diff --git a/.gitignore b/.gitignore
index 963b8a4..3679a33 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,9 +1,6 @@
 /.project
 /target
+.DS_Store
 infer-out
-bazel-bin
-bazel-genfiles
-bazel-jgit
-bazel-out
-bazel-testlogs
+bazel-*
 *~
diff --git a/Documentation/technical/reftable.md b/Documentation/technical/reftable.md
new file mode 100644
index 0000000..47c61a3
--- /dev/null
+++ b/Documentation/technical/reftable.md
@@ -0,0 +1,955 @@
+# reftable
+
+[TOC]
+
+## Overview
+
+### Problem statement
+
+Some repositories contain a lot of references (e.g.  android at 866k,
+rails at 31k).  The existing packed-refs format takes up a lot of
+space (e.g.  62M), and does not scale with additional references.
+Lookup of a single reference requires linearly scanning the file.
+
+Atomic pushes modifying multiple references require copying the
+entire packed-refs file, which can be a considerable amount of data
+moved (e.g. 62M in, 62M out) for even small transactions (2 refs
+modified).
+
+Repositories with many loose references occupy a large number of disk
+blocks from the local file system, as each reference is its own file
+storing 41 bytes (and another file for the corresponding reflog).
+This negatively affects the number of inodes available when a large
+number of repositories are stored on the same filesystem.  Readers can
+be penalized due to the larger number of syscalls required to traverse
+and read the `$GIT_DIR/refs` directory.
+
+### Objectives
+
+- Near constant time lookup for any single reference, even when the
+  repository is cold and not in process or kernel cache.
+- Near constant time verification if a SHA-1 is referred to by at
+  least one reference (for allow-tip-sha1-in-want).
+- Efficient lookup of an entire namespace, such as `refs/tags/`.
+- Support atomic push with `O(size_of_update)` operations.
+- Combine reflog storage with ref storage for small transactions.
+- Separate reflog storage for base refs and historical logs.
+
+### Description
+
+A reftable file is a portable binary file format customized for
+reference storage. References are sorted, enabling linear scans,
+binary search lookup, and range scans.
+
+Storage in the file is organized into variable sized blocks.  Prefix
+compression is used within a single block to reduce disk space.  Block
+size and alignment is tunable by the writer.
+
+### Performance
+
+Space used, packed-refs vs. reftable:
+
+repository | packed-refs | reftable | % original | avg ref  | avg obj
+-----------|------------:|---------:|-----------:|---------:|--------:
+android    |      62.2 M |   36.1 M |     58.0%  | 33 bytes | 5 bytes
+rails      |       1.8 M |    1.1 M |     57.7%  | 29 bytes | 4 bytes
+git        |      78.7 K |   48.1 K |     61.0%  | 50 bytes | 4 bytes
+git (heads)|       332 b |    269 b |     81.0%  | 33 bytes | 0 bytes
+
+Scan (read 866k refs), by reference name lookup (single ref from 866k
+refs), and by SHA-1 lookup (refs with that SHA-1, from 866k refs):
+
+format      | cache | scan    | by name        | by SHA-1
+------------|------:|--------:|---------------:|---------------:
+packed-refs | cold  |  402 ms | 409,660.1 usec | 412,535.8 usec
+packed-refs | hot   |         |   6,844.6 usec |  20,110.1 usec
+reftable    | cold  |  112 ms |      33.9 usec |     323.2 usec
+reftable    | hot   |         |      20.2 usec |     320.8 usec
+
+Space used for 149,932 log entries for 43,061 refs,
+reflog vs. reftable:
+
+format        | size  | avg entry
+--------------|------:|-----------:
+$GIT_DIR/logs | 173 M | 1209 bytes
+reftable      |   5 M |   37 bytes
+
+## Details
+
+### Peeling
+
+References stored in a reftable are peeled, a record for an annotated
+(or signed) tag records both the tag object, and the object it refers
+to.
+
+### Reference name encoding
+
+Reference names are an uninterpreted sequence of bytes that must pass
+[git-check-ref-format][ref-fmt] as a valid reference name.
+
+[ref-fmt]: https://git-scm.com/docs/git-check-ref-format
+
+### Network byte order
+
+All multi-byte, fixed width fields are in network byte order.
+
+### Ordering
+
+Blocks are lexicographically ordered by their first reference.
+
+### Directory/file conflicts
+
+The reftable format accepts both `refs/heads/foo` and
+`refs/heads/foo/bar` as distinct references.
+
+This property is useful for retaining log records in reftable, but may
+confuse versions of Git using `$GIT_DIR/refs` directory tree to
+maintain references.  Users of reftable may choose to continue to
+reject `foo` and `foo/bar` type conflicts to prevent problems for
+peers.
+
+## File format
+
+### Structure
+
+A reftable file has the following high-level structure:
+
+    first_block {
+      header
+      first_ref_block
+    }
+    ref_block*
+    ref_index*
+    obj_block*
+    obj_index*
+    log_block*
+    log_index*
+    footer
+
+A log-only file omits the `ref_block`, `ref_index`, `obj_block` and
+`obj_index` sections, containing only the file header and log block:
+
+    first_block {
+      header
+    }
+    log_block*
+    log_index*
+    footer
+
+in a log-only file the first log block immediately follows the file
+header, without padding to block alignment.
+
+### Block size
+
+The file's block size is arbitrarily determined by the writer, and
+does not have to be a power of 2.  The block size must be larger than
+the longest reference name or log entry used in the repository, as
+references cannot span blocks.
+
+Powers of two that are friendly to the virtual memory system or
+filesystem (such as 4k or 8k) are recommended.  Larger sizes (64k) can
+yield better compression, with a possible increased cost incurred by
+readers during access.
+
+The largest block size is `16777215` bytes (15.99 MiB).
+
+### Block alignment
+
+Writers may choose to align blocks at multiples of the block size by
+including `padding` filled with NUL bytes at the end of a block to
+round out to the chosen alignment.  When alignment is used, writers
+must specify the alignment with the file header's `block_size` field.
+
+Block alignment is not required by the file format.  Unaligned files
+must set `block_size = 0` in the file header, and omit `padding`.
+Unaligned files with more than one ref block must include the
+[ref index](#Ref-index) to support fast lookup.  Readers must be
+able to read both aligned and non-aligned files.
+
+Very small files (e.g. 1 only ref block) may omit `padding` and the
+ref index to reduce total file size.
+
+### Header
+
+A 24-byte header appears at the beginning of the file:
+
+    'REFT'
+    uint8( version_number = 1 )
+    uint24( block_size )
+    uint64( min_update_index )
+    uint64( max_update_index )
+
+Aligned files must specify `block_size` to configure readers with the
+expected block alignment.  Unaligned files must set `block_size = 0`.
+
+The `min_update_index` and `max_update_index` describe bounds for the
+`update_index` field of all log records in this file.  When reftables
+are used in a stack for [transactions](#Update-transactions), these
+fields can order the files such that the prior file's
+`max_update_index + 1` is the next file's `min_update_index`.
+
+### First ref block
+
+The first ref block shares the same block as the file header, and is
+24 bytes smaller than all other blocks in the file.  The first block
+immediately begins after the file header, at position 24.
+
+If the first block is a log block (a log-only file), its block header
+begins immediately at position 24.
+
+### Ref block format
+
+A ref block is written as:
+
+    'r'
+    uint24( block_len )
+    ref_record+
+    uint24( restart_offset )+
+    uint16( restart_count )
+
+    padding?
+
+Blocks begin with `block_type = 'r'` and a 3-byte `block_len` which
+encodes the number of bytes in the block up to, but not including the
+optional `padding`.  This is always less than or equal to the file's
+block size.  In the first ref block, `block_len` includes 24 bytes
+for the file header.
+
+The 2-byte `restart_count` stores the number of entries in the
+`restart_offset` list, which must not be empty.  Readers can use
+`restart_count` to binary search between restarts before starting a
+linear scan.
+
+Exactly `restart_count` 3-byte `restart_offset` values precedes the
+`restart_count`.  Offsets are relative to the start of the block and
+refer to the first byte of any `ref_record` whose name has not been
+prefix compressed.  Entries in the `restart_offset` list must be
+sorted, ascending.  Readers can start linear scans from any of these
+records.
+
+A variable number of `ref_record` fill the middle of the block,
+describing reference names and values.  The format is described below.
+
+As the first ref block shares the first file block with the file
+header, all `restart_offset` in the first block are relative to the
+start of the file (position 0), and include the file header.  This
+forces the first `restart_offset` to be `28`.
+
+#### ref record
+
+A `ref_record` describes a single reference, storing both the name and
+its value(s). Records are formatted as:
+
+    varint( prefix_length )
+    varint( (suffix_length << 3) | value_type )
+    suffix
+    varint( update_index_delta )
+    value?
+
+The `prefix_length` field specifies how many leading bytes of the
+prior reference record's name should be copied to obtain this
+reference's name.  This must be 0 for the first reference in any
+block, and also must be 0 for any `ref_record` whose offset is listed
+in the `restart_offset` table at the end of the block.
+
+Recovering a reference name from any `ref_record` is a simple concat:
+
+    this_name = prior_name[0..prefix_length] + suffix
+
+The `suffix_length` value provides the number of bytes available in
+`suffix` to copy from `suffix` to complete the reference name.
+
+The `update_index` that last modified the reference can be obtained by
+adding `update_index_delta` to the `min_update_index` from the file
+header: `min_update_index + update_index_delta`.
+
+The `value` follows.  Its format is determined by `value_type`, one of
+the following:
+
+- `0x0`: deletion; no value data (see transactions, below)
+- `0x1`: one 20-byte object id; value of the ref
+- `0x2`: two 20-byte object ids; value of the ref, peeled target
+- `0x3`: symbolic reference: `varint( target_len ) target`
+
+Symbolic references use `0x3`, followed by the complete name of the
+reference target.  No compression is applied to the target name.
+
+Types `0x4..0x7` are reserved for future use.
+
+### Ref index
+
+The ref index stores the name of the last reference from every ref
+block in the file, enabling reduced disk seeks for lookups.  Any
+reference can be found by searching the index, identifying the
+containing block, and searching within that block.
+
+The index may be organized into a multi-level index, where the 1st
+level index block points to additional ref index blocks (2nd level),
+which may in turn point to either additional index blocks (e.g. 3rd
+level) or ref blocks (leaf level).  Disk reads required to access a
+ref go up with higher index levels.  Multi-level indexes may be
+required to ensure no single index block exceeds the file format's max
+block size of `16777215` bytes (15.99 MiB).  To acheive constant O(1)
+disk seeks for lookups the index must be a single level, which is
+permitted to exceed the file's configured block size, but not the
+format's max block size of 15.99 MiB.
+
+If present, the ref index block(s) appears after the last ref block.
+
+If there are at least 4 ref blocks, a ref index block should be
+written to improve lookup times.  Cold reads using the index require
+2 disk reads (read index, read block), and binary searching < 4 blocks
+also requires <= 2 reads.  Omitting the index block from smaller files
+saves space.
+
+If the file is unaligned and contains more than one ref block, the ref
+index must be written.
+
+Index block format:
+
+    'i'
+    uint24( block_len )
+    index_record+
+    uint24( restart_offset )+
+    uint16( restart_count )
+
+    padding?
+
+The index blocks begin with `block_type = 'i'` and a 3-byte
+`block_len` which encodes the number of bytes in the block,
+up to but not including the optional `padding`.
+
+The `restart_offset` and `restart_count` fields are identical in
+format, meaning and usage as in ref blocks.
+
+To reduce the number of reads required for random access in very large
+files the index block may be larger than other blocks.  However,
+readers must hold the entire index in memory to benefit from this, so
+it's a time-space tradeoff in both file size and reader memory.
+
+Increasing the file's block size decreases the index size.
+Alternatively a multi-level index may be used, keeping index blocks
+within the file's block size, but increasing the number of blocks
+that need to be accessed.
+
+#### index record
+
+An index record describes the last entry in another block.
+Index records are written as:
+
+    varint( prefix_length )
+    varint( (suffix_length << 3) | 0 )
+    suffix
+    varint( block_position )
+
+Index records use prefix compression exactly like `ref_record`.
+
+Index records store `block_position` after the suffix, specifying the
+absolute position in bytes (from the start of the file) of the block
+that ends with this reference. Readers can seek to `block_position` to
+begin reading the block header.
+
+Readers must examine the block header at `block_position` to determine
+if the next block is another level index block, or the leaf-level ref
+block.
+
+#### Reading the index
+
+Readers loading the ref index must first read the footer (below) to
+obtain `ref_index_position`. If not present, the position will be 0.
+The `ref_index_position` is for the 1st level root of the ref index.
+
+### Obj block format
+
+Object blocks are optional.  Writers may choose to omit object blocks,
+especially if readers will not use the SHA-1 to ref mapping.
+
+Object blocks use unique, abbreviated 2-20 byte SHA-1 keys, mapping
+to ref blocks containing references pointing to that object directly,
+or as the peeled value of an annotated tag.  Like ref blocks, object
+blocks use the file's standard block size. The abbrevation length is
+available in the footer as `obj_id_len`.
+
+To save space in small files, object blocks may be omitted if the ref
+index is not present, as brute force search will only need to read a
+few ref blocks.  When missing, readers should brute force a linear
+search of all references to lookup by SHA-1.
+
+An object block is written as:
+
+    'o'
+    uint24( block_len )
+    obj_record+
+    uint24( restart_offset )+
+    uint16( restart_count )
+
+    padding?
+
+Fields are identical to ref block.  Binary search using the restart
+table works the same as in reference blocks.
+
+Because object identifiers are abbreviated by writers to the shortest
+unique abbreviation within the reftable, obj key lengths are variable
+between 2 and 20 bytes.  Readers must compare only for common prefix
+match within an obj block or obj index.
+
+#### obj record
+
+An `obj_record` describes a single object abbreviation, and the blocks
+containing references using that unique abbreviation:
+
+    varint( prefix_length )
+    varint( (suffix_length << 3) | cnt_3 )
+    suffix
+    varint( cnt_large )?
+    varint( position_delta )*
+
+Like in reference blocks, abbreviations are prefix compressed within
+an obj block.  On large reftables with many unique objects, higher
+block sizes (64k), and higher restart interval (128), a
+`prefix_length` of 2 or 3 and `suffix_length` of 3 may be common in
+obj records (unique abbreviation of 5-6 raw bytes, 10-12 hex digits).
+
+Each record contains `position_count` number of positions for matching
+ref blocks.  For 1-7 positions the count is stored in `cnt_3`.  When
+`cnt_3 = 0` the actual count follows in a varint, `cnt_large`.
+
+The use of `cnt_3` bets most objects are pointed to by only a single
+reference, some may be pointed to by a couple of references, and very
+few (if any) are pointed to by more than 7 references.
+
+A special case exists when `cnt_3 = 0` and `cnt_large = 0`: there
+are no `position_delta`, but at least one reference starts with this
+abbreviation.  A reader that needs exact reference names must scan all
+references to find which specific references have the desired object.
+Writers should use this format when the `position_delta` list would have
+overflowed the file's block size due to a high number of references
+pointing to the same object.
+
+The first `position_delta` is the position from the start of the file.
+Additional `position_delta` entries are sorted ascending and relative
+to the prior entry, e.g.  a reader would perform:
+
+    pos = position_delta[0]
+    prior = pos
+    for (j = 1; j < position_count; j++) {
+      pos = prior + position_delta[j]
+      prior = pos
+    }
+
+With a position in hand, a reader must linearly scan the ref block,
+starting from the first `ref_record`, testing each reference's SHA-1s
+(for `value_type = 0x1` or `0x2`) for full equality.  Faster searching
+by SHA-1 within a single ref block is not supported by the reftable
+format.  Smaller block sizes reduce the number of candidates this step
+must consider.
+
+### Obj index
+
+The obj index stores the abbreviation from the last entry for every
+obj block in the file, enabling reduced disk seeks for all lookups.
+It is formatted exactly the same as the ref index, but refers to obj
+blocks.
+
+The obj index should be present if obj blocks are present, as
+obj blocks should only be written in larger files.
+
+Readers loading the obj index must first read the footer (below) to
+obtain `obj_index_position`.  If not present, the position will be 0.
+
+### Log block format
+
+Unlike ref and obj blocks, log blocks are always unaligned.
+
+Log blocks are variable in size, and do not match the `block_size`
+specified in the file header or footer.  Writers should choose an
+appropriate buffer size to prepare a log block for deflation, such as
+`2 * block_size`.
+
+A log block is written as:
+
+    'g'
+    uint24( block_len )
+    zlib_deflate {
+      log_record+
+      uint24( restart_offset )+
+      uint16( restart_count )
+    }
+
+Log blocks look similar to ref blocks, except `block_type = 'g'`.
+
+The 4-byte block header is followed by the deflated block contents
+using zlib deflate.  The `block_len` in the header is the inflated
+size (including 4-byte block header), and should be used by readers to
+preallocate the inflation output buffer.  A log block's `block_len`
+may exceed the file's block size.
+
+Offsets within the log block (e.g.  `restart_offset`) still include
+the 4-byte header.  Readers may prefer prefixing the inflation output
+buffer with the 4-byte header.
+
+Within the deflate container, a variable number of `log_record`
+describe reference changes.  The log record format is described
+below.  See ref block format (above) for a description of
+`restart_offset` and `restart_count`.
+
+Because log blocks have no alignment or padding between blocks,
+readers must keep track of the bytes consumed by the inflater to
+know where the next log block begins.
+
+#### log record
+
+Log record keys are structured as:
+
+    ref_name '\0' reverse_int64( update_index )
+
+where `update_index` is the unique transaction identifier.  The
+`update_index` field must be unique within the scope of a `ref_name`.
+See the update transactions section below for further details.
+
+The `reverse_int64` function inverses the value so lexographical
+ordering the network byte order encoding sorts the more recent records
+with higher `update_index` values first:
+
+    reverse_int64(int64 t) {
+      return 0xffffffffffffffff - t;
+    }
+
+Log records have a similar starting structure to ref and index
+records, utilizing the same prefix compression scheme applied to the
+log record key described above.
+
+```
+    varint( prefix_length )
+    varint( (suffix_length << 3) | log_type )
+    suffix
+    log_data {
+      old_id
+      new_id
+      varint( name_length    )  name
+      varint( email_length   )  email
+      varint( time_seconds )
+      sint16( tz_offset )
+      varint( message_length )  message
+    }?
+```
+
+Log record entries use `log_type` to indicate what follows:
+
+- `0x0`: deletion; no log data.
+- `0x1`: standard git reflog data using `log_data` above.
+
+The `log_type = 0x0` is mostly useful for `git stash drop`, removing
+an entry from the reflog of `refs/stash` in a transaction file
+(below), without needing to rewrite larger files.  Readers reading a
+stack of reflogs must treat this as a deletion.
+
+For `log_type = 0x1`, the `log_data` section follows
+[git update-ref][update-ref] logging, and includes:
+
+- two 20-byte SHA-1s (old id, new id)
+- varint string of committer's name
+- varint string of committer's email
+- varint time in seconds since epoch (Jan 1, 1970)
+- 2-byte timezone offset in minutes (signed)
+- varint string of message
+
+`tz_offset` is the absolute number of minutes from GMT the committer
+was at the time of the update.  For example `GMT-0800` is encoded in
+reftable as `sint16(-480)` and `GMT+0230` is `sint16(150)`.
+
+The committer email does not contain `<` or `>`, it's the value
+normally found between the `<>` in a git commit object header.
+
+The `message_length` may be 0, in which case there was no message
+supplied for the update.
+
+[update-ref]: https://git-scm.com/docs/git-update-ref#_logging_updates
+
+#### Reading the log
+
+Readers accessing the log must first read the footer (below) to
+determine the `log_position`.  The first block of the log begins at
+`log_position` bytes since the start of the file.  The `log_position`
+is not block aligned.
+
+#### Importing logs
+
+When importing from `$GIT_DIR/logs` writers should globally order all
+log records roughly by timestamp while preserving file order, and
+assign unique, increasing `update_index` values for each log line.
+Newer log records get higher `update_index` values.
+
+Although an import may write only a single reftable file, the reftable
+file must span many unique `update_index`, as each log line requires
+its own `update_index` to preserve semantics.
+
+### Log index
+
+The log index stores the log key (`refname \0 reverse_int64(update_index)`)
+for the last log record of every log block in the file, supporting
+bounded-time lookup.
+
+A log index block must be written if 2 or more log blocks are written
+to the file.  If present, the log index appears after the last log
+block.  There is no padding used to align the log index to block
+alignment.
+
+Log index format is identical to ref index, except the keys are 9
+bytes longer to include `'\0'` and the 8-byte
+`reverse_int64(update_index)`.  Records use `block_position` to
+refer to the start of a log block.
+
+#### Reading the index
+
+Readers loading the log index must first read the footer (below) to
+obtain `log_index_position`. If not present, the position will be 0.
+
+### Footer
+
+After the last block of the file, a file footer is written.  It begins
+like the file header, but is extended with additional data.
+
+A 68-byte footer appears at the end:
+
+```
+    'REFT'
+    uint8( version_number = 1 )
+    uint24( block_size )
+    uint64( min_update_index )
+    uint64( max_update_index )
+
+    uint64( ref_index_position )
+    uint64( (obj_position << 5) | obj_id_len )
+    uint64( obj_index_position )
+
+    uint64( log_position )
+    uint64( log_index_position )
+
+    uint32( CRC-32 of above )
+```
+
+If a section is missing (e.g. ref index) the corresponding position
+field (e.g. `ref_index_position`) will be 0.
+
+- `obj_position`: byte position for the first obj block.
+- `obj_id_len`: number of bytes used to abbreviate object identifiers
+  in obj blocks.
+- `log_position`: byte position for the first log block.
+- `ref_index_position`: byte position for the start of the ref index.
+- `obj_index_position`: byte position for the start of the obj index.
+- `log_index_position`: byte position for the start of the log index.
+
+#### Reading the footer
+
+Readers must seek to `file_length - 68` to access the footer.  A
+trusted external source (such as `stat(2)`) is necessary to obtain
+`file_length`.  When reading the footer, readers must verify:
+
+- 4-byte magic is correct
+- 1-byte version number is recognized
+- 4-byte CRC-32 matches the other 64 bytes (including magic, and version)
+
+Once verified, the other fields of the footer can be accessed.
+
+### Varint encoding
+
+Varint encoding is identical to the ofs-delta encoding method used
+within pack files.
+
+Decoder works such as:
+
+    val = buf[ptr] & 0x7f
+    while (buf[ptr] & 0x80) {
+      ptr++
+      val = ((val + 1) << 7) | (buf[ptr] & 0x7f)
+    }
+
+### Binary search
+
+Binary search within a block is supported by the `restart_offset`
+fields at the end of the block.  Readers can binary search through the
+restart table to locate between which two restart points the sought
+reference or key should appear.
+
+Each record identified by a `restart_offset` stores the complete key
+in the `suffix` field of the record, making the compare operation
+during binary search straightforward.
+
+Once a restart point lexicographically before the sought reference has
+been identified, readers can linearly scan through the following
+record entries to locate the sought record, terminating if the current
+record sorts after (and therefore the sought key is not present).
+
+#### Restart point selection
+
+Writers determine the restart points at file creation.  The process is
+arbitrary, but every 16 or 64 records is recommended.  Every 16 may
+be more suitable for smaller block sizes (4k or 8k), every 64 for
+larger block sizes (64k).
+
+More frequent restart points reduces prefix compression and increases
+space consumed by the restart table, both of which increase file size.
+
+Less frequent restart points makes prefix compression more effective,
+decreasing overall file size, with increased penalities for readers
+walking through more records after the binary search step.
+
+A maximum of `65535` restart points per block is supported.
+
+## Considerations
+
+### Lightweight refs dominate
+
+The reftable format assumes the vast majority of references are single
+SHA-1 valued with common prefixes, such as Gerrit Code Review's
+`refs/changes/` namespace, GitHub's `refs/pulls/` namespace, or many
+lightweight tags in the `refs/tags/` namespace.
+
+Annotated tags storing the peeled object cost an additional 20 bytes
+per reference.
+
+### Low overhead
+
+A reftable with very few references (e.g. git.git with 5 heads)
+is 269 bytes for reftable, vs. 332 bytes for packed-refs.  This
+supports reftable scaling down for transaction logs (below).
+
+### Block size
+
+For a Gerrit Code Review type repository with many change refs, larger
+block sizes (64 KiB) and less frequent restart points (every 64) yield
+better compression due to more references within the block compressing
+against the prior reference.
+
+Larger block sizes reduce the index size, as the reftable will
+require fewer blocks to store the same number of references.
+
+### Minimal disk seeks
+
+Assuming the index block has been loaded into memory, binary searching
+for any single reference requires exactly 1 disk seek to load the
+containing block.
+
+### Scans and lookups dominate
+
+Scanning all references and lookup by name (or namespace such as
+`refs/heads/`) are the most common activities performed on repositories.
+SHA-1s are stored directly with references to optimize this use case.
+
+### Logs are infrequently read
+
+Logs are infrequently accessed, but can be large.  Deflating log
+blocks saves disk space, with some increased penalty at read time.
+
+Logs are stored in an isolated section from refs, reducing the burden
+on reference readers that want to ignore logs.  Further, historical
+logs can be isolated into log-only files.
+
+### Logs are read backwards
+
+Logs are frequently accessed backwards (most recent N records for
+master to answer `master@{4}`), so log records are grouped by
+reference, and sorted descending by update index.
+
+## Repository format
+
+### Version 1
+
+A repository must set its `$GIT_DIR/config` to configure reftable:
+
+    [core]
+        repositoryformatversion = 1
+    [extensions]
+        refStorage = reftable
+
+### Layout
+
+The `$GIT_DIR/refs` path is a file when reftable is configured, not a
+directory.  This prevents loose references from being stored.
+
+A collection of reftable files are stored in the `$GIT_DIR/reftable/`
+directory:
+
+    00000001.log
+    00000001.ref
+    00000002.ref
+
+where reftable files are named by a unique name such as produced by
+the function `${update_index}.ref`.
+
+Log-only files use the `.log` extension, while ref-only and mixed ref
+and log files use `.ref`.  extension.
+
+The stack ordering file is `$GIT_DIR/refs` and lists the current
+files, one per line, in order, from oldest (base) to newest (most
+recent):
+
+    $ cat .git/refs
+    00000001.log
+    00000001.ref
+    00000002.ref
+
+Readers must read `$GIT_DIR/refs` to determine which files are
+relevant right now, and search through the stack in reverse order
+(last reftable is examined first).
+
+Reftable files not listed in `refs` may be new (and about to be added
+to the stack by the active writer), or ancient and ready to be pruned.
+
+### Readers
+
+Readers can obtain a consistent snapshot of the reference space by
+following:
+
+1.  Open and read the `refs` file.
+2.  Open each of the reftable files that it mentions.
+3.  If any of the files is missing, goto 1.
+4.  Read from the now-open files as long as necessary.
+
+### Update transactions
+
+Although reftables are immutable, mutations are supported by writing a
+new reftable and atomically appending it to the stack:
+
+1. Acquire `refs.lock`.
+2. Read `refs` to determine current reftables.
+3. Select `update_index` to be most recent file's `max_update_index + 1`.
+4. Prepare temp reftable `${update_index}_XXXXXX`, including log entries.
+5. Rename `${update_index}_XXXXXX` to `${update_index}.ref`.
+6. Copy `refs` to `refs.lock`, appending file from (5).
+7. Rename `refs.lock` to `refs`.
+
+During step 4 the new file's `min_update_index` and `max_update_index`
+are both set to the `update_index` selected by step 3.  All log
+records for the transaction use the same `update_index` in their keys.
+This enables later correlation of which references were updated by the
+same transaction.
+
+Because a single `refs.lock` file is used to manage locking, the
+repository is single-threaded for writers.  Writers may have to
+busy-spin (with backoff) around creating `refs.lock`, for up to an
+acceptable wait period, aborting if the repository is too busy to
+mutate.  Application servers wrapped around repositories (e.g.  Gerrit
+Code Review) can layer their own lock/wait queue to improve fairness
+to writers.
+
+### Reference deletions
+
+Deletion of any reference can be explicitly stored by setting the
+`type` to `0x0` and omitting the `value` field of the `ref_record`.
+This serves as a tombstone, overriding any assertions about the
+existence of the reference from earlier files in the stack.
+
+### Compaction
+
+A partial stack of reftables can be compacted by merging references
+using a straightforward merge join across reftables, selecting the
+most recent value for output, and omitting deleted references that do
+not appear in remaining, lower reftables.
+
+A compacted reftable should set its `min_update_index` to the smallest of
+the input files' `min_update_index`, and its `max_update_index`
+likewise to the largest input `max_update_index`.
+
+For sake of illustration, assume the stack currently consists of
+reftable files (from oldest to newest): A, B, C, and D. The compactor
+is going to compact B and C, leaving A and D alone.
+
+1.  Obtain lock `refs.lock` and read the `refs` file.
+2.  Obtain locks `B.lock` and `C.lock`.
+    Ownership of these locks prevents other processes from trying
+    to compact these files.
+3.  Release `refs.lock`.
+4.  Compact `B` and `C` into a temp file `${min_update_index}_XXXXXX`.
+5.  Reacquire lock `refs.lock`.
+6.  Verify that `B` and `C` are still in the stack, in that order. This
+    should always be the case, assuming that other processes are adhering
+    to the locking protocol.
+7.  Rename `${min_update_index}_XXXXXX` to `${min_update_index}_2.ref`.
+8.  Write the new stack to `refs.lock`, replacing `B` and `C` with the
+    file from (4).
+9.  Rename `refs.lock` to `refs`.
+10. Delete `B` and `C`, perhaps after a short sleep to avoid forcing
+    readers to backtrack.
+
+This strategy permits compactions to proceed independently of updates.
+
+## Alternatives considered
+
+### bzip packed-refs
+
+`bzip2` can significantly shrink a large packed-refs file (e.g. 62
+MiB compresses to 23 MiB, 37%).  However the bzip format does not support
+random access to a single reference. Readers must inflate and discard
+while performing a linear scan.
+
+Breaking packed-refs into chunks (individually compressing each chunk)
+would reduce the amount of data a reader must inflate, but still
+leaves the problem of indexing chunks to support readers efficiently
+locating the correct chunk.
+
+Given the compression achieved by reftable's encoding, it does not
+seem necessary to add the complexity of bzip/gzip/zlib.
+
+### Michael Haggerty's alternate format
+
+Michael Haggerty proposed [an alternate][mh-alt] format to reftable on
+the Git mailing list.  This format uses smaller chunks, without the
+restart table, and avoids block alignment with padding.  Reflog entries
+immediately follow each ref, and are thus interleaved between refs.
+
+Performance testing indicates reftable is faster for lookups (51%
+faster, 11.2 usec vs.  5.4 usec), although reftable produces a
+slightly larger file (+ ~3.2%, 28.3M vs 29.2M):
+
+format    |  size  | seek cold | seek hot  |
+---------:|-------:|----------:|----------:|
+mh-alt    | 28.3 M | 23.4 usec | 11.2 usec |
+reftable  | 29.2 M | 19.9 usec |  5.4 usec |
+
+[mh-alt]: https://public-inbox.org/git/CAMy9T_HCnyc1g8XWOOWhe7nN0aEFyyBskV2aOMb_fe+wGvEJ7A@mail.gmail.com/
+
+### JGit Ketch RefTree
+
+[JGit Ketch][ketch] proposed [RefTree][reftree], an encoding of
+references inside Git tree objects stored as part of the repository's
+object database.
+
+The RefTree format adds additional load on the object database storage
+layer (more loose objects, more objects in packs), and relies heavily
+on the packer's delta compression to save space.  Namespaces which are
+flat (e.g.  thousands of tags in refs/tags) initially create very
+large loose objects, and so RefTree does not address the problem of
+copying many references to modify a handful.
+
+Flat namespaces are not efficiently searchable in RefTree, as tree
+objects in canonical formatting cannot be binary searched. This fails
+the need to handle a large number of references in a single namespace,
+such as GitHub's `refs/pulls`, or a project with many tags.
+
+[ketch]: https://dev.eclipse.org/mhonarc/lists/jgit-dev/msg03073.html
+[reftree]: https://public-inbox.org/git/CAJo=hJvnAPNAdDcAAwAvU9C4RVeQdoS3Ev9WTguHx4fD0V_nOg@mail.gmail.com/
+
+### LMDB
+
+David Turner proposed [using LMDB][dt-lmdb], as LMDB is lightweight
+(64k of runtime code) and GPL-compatible license.
+
+A downside of LMDB is its reliance on a single C implementation.  This
+makes embedding inside JGit (a popular reimplemenation of Git)
+difficult, and hoisting onto virtual storage (for JGit DFS) virtually
+impossible.
+
+A common format that can be supported by all major Git implementations
+(git-core, JGit, libgit2) is strongly preferred.
+
+[dt-lmdb]: https://public-inbox.org/git/1455772670-21142-26-git-send-email-dturner@twopensource.com/
+
+## Future
+
+### Longer hashes
+
+Version will bump (e.g.  2) to indicate `value` uses a different
+object id length other than 20.  The length could be stored in an
+expanded file header, or hardcoded as part of the version.
diff --git a/WORKSPACE b/WORKSPACE
index f2fecb5..afd58b2 100644
--- a/WORKSPACE
+++ b/WORKSPACE
@@ -77,8 +77,8 @@
 
 maven_jar(
     name = "args4j",
-    artifact = "args4j:args4j:2.0.15",
-    sha1 = "139441471327b9cc6d56436cb2a31e60eb6ed2ba",
+    artifact = "args4j:args4j:2.33",
+    sha1 = "bd87a75374a6d6523de82fef51fc3cfe9baf9fc9",
 )
 
 maven_jar(
diff --git a/lib/BUILD b/lib/BUILD
index 346e1fd..a3936ee 100644
--- a/lib/BUILD
+++ b/lib/BUILD
@@ -106,7 +106,10 @@
 
 java_library(
     name = "jsch",
-    visibility = ["//org.eclipse.jgit:__pkg__"],
+    visibility = [
+        "//org.eclipse.jgit:__pkg__",
+        "//org.eclipse.jgit.test:__pkg__",
+    ],
     exports = ["@jsch//jar"],
 )
 
diff --git a/org.eclipse.jgit.ant.test/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.ant.test/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.ant.test/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.ant.test/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.ant.test/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.ant.test/.settings/org.eclipse.pde.api.tools.prefs
index fb04636..c0030de 100644
--- a/org.eclipse.jgit.ant.test/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.ant.test/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,4 +1,4 @@
-#Tue Oct 18 02:04:38 CEST 2011
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -8,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -47,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -58,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -75,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -83,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.ant.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.ant.test/META-INF/MANIFEST.MF
index 5889109..8102156 100644
--- a/org.eclipse.jgit.ant.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.ant.test/META-INF/MANIFEST.MF
@@ -3,13 +3,13 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.ant.test
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: org.apache.tools.ant,
- org.eclipse.jgit.ant.tasks;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.junit;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)",
+ org.eclipse.jgit.ant.tasks;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.junit;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)",
  org.hamcrest.core;version="[1.1.0,2.0.0)",
  org.junit;version="[4.0.0,5.0.0)"
diff --git a/org.eclipse.jgit.ant.test/pom.xml b/org.eclipse.jgit.ant.test/pom.xml
index 386ecd2..8c6c44a 100644
--- a/org.eclipse.jgit.ant.test/pom.xml
+++ b/org.eclipse.jgit.ant.test/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.ant.test</artifactId>
diff --git a/org.eclipse.jgit.ant/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.ant/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.ant/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.ant/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.ant/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.ant/.settings/org.eclipse.pde.api.tools.prefs
index cd148d9..c0030de 100644
--- a/org.eclipse.jgit.ant/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.ant/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,4 +1,4 @@
-#Tue Oct 18 00:52:01 CEST 2011
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -8,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -47,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -58,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -75,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -83,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.ant/META-INF/MANIFEST.MF b/org.eclipse.jgit.ant/META-INF/MANIFEST.MF
index be009d1..c8f0309 100644
--- a/org.eclipse.jgit.ant/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.ant/META-INF/MANIFEST.MF
@@ -2,11 +2,11 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: org.eclipse.jgit.ant
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: org.apache.tools.ant,
-  org.eclipse.jgit.storage.file;version="[4.8.1,4.9.0)"
+  org.eclipse.jgit.storage.file;version="[4.9.6,4.10.0)"
 Bundle-Localization: plugin
 Bundle-Vendor: %Provider-Name
-Export-Package: org.eclipse.jgit.ant.tasks;version="4.8.1";
+Export-Package: org.eclipse.jgit.ant.tasks;version="4.9.6";
  uses:="org.apache.tools.ant.types,org.apache.tools.ant"
diff --git a/org.eclipse.jgit.ant/pom.xml b/org.eclipse.jgit.ant/pom.xml
index 5712d29..31a2555 100644
--- a/org.eclipse.jgit.ant/pom.xml
+++ b/org.eclipse.jgit.ant/pom.xml
@@ -48,7 +48,7 @@
 	<parent>
 		<groupId>org.eclipse.jgit</groupId>
 		<artifactId>org.eclipse.jgit-parent</artifactId>
-		<version>4.8.1-SNAPSHOT</version>
+		<version>4.9.6-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>org.eclipse.jgit.ant</artifactId>
diff --git a/org.eclipse.jgit.archive/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.archive/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.archive/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.archive/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.archive/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.archive/.settings/org.eclipse.pde.api.tools.prefs
index cd148d9..c0030de 100644
--- a/org.eclipse.jgit.archive/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.archive/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,4 +1,4 @@
-#Tue Oct 18 00:52:01 CEST 2011
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -8,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -47,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -58,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -75,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -83,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.archive/META-INF/MANIFEST.MF b/org.eclipse.jgit.archive/META-INF/MANIFEST.MF
index 4080946..2d41611 100644
--- a/org.eclipse.jgit.archive/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.archive/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.archive
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-Localization: plugin
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
@@ -12,15 +12,15 @@
  org.apache.commons.compress.compressors.bzip2;version="[1.4,2.0)",
  org.apache.commons.compress.compressors.gzip;version="[1.4,2.0)",
  org.apache.commons.compress.compressors.xz;version="[1.4,2.0)",
- org.eclipse.jgit.api;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.nls;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revwalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)",
+ org.eclipse.jgit.api;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.nls;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revwalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)",
  org.osgi.framework;version="[1.3.0,2.0.0)"
 Bundle-ActivationPolicy: lazy
 Bundle-Activator: org.eclipse.jgit.archive.FormatActivator
-Export-Package: org.eclipse.jgit.archive;version="4.8.1";
+Export-Package: org.eclipse.jgit.archive;version="4.9.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.api,
    org.apache.commons.compress.archivers,
diff --git a/org.eclipse.jgit.archive/META-INF/SOURCE-MANIFEST.MF b/org.eclipse.jgit.archive/META-INF/SOURCE-MANIFEST.MF
index c03191a..a9c01cc 100644
--- a/org.eclipse.jgit.archive/META-INF/SOURCE-MANIFEST.MF
+++ b/org.eclipse.jgit.archive/META-INF/SOURCE-MANIFEST.MF
@@ -3,5 +3,5 @@
 Bundle-Name: org.eclipse.jgit.archive - Sources
 Bundle-SymbolicName: org.eclipse.jgit.archive.source
 Bundle-Vendor: Eclipse.org - JGit
-Bundle-Version: 4.8.1.qualifier
-Eclipse-SourceBundle: org.eclipse.jgit.archive;version="4.8.1.qualifier";roots="."
+Bundle-Version: 4.9.6.qualifier
+Eclipse-SourceBundle: org.eclipse.jgit.archive;version="4.9.6.qualifier";roots="."
diff --git a/org.eclipse.jgit.archive/pom.xml b/org.eclipse.jgit.archive/pom.xml
index eea1d80..d4c5946 100644
--- a/org.eclipse.jgit.archive/pom.xml
+++ b/org.eclipse.jgit.archive/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.archive</artifactId>
diff --git a/org.eclipse.jgit.http.apache/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.http.apache/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.http.apache/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.http.apache/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.http.apache/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.http.apache/.settings/org.eclipse.pde.api.tools.prefs
index cd148d9..c0030de 100644
--- a/org.eclipse.jgit.http.apache/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.http.apache/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,4 +1,4 @@
-#Tue Oct 18 00:52:01 CEST 2011
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -8,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -47,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -58,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -75,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -83,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.http.apache/META-INF/MANIFEST.MF b/org.eclipse.jgit.http.apache/META-INF/MANIFEST.MF
index 2fc4543..3a1a401 100644
--- a/org.eclipse.jgit.http.apache/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.http.apache/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: org.eclipse.jgit.http.apache
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Localization: plugin
 Bundle-Vendor: %Provider-Name
@@ -22,10 +22,10 @@
  org.apache.http.impl.client;version="[4.3.0,5.0.0)",
  org.apache.http.impl.conn;version="[4.3.0,5.0.0)",
  org.apache.http.params;version="[4.3.0,5.0.0)",
- org.eclipse.jgit.nls;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport.http;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)"
-Export-Package: org.eclipse.jgit.transport.http.apache;version="4.8.1";
+ org.eclipse.jgit.nls;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport.http;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)"
+Export-Package: org.eclipse.jgit.transport.http.apache;version="4.9.6";
   uses:="org.apache.http.client,
    org.eclipse.jgit.transport.http,
    org.apache.http.entity,
diff --git a/org.eclipse.jgit.http.apache/pom.xml b/org.eclipse.jgit.http.apache/pom.xml
index 068e367..1ff8731 100644
--- a/org.eclipse.jgit.http.apache/pom.xml
+++ b/org.eclipse.jgit.http.apache/pom.xml
@@ -48,7 +48,7 @@
 	<parent>
 		<groupId>org.eclipse.jgit</groupId>
 		<artifactId>org.eclipse.jgit-parent</artifactId>
-		<version>4.8.1-SNAPSHOT</version>
+		<version>4.9.6-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>org.eclipse.jgit.http.apache</artifactId>
diff --git a/org.eclipse.jgit.http.server/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.http.server/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.http.server/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.http.server/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.http.server/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.http.server/.settings/org.eclipse.pde.api.tools.prefs
index cd148d9..c0030de 100644
--- a/org.eclipse.jgit.http.server/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.http.server/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,4 +1,4 @@
-#Tue Oct 18 00:52:01 CEST 2011
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -8,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -47,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -58,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -75,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -83,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.http.server/META-INF/MANIFEST.MF b/org.eclipse.jgit.http.server/META-INF/MANIFEST.MF
index 2b51b4b..aea610a 100644
--- a/org.eclipse.jgit.http.server/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.http.server/META-INF/MANIFEST.MF
@@ -2,13 +2,13 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.http.server
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
-Export-Package: org.eclipse.jgit.http.server;version="4.8.1",
- org.eclipse.jgit.http.server.glue;version="4.8.1";
+Export-Package: org.eclipse.jgit.http.server;version="4.9.6",
+ org.eclipse.jgit.http.server.glue;version="4.9.6";
   uses:="javax.servlet,javax.servlet.http",
- org.eclipse.jgit.http.server.resolver;version="4.8.1";
+ org.eclipse.jgit.http.server.resolver;version="4.9.6";
   uses:="org.eclipse.jgit.transport.resolver,
    org.eclipse.jgit.lib,
    org.eclipse.jgit.transport,
@@ -17,12 +17,12 @@
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: javax.servlet;version="[2.5.0,3.2.0)",
  javax.servlet.http;version="[2.5.0,3.2.0)",
- org.eclipse.jgit.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.dfs;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.file;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.nls;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revwalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport.resolver;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)"
+ org.eclipse.jgit.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.dfs;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.file;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.nls;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revwalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport.resolver;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)"
diff --git a/org.eclipse.jgit.http.server/pom.xml b/org.eclipse.jgit.http.server/pom.xml
index a011594..afaa409 100644
--- a/org.eclipse.jgit.http.server/pom.xml
+++ b/org.eclipse.jgit.http.server/pom.xml
@@ -52,7 +52,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.http.server</artifactId>
diff --git a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/GitSmartHttpTools.java b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/GitSmartHttpTools.java
index 03c9d8d..cfe4822 100644
--- a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/GitSmartHttpTools.java
+++ b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/GitSmartHttpTools.java
@@ -201,7 +201,7 @@ public static void sendError(HttpServletRequest req,
 		} else {
 			if (httpStatus < 400)
 				ServletUtils.consumeRequestBody(req);
-			res.sendError(httpStatus);
+			res.sendError(httpStatus, textForGit);
 		}
 	}
 
diff --git a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ServletUtils.java b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ServletUtils.java
index 1336d6e..c7fbaf6 100644
--- a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ServletUtils.java
+++ b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ServletUtils.java
@@ -112,7 +112,7 @@ public static InputStream getInputStream(final HttpServletRequest req)
 			throws IOException {
 		InputStream in = req.getInputStream();
 		final String enc = req.getHeader(HDR_CONTENT_ENCODING);
-		if (ENCODING_GZIP.equals(enc) || ENCODING_X_GZIP.equals(enc)) //$NON-NLS-1$
+		if (ENCODING_GZIP.equals(enc) || ENCODING_X_GZIP.equals(enc))
 			in = new GZIPInputStream(in);
 		else if (enc != null)
 			throw new IOException(MessageFormat.format(HttpServerText.get().encodingNotSupportedByThisLibrary
diff --git a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/glue/ServletBinder.java b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/glue/ServletBinder.java
index 9c3ed50..47443f5 100644
--- a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/glue/ServletBinder.java
+++ b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/glue/ServletBinder.java
@@ -60,4 +60,4 @@ public interface ServletBinder {
 	 *            the servlet to execute on this path.
 	 */
 	public void with(HttpServlet servlet);
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/AsIsFileService.java b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/AsIsFileService.java
index 88ad472..d20fe9f 100644
--- a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/AsIsFileService.java
+++ b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/AsIsFileService.java
@@ -47,7 +47,6 @@
 
 import org.eclipse.jgit.http.server.GitServlet;
 import org.eclipse.jgit.lib.Config;
-import org.eclipse.jgit.lib.Config.SectionParser;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.transport.resolver.ServiceNotAuthorizedException;
 import org.eclipse.jgit.transport.resolver.ServiceNotEnabledException;
@@ -71,13 +70,6 @@ public void access(HttpServletRequest req, Repository db)
 		}
 	};
 
-	private static final SectionParser<ServiceConfig> CONFIG = new SectionParser<ServiceConfig>() {
-		@Override
-		public ServiceConfig parse(final Config cfg) {
-			return new ServiceConfig(cfg);
-		}
-	};
-
 	private static class ServiceConfig {
 		final boolean enabled;
 
@@ -96,7 +88,7 @@ private static class ServiceConfig {
 	 *         {@code true}.
 	 */
 	protected static boolean isEnabled(Repository db) {
-		return db.getConfig().get(CONFIG).enabled;
+		return db.getConfig().get(ServiceConfig::new).enabled;
 	}
 
 	/**
diff --git a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/DefaultReceivePackFactory.java b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/DefaultReceivePackFactory.java
index 04e192b..c0ffbb6 100644
--- a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/DefaultReceivePackFactory.java
+++ b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/DefaultReceivePackFactory.java
@@ -46,7 +46,6 @@
 import javax.servlet.http.HttpServletRequest;
 
 import org.eclipse.jgit.lib.Config;
-import org.eclipse.jgit.lib.Config.SectionParser;
 import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.transport.ReceivePack;
@@ -68,13 +67,6 @@
  */
 public class DefaultReceivePackFactory implements
 		ReceivePackFactory<HttpServletRequest> {
-	private static final SectionParser<ServiceConfig> CONFIG = new SectionParser<ServiceConfig>() {
-		@Override
-		public ServiceConfig parse(final Config cfg) {
-			return new ServiceConfig(cfg);
-		}
-	};
-
 	private static class ServiceConfig {
 		final boolean set;
 
@@ -89,7 +81,7 @@ private static class ServiceConfig {
 	@Override
 	public ReceivePack create(final HttpServletRequest req, final Repository db)
 			throws ServiceNotEnabledException, ServiceNotAuthorizedException {
-		final ServiceConfig cfg = db.getConfig().get(CONFIG);
+		final ServiceConfig cfg = db.getConfig().get(ServiceConfig::new);
 		String user = req.getRemoteUser();
 
 		if (cfg.set) {
diff --git a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/DefaultUploadPackFactory.java b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/DefaultUploadPackFactory.java
index d01e2ef..642623b 100644
--- a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/DefaultUploadPackFactory.java
+++ b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/DefaultUploadPackFactory.java
@@ -46,7 +46,6 @@
 import javax.servlet.http.HttpServletRequest;
 
 import org.eclipse.jgit.lib.Config;
-import org.eclipse.jgit.lib.Config.SectionParser;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.transport.UploadPack;
 import org.eclipse.jgit.transport.resolver.ServiceNotAuthorizedException;
@@ -61,13 +60,6 @@
  */
 public class DefaultUploadPackFactory implements
 		UploadPackFactory<HttpServletRequest> {
-	private static final SectionParser<ServiceConfig> CONFIG = new SectionParser<ServiceConfig>() {
-		@Override
-		public ServiceConfig parse(final Config cfg) {
-			return new ServiceConfig(cfg);
-		}
-	};
-
 	private static class ServiceConfig {
 		final boolean enabled;
 
@@ -79,7 +71,7 @@ private static class ServiceConfig {
 	@Override
 	public UploadPack create(final HttpServletRequest req, final Repository db)
 			throws ServiceNotEnabledException, ServiceNotAuthorizedException {
-		if (db.getConfig().get(CONFIG).enabled)
+		if (db.getConfig().get(ServiceConfig::new).enabled)
 			return new UploadPack(db);
 		else
 			throw new ServiceNotEnabledException();
diff --git a/org.eclipse.jgit.http.test/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.http.test/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.http.test/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.http.test/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.http.test/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.http.test/.settings/org.eclipse.pde.api.tools.prefs
index cd148d9..c0030de 100644
--- a/org.eclipse.jgit.http.test/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.http.test/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,4 +1,4 @@
-#Tue Oct 18 00:52:01 CEST 2011
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -8,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -47,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -58,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -75,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -83,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.http.test/BUILD b/org.eclipse.jgit.http.test/BUILD
index ce2d611..85a2242 100644
--- a/org.eclipse.jgit.http.test/BUILD
+++ b/org.eclipse.jgit.http.test/BUILD
@@ -34,6 +34,7 @@
     srcs = glob(["src/**/*.java"]),
     deps = [
         "//lib:junit",
+        "//lib:servlet-api",
         "//org.eclipse.jgit.http.server:jgit-servlet",
         "//org.eclipse.jgit:jgit",
         "//org.eclipse.jgit.junit.http:junit-http",
diff --git a/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF
index 811585e..691b888 100644
--- a/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF
@@ -2,12 +2,14 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.http.test
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-Localization: plugin
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: javax.servlet;version="[2.5.0,3.2.0)",
  javax.servlet.http;version="[2.5.0,3.2.0)",
+ org.apache.commons.codec;version="[1.6.0, 2.0.0)",
+ org.apache.commons.codec.binary;version="[1.6.0, 2.0.0)",
  org.eclipse.jetty.continuation;version="[9.4.5,10.0.0)",
  org.eclipse.jetty.http;version="[9.4.5,10.0.0)",
  org.eclipse.jetty.io;version="[9.4.5,10.0.0)",
@@ -22,24 +24,24 @@
  org.eclipse.jetty.util.log;version="[9.4.5,10.0.0)",
  org.eclipse.jetty.util.security;version="[9.4.5,10.0.0)",
  org.eclipse.jetty.util.thread;version="[9.4.5,10.0.0)",
- org.eclipse.jgit.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.http.server;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.http.server.glue;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.http.server.resolver;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.dfs;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.file;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.junit;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.junit.http;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.nls;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revwalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.storage.file;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport.http;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport.http.apache;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport.resolver;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)",
+ org.eclipse.jgit.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.http.server;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.http.server.glue;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.http.server.resolver;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.dfs;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.file;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.junit;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.junit.http;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.nls;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revwalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.storage.file;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport.http;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport.http.apache;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport.resolver;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)",
  org.hamcrest.core;version="[1.1.0,2.0.0)",
  org.junit;version="[4.0.0,5.0.0)",
  org.junit.runner;version="[4.0.0,5.0.0)",
diff --git a/org.eclipse.jgit.http.test/pom.xml b/org.eclipse.jgit.http.test/pom.xml
index 1538601..a5c795a 100644
--- a/org.eclipse.jgit.http.test/pom.xml
+++ b/org.eclipse.jgit.http.test/pom.xml
@@ -51,7 +51,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.http.test</artifactId>
@@ -87,14 +87,12 @@
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit.junit.http</artifactId>
       <version>${project.version}</version>
-      <scope>test</scope>
     </dependency>
 
     <dependency>
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit.junit</artifactId>
       <version>${project.version}</version>
-      <scope>test</scope>
     </dependency>
 
     <dependency>
@@ -107,7 +105,6 @@
     <dependency>
       <groupId>org.eclipse.jetty</groupId>
       <artifactId>jetty-servlet</artifactId>
-      <scope>test</scope>
     </dependency>
   </dependencies>
 
diff --git a/org.eclipse.jgit.http.test/src/org/eclipse/jgit/http/test/TestRepositoryResolver.java b/org.eclipse.jgit.http.test/src/org/eclipse/jgit/http/test/TestRepositoryResolver.java
new file mode 100644
index 0000000..334e57c
--- /dev/null
+++ b/org.eclipse.jgit.http.test/src/org/eclipse/jgit/http/test/TestRepositoryResolver.java
@@ -0,0 +1,85 @@
+/*
+ * Copyright (C) 2016, 2017 Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.http.test;
+
+import javax.servlet.http.HttpServletRequest;
+
+import org.eclipse.jgit.errors.RepositoryNotFoundException;
+import org.eclipse.jgit.junit.TestRepository;
+import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.transport.resolver.RepositoryResolver;
+import org.eclipse.jgit.transport.resolver.ServiceNotEnabledException;
+
+/** A simple repository resolver for tests. */
+public final class TestRepositoryResolver
+		implements RepositoryResolver<HttpServletRequest> {
+
+	private final TestRepository<Repository> repo;
+
+	private final String repoName;
+
+	/**
+	 * Creates a new {@link TestRepositoryResolver} that resolves the given name to
+	 * the given repository.
+	 *
+	 * @param repo
+	 *            to resolve to
+	 * @param repoName
+	 *            to match
+	 */
+	public TestRepositoryResolver(TestRepository<Repository> repo, String repoName) {
+		this.repo = repo;
+		this.repoName = repoName;
+	}
+
+	@Override
+	public Repository open(HttpServletRequest req, String name)
+			throws RepositoryNotFoundException, ServiceNotEnabledException {
+		if (!name.equals(repoName)) {
+			throw new RepositoryNotFoundException(name);
+		}
+		Repository db = repo.getRepository();
+		db.incrementOpen();
+		return db;
+	}
+}
diff --git a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DumbClientSmartServerTest.java b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DumbClientSmartServerTest.java
index 06bfd79..727f9ba 100644
--- a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DumbClientSmartServerTest.java
+++ b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DumbClientSmartServerTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2010, Google Inc.
+ * Copyright (C) 2010, 2017 Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -60,12 +60,9 @@
 import java.util.List;
 import java.util.Map;
 
-import javax.servlet.http.HttpServletRequest;
-
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
 import org.eclipse.jgit.errors.NotSupportedException;
-import org.eclipse.jgit.errors.RepositoryNotFoundException;
 import org.eclipse.jgit.http.server.GitServlet;
 import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.junit.http.AccessEvent;
@@ -84,8 +81,6 @@
 import org.eclipse.jgit.transport.http.HttpConnectionFactory;
 import org.eclipse.jgit.transport.http.JDKHttpConnectionFactory;
 import org.eclipse.jgit.transport.http.apache.HttpClientConnectionFactory;
-import org.eclipse.jgit.transport.resolver.RepositoryResolver;
-import org.eclipse.jgit.transport.resolver.ServiceNotEnabledException;
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
@@ -124,19 +119,7 @@ public void setUp() throws Exception {
 
 		ServletContextHandler app = server.addContext("/git");
 		GitServlet gs = new GitServlet();
-		gs.setRepositoryResolver(new RepositoryResolver<HttpServletRequest>() {
-			@Override
-			public Repository open(HttpServletRequest req, String name)
-					throws RepositoryNotFoundException,
-					ServiceNotEnabledException {
-				if (!name.equals(srcName))
-					throw new RepositoryNotFoundException(name);
-
-				final Repository db = src.getRepository();
-				db.incrementOpen();
-				return db;
-			}
-		});
+		gs.setRepositoryResolver(new TestRepositoryResolver(src, srcName));
 		app.addServlet(new ServletHolder(gs), "/*");
 
 		server.setUp();
diff --git a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/SmartClientSmartServerSslTest.java b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/SmartClientSmartServerSslTest.java
new file mode 100644
index 0000000..7deb0d8
--- /dev/null
+++ b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/SmartClientSmartServerSslTest.java
@@ -0,0 +1,341 @@
+/*
+ * Copyright (C) 2017 Thomas Wolf <thomas.wolf@paranor.ch>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.http.test;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.EnumSet;
+import java.util.List;
+
+import javax.servlet.DispatcherType;
+import javax.servlet.Filter;
+import javax.servlet.FilterChain;
+import javax.servlet.FilterConfig;
+import javax.servlet.ServletException;
+import javax.servlet.ServletRequest;
+import javax.servlet.ServletResponse;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.eclipse.jetty.servlet.FilterHolder;
+import org.eclipse.jetty.servlet.ServletContextHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.eclipse.jgit.errors.TransportException;
+import org.eclipse.jgit.errors.UnsupportedCredentialItem;
+import org.eclipse.jgit.http.server.GitServlet;
+import org.eclipse.jgit.junit.TestRepository;
+import org.eclipse.jgit.junit.http.AccessEvent;
+import org.eclipse.jgit.junit.http.AppServer;
+import org.eclipse.jgit.junit.http.HttpTestCase;
+import org.eclipse.jgit.lib.ConfigConstants;
+import org.eclipse.jgit.lib.NullProgressMonitor;
+import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.revwalk.RevBlob;
+import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.transport.CredentialItem;
+import org.eclipse.jgit.transport.CredentialsProvider;
+import org.eclipse.jgit.transport.HttpTransport;
+import org.eclipse.jgit.transport.Transport;
+import org.eclipse.jgit.transport.URIish;
+import org.eclipse.jgit.transport.UsernamePasswordCredentialsProvider;
+import org.eclipse.jgit.transport.http.HttpConnectionFactory;
+import org.eclipse.jgit.transport.http.JDKHttpConnectionFactory;
+import org.eclipse.jgit.transport.http.apache.HttpClientConnectionFactory;
+import org.eclipse.jgit.util.HttpSupport;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+@RunWith(Parameterized.class)
+public class SmartClientSmartServerSslTest extends HttpTestCase {
+
+	// We run these tests with a server on localhost with a self-signed
+	// certificate. We don't do authentication tests here, so there's no need
+	// for username and password.
+	//
+	// But the server certificate will not validate. We know that Transport will
+	// ask whether we trust the server all the same. This credentials provider
+	// blindly trusts the self-signed certificate by answering "Yes" to all
+	// questions.
+	private CredentialsProvider testCredentials = new CredentialsProvider() {
+
+		@Override
+		public boolean isInteractive() {
+			return false;
+		}
+
+		@Override
+		public boolean supports(CredentialItem... items) {
+			for (CredentialItem item : items) {
+				if (item instanceof CredentialItem.InformationalMessage) {
+					continue;
+				}
+				if (item instanceof CredentialItem.YesNoType) {
+					continue;
+				}
+				return false;
+			}
+			return true;
+		}
+
+		@Override
+		public boolean get(URIish uri, CredentialItem... items)
+				throws UnsupportedCredentialItem {
+			for (CredentialItem item : items) {
+				if (item instanceof CredentialItem.InformationalMessage) {
+					continue;
+				}
+				if (item instanceof CredentialItem.YesNoType) {
+					((CredentialItem.YesNoType) item).setValue(true);
+					continue;
+				}
+				return false;
+			}
+			return true;
+		}
+	};
+
+	private URIish remoteURI;
+
+	private URIish secureURI;
+
+	private RevBlob A_txt;
+
+	private RevCommit A, B;
+
+	@Parameters
+	public static Collection<Object[]> data() {
+		// run all tests with both connection factories we have
+		return Arrays.asList(new Object[][] {
+				{ new JDKHttpConnectionFactory() },
+				{ new HttpClientConnectionFactory() } });
+	}
+
+	public SmartClientSmartServerSslTest(HttpConnectionFactory cf) {
+		HttpTransport.setConnectionFactory(cf);
+	}
+
+	@Override
+	protected AppServer createServer() {
+		return new AppServer(0, 0);
+	}
+
+	@Override
+	@Before
+	public void setUp() throws Exception {
+		super.setUp();
+
+		final TestRepository<Repository> src = createTestRepository();
+		final String srcName = src.getRepository().getDirectory().getName();
+		src.getRepository()
+				.getConfig()
+				.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
+						ConfigConstants.CONFIG_KEY_LOGALLREFUPDATES, true);
+
+		GitServlet gs = new GitServlet();
+
+		ServletContextHandler app = addNormalContext(gs, src, srcName);
+
+		server.setUp();
+
+		remoteURI = toURIish(app, srcName);
+		secureURI = new URIish(rewriteUrl(remoteURI.toString(), "https",
+				server.getSecurePort()));
+
+		A_txt = src.blob("A");
+		A = src.commit().add("A_txt", A_txt).create();
+		B = src.commit().parent(A).add("A_txt", "C").add("B", "B").create();
+		src.update(master, B);
+
+		src.update("refs/garbage/a/very/long/ref/name/to/compress", B);
+	}
+
+	private ServletContextHandler addNormalContext(GitServlet gs, TestRepository<Repository> src, String srcName) {
+		ServletContextHandler app = server.addContext("/git");
+		app.addFilter(new FilterHolder(new Filter() {
+
+			@Override
+			public void init(FilterConfig filterConfig)
+					throws ServletException {
+				// empty
+			}
+
+			// Redirects http to https for requests containing "/https/".
+			@Override
+			public void doFilter(ServletRequest request,
+					ServletResponse response, FilterChain chain)
+					throws IOException, ServletException {
+				final HttpServletResponse httpServletResponse = (HttpServletResponse) response;
+				final HttpServletRequest httpServletRequest = (HttpServletRequest) request;
+				final StringBuffer fullUrl = httpServletRequest.getRequestURL();
+				if (httpServletRequest.getQueryString() != null) {
+					fullUrl.append("?")
+							.append(httpServletRequest.getQueryString());
+				}
+				String urlString = rewriteUrl(fullUrl.toString(), "https",
+						server.getSecurePort());
+				httpServletResponse
+						.setStatus(HttpServletResponse.SC_MOVED_PERMANENTLY);
+				httpServletResponse.setHeader(HttpSupport.HDR_LOCATION,
+						urlString.replace("/https/", "/"));
+			}
+
+			@Override
+			public void destroy() {
+				// empty
+			}
+		}), "/https/*", EnumSet.of(DispatcherType.REQUEST));
+		app.addFilter(new FilterHolder(new Filter() {
+
+			@Override
+			public void init(FilterConfig filterConfig)
+					throws ServletException {
+				// empty
+			}
+
+			// Redirects https back to http for requests containing "/back/".
+			@Override
+			public void doFilter(ServletRequest request,
+					ServletResponse response, FilterChain chain)
+					throws IOException, ServletException {
+				final HttpServletResponse httpServletResponse = (HttpServletResponse) response;
+				final HttpServletRequest httpServletRequest = (HttpServletRequest) request;
+				final StringBuffer fullUrl = httpServletRequest.getRequestURL();
+				if (httpServletRequest.getQueryString() != null) {
+					fullUrl.append("?")
+							.append(httpServletRequest.getQueryString());
+				}
+				String urlString = rewriteUrl(fullUrl.toString(), "http",
+						server.getPort());
+				httpServletResponse
+						.setStatus(HttpServletResponse.SC_MOVED_PERMANENTLY);
+				httpServletResponse.setHeader(HttpSupport.HDR_LOCATION,
+						urlString.replace("/back/", "/"));
+			}
+
+			@Override
+			public void destroy() {
+				// empty
+			}
+		}), "/back/*", EnumSet.of(DispatcherType.REQUEST));
+		gs.setRepositoryResolver(new TestRepositoryResolver(src, srcName));
+		app.addServlet(new ServletHolder(gs), "/*");
+		return app;
+	}
+
+	@Test
+	public void testInitialClone_ViaHttps() throws Exception {
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		try (Transport t = Transport.open(dst, secureURI)) {
+			t.setCredentialsProvider(testCredentials);
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+		}
+		assertTrue(dst.hasObject(A_txt));
+		assertEquals(B, dst.exactRef(master).getObjectId());
+		fsck(dst, B);
+
+		List<AccessEvent> requests = getRequests();
+		assertEquals(2, requests.size());
+	}
+
+	@Test
+	public void testInitialClone_RedirectToHttps() throws Exception {
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		URIish cloneFrom = extendPath(remoteURI, "/https");
+		try (Transport t = Transport.open(dst, cloneFrom)) {
+			t.setCredentialsProvider(testCredentials);
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+		}
+		assertTrue(dst.hasObject(A_txt));
+		assertEquals(B, dst.exactRef(master).getObjectId());
+		fsck(dst, B);
+
+		List<AccessEvent> requests = getRequests();
+		assertEquals(3, requests.size());
+	}
+
+	@Test
+	public void testInitialClone_RedirectBackToHttp() throws Exception {
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		URIish cloneFrom = extendPath(secureURI, "/back");
+		try (Transport t = Transport.open(dst, cloneFrom)) {
+			t.setCredentialsProvider(testCredentials);
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			fail("Should have failed (redirect from https to http)");
+		} catch (TransportException e) {
+			assertTrue(e.getMessage().contains("not allowed"));
+		}
+	}
+
+	@Test
+	public void testInitialClone_SslFailure() throws Exception {
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		try (Transport t = Transport.open(dst, secureURI)) {
+			// Set a credentials provider that doesn't handle questions
+			t.setCredentialsProvider(
+					new UsernamePasswordCredentialsProvider("any", "anypwd"));
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			fail("Should have failed (SSL certificate not trusted)");
+		} catch (TransportException e) {
+			assertTrue(e.getMessage().contains("Secure connection"));
+		}
+	}
+
+}
diff --git a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/SmartClientSmartServerTest.java b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/SmartClientSmartServerTest.java
index ed223c9..51b7990 100644
--- a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/SmartClientSmartServerTest.java
+++ b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/SmartClientSmartServerTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2010, Google Inc.
+ * Copyright (C) 2010, 2017 Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -57,17 +57,21 @@
 import java.io.PrintWriter;
 import java.net.URISyntaxException;
 import java.nio.charset.StandardCharsets;
+import java.text.MessageFormat;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.EnumSet;
 import java.util.List;
 import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import javax.servlet.DispatcherType;
 import javax.servlet.Filter;
 import javax.servlet.FilterChain;
 import javax.servlet.FilterConfig;
+import javax.servlet.RequestDispatcher;
 import javax.servlet.ServletException;
 import javax.servlet.ServletRequest;
 import javax.servlet.ServletResponse;
@@ -78,8 +82,8 @@
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
 import org.eclipse.jgit.errors.RemoteRepositoryException;
-import org.eclipse.jgit.errors.RepositoryNotFoundException;
 import org.eclipse.jgit.errors.TransportException;
+import org.eclipse.jgit.errors.UnsupportedCredentialItem;
 import org.eclipse.jgit.http.server.GitServlet;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.internal.storage.dfs.DfsRepositoryDescription;
@@ -101,18 +105,22 @@
 import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.revwalk.RevBlob;
 import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.storage.file.FileBasedConfig;
+import org.eclipse.jgit.transport.CredentialItem;
+import org.eclipse.jgit.transport.CredentialsProvider;
 import org.eclipse.jgit.transport.FetchConnection;
 import org.eclipse.jgit.transport.HttpTransport;
 import org.eclipse.jgit.transport.RemoteRefUpdate;
 import org.eclipse.jgit.transport.Transport;
 import org.eclipse.jgit.transport.TransportHttp;
 import org.eclipse.jgit.transport.URIish;
+import org.eclipse.jgit.transport.UsernamePasswordCredentialsProvider;
 import org.eclipse.jgit.transport.http.HttpConnectionFactory;
 import org.eclipse.jgit.transport.http.JDKHttpConnectionFactory;
 import org.eclipse.jgit.transport.http.apache.HttpClientConnectionFactory;
-import org.eclipse.jgit.transport.resolver.RepositoryResolver;
-import org.eclipse.jgit.transport.resolver.ServiceNotEnabledException;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.HttpSupport;
+import org.eclipse.jgit.util.SystemReader;
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
@@ -125,12 +133,19 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 
 	private Repository remoteRepository;
 
+	private CredentialsProvider testCredentials = new UsernamePasswordCredentialsProvider(
+			AppServer.username, AppServer.password);
+
 	private URIish remoteURI;
 
 	private URIish brokenURI;
 
 	private URIish redirectURI;
 
+	private URIish authURI;
+
+	private URIish authOnPostURI;
+
 	private RevBlob A_txt;
 
 	private RevCommit A, B;
@@ -165,7 +180,11 @@ public void setUp() throws Exception {
 
 		ServletContextHandler broken = addBrokenContext(gs, src, srcName);
 
-		ServletContextHandler redirect = addRedirectContext(gs, src, srcName);
+		ServletContextHandler redirect = addRedirectContext(gs);
+
+		ServletContextHandler auth = addAuthContext(gs, "auth");
+
+		ServletContextHandler authOnPost = addAuthContext(gs, "pauth", "POST");
 
 		server.setUp();
 
@@ -173,6 +192,8 @@ public void setUp() throws Exception {
 		remoteURI = toURIish(app, srcName);
 		brokenURI = toURIish(broken, srcName);
 		redirectURI = toURIish(redirect, srcName);
+		authURI = toURIish(auth, srcName);
+		authOnPostURI = toURIish(authOnPost, srcName);
 
 		A_txt = src.blob("A");
 		A = src.commit().add("A_txt", A_txt).create();
@@ -184,7 +205,52 @@ public void setUp() throws Exception {
 
 	private ServletContextHandler addNormalContext(GitServlet gs, TestRepository<Repository> src, String srcName) {
 		ServletContextHandler app = server.addContext("/git");
-		gs.setRepositoryResolver(new TestRepoResolver(src, srcName));
+		app.addFilter(new FilterHolder(new Filter() {
+
+			@Override
+			public void init(FilterConfig filterConfig)
+					throws ServletException {
+				// empty
+			}
+
+			// Does an internal forward for GET requests containing "/post/",
+			// and issues a 301 redirect on POST requests for such URLs. Used
+			// in the POST redirect tests.
+			@Override
+			public void doFilter(ServletRequest request,
+					ServletResponse response, FilterChain chain)
+					throws IOException, ServletException {
+				final HttpServletResponse httpServletResponse = (HttpServletResponse) response;
+				final HttpServletRequest httpServletRequest = (HttpServletRequest) request;
+				final StringBuffer fullUrl = httpServletRequest.getRequestURL();
+				if (httpServletRequest.getQueryString() != null) {
+					fullUrl.append("?")
+							.append(httpServletRequest.getQueryString());
+				}
+				String urlString = fullUrl.toString();
+				if ("POST".equalsIgnoreCase(httpServletRequest.getMethod())) {
+					httpServletResponse.setStatus(
+							HttpServletResponse.SC_MOVED_PERMANENTLY);
+					httpServletResponse.setHeader(HttpSupport.HDR_LOCATION,
+							urlString.replace("/post/", "/"));
+				} else {
+					String path = httpServletRequest.getPathInfo();
+					path = path.replace("/post/", "/");
+					if (httpServletRequest.getQueryString() != null) {
+						path += '?' + httpServletRequest.getQueryString();
+					}
+					RequestDispatcher dispatcher = httpServletRequest
+							.getRequestDispatcher(path);
+					dispatcher.forward(httpServletRequest, httpServletResponse);
+				}
+			}
+
+			@Override
+			public void destroy() {
+				// empty
+			}
+		}), "/post/*", EnumSet.of(DispatcherType.REQUEST));
+		gs.setRepositoryResolver(new TestRepositoryResolver(src, srcName));
 		app.addServlet(new ServletHolder(gs), "/*");
 		return app;
 	}
@@ -222,12 +288,28 @@ public void destroy() {
 		return broken;
 	}
 
-	@SuppressWarnings("unused")
-	private ServletContextHandler addRedirectContext(GitServlet gs,
-			TestRepository<Repository> src, String srcName) {
+	private ServletContextHandler addAuthContext(GitServlet gs,
+			String contextPath, String... methods) {
+		ServletContextHandler auth = server.addContext('/' + contextPath);
+		auth.addServlet(new ServletHolder(gs), "/*");
+		return server.authBasic(auth, methods);
+	}
+
+	private ServletContextHandler addRedirectContext(GitServlet gs) {
 		ServletContextHandler redirect = server.addContext("/redirect");
 		redirect.addFilter(new FilterHolder(new Filter() {
 
+			// Enables tests for different codes, and for multiple redirects.
+			// First parameter is the number of redirects, second one is the
+			// redirect status code that should be used
+			private Pattern responsePattern = Pattern
+					.compile("/response/(\\d+)/(30[1237])/");
+
+			// Enables tests to specify the context that the request should be
+			// redirected to in the end. If not present, redirects got to the
+			// normal /git context.
+			private Pattern targetPattern = Pattern.compile("/target(/\\w+)/");
+
 			@Override
 			public void init(FilterConfig filterConfig)
 					throws ServletException {
@@ -245,10 +327,50 @@ public void doFilter(ServletRequest request,
 					fullUrl.append("?")
 							.append(httpServletRequest.getQueryString());
 				}
-				httpServletResponse
-						.setStatus(HttpServletResponse.SC_MOVED_PERMANENTLY);
+				String urlString = fullUrl.toString();
+				if (urlString.contains("/loop/")) {
+					urlString = urlString.replace("/loop/", "/loop/x/");
+					if (urlString.contains("/loop/x/x/x/x/x/x/x/x/")) {
+						// Go back to initial.
+						urlString = urlString.replace("/loop/x/x/x/x/x/x/x/x/",
+								"/loop/");
+					}
+					httpServletResponse.setStatus(
+							HttpServletResponse.SC_MOVED_TEMPORARILY);
+					httpServletResponse.setHeader(HttpSupport.HDR_LOCATION,
+							urlString);
+					return;
+				}
+				int responseCode = HttpServletResponse.SC_MOVED_PERMANENTLY;
+				int nofRedirects = 0;
+				Matcher matcher = responsePattern.matcher(urlString);
+				if (matcher.find()) {
+					nofRedirects = Integer
+							.parseUnsignedInt(matcher.group(1));
+					responseCode = Integer.parseUnsignedInt(matcher.group(2));
+					if (--nofRedirects <= 0) {
+						urlString = urlString.substring(0, matcher.start())
+								+ '/' + urlString.substring(matcher.end());
+					} else {
+						urlString = urlString.substring(0, matcher.start())
+								+ "/response/" + nofRedirects + "/"
+								+ responseCode + '/'
+								+ urlString.substring(matcher.end());
+					}
+				}
+				httpServletResponse.setStatus(responseCode);
+				if (nofRedirects <= 0) {
+					String targetContext = "/git";
+					matcher = targetPattern.matcher(urlString);
+					if (matcher.find()) {
+						urlString = urlString.substring(0, matcher.start())
+								+ '/' + urlString.substring(matcher.end());
+						targetContext = matcher.group(1);
+					}
+					urlString = urlString.replace("/redirect", targetContext);
+				}
 				httpServletResponse.setHeader(HttpSupport.HDR_LOCATION,
-						fullUrl.toString().replace("/redirect", "/git"));
+						urlString);
 			}
 
 			@Override
@@ -373,13 +495,332 @@ public void testInitialClone_Small() throws Exception {
 				.getResponseHeader(HDR_CONTENT_TYPE));
 	}
 
+	private void initialClone_Redirect(int nofRedirects, int code)
+			throws Exception {
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		URIish cloneFrom = redirectURI;
+		if (code != 301 || nofRedirects > 1) {
+			cloneFrom = extendPath(cloneFrom,
+					"/response/" + nofRedirects + "/" + code);
+		}
+		try (Transport t = Transport.open(dst, cloneFrom)) {
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+		}
+
+		assertTrue(dst.hasObject(A_txt));
+		assertEquals(B, dst.exactRef(master).getObjectId());
+		fsck(dst, B);
+
+		List<AccessEvent> requests = getRequests();
+		assertEquals(2 + nofRedirects, requests.size());
+
+		int n = 0;
+		while (n < nofRedirects) {
+			AccessEvent redirect = requests.get(n++);
+			assertEquals(code, redirect.getStatus());
+		}
+
+		AccessEvent info = requests.get(n++);
+		assertEquals("GET", info.getMethod());
+		assertEquals(join(remoteURI, "info/refs"), info.getPath());
+		assertEquals(1, info.getParameters().size());
+		assertEquals("git-upload-pack", info.getParameter("service"));
+		assertEquals(200, info.getStatus());
+		assertEquals("application/x-git-upload-pack-advertisement",
+				info.getResponseHeader(HDR_CONTENT_TYPE));
+		assertEquals("gzip", info.getResponseHeader(HDR_CONTENT_ENCODING));
+
+		AccessEvent service = requests.get(n++);
+		assertEquals("POST", service.getMethod());
+		assertEquals(join(remoteURI, "git-upload-pack"), service.getPath());
+		assertEquals(0, service.getParameters().size());
+		assertNotNull("has content-length",
+				service.getRequestHeader(HDR_CONTENT_LENGTH));
+		assertNull("not chunked",
+				service.getRequestHeader(HDR_TRANSFER_ENCODING));
+
+		assertEquals(200, service.getStatus());
+		assertEquals("application/x-git-upload-pack-result",
+				service.getResponseHeader(HDR_CONTENT_TYPE));
+	}
+
 	@Test
-	public void testInitialClone_RedirectSmall() throws Exception {
+	public void testInitialClone_Redirect301Small() throws Exception {
+		initialClone_Redirect(1, 301);
+	}
+
+	@Test
+	public void testInitialClone_Redirect302Small() throws Exception {
+		initialClone_Redirect(1, 302);
+	}
+
+	@Test
+	public void testInitialClone_Redirect303Small() throws Exception {
+		initialClone_Redirect(1, 303);
+	}
+
+	@Test
+	public void testInitialClone_Redirect307Small() throws Exception {
+		initialClone_Redirect(1, 307);
+	}
+
+	@Test
+	public void testInitialClone_RedirectMultiple() throws Exception {
+		initialClone_Redirect(4, 302);
+	}
+
+	@Test
+	public void testInitialClone_RedirectMax() throws Exception {
+		FileBasedConfig userConfig = SystemReader.getInstance()
+				.openUserConfig(null, FS.DETECTED);
+		userConfig.setInt("http", null, "maxRedirects", 4);
+		userConfig.save();
+		initialClone_Redirect(4, 302);
+	}
+
+	@Test
+	public void testInitialClone_RedirectTooOften() throws Exception {
+		FileBasedConfig userConfig = SystemReader.getInstance()
+				.openUserConfig(null, FS.DETECTED);
+		userConfig.setInt("http", null, "maxRedirects", 3);
+		userConfig.save();
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		URIish cloneFrom = extendPath(redirectURI, "/response/4/302");
+		String remoteUri = cloneFrom.toString();
+		try (Transport t = Transport.open(dst, cloneFrom)) {
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			fail("Should have failed (too many redirects)");
+		} catch (TransportException e) {
+			String expectedMessageBegin = remoteUri.toString() + ": "
+					+ MessageFormat.format(JGitText.get().redirectLimitExceeded,
+							"3", remoteUri.replace("/4/", "/1/") + '/', "");
+			String message = e.getMessage();
+			if (message.length() > expectedMessageBegin.length()) {
+				message = message.substring(0, expectedMessageBegin.length());
+			}
+			assertEquals(expectedMessageBegin, message);
+		}
+	}
+
+	@Test
+	public void testInitialClone_RedirectLoop() throws Exception {
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		URIish cloneFrom = extendPath(redirectURI, "/loop");
+		try (Transport t = Transport.open(dst, cloneFrom)) {
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			fail("Should have failed (redirect loop)");
+		} catch (TransportException e) {
+			assertTrue(e.getMessage().contains("Redirected more than"));
+		}
+	}
+
+	@Test
+	public void testInitialClone_RedirectOnPostAllowed() throws Exception {
+		FileBasedConfig userConfig = SystemReader.getInstance()
+				.openUserConfig(null, FS.DETECTED);
+		userConfig.setString("http", null, "followRedirects", "true");
+		userConfig.save();
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		URIish cloneFrom = extendPath(remoteURI, "/post");
+		try (Transport t = Transport.open(dst, cloneFrom)) {
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+		}
+
+		assertTrue(dst.hasObject(A_txt));
+		assertEquals(B, dst.exactRef(master).getObjectId());
+		fsck(dst, B);
+
+		List<AccessEvent> requests = getRequests();
+		assertEquals(3, requests.size());
+
+		AccessEvent info = requests.get(0);
+		assertEquals("GET", info.getMethod());
+		assertEquals(join(cloneFrom, "info/refs"), info.getPath());
+		assertEquals(1, info.getParameters().size());
+		assertEquals("git-upload-pack", info.getParameter("service"));
+		assertEquals(200, info.getStatus());
+		assertEquals("application/x-git-upload-pack-advertisement",
+				info.getResponseHeader(HDR_CONTENT_TYPE));
+		assertEquals("gzip", info.getResponseHeader(HDR_CONTENT_ENCODING));
+
+		AccessEvent redirect = requests.get(1);
+		assertEquals("POST", redirect.getMethod());
+		assertEquals(301, redirect.getStatus());
+
+		AccessEvent service = requests.get(2);
+		assertEquals("POST", service.getMethod());
+		assertEquals(join(remoteURI, "git-upload-pack"), service.getPath());
+		assertEquals(0, service.getParameters().size());
+		assertNotNull("has content-length",
+				service.getRequestHeader(HDR_CONTENT_LENGTH));
+		assertNull("not chunked",
+				service.getRequestHeader(HDR_TRANSFER_ENCODING));
+
+		assertEquals(200, service.getStatus());
+		assertEquals("application/x-git-upload-pack-result",
+				service.getResponseHeader(HDR_CONTENT_TYPE));
+	}
+
+	@Test
+	public void testInitialClone_RedirectOnPostForbidden() throws Exception {
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		URIish cloneFrom = extendPath(remoteURI, "/post");
+		try (Transport t = Transport.open(dst, cloneFrom)) {
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			fail("Should have failed (redirect on POST)");
+		} catch (TransportException e) {
+			assertTrue(e.getMessage().contains("301"));
+		}
+	}
+
+	@Test
+	public void testInitialClone_RedirectForbidden() throws Exception {
+		FileBasedConfig userConfig = SystemReader.getInstance()
+				.openUserConfig(null, FS.DETECTED);
+		userConfig.setString("http", null, "followRedirects", "false");
+		userConfig.save();
+
 		Repository dst = createBareRepository();
 		assertFalse(dst.hasObject(A_txt));
 
 		try (Transport t = Transport.open(dst, redirectURI)) {
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			fail("Should have failed (redirects forbidden)");
+		} catch (TransportException e) {
+			assertTrue(
+					e.getMessage().contains("http.followRedirects is false"));
+		}
+	}
+
+	@Test
+	public void testInitialClone_WithAuthentication() throws Exception {
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		try (Transport t = Transport.open(dst, authURI)) {
+			t.setCredentialsProvider(testCredentials);
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+		}
+
+		assertTrue(dst.hasObject(A_txt));
+		assertEquals(B, dst.exactRef(master).getObjectId());
+		fsck(dst, B);
+
+		List<AccessEvent> requests = getRequests();
+		assertEquals(3, requests.size());
+
+		AccessEvent info = requests.get(0);
+		assertEquals("GET", info.getMethod());
+		assertEquals(401, info.getStatus());
+
+		info = requests.get(1);
+		assertEquals("GET", info.getMethod());
+		assertEquals(join(authURI, "info/refs"), info.getPath());
+		assertEquals(1, info.getParameters().size());
+		assertEquals("git-upload-pack", info.getParameter("service"));
+		assertEquals(200, info.getStatus());
+		assertEquals("application/x-git-upload-pack-advertisement",
+				info.getResponseHeader(HDR_CONTENT_TYPE));
+		assertEquals("gzip", info.getResponseHeader(HDR_CONTENT_ENCODING));
+
+		AccessEvent service = requests.get(2);
+		assertEquals("POST", service.getMethod());
+		assertEquals(join(authURI, "git-upload-pack"), service.getPath());
+		assertEquals(0, service.getParameters().size());
+		assertNotNull("has content-length",
+				service.getRequestHeader(HDR_CONTENT_LENGTH));
+		assertNull("not chunked",
+				service.getRequestHeader(HDR_TRANSFER_ENCODING));
+
+		assertEquals(200, service.getStatus());
+		assertEquals("application/x-git-upload-pack-result",
+				service.getResponseHeader(HDR_CONTENT_TYPE));
+	}
+
+	@Test
+	public void testInitialClone_WithAuthenticationNoCredentials()
+			throws Exception {
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		try (Transport t = Transport.open(dst, authURI)) {
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			fail("Should not have succeeded -- no authentication");
+		} catch (TransportException e) {
+			String msg = e.getMessage();
+			assertTrue("Unexpected exception message: " + msg,
+					msg.contains("no CredentialsProvider"));
+		}
+		List<AccessEvent> requests = getRequests();
+		assertEquals(1, requests.size());
+
+		AccessEvent info = requests.get(0);
+		assertEquals("GET", info.getMethod());
+		assertEquals(401, info.getStatus());
+	}
+
+	@Test
+	public void testInitialClone_WithAuthenticationWrongCredentials()
+			throws Exception {
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		try (Transport t = Transport.open(dst, authURI)) {
+			t.setCredentialsProvider(new UsernamePasswordCredentialsProvider(
+					AppServer.username, "wrongpassword"));
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			fail("Should not have succeeded -- wrong password");
+		} catch (TransportException e) {
+			String msg = e.getMessage();
+			assertTrue("Unexpected exception message: " + msg,
+					msg.contains("auth"));
+		}
+		List<AccessEvent> requests = getRequests();
+		// Once without authentication plus three re-tries with authentication
+		assertEquals(4, requests.size());
+
+		for (AccessEvent event : requests) {
+			assertEquals("GET", event.getMethod());
+			assertEquals(401, event.getStatus());
+		}
+	}
+
+	@Test
+	public void testInitialClone_WithAuthenticationAfterRedirect()
+			throws Exception {
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		URIish cloneFrom = extendPath(redirectURI, "/target/auth");
+		CredentialsProvider uriSpecificCredentialsProvider = new UsernamePasswordCredentialsProvider(
+				"unknown", "none") {
+			@Override
+			public boolean get(URIish uri, CredentialItem... items)
+					throws UnsupportedCredentialItem {
+				// Only return the true credentials if the uri path starts with
+				// /auth. This ensures that we do provide the correct
+				// credentials only for the URi after the redirect, making the
+				// test fail if we should be asked for the credentials for the
+				// original URI.
+				if (uri.getPath().startsWith("/auth")) {
+					return testCredentials.get(uri, items);
+				}
+				return super.get(uri, items);
+			}
+		};
+		try (Transport t = Transport.open(dst, cloneFrom)) {
+			t.setCredentialsProvider(uriSpecificCredentialsProvider);
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
 		}
 
 		assertTrue(dst.hasObject(A_txt));
@@ -389,12 +830,19 @@ public void testInitialClone_RedirectSmall() throws Exception {
 		List<AccessEvent> requests = getRequests();
 		assertEquals(4, requests.size());
 
-		AccessEvent firstRedirect = requests.get(0);
-		assertEquals(301, firstRedirect.getStatus());
+		AccessEvent redirect = requests.get(0);
+		assertEquals("GET", redirect.getMethod());
+		assertEquals(join(cloneFrom, "info/refs"), redirect.getPath());
+		assertEquals(301, redirect.getStatus());
 
 		AccessEvent info = requests.get(1);
 		assertEquals("GET", info.getMethod());
-		assertEquals(join(remoteURI, "info/refs"), info.getPath());
+		assertEquals(join(authURI, "info/refs"), info.getPath());
+		assertEquals(401, info.getStatus());
+
+		info = requests.get(2);
+		assertEquals("GET", info.getMethod());
+		assertEquals(join(authURI, "info/refs"), info.getPath());
 		assertEquals(1, info.getParameters().size());
 		assertEquals("git-upload-pack", info.getParameter("service"));
 		assertEquals(200, info.getStatus());
@@ -402,12 +850,56 @@ public void testInitialClone_RedirectSmall() throws Exception {
 				info.getResponseHeader(HDR_CONTENT_TYPE));
 		assertEquals("gzip", info.getResponseHeader(HDR_CONTENT_ENCODING));
 
-		AccessEvent secondRedirect = requests.get(2);
-		assertEquals(301, secondRedirect.getStatus());
-
 		AccessEvent service = requests.get(3);
 		assertEquals("POST", service.getMethod());
-		assertEquals(join(remoteURI, "git-upload-pack"), service.getPath());
+		assertEquals(join(authURI, "git-upload-pack"), service.getPath());
+		assertEquals(0, service.getParameters().size());
+		assertNotNull("has content-length",
+				service.getRequestHeader(HDR_CONTENT_LENGTH));
+		assertNull("not chunked",
+				service.getRequestHeader(HDR_TRANSFER_ENCODING));
+
+		assertEquals(200, service.getStatus());
+		assertEquals("application/x-git-upload-pack-result",
+				service.getResponseHeader(HDR_CONTENT_TYPE));
+	}
+
+	@Test
+	public void testInitialClone_WithAuthenticationOnPostOnly()
+			throws Exception {
+		Repository dst = createBareRepository();
+		assertFalse(dst.hasObject(A_txt));
+
+		try (Transport t = Transport.open(dst, authOnPostURI)) {
+			t.setCredentialsProvider(testCredentials);
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+		}
+
+		assertTrue(dst.hasObject(A_txt));
+		assertEquals(B, dst.exactRef(master).getObjectId());
+		fsck(dst, B);
+
+		List<AccessEvent> requests = getRequests();
+		assertEquals(3, requests.size());
+
+		AccessEvent info = requests.get(0);
+		assertEquals("GET", info.getMethod());
+		assertEquals(join(authOnPostURI, "info/refs"), info.getPath());
+		assertEquals(1, info.getParameters().size());
+		assertEquals("git-upload-pack", info.getParameter("service"));
+		assertEquals(200, info.getStatus());
+		assertEquals("application/x-git-upload-pack-advertisement",
+				info.getResponseHeader(HDR_CONTENT_TYPE));
+		assertEquals("gzip", info.getResponseHeader(HDR_CONTENT_ENCODING));
+
+		AccessEvent service = requests.get(1);
+		assertEquals("POST", service.getMethod());
+		assertEquals(join(authOnPostURI, "git-upload-pack"), service.getPath());
+		assertEquals(401, service.getStatus());
+
+		service = requests.get(2);
+		assertEquals("POST", service.getMethod());
+		assertEquals(join(authOnPostURI, "git-upload-pack"), service.getPath());
 		assertEquals(0, service.getParameters().size());
 		assertNotNull("has content-length",
 				service.getRequestHeader(HDR_CONTENT_LENGTH));
@@ -619,7 +1111,7 @@ public void testFetch_RefsUnreadableOnUpload() throws Exception {
 
 			ServletContextHandler app = noRefServer.addContext("/git");
 			GitServlet gs = new GitServlet();
-			gs.setRepositoryResolver(new TestRepoResolver(repo, repoName));
+			gs.setRepositoryResolver(new TestRepositoryResolver(repo, repoName));
 			app.addServlet(new ServletHolder(gs), "/*");
 			noRefServer.setUp();
 
@@ -822,28 +1314,4 @@ private void enableReceivePack() throws IOException {
 		cfg.save();
 	}
 
-	private final class TestRepoResolver
-			implements RepositoryResolver<HttpServletRequest> {
-
-		private final TestRepository<Repository> repo;
-
-		private final String repoName;
-
-		private TestRepoResolver(TestRepository<Repository> repo,
-				String repoName) {
-			this.repo = repo;
-			this.repoName = repoName;
-		}
-
-		@Override
-		public Repository open(HttpServletRequest req, String name)
-				throws RepositoryNotFoundException, ServiceNotEnabledException {
-			if (!name.equals(repoName))
-				throw new RepositoryNotFoundException(name);
-
-			Repository db = repo.getRepository();
-			db.incrementOpen();
-			return db;
-		}
-	}
 }
diff --git a/org.eclipse.jgit.junit.http/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.junit.http/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.junit.http/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.junit.http/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.junit.http/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.junit.http/.settings/org.eclipse.pde.api.tools.prefs
index cd148d9..c0030de 100644
--- a/org.eclipse.jgit.junit.http/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.junit.http/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,4 +1,4 @@
-#Tue Oct 18 00:52:01 CEST 2011
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -8,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -47,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -58,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -75,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -83,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.junit.http/META-INF/MANIFEST.MF b/org.eclipse.jgit.junit.http/META-INF/MANIFEST.MF
index 00a7a65..71feeca 100644
--- a/org.eclipse.jgit.junit.http/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.junit.http/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.junit.http
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
@@ -20,16 +20,17 @@
  org.eclipse.jetty.util.component;version="[9.4.5,10.0.0)",
  org.eclipse.jetty.util.log;version="[9.4.5,10.0.0)",
  org.eclipse.jetty.util.security;version="[9.4.5,10.0.0)",
- org.eclipse.jgit.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.http.server;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.file;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.junit;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revwalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport.resolver;version="[4.8.1,4.9.0)",
+ org.eclipse.jetty.util.ssl;version="[9.4.5,10.0.0)",
+ org.eclipse.jgit.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.http.server;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.file;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.junit;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revwalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport.resolver;version="[4.9.6,4.10.0)",
  org.junit;version="[4.0.0,5.0.0)"
-Export-Package: org.eclipse.jgit.junit.http;version="4.8.1";
+Export-Package: org.eclipse.jgit.junit.http;version="4.9.6";
   uses:="org.eclipse.jgit.transport,
    org.eclipse.jgit.junit,
    javax.servlet.http,
diff --git a/org.eclipse.jgit.junit.http/pom.xml b/org.eclipse.jgit.junit.http/pom.xml
index 0c1acf9..cd750f1 100644
--- a/org.eclipse.jgit.junit.http/pom.xml
+++ b/org.eclipse.jgit.junit.http/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.junit.http</artifactId>
diff --git a/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/AppServer.java b/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/AppServer.java
index 28c0f21..e257cf6 100644
--- a/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/AppServer.java
+++ b/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/AppServer.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2010, 2012 Google Inc.
+ * Copyright (C) 2010, 2017 Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -46,15 +46,20 @@
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 
+import java.io.File;
+import java.io.IOException;
 import java.net.InetAddress;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.UnknownHostException;
+import java.nio.file.Files;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Locale;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.ConcurrentMap;
 
+import org.eclipse.jetty.http.HttpVersion;
 import org.eclipse.jetty.security.AbstractLoginService;
 import org.eclipse.jetty.security.Authenticator;
 import org.eclipse.jetty.security.ConstraintMapping;
@@ -65,10 +70,12 @@
 import org.eclipse.jetty.server.HttpConnectionFactory;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.server.ServerConnector;
+import org.eclipse.jetty.server.SslConnectionFactory;
 import org.eclipse.jetty.server.handler.ContextHandlerCollection;
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.util.security.Constraint;
 import org.eclipse.jetty.util.security.Password;
+import org.eclipse.jetty.util.ssl.SslContextFactory;
 import org.eclipse.jgit.transport.URIish;
 
 /**
@@ -88,6 +95,12 @@ public class AppServer {
 	/** Password for {@link #username} in secured access areas. */
 	public static final String password = "letmein";
 
+	/** SSL keystore password; must have at least 6 characters. */
+	private static final String keyPassword = "mykeys";
+
+	/** Role for authentication. */
+	private static final String authRole = "can-access";
+
 	static {
 		// Install a logger that throws warning messages.
 		//
@@ -97,48 +110,141 @@ public class AppServer {
 
 	private final Server server;
 
+	private final HttpConfiguration config;
+
 	private final ServerConnector connector;
 
+	private final HttpConfiguration secureConfig;
+
+	private final ServerConnector secureConnector;
+
 	private final ContextHandlerCollection contexts;
 
 	private final TestRequestLog log;
 
+	private List<File> filesToDelete = new ArrayList<>();
+
 	public AppServer() {
-		this(0);
+		this(0, -1);
 	}
 
 	/**
 	 * @param port
-	 *            the http port number
+	 *            the http port number; may be zero to allocate a port
+	 *            dynamically
 	 * @since 4.2
 	 */
 	public AppServer(int port) {
+		this(port, -1);
+	}
+
+	/**
+	 * @param port
+	 *            for http, may be zero to allocate a port dynamically
+	 * @param sslPort
+	 *            for https,may be zero to allocate a port dynamically. If
+	 *            negative, the server will be set up without https support.
+	 * @since 4.9
+	 */
+	public AppServer(int port, int sslPort) {
 		server = new Server();
 
-		HttpConfiguration http_config = new HttpConfiguration();
-		http_config.setSecureScheme("https");
-		http_config.setSecurePort(8443);
-		http_config.setOutputBufferSize(32768);
+		config = new HttpConfiguration();
+		config.setSecureScheme("https");
+		config.setSecurePort(0);
+		config.setOutputBufferSize(32768);
 
 		connector = new ServerConnector(server,
-				new HttpConnectionFactory(http_config));
+				new HttpConnectionFactory(config));
 		connector.setPort(port);
+		String ip;
+		String hostName;
 		try {
 			final InetAddress me = InetAddress.getByName("localhost");
-			connector.setHost(me.getHostAddress());
+			ip = me.getHostAddress();
+			connector.setHost(ip);
+			hostName = InetAddress.getLocalHost().getCanonicalHostName();
 		} catch (UnknownHostException e) {
 			throw new RuntimeException("Cannot find localhost", e);
 		}
 
+		if (sslPort >= 0) {
+			SslContextFactory sslContextFactory = createTestSslContextFactory(
+					hostName);
+			secureConfig = new HttpConfiguration(config);
+			secureConnector = new ServerConnector(server,
+					new SslConnectionFactory(sslContextFactory,
+							HttpVersion.HTTP_1_1.asString()),
+					new HttpConnectionFactory(secureConfig));
+			secureConnector.setPort(sslPort);
+			secureConnector.setHost(ip);
+		} else {
+			secureConfig = null;
+			secureConnector = null;
+		}
+
 		contexts = new ContextHandlerCollection();
 
 		log = new TestRequestLog();
 		log.setHandler(contexts);
 
-		server.setConnectors(new Connector[] { connector });
+		if (secureConnector == null) {
+			server.setConnectors(new Connector[] { connector });
+		} else {
+			server.setConnectors(
+					new Connector[] { connector, secureConnector });
+		}
 		server.setHandler(log);
 	}
 
+	private SslContextFactory createTestSslContextFactory(String hostName) {
+		SslContextFactory factory = new SslContextFactory(true);
+
+		String dName = "CN=,OU=,O=,ST=,L=,C=";
+
+		try {
+			File tmpDir = Files.createTempDirectory("jks").toFile();
+			tmpDir.deleteOnExit();
+			makePrivate(tmpDir);
+			File keyStore = new File(tmpDir, "keystore.jks");
+			Runtime.getRuntime().exec(
+					new String[] {
+							"keytool", //
+							"-keystore", keyStore.getAbsolutePath(), //
+							"-storepass", keyPassword,
+							"-alias", hostName, //
+							"-genkeypair", //
+							"-keyalg", "RSA", //
+							"-keypass", keyPassword, //
+							"-dname", dName, //
+							"-validity", "2" //
+					}).waitFor();
+			keyStore.deleteOnExit();
+			makePrivate(keyStore);
+			filesToDelete.add(keyStore);
+			filesToDelete.add(tmpDir);
+			factory.setKeyStorePath(keyStore.getAbsolutePath());
+			factory.setKeyStorePassword(keyPassword);
+			factory.setKeyManagerPassword(keyPassword);
+			factory.setTrustStorePath(keyStore.getAbsolutePath());
+			factory.setTrustStorePassword(keyPassword);
+		} catch (InterruptedException | IOException e) {
+			throw new RuntimeException("Cannot create ssl key/certificate", e);
+		}
+		return factory;
+	}
+
+	private void makePrivate(File file) {
+		file.setReadable(false);
+		file.setWritable(false);
+		file.setExecutable(false);
+		file.setReadable(true, true);
+		file.setWritable(true, true);
+		if (file.isDirectory()) {
+			file.setExecutable(true, true);
+		}
+	}
+
 	/**
 	 * Create a new servlet context within the server.
 	 * <p>
@@ -162,9 +268,10 @@ public ServletContextHandler addContext(String path) {
 		return ctx;
 	}
 
-	public ServletContextHandler authBasic(ServletContextHandler ctx) {
+	public ServletContextHandler authBasic(ServletContextHandler ctx,
+			String... methods) {
 		assertNotYetSetUp();
-		auth(ctx, new BasicAuthenticator());
+		auth(ctx, new BasicAuthenticator(), methods);
 		return ctx;
 	}
 
@@ -199,22 +306,36 @@ protected UserPrincipal loadUserInfo(String user) {
 		}
 	}
 
-	private void auth(ServletContextHandler ctx, Authenticator authType) {
-		final String role = "can-access";
-
-		AbstractLoginService users = new TestMappedLoginService(role);
+	private ConstraintMapping createConstraintMapping() {
 		ConstraintMapping cm = new ConstraintMapping();
 		cm.setConstraint(new Constraint());
 		cm.getConstraint().setAuthenticate(true);
 		cm.getConstraint().setDataConstraint(Constraint.DC_NONE);
-		cm.getConstraint().setRoles(new String[] { role });
+		cm.getConstraint().setRoles(new String[] { authRole });
 		cm.setPathSpec("/*");
+		return cm;
+	}
+
+	private void auth(ServletContextHandler ctx, Authenticator authType,
+			String... methods) {
+		AbstractLoginService users = new TestMappedLoginService(authRole);
+		List<ConstraintMapping> mappings = new ArrayList<>();
+		if (methods == null || methods.length == 0) {
+			mappings.add(createConstraintMapping());
+		} else {
+			for (String method : methods) {
+				ConstraintMapping cm = createConstraintMapping();
+				cm.setMethod(method.toUpperCase(Locale.ROOT));
+				mappings.add(cm);
+			}
+		}
 
 		ConstraintSecurityHandler sec = new ConstraintSecurityHandler();
 		sec.setRealmName(realm);
 		sec.setAuthenticator(authType);
 		sec.setLoginService(users);
-		sec.setConstraintMappings(new ConstraintMapping[] { cm });
+		sec.setConstraintMappings(
+				mappings.toArray(new ConstraintMapping[mappings.size()]));
 		sec.setHandler(ctx);
 
 		contexts.removeHandler(ctx);
@@ -231,6 +352,10 @@ public void setUp() throws Exception {
 		RecordingLogger.clear();
 		log.clear();
 		server.start();
+		config.setSecurePort(getSecurePort());
+		if (secureConfig != null) {
+			secureConfig.setSecurePort(getSecurePort());
+		}
 	}
 
 	/**
@@ -243,6 +368,10 @@ public void tearDown() throws Exception {
 		RecordingLogger.clear();
 		log.clear();
 		server.stop();
+		for (File f : filesToDelete) {
+			f.delete();
+		}
+		filesToDelete.clear();
 	}
 
 	/**
@@ -272,6 +401,12 @@ public int getPort() {
 		return connector.getLocalPort();
 	}
 
+	/** @return the HTTPS port or -1 if not configured. */
+	public int getSecurePort() {
+		assertAlreadySetUp();
+		return secureConnector != null ? secureConnector.getLocalPort() : -1;
+	}
+
 	/** @return all requests since the server was started. */
 	public List<AccessEvent> getRequests() {
 		return new ArrayList<>(log.getEvents());
diff --git a/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/HttpTestCase.java b/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/HttpTestCase.java
index 1b94e02..eabb0f2 100644
--- a/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/HttpTestCase.java
+++ b/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/HttpTestCase.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2009-2010, Google Inc.
+ * Copyright (C) 2009-2017, Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -77,7 +77,7 @@ public abstract class HttpTestCase extends LocalDiskRepositoryTestCase {
 	@Override
 	public void setUp() throws Exception {
 		super.setUp();
-		server = new AppServer();
+		server = createServer();
 	}
 
 	@Override
@@ -86,6 +86,20 @@ public void tearDown() throws Exception {
 		super.tearDown();
 	}
 
+	/**
+	 * Creates the {@linkAppServer}.This default implementation creates a server
+	 * without SSLsupport listening for HTTP connections on a dynamically chosen
+	 * port, which can be gotten once the server has been started via its
+	 * {@link AppServer#getPort()} method. Subclasses may override if they need
+	 * a more specialized server.
+	 *
+	 * @return the {@link AppServer}.
+	 * @since 4.9
+	 */
+	protected AppServer createServer() {
+		return new AppServer();
+	}
+
 	protected TestRepository<Repository> createTestRepository()
 			throws IOException {
 		return new TestRepository<>(createBareRepository());
@@ -165,4 +179,37 @@ public static String join(URIish base, String path) {
 			dir += "/";
 		return dir + path;
 	}
+
+	protected static String rewriteUrl(String url, String newProtocol,
+			int newPort) {
+		String newUrl = url;
+		if (newProtocol != null && !newProtocol.isEmpty()) {
+			int schemeEnd = newUrl.indexOf("://");
+			if (schemeEnd >= 0) {
+				newUrl = newProtocol + newUrl.substring(schemeEnd);
+			}
+		}
+		if (newPort > 0) {
+			newUrl = newUrl.replaceFirst(":\\d+/", ":" + newPort + "/");
+		} else {
+			// Remove the port, if any
+			newUrl = newUrl.replaceFirst(":\\d+/", "/");
+		}
+		return newUrl;
+	}
+
+	protected static URIish extendPath(URIish uri, String pathComponents)
+			throws URISyntaxException {
+		String raw = uri.toString();
+		String newComponents = pathComponents;
+		if (!newComponents.startsWith("/")) {
+			newComponents = '/' + newComponents;
+		}
+		if (!newComponents.endsWith("/")) {
+			newComponents += '/';
+		}
+		int i = raw.lastIndexOf('/');
+		raw = raw.substring(0, i) + newComponents + raw.substring(i + 1);
+		return new URIish(raw);
+	}
 }
diff --git a/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/MockServletConfig.java b/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/MockServletConfig.java
index 9defcd9..03c0816 100644
--- a/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/MockServletConfig.java
+++ b/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/MockServletConfig.java
@@ -88,4 +88,4 @@ public String getServletName() {
 	public ServletContext getServletContext() {
 		return null;
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/SimpleHttpServer.java b/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/SimpleHttpServer.java
index 605c69a..0ea0721 100644
--- a/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/SimpleHttpServer.java
+++ b/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/SimpleHttpServer.java
@@ -69,9 +69,15 @@ public class SimpleHttpServer {
 
 	private URIish uri;
 
+	private URIish secureUri;
+
 	public SimpleHttpServer(Repository repository) {
+		this(repository, false);
+	}
+
+	public SimpleHttpServer(Repository repository, boolean withSsl) {
 		this.db = repository;
-		server = new AppServer();
+		server = new AppServer(0, withSsl ? 0 : -1);
 	}
 
 	public void start() throws Exception {
@@ -79,6 +85,10 @@ public void start() throws Exception {
 		server.setUp();
 		final String srcName = db.getDirectory().getName();
 		uri = toURIish(sBasic, srcName);
+		int sslPort = server.getSecurePort();
+		if (sslPort > 0) {
+			secureUri = uri.setPort(sslPort).setScheme("https");
+		}
 	}
 
 	public void stop() throws Exception {
@@ -89,6 +99,10 @@ public URIish getUri() {
 		return uri;
 	}
 
+	public URIish getSecureUri() {
+		return secureUri;
+	}
+
 	private ServletContextHandler smart(final String path) {
 		GitServlet gs = new GitServlet();
 		gs.setRepositoryResolver(new RepositoryResolver<HttpServletRequest>() {
diff --git a/org.eclipse.jgit.junit/.settings/.api_filters b/org.eclipse.jgit.junit/.settings/.api_filters
deleted file mode 100644
index a70ce77..0000000
--- a/org.eclipse.jgit.junit/.settings/.api_filters
+++ /dev/null
@@ -1,35 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<component id="org.eclipse.jgit.junit" version="2">
-    <resource path="src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java" type="org.eclipse.jgit.junit.LocalDiskRepositoryTestCase">
-        <filter comment="OK to use internal implementation in tests" id="643842064">
-            <message_arguments>
-                <message_argument value="FileRepository"/>
-                <message_argument value="LocalDiskRepositoryTestCase"/>
-                <message_argument value="createBareRepository()"/>
-            </message_arguments>
-        </filter>
-        <filter comment="OK to use internal implementation in tests" id="643842064">
-            <message_arguments>
-                <message_argument value="FileRepository"/>
-                <message_argument value="LocalDiskRepositoryTestCase"/>
-                <message_argument value="createRepository(boolean, boolean)"/>
-            </message_arguments>
-        </filter>
-        <filter comment="OK to use internal implementation in tests" id="643842064">
-            <message_arguments>
-                <message_argument value="FileRepository"/>
-                <message_argument value="LocalDiskRepositoryTestCase"/>
-                <message_argument value="createWorkRepository()"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/junit/RepositoryTestCase.java" type="org.eclipse.jgit.junit.RepositoryTestCase">
-        <filter comment="OK to use internal implementation in tests" id="627060751">
-            <message_arguments>
-                <message_argument value="FileRepository"/>
-                <message_argument value="RepositoryTestCase"/>
-                <message_argument value="db"/>
-            </message_arguments>
-        </filter>
-    </resource>
-</component>
diff --git a/org.eclipse.jgit.junit/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.junit/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.junit/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.junit/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.junit/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.junit/.settings/org.eclipse.pde.api.tools.prefs
index cd148d9..c0030de 100644
--- a/org.eclipse.jgit.junit/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.junit/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,4 +1,4 @@
-#Tue Oct 18 00:52:01 CEST 2011
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -8,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -47,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -58,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -75,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -83,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.junit/META-INF/MANIFEST.MF b/org.eclipse.jgit.junit/META-INF/MANIFEST.MF
index c864c5c..fb1454e 100644
--- a/org.eclipse.jgit.junit/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.junit/META-INF/MANIFEST.MF
@@ -2,31 +2,31 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.junit
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Import-Package: org.eclipse.jgit.api;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.api.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.dircache;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.file;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.pack;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.merge;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revwalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.storage.file;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.treewalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.treewalk.filter;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util.io;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util.time;version="[4.8.1,4.9.0)",
+Import-Package: org.eclipse.jgit.api;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.api.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.dircache;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.file;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.pack;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.merge;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revwalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.storage.file;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.treewalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.treewalk.filter;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util.io;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util.time;version="[4.9.6,4.10.0)",
  org.junit;version="[4.0.0,5.0.0)",
  org.junit.rules;version="[4.9.0,5.0.0)",
  org.junit.runner;version="[4.0.0,5.0.0)",
  org.junit.runners.model;version="[4.5.0,5.0.0)"
-Export-Package: org.eclipse.jgit.junit;version="4.8.1";
+Export-Package: org.eclipse.jgit.junit;version="4.9.6";
   uses:="org.eclipse.jgit.dircache,
    org.eclipse.jgit.lib,
    org.eclipse.jgit.revwalk,
@@ -35,4 +35,4 @@
    org.eclipse.jgit.util,
    org.eclipse.jgit.storage.file,
    org.eclipse.jgit.api",
- org.eclipse.jgit.junit.time;version="4.8.1"
+ org.eclipse.jgit.junit.time;version="4.9.6"
diff --git a/org.eclipse.jgit.junit/pom.xml b/org.eclipse.jgit.junit/pom.xml
index 3f843e6..3f76e23 100644
--- a/org.eclipse.jgit.junit/pom.xml
+++ b/org.eclipse.jgit.junit/pom.xml
@@ -52,7 +52,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.junit</artifactId>
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/JGitTestUtil.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/JGitTestUtil.java
index 2962e71..5bf61f0 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/JGitTestUtil.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/JGitTestUtil.java
@@ -258,4 +258,27 @@ public static Path writeLink(Repository db, String link,
 				target);
 	}
 
+	/**
+	 * Concatenate byte arrays.
+	 *
+	 * @param b
+	 *            byte arrays to combine together.
+	 * @return a single byte array that contains all bytes copied from input
+	 *         byte arrays.
+	 * @since 4.9
+	 */
+	public static byte[] concat(byte[]... b) {
+		int n = 0;
+		for (byte[] a : b) {
+			n += a.length;
+		}
+
+		byte[] data = new byte[n];
+		n = 0;
+		for (byte[] a : b) {
+			System.arraycopy(a, 0, data, n, a.length);
+			n += a.length;
+		}
+		return data;
+	}
 }
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/Repeat.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/Repeat.java
index 22b5007..a3c869f 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/Repeat.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/Repeat.java
@@ -50,4 +50,4 @@
 @Target({ java.lang.annotation.ElementType.METHOD })
 public @interface Repeat {
 	public abstract int n();
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepeatRule.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepeatRule.java
index 75e1a67..4230073 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepeatRule.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepeatRule.java
@@ -128,4 +128,4 @@ public Statement apply(Statement statement, Description description) {
 		}
 		return result;
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/StrictWorkMonitor.java
similarity index 73%
copy from org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
copy to org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/StrictWorkMonitor.java
index 98a2a94..22b69a3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/StrictWorkMonitor.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2011, Google Inc.
+ * Copyright (C) 2017 Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -41,20 +41,38 @@
  * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.eclipse.jgit.internal.storage.dfs;
+package org.eclipse.jgit.junit;
 
-import java.util.concurrent.atomic.AtomicLong;
+import static org.junit.Assert.assertEquals;
 
-final class DfsPackKey {
-	final int hash;
+import org.eclipse.jgit.lib.ProgressMonitor;
 
-	final AtomicLong cachedSize;
+public final class StrictWorkMonitor implements ProgressMonitor {
+	private int lastWork, totalWork;
 
-	DfsPackKey() {
-		// Multiply by 31 here so we can more directly combine with another
-		// value without doing the multiply there.
-		//
-		hash = System.identityHashCode(this) * 31;
-		cachedSize = new AtomicLong();
+	@Override
+	public void start(int totalTasks) {
+		// empty
+	}
+
+	@Override
+	public void beginTask(String title, int total) {
+		this.totalWork = total;
+		lastWork = 0;
+	}
+
+	@Override
+	public void update(int completed) {
+		lastWork += completed;
+	}
+
+	@Override
+	public void endTask() {
+		assertEquals("Units of work recorded", totalWork, lastWork);
+	}
+
+	@Override
+	public boolean isCancelled() {
+		return false;
 	}
 }
diff --git a/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.pde.api.tools.prefs
index d585687..c0030de 100644
--- a/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,3 +1,4 @@
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -7,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -46,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -57,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -74,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -82,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.lfs.server.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.lfs.server.test/META-INF/MANIFEST.MF
index f7960c7..a0099e4 100644
--- a/org.eclipse.jgit.lfs.server.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.lfs.server.test/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.lfs.server.test
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-Localization: plugin
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
@@ -27,11 +27,11 @@
  org.eclipse.jetty.util.log;version="[9.4.5,10.0.0)",
  org.eclipse.jetty.util.security;version="[9.4.5,10.0.0)",
  org.eclipse.jetty.util.thread;version="[9.4.5,10.0.0)",
- org.eclipse.jgit.junit.http;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs.server.fs;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs.test;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)",
+ org.eclipse.jgit.junit.http;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs.server.fs;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs.test;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)",
  org.hamcrest.core;version="[1.1.0,2.0.0)",
  org.junit;version="[4.0.0,5.0.0)",
  org.junit.runner;version="[4.0.0,5.0.0)",
diff --git a/org.eclipse.jgit.lfs.server.test/pom.xml b/org.eclipse.jgit.lfs.server.test/pom.xml
index 9fd7080..848e29f 100644
--- a/org.eclipse.jgit.lfs.server.test/pom.xml
+++ b/org.eclipse.jgit.lfs.server.test/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.lfs.server.test</artifactId>
diff --git a/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/DownloadTest.java b/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/DownloadTest.java
index f92e638..303d8056 100644
--- a/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/DownloadTest.java
+++ b/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/DownloadTest.java
@@ -81,7 +81,7 @@ public void testDownloadInvalidPathInfo()
 			fail("expected RuntimeException");
 		} catch (RuntimeException e) {
 			String error = String.format(
-					"Invalid pathInfo '/%s' does not match '/{SHA-256}'", id);
+					"Invalid pathInfo: '/%s' does not match '/{SHA-256}'", id);
 			assertEquals(formatErrorMessage(SC_UNPROCESSABLE_ENTITY, error),
 					e.getMessage());
 		}
@@ -97,7 +97,7 @@ public void testDownloadInvalidId()
 			getContent(id, f);
 			fail("expected RuntimeException");
 		} catch (RuntimeException e) {
-			String error = String.format("Invalid id: : %s", id);
+			String error = String.format("Invalid id: %s", id);
 			assertEquals(formatErrorMessage(SC_UNPROCESSABLE_ENTITY, error),
 					e.getMessage());
 		}
@@ -129,7 +129,7 @@ public void testLargeFileDownload() throws Exception {
 		long start = System.nanoTime();
 		long len = getContent(id, f2);
 		System.out.println(
-				MessageFormat.format("dowloaded 10 MiB random data in {0}ms",
+				MessageFormat.format("downloaded 10 MiB random data in {0}ms",
 						(System.nanoTime() - start) / 1e6));
 		assertEquals(expectedLen, len);
 		FileUtils.delete(f.toFile(), FileUtils.RETRY);
@@ -138,7 +138,7 @@ public void testLargeFileDownload() throws Exception {
 
 	@SuppressWarnings("boxing")
 	private String formatErrorMessage(int status, String message) {
-		return String.format("Status: %d {\n  \"message\": \"%s\"\n}", status,
+		return String.format("Status: %d {\"message\":\"%s\"}", status,
 				message);
 	}
 }
diff --git a/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/LfsServerTest.java b/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/LfsServerTest.java
index e10660d..5da502e 100644
--- a/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/LfsServerTest.java
+++ b/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/LfsServerTest.java
@@ -265,4 +265,4 @@ protected long createPseudoRandomContentFile(Path f, long size)
 		}
 		return Files.size(f);
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.lfs.server/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.lfs.server/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.lfs.server/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.lfs.server/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.lfs.server/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.lfs.server/.settings/org.eclipse.pde.api.tools.prefs
index 3294d4f..112e3c3 100644
--- a/org.eclipse.jgit.lfs.server/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.lfs.server/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,3 +1,4 @@
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -10,6 +11,7 @@
 API_USE_SCAN_FIELD_SEVERITY=Error
 API_USE_SCAN_METHOD_SEVERITY=Error
 API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -49,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -87,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.lfs.server/META-INF/MANIFEST.MF b/org.eclipse.jgit.lfs.server/META-INF/MANIFEST.MF
index 3366e1f..0bb9cfb 100644
--- a/org.eclipse.jgit.lfs.server/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.lfs.server/META-INF/MANIFEST.MF
@@ -2,19 +2,19 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.lfs.server
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
-Export-Package: org.eclipse.jgit.lfs.server;version="4.8.1";
+Export-Package: org.eclipse.jgit.lfs.server;version="4.9.6";
   uses:="javax.servlet.http,
    org.eclipse.jgit.lfs.lib",
- org.eclipse.jgit.lfs.server.fs;version="4.8.1";
+ org.eclipse.jgit.lfs.server.fs;version="4.9.6";
   uses:="javax.servlet,
    javax.servlet.http,
    org.eclipse.jgit.lfs.server,
    org.eclipse.jgit.lfs.lib",
- org.eclipse.jgit.lfs.server.internal;version="4.8.1";x-internal:=true,
- org.eclipse.jgit.lfs.server.s3;version="4.8.1";
+ org.eclipse.jgit.lfs.server.internal;version="4.9.6";x-internal:=true,
+ org.eclipse.jgit.lfs.server.s3;version="4.9.6";
   uses:="org.eclipse.jgit.lfs.server,
    org.eclipse.jgit.lfs.lib"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
@@ -24,14 +24,14 @@
  javax.servlet.http;version="[3.1.0,4.0.0)",
  org.apache.http;version="[4.3.0,5.0.0)",
  org.apache.http.client;version="[4.3.0,5.0.0)",
- org.eclipse.jgit.annotations;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.file;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs.internal;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.nls;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport.http;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport.http.apache;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)",
+ org.eclipse.jgit.annotations;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.file;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs.internal;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.nls;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport.http;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport.http.apache;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)",
  org.slf4j;version="[1.7.0,2.0.0)"
diff --git a/org.eclipse.jgit.lfs.server/pom.xml b/org.eclipse.jgit.lfs.server/pom.xml
index f247cae..b2d91c9 100644
--- a/org.eclipse.jgit.lfs.server/pom.xml
+++ b/org.eclipse.jgit.lfs.server/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.lfs.server</artifactId>
diff --git a/org.eclipse.jgit.lfs.server/resources/org/eclipse/jgit/lfs/server/internal/LfsServerText.properties b/org.eclipse.jgit.lfs.server/resources/org/eclipse/jgit/lfs/server/internal/LfsServerText.properties
index b2b487e..6597145 100644
--- a/org.eclipse.jgit.lfs.server/resources/org/eclipse/jgit/lfs/server/internal/LfsServerText.properties
+++ b/org.eclipse.jgit.lfs.server/resources/org/eclipse/jgit/lfs/server/internal/LfsServerText.properties
@@ -1,5 +1,5 @@
 failedToCalcSignature=Failed to calculate a request signature: {0}
-invalidPathInfo=Invalid pathInfo ''{0}'' does not match ''/'{'SHA-256'}'''
+invalidPathInfo=Invalid pathInfo: ''{0}'' does not match ''/'{'SHA-256'}'''
 objectNotFound=Object ''{0}'' not found
 undefinedS3AccessKey=S3 configuration: 'accessKey' is undefined
 undefinedS3Bucket=S3 configuration: 'bucket' is undefined
diff --git a/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/TransferHandler.java b/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/TransferHandler.java
index 86ca2d3..4fea92e 100644
--- a/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/TransferHandler.java
+++ b/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/TransferHandler.java
@@ -164,4 +164,4 @@ private void addObjectInfo(Response.Body body, LfsObject o)
 	}
 
 	abstract Response.Body process() throws IOException;
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/fs/FileLfsServlet.java b/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/fs/FileLfsServlet.java
index 15c4448..d02d466 100644
--- a/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/fs/FileLfsServlet.java
+++ b/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/fs/FileLfsServlet.java
@@ -216,10 +216,9 @@ protected static void sendError(HttpServletResponse rsp, int status, String mess
 	}
 
 	private static Gson createGson() {
-		GsonBuilder gb = new GsonBuilder()
-				.setFieldNamingPolicy(
-						FieldNamingPolicy.LOWER_CASE_WITH_UNDERSCORES)
-				.setPrettyPrinting().disableHtmlEscaping();
-		return gb.create();
+		return new GsonBuilder()
+				.setFieldNamingPolicy(FieldNamingPolicy.LOWER_CASE_WITH_UNDERSCORES)
+				.disableHtmlEscaping()
+				.create();
 	}
 }
diff --git a/org.eclipse.jgit.lfs.test/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.lfs.test/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.lfs.test/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.lfs.test/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.lfs.test/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.lfs.test/.settings/org.eclipse.pde.api.tools.prefs
index d585687..c0030de 100644
--- a/org.eclipse.jgit.lfs.test/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.lfs.test/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,3 +1,4 @@
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -7,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -46,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -57,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -74,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -82,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF
index 2bdbb59..b20f8d4 100644
--- a/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF
@@ -2,23 +2,23 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.lfs.test
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-Localization: plugin
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Import-Package: org.eclipse.jgit.internal.storage.dfs;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.junit;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revwalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.treewalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.treewalk.filter;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)",
+Import-Package: org.eclipse.jgit.internal.storage.dfs;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.junit;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revwalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.treewalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.treewalk.filter;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)",
  org.hamcrest.core;version="[1.1.0,2.0.0)",
  org.junit;version="[4.0.0,5.0.0)",
  org.junit.runner;version="[4.0.0,5.0.0)",
  org.junit.runners;version="[4.0.0,5.0.0)"
-Export-Package: org.eclipse.jgit.lfs.test;version="4.8.1";x-friends:="org.eclipse.jgit.lfs.server.test"
+Export-Package: org.eclipse.jgit.lfs.test;version="4.9.6";x-friends:="org.eclipse.jgit.lfs.server.test"
 
diff --git a/org.eclipse.jgit.lfs.test/pom.xml b/org.eclipse.jgit.lfs.test/pom.xml
index f599ca0..20e8199 100644
--- a/org.eclipse.jgit.lfs.test/pom.xml
+++ b/org.eclipse.jgit.lfs.test/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.lfs.test</artifactId>
diff --git a/org.eclipse.jgit.lfs.test/tst/org/eclipse/jgit/lfs/lib/LongObjectIdTest.java b/org.eclipse.jgit.lfs.test/tst/org/eclipse/jgit/lfs/lib/LongObjectIdTest.java
index e754d6f..31ab783 100644
--- a/org.eclipse.jgit.lfs.test/tst/org/eclipse/jgit/lfs/lib/LongObjectIdTest.java
+++ b/org.eclipse.jgit.lfs.test/tst/org/eclipse/jgit/lfs/lib/LongObjectIdTest.java
@@ -291,6 +291,8 @@ public void testCompareTo() {
 				"0123456789abcdef0123456789abcdef0123456789abcdef0123456789abcdef");
 		assertEquals(0, id1.compareTo(LongObjectId.fromString(
 				"0123456789abcdef0123456789abcdef0123456789abcdef0123456789abcdef")));
+		AnyLongObjectId self = id1;
+		assertEquals(0, id1.compareTo(self));
 
 		assertEquals(-1, id1.compareTo(LongObjectId.fromString(
 				"1123456789abcdef0123456789abcdef0123456789abcdef0123456789abcdef")));
diff --git a/org.eclipse.jgit.lfs/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.lfs/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.lfs/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.lfs/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.lfs/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.lfs/.settings/org.eclipse.pde.api.tools.prefs
index 3294d4f..112e3c3 100644
--- a/org.eclipse.jgit.lfs/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.lfs/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,3 +1,4 @@
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -10,6 +11,7 @@
 API_USE_SCAN_FIELD_SEVERITY=Error
 API_USE_SCAN_METHOD_SEVERITY=Error
 API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -49,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -87,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF b/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF
index 489fd12..d97c85e 100644
--- a/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF
@@ -2,20 +2,20 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.lfs
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
-Export-Package: org.eclipse.jgit.lfs;version="4.8.1",
- org.eclipse.jgit.lfs.errors;version="4.8.1",
- org.eclipse.jgit.lfs.internal;version="4.8.1";x-friends:="org.eclipse.jgit.lfs.test,org.eclipse.jgit.lfs.server.fs,org.eclipse.jgit.lfs.server",
- org.eclipse.jgit.lfs.lib;version="4.8.1"
+Export-Package: org.eclipse.jgit.lfs;version="4.9.6",
+ org.eclipse.jgit.lfs.errors;version="4.9.6",
+ org.eclipse.jgit.lfs.internal;version="4.9.6";x-friends:="org.eclipse.jgit.lfs.test,org.eclipse.jgit.lfs.server.fs,org.eclipse.jgit.lfs.server",
+ org.eclipse.jgit.lfs.lib;version="4.9.6"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Import-Package: org.eclipse.jgit.annotations;version="[4.8.1,4.9.0)";resolution:=optional,
- org.eclipse.jgit.attributes;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.file;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.nls;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.treewalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.treewalk.filter;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)"
+Import-Package: org.eclipse.jgit.annotations;version="[4.9.6,4.10.0)";resolution:=optional,
+ org.eclipse.jgit.attributes;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.file;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.nls;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.treewalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.treewalk.filter;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)"
diff --git a/org.eclipse.jgit.lfs/pom.xml b/org.eclipse.jgit.lfs/pom.xml
index 98216fb..04423ea 100644
--- a/org.eclipse.jgit.lfs/pom.xml
+++ b/org.eclipse.jgit.lfs/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.lfs</artifactId>
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/errors/InvalidLongObjectIdException.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/errors/InvalidLongObjectIdException.java
index 1f6e2d1..44ac317 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/errors/InvalidLongObjectIdException.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/errors/InvalidLongObjectIdException.java
@@ -80,7 +80,7 @@ public InvalidLongObjectIdException(String idString) {
 
 	private static String asAscii(byte[] bytes, int offset, int length) {
 		try {
-			return ": " + new String(bytes, offset, length, "US-ASCII"); //$NON-NLS-1$ //$NON-NLS-2$
+			return new String(bytes, offset, length, "US-ASCII"); //$NON-NLS-1$
 		} catch (UnsupportedEncodingException e2) {
 			return ""; //$NON-NLS-1$
 		} catch (StringIndexOutOfBoundsException e2) {
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/AtomicObjectOutputStream.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/AtomicObjectOutputStream.java
index 867cca5..1598b9e 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/AtomicObjectOutputStream.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/AtomicObjectOutputStream.java
@@ -146,4 +146,4 @@ public void abort() {
 		locked.unlock();
 		aborted = true;
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/feature.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/feature.xml
index 0d9c4b2..5853d82 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/feature.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.eclipse.jgit"
       label="%featureName"
-      version="4.8.1.qualifier"
+      version="4.9.6.qualifier"
       provider-name="%providerName">
 
    <description url="http://www.eclipse.org/jgit/">
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/pom.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/pom.xml
index c6ae404..9280b96 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/pom.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>jgit.tycho.parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.http.apache.feature/feature.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.http.apache.feature/feature.xml
index c2662fc..7a1e2cf 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.http.apache.feature/feature.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.http.apache.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.eclipse.jgit.http.apache"
       label="%featureName"
-      version="4.8.1.qualifier"
+      version="4.9.6.qualifier"
       provider-name="%providerName">
 
    <description url="http://www.eclipse.org/jgit/">
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.http.apache.feature/pom.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.http.apache.feature/pom.xml
index 4fa4fca..c830e4d 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.http.apache.feature/pom.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.http.apache.feature/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>jgit.tycho.parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.junit.feature/feature.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.junit.feature/feature.xml
index 408b1d8..06a732b 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.junit.feature/feature.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.junit.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.eclipse.jgit.junit"
       label="%featureName"
-      version="4.8.1.qualifier"
+      version="4.9.6.qualifier"
       provider-name="%providerName">
 
    <description url="http://www.eclipse.org/jgit/">
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.junit.feature/pom.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.junit.feature/pom.xml
index bdaa809..8c09b5d 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.junit.feature/pom.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.junit.feature/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>jgit.tycho.parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.lfs.feature/feature.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.lfs.feature/feature.xml
index 7113e7b..a7e0e25 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.lfs.feature/feature.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.lfs.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.eclipse.jgit.lfs"
       label="%featureName"
-      version="4.8.1.qualifier"
+      version="4.9.6.qualifier"
       provider-name="%providerName">
 
    <description url="http://www.eclipse.org/jgit/">
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.lfs.feature/pom.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.lfs.feature/pom.xml
index b39af8c..4300712 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.lfs.feature/pom.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.lfs.feature/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>jgit.tycho.parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.feature/feature.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.feature/feature.xml
index 1129615..bf31b46 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.feature/feature.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.eclipse.jgit.pgm"
       label="%featureName"
-      version="4.8.1.qualifier"
+      version="4.9.6.qualifier"
       provider-name="%providerName">
 
    <description url="http://www.eclipse.org/jgit/">
@@ -31,8 +31,8 @@
          version="0.0.0"/>
 
    <requires>
-      <import feature="org.eclipse.jgit" version="4.8.1" match="equivalent"/>
-      <import feature="org.eclipse.jgit.lfs" version="4.8.1" match="equivalent"/>
+      <import feature="org.eclipse.jgit" version="4.9.6" match="equivalent"/>
+      <import feature="org.eclipse.jgit.lfs" version="4.9.6" match="equivalent"/>
    </requires>
 
    <plugin
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.feature/pom.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.feature/pom.xml
index b8cb2c8..291b360 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.feature/pom.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.feature/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>jgit.tycho.parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.source.feature/feature.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.source.feature/feature.xml
index 0556fb5..9bb704c 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.source.feature/feature.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.source.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.eclipse.jgit.pgm.source"
       label="%featureName"
-      version="4.8.1.qualifier"
+      version="4.9.6.qualifier"
       provider-name="%providerName">
 
    <description url="http://www.eclipse.org/jgit/">
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.source.feature/pom.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.source.feature/pom.xml
index 70813bc..14f74da 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.source.feature/pom.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.source.feature/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>jgit.tycho.parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.repository/pom.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.repository/pom.xml
index 432c5d4..d622c28 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.repository/pom.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.repository/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>jgit.tycho.parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.repository</artifactId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.source.feature/feature.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.source.feature/feature.xml
index 5834a0c..f437e2e 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.source.feature/feature.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.source.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.eclipse.jgit.source"
       label="%featureName"
-      version="4.8.1.qualifier"
+      version="4.9.6.qualifier"
       provider-name="%providerName">
 
    <description url="http://www.eclipse.org/jgit/">
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.source.feature/pom.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.source.feature/pom.xml
index ec57876..6b8bad9 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.source.feature/pom.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.source.feature/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>jgit.tycho.parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/META-INF/MANIFEST.MF b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/META-INF/MANIFEST.MF
index a43734b..c71984d 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/META-INF/MANIFEST.MF
@@ -2,4 +2,4 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: JGit Target Platform Bundle
 Bundle-SymbolicName: org.eclipse.jgit.target
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.target b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.target
index 8051080..b4b3908 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.target
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.target
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/mbarbero/fr.obeo.releng.targetplatform -->
-<target name="jgit-4.5" sequenceNumber="1502749391">
+<target name="jgit-4.5" sequenceNumber="1504052010">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.5.v20170502"/>
@@ -63,6 +63,8 @@
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.apache.ant" version="1.9.6.v201510161327"/>
       <unit id="org.apache.ant.source" version="1.9.6.v201510161327"/>
+      <unit id="org.apache.commons.codec" version="1.9.0.v20170208-1614"/>
+      <unit id="org.apache.commons.codec.source" version="1.9.0.v20170208-1614"/>
       <unit id="org.apache.commons.compress" version="1.6.0.v201310281400"/>
       <unit id="org.apache.commons.compress.source" version="1.6.0.v201310281400"/>
       <unit id="org.apache.commons.logging" version="1.1.1.v201101211721"/>
@@ -73,8 +75,8 @@
       <unit id="org.apache.httpcomponents.httpclient.source" version="4.3.6.v201511171540"/>
       <unit id="org.apache.log4j" version="1.2.15.v201012070815"/>
       <unit id="org.apache.log4j.source" version="1.2.15.v201012070815"/>
-      <unit id="org.kohsuke.args4j" version="2.0.21.v201301150030"/>
-      <unit id="org.kohsuke.args4j.source" version="2.0.21.v201301150030"/>
+      <unit id="org.kohsuke.args4j" version="2.33.0.v20160323-2218"/>
+      <unit id="org.kohsuke.args4j.source" version="2.33.0.v20160323-2218"/>
       <unit id="org.hamcrest.core" version="1.3.0.v201303031735"/>
       <unit id="org.hamcrest.core.source" version="1.3.0.v201303031735"/>
       <unit id="org.hamcrest.library" version="1.3.0.v201505072020"/>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target
index b6bbcda..48cd300 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/mbarbero/fr.obeo.releng.targetplatform -->
-<target name="jgit-4.6" sequenceNumber="1502749371">
+<target name="jgit-4.6" sequenceNumber="1504051999">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.5.v20170502"/>
@@ -25,6 +25,8 @@
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.apache.ant" version="1.9.6.v201510161327"/>
       <unit id="org.apache.ant.source" version="1.9.6.v201510161327"/>
+      <unit id="org.apache.commons.codec" version="1.9.0.v20170208-1614"/>
+      <unit id="org.apache.commons.codec.source" version="1.9.0.v20170208-1614"/>
       <unit id="org.apache.commons.compress" version="1.6.0.v201310281400"/>
       <unit id="org.apache.commons.compress.source" version="1.6.0.v201310281400"/>
       <unit id="org.apache.commons.logging" version="1.1.1.v201101211721"/>
@@ -35,8 +37,8 @@
       <unit id="org.apache.httpcomponents.httpclient.source" version="4.3.6.v201511171540"/>
       <unit id="org.apache.log4j" version="1.2.15.v201012070815"/>
       <unit id="org.apache.log4j.source" version="1.2.15.v201012070815"/>
-      <unit id="org.kohsuke.args4j" version="2.0.21.v201301150030"/>
-      <unit id="org.kohsuke.args4j.source" version="2.0.21.v201301150030"/>
+      <unit id="org.kohsuke.args4j" version="2.33.0.v20160323-2218"/>
+      <unit id="org.kohsuke.args4j.source" version="2.33.0.v20160323-2218"/>
       <unit id="org.hamcrest.core" version="1.3.0.v201303031735"/>
       <unit id="org.hamcrest.core.source" version="1.3.0.v201303031735"/>
       <unit id="org.hamcrest.library" version="1.3.0.v201505072020"/>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.target b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.target
index 6071c8f..4ac65dd 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.target
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.target
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/mbarbero/fr.obeo.releng.targetplatform -->
-<target name="jgit-4.7" sequenceNumber="1502749365">
+<target name="jgit-4.7" sequenceNumber="1504051975">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.5.v20170502"/>
@@ -25,6 +25,8 @@
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.apache.ant" version="1.9.6.v201510161327"/>
       <unit id="org.apache.ant.source" version="1.9.6.v201510161327"/>
+      <unit id="org.apache.commons.codec" version="1.9.0.v20170208-1614"/>
+      <unit id="org.apache.commons.codec.source" version="1.9.0.v20170208-1614"/>
       <unit id="org.apache.commons.compress" version="1.6.0.v201310281400"/>
       <unit id="org.apache.commons.compress.source" version="1.6.0.v201310281400"/>
       <unit id="org.apache.commons.logging" version="1.1.1.v201101211721"/>
@@ -35,8 +37,8 @@
       <unit id="org.apache.httpcomponents.httpclient.source" version="4.3.6.v201511171540"/>
       <unit id="org.apache.log4j" version="1.2.15.v201012070815"/>
       <unit id="org.apache.log4j.source" version="1.2.15.v201012070815"/>
-      <unit id="org.kohsuke.args4j" version="2.0.21.v201301150030"/>
-      <unit id="org.kohsuke.args4j.source" version="2.0.21.v201301150030"/>
+      <unit id="org.kohsuke.args4j" version="2.33.0.v20160323-2218"/>
+      <unit id="org.kohsuke.args4j.source" version="2.33.0.v20160323-2218"/>
       <unit id="org.hamcrest.core" version="1.3.0.v201303031735"/>
       <unit id="org.hamcrest.core.source" version="1.3.0.v201303031735"/>
       <unit id="org.hamcrest.library" version="1.3.0.v201505072020"/>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.target b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.target
new file mode 100644
index 0000000..d82fe3e
--- /dev/null
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.target
@@ -0,0 +1,72 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?pde?>
+<!-- generated with https://github.com/mbarbero/fr.obeo.releng.targetplatform -->
+<target name="jgit-4.8" sequenceNumber="1535021913">
+  <locations>
+    <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
+      <unit id="org.eclipse.jetty.client" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.client.source" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.continuation" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.continuation.source" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.http" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.http.source" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.io" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.io.source" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.security" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.security.source" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.server" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.server.source" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.servlet" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.servlet.source" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.util" version="9.4.5.v20170502"/>
+      <unit id="org.eclipse.jetty.util.source" version="9.4.5.v20170502"/>
+      <repository id="jetty-9.4.5" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.5.v20170502/"/>
+    </location>
+    <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
+      <unit id="org.apache.ant" version="1.9.6.v201510161327"/>
+      <unit id="org.apache.ant.source" version="1.9.6.v201510161327"/>
+      <unit id="org.apache.commons.codec" version="1.9.0.v20170208-1614"/>
+      <unit id="org.apache.commons.codec.source" version="1.9.0.v20170208-1614"/>
+      <unit id="org.apache.commons.compress" version="1.6.0.v201310281400"/>
+      <unit id="org.apache.commons.compress.source" version="1.6.0.v201310281400"/>
+      <unit id="org.apache.commons.logging" version="1.1.1.v201101211721"/>
+      <unit id="org.apache.commons.logging.source" version="1.1.1.v201101211721"/>
+      <unit id="org.apache.httpcomponents.httpcore" version="4.3.3.v201411290715"/>
+      <unit id="org.apache.httpcomponents.httpcore.source" version="4.3.3.v201411290715"/>
+      <unit id="org.apache.httpcomponents.httpclient" version="4.3.6.v201511171540"/>
+      <unit id="org.apache.httpcomponents.httpclient.source" version="4.3.6.v201511171540"/>
+      <unit id="org.apache.log4j" version="1.2.15.v201012070815"/>
+      <unit id="org.apache.log4j.source" version="1.2.15.v201012070815"/>
+      <unit id="org.kohsuke.args4j" version="2.33.0.v20160323-2218"/>
+      <unit id="org.kohsuke.args4j.source" version="2.33.0.v20160323-2218"/>
+      <unit id="org.hamcrest.core" version="1.3.0.v20180420-1519"/>
+      <unit id="org.hamcrest.core.source" version="1.3.0.v20180420-1519"/>
+      <unit id="org.hamcrest.library" version="1.3.0.v20180524-2246"/>
+      <unit id="org.hamcrest.library.source" version="1.3.0.v20180524-2246"/>
+      <unit id="javaewah" version="1.1.6.v20160919-1400"/>
+      <unit id="javaewah.source" version="1.1.6.v20160919-1400"/>
+      <unit id="org.objenesis" version="1.0.0.v201505121915"/>
+      <unit id="org.objenesis.source" version="1.0.0.v201505121915"/>
+      <unit id="org.mockito" version="1.8.4.v201303031500"/>
+      <unit id="org.mockito.source" version="1.8.4.v201303031500"/>
+      <unit id="com.google.gson" version="2.2.4.v201311231704"/>
+      <unit id="com.jcraft.jsch" version="0.1.54.v20170116-1932"/>
+      <unit id="com.jcraft.jsch.source" version="0.1.54.v20170116-1932"/>
+      <unit id="org.junit" version="4.12.0.v201504281640"/>
+      <unit id="org.junit.source" version="4.12.0.v201504281640"/>
+      <unit id="javax.servlet" version="3.1.0.v201410161800"/>
+      <unit id="javax.servlet.source" version="3.1.0.v201410161800"/>
+      <unit id="org.tukaani.xz" version="1.3.0.v201308270617"/>
+      <unit id="org.tukaani.xz.source" version="1.3.0.v201308270617"/>
+      <unit id="org.slf4j.api" version="1.7.2.v20121108-1250"/>
+      <unit id="org.slf4j.api.source" version="1.7.2.v20121108-1250"/>
+      <unit id="org.slf4j.impl.log4j12" version="1.7.2.v20131105-2200"/>
+      <unit id="org.slf4j.impl.log4j12.source" version="1.7.2.v20131105-2200"/>
+      <repository location="http://download.eclipse.org/tools/orbit/downloads/drops/R20180606145124/repository"/>
+    </location>
+    <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
+      <unit id="org.eclipse.osgi" version="0.0.0"/>
+      <repository location="http://download.eclipse.org/releases/photon/"/>
+    </location>
+  </locations>
+</target>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.tpd
new file mode 100644
index 0000000..cd1954f
--- /dev/null
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.tpd
@@ -0,0 +1,8 @@
+target "jgit-4.8" with source configurePhase
+
+include "projects/jetty-9.4.5.tpd"
+include "orbit/R20180606145124-Photon.tpd"
+
+location "http://download.eclipse.org/releases/photon/" {
+	org.eclipse.osgi lazy
+}
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20170516192513-Oxygen.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20170516192513-Oxygen.tpd
index ef19fa6..f4cb572 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20170516192513-Oxygen.tpd
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20170516192513-Oxygen.tpd
@@ -4,6 +4,8 @@
 location "http://download.eclipse.org/tools/orbit/downloads/drops/R20170516192513/repository" {
 	org.apache.ant [1.9.6.v201510161327,1.9.6.v201510161327]
 	org.apache.ant.source [1.9.6.v201510161327,1.9.6.v201510161327]
+	org.apache.commons.codec [1.9.0.v20170208-1614,1.9.0.v20170208-1614]
+	org.apache.commons.codec.source [1.9.0.v20170208-1614,1.9.0.v20170208-1614]
 	org.apache.commons.compress [1.6.0.v201310281400,1.6.0.v201310281400]
 	org.apache.commons.compress.source [1.6.0.v201310281400,1.6.0.v201310281400]
 	org.apache.commons.logging [1.1.1.v201101211721,1.1.1.v201101211721]
@@ -14,8 +16,8 @@
 	org.apache.httpcomponents.httpclient.source [4.3.6.v201511171540,4.3.6.v201511171540]
 	org.apache.log4j [1.2.15.v201012070815,1.2.15.v201012070815]
 	org.apache.log4j.source [1.2.15.v201012070815,1.2.15.v201012070815]
-	org.kohsuke.args4j [2.0.21.v201301150030,2.0.21.v201301150030]
-	org.kohsuke.args4j.source [2.0.21.v201301150030,2.0.21.v201301150030]
+	org.kohsuke.args4j [2.33.0.v20160323-2218,2.33.0.v20160323-2218]
+	org.kohsuke.args4j.source [2.33.0.v20160323-2218,2.33.0.v20160323-2218]
 	org.hamcrest.core [1.3.0.v201303031735,1.3.0.v201303031735]
 	org.hamcrest.core.source [1.3.0.v201303031735,1.3.0.v201303031735]
 	org.hamcrest.library [1.3.0.v201505072020,1.3.0.v201505072020]
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20180606145124-Photon.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20180606145124-Photon.tpd
new file mode 100644
index 0000000..a7ad1a4
--- /dev/null
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20180606145124-Photon.tpd
@@ -0,0 +1,44 @@
+target "R20180606145124-Photon" with source configurePhase
+// see http://download.eclipse.org/tools/orbit/downloads/
+
+location "http://download.eclipse.org/tools/orbit/downloads/drops/R20180606145124/repository" {
+	org.apache.ant [1.9.6.v201510161327,1.9.6.v201510161327]
+	org.apache.ant.source [1.9.6.v201510161327,1.9.6.v201510161327]
+	org.apache.commons.codec [1.9.0.v20170208-1614,1.9.0.v20170208-1614]
+	org.apache.commons.codec.source [1.9.0.v20170208-1614,1.9.0.v20170208-1614]
+	org.apache.commons.compress [1.6.0.v201310281400,1.6.0.v201310281400]
+	org.apache.commons.compress.source [1.6.0.v201310281400,1.6.0.v201310281400]
+	org.apache.commons.logging [1.1.1.v201101211721,1.1.1.v201101211721]
+	org.apache.commons.logging.source [1.1.1.v201101211721,1.1.1.v201101211721]
+	org.apache.httpcomponents.httpcore [4.3.3.v201411290715,4.3.3.v201411290715]
+	org.apache.httpcomponents.httpcore.source [4.3.3.v201411290715,4.3.3.v201411290715]
+	org.apache.httpcomponents.httpclient [4.3.6.v201511171540,4.3.6.v201511171540]
+	org.apache.httpcomponents.httpclient.source [4.3.6.v201511171540,4.3.6.v201511171540]
+	org.apache.log4j [1.2.15.v201012070815,1.2.15.v201012070815]
+	org.apache.log4j.source [1.2.15.v201012070815,1.2.15.v201012070815]
+	org.kohsuke.args4j [2.33.0.v20160323-2218,2.33.0.v20160323-2218]
+	org.kohsuke.args4j.source [2.33.0.v20160323-2218,2.33.0.v20160323-2218]
+	org.hamcrest.core [1.3.0.v20180420-1519,1.3.0.v20180420-1519]
+	org.hamcrest.core.source [1.3.0.v20180420-1519,1.3.0.v20180420-1519]
+	org.hamcrest.library [1.3.0.v20180524-2246,1.3.0.v20180524-2246]
+	org.hamcrest.library.source [1.3.0.v20180524-2246,1.3.0.v20180524-2246]
+	javaewah [1.1.6.v20160919-1400,1.1.6.v20160919-1400]
+	javaewah.source [1.1.6.v20160919-1400,1.1.6.v20160919-1400]
+	org.objenesis [1.0.0.v201505121915,1.0.0.v201505121915]
+	org.objenesis.source [1.0.0.v201505121915,1.0.0.v201505121915]
+	org.mockito [1.8.4.v201303031500,1.8.4.v201303031500]
+	org.mockito.source [1.8.4.v201303031500,1.8.4.v201303031500]
+	com.google.gson [2.2.4.v201311231704,2.2.4.v201311231704]
+	com.jcraft.jsch [0.1.54.v20170116-1932,0.1.54.v20170116-1932]
+	com.jcraft.jsch.source [0.1.54.v20170116-1932,0.1.54.v20170116-1932]
+	org.junit [4.12.0.v201504281640,4.12.0.v201504281640]
+	org.junit.source [4.12.0.v201504281640,4.12.0.v201504281640]
+	javax.servlet [3.1.0.v201410161800,3.1.0.v201410161800]
+	javax.servlet.source [3.1.0.v201410161800,3.1.0.v201410161800]
+	org.tukaani.xz [1.3.0.v201308270617,1.3.0.v201308270617]
+	org.tukaani.xz.source [1.3.0.v201308270617,1.3.0.v201308270617]
+	org.slf4j.api [1.7.2.v20121108-1250,1.7.2.v20121108-1250]
+	org.slf4j.api.source [1.7.2.v20121108-1250,1.7.2.v20121108-1250]
+	org.slf4j.impl.log4j12 [1.7.2.v20131105-2200,1.7.2.v20131105-2200]
+	org.slf4j.impl.log4j12.source [1.7.2.v20131105-2200,1.7.2.v20131105-2200]
+}
\ No newline at end of file
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/pom.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/pom.xml
index d1934e7..3893479 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/pom.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/pom.xml
@@ -49,7 +49,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>jgit.tycho.parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.target</artifactId>
diff --git a/org.eclipse.jgit.packaging/pom.xml b/org.eclipse.jgit.packaging/pom.xml
index 2613686..efbd4ab 100644
--- a/org.eclipse.jgit.packaging/pom.xml
+++ b/org.eclipse.jgit.packaging/pom.xml
@@ -53,7 +53,7 @@
 
   <groupId>org.eclipse.jgit</groupId>
   <artifactId>jgit.tycho.parent</artifactId>
-  <version>4.8.1-SNAPSHOT</version>
+  <version>4.9.6-SNAPSHOT</version>
   <packaging>pom</packaging>
 
   <name>JGit Tycho Parent</name>
diff --git a/org.eclipse.jgit.pgm.test/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.pgm.test/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.pgm.test/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.pgm.test/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.pgm.test/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.pgm.test/.settings/org.eclipse.pde.api.tools.prefs
index cd148d9..c0030de 100644
--- a/org.eclipse.jgit.pgm.test/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.pgm.test/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,4 +1,4 @@
-#Tue Oct 18 00:52:01 CEST 2011
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -8,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -47,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -58,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -75,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -83,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.pgm.test/BUILD b/org.eclipse.jgit.pgm.test/BUILD
index 5d4a175..5bedf9a 100644
--- a/org.eclipse.jgit.pgm.test/BUILD
+++ b/org.eclipse.jgit.pgm.test/BUILD
@@ -13,6 +13,7 @@
     tags = ["pgm"],
     deps = [
         ":helpers",
+        "//lib:args4j",
         "//lib:commons-compress",
         "//lib:javaewah",
         "//lib:junit",
diff --git a/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF
index 37bef75..9a483b4 100644
--- a/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF
@@ -2,30 +2,30 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.pgm.test
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-Localization: plugin
 Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Import-Package: org.eclipse.jgit.api;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.api.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.diff;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.dircache;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.file;version="4.8.1",
- org.eclipse.jgit.junit;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.merge;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.pgm;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.pgm.internal;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.pgm.opt;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revwalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.storage.file;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.treewalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util.io;version="[4.8.1,4.9.0)",
+Import-Package: org.eclipse.jgit.api;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.api.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.diff;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.dircache;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.file;version="4.9.6",
+ org.eclipse.jgit.junit;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.merge;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.pgm;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.pgm.internal;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.pgm.opt;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revwalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.storage.file;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.treewalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util.io;version="[4.9.6,4.10.0)",
  org.hamcrest.core;bundle-version="[1.1.0,2.0.0)",
  org.junit;version="[4.11.0,5.0.0)",
  org.junit.rules;version="[4.11.0,5.0.0)",
- org.kohsuke.args4j;version="[2.0.12,2.1.0)"
+ org.kohsuke.args4j;version="[2.33.0,3.0.0)"
 Require-Bundle: org.tukaani.xz;bundle-version="[1.3.0,2.0.0)"
diff --git a/org.eclipse.jgit.pgm.test/pom.xml b/org.eclipse.jgit.pgm.test/pom.xml
index ee234d8..3eba065 100644
--- a/org.eclipse.jgit.pgm.test/pom.xml
+++ b/org.eclipse.jgit.pgm.test/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.pgm.test</artifactId>
diff --git a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/CheckoutTest.java b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/CheckoutTest.java
index 4b86b60..a98dd1c 100644
--- a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/CheckoutTest.java
+++ b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/CheckoutTest.java
@@ -71,6 +71,23 @@
 import org.junit.Test;
 
 public class CheckoutTest extends CLIRepositoryTestCase {
+	/**
+	 * Executes specified git command (with arguments), captures exception and
+	 * returns its message as an array of lines. Throws an AssertionError if no
+	 * exception is thrown.
+	 *
+	 * @param command
+	 *            a valid git command line, e.g. "git branch -h"
+	 * @return message contained within the exception
+	 */
+	private String[] executeExpectingException(String command) {
+		try {
+			execute(command);
+			throw new AssertionError("Expected Die");
+		} catch (Exception e) {
+			return e.getMessage().split(System.lineSeparator());
+		}
+	}
 
 	@Test
 	public void testCheckoutSelf() throws Exception {
@@ -107,7 +124,7 @@ public void testCheckoutNewBranch() throws Exception {
 	public void testCheckoutNonExistingBranch() throws Exception {
 		assertStringArrayEquals(
 				"error: pathspec 'side' did not match any file(s) known to git.",
-				execute("git checkout side"));
+				executeExpectingException("git checkout side"));
 	}
 
 	@Test
@@ -131,7 +148,7 @@ public void testCheckoutNewBranchOnBranchToBeBorn() throws Exception {
 	public void testCheckoutUnresolvedHead() throws Exception {
 		assertStringArrayEquals(
 				"error: pathspec 'HEAD' did not match any file(s) known to git.",
-				execute("git checkout HEAD"));
+				executeExpectingException("git checkout HEAD"));
 	}
 
 	@Test
@@ -159,7 +176,8 @@ public void testCheckoutExistingBranchWithConflict() throws Exception {
 			writeTrashFile("a", "New Hello world a");
 			git.add().addFilepattern(".").call();
 
-			String[] execute = execute("git checkout branch_1");
+			String[] execute = executeExpectingException(
+					"git checkout branch_1");
 			assertEquals(
 					"error: Your local changes to the following files would be overwritten by checkout:",
 					execute[0]);
diff --git a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/DescribeTest.java b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/DescribeTest.java
index 086e72e..e97762d 100644
--- a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/DescribeTest.java
+++ b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/DescribeTest.java
@@ -46,6 +46,7 @@
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
 
 import java.util.Arrays;
 
@@ -71,6 +72,12 @@ private void initialCommitAndTag() throws Exception {
 		git.tag().setName("v1.0").call();
 	}
 
+	private void secondCommit() throws Exception {
+		writeTrashFile("greeting", "Hello, world!");
+		git.add().addFilepattern("greeting").call();
+		git.commit().setMessage("2nd commit").call();
+	}
+
 	@Test
 	public void testNoHead() throws Exception {
 		assertEquals(CLIText.fatalError(CLIText.get().noNamesFound),
@@ -94,9 +101,7 @@ public void testDescribeTag() throws Exception {
 	@Test
 	public void testDescribeCommit() throws Exception {
 		initialCommitAndTag();
-		writeTrashFile("greeting", "Hello, world!");
-		git.add().addFilepattern("greeting").call();
-		git.commit().setMessage("2nd commit").call();
+		secondCommit();
 		assertArrayEquals(new String[] { "v1.0-1-g56f6ceb", "" },
 				execute("git describe"));
 	}
@@ -109,6 +114,47 @@ public void testDescribeTagLong() throws Exception {
 	}
 
 	@Test
+	public void testDescribeCommitMatch() throws Exception {
+		initialCommitAndTag();
+		secondCommit();
+		assertArrayEquals(new String[] { "v1.0-1-g56f6ceb", "" },
+				execute("git describe --match v1.*"));
+	}
+
+	@Test
+	public void testDescribeCommitMatch2() throws Exception {
+		initialCommitAndTag();
+		secondCommit();
+		git.tag().setName("v2.0").call();
+		assertArrayEquals(new String[] { "v1.0-1-g56f6ceb", "" },
+				execute("git describe --match v1.*"));
+	}
+
+	@Test
+	public void testDescribeCommitMultiMatch() throws Exception {
+		initialCommitAndTag();
+		secondCommit();
+		git.tag().setName("v2.0.0").call();
+		git.tag().setName("v2.1.1").call();
+		assertArrayEquals("git yields v2.0.0", new String[] { "v2.0.0", "" },
+				execute("git describe --match v2.0* --match v2.1.*"));
+	}
+
+	@Test
+	public void testDescribeCommitNoMatch() throws Exception {
+		initialCommitAndTag();
+		writeTrashFile("greeting", "Hello, world!");
+		secondCommit();
+		try {
+			execute("git describe --match 1.*");
+			fail("git describe should not find any tag matching 1.*");
+		} catch (Die e) {
+			assertEquals("No names found, cannot describe anything.",
+					e.getMessage());
+		}
+	}
+
+	@Test
 	public void testHelpArgumentBeforeUnknown() throws Exception {
 		String[] output = execute("git describe -h -XYZ");
 		String all = Arrays.toString(output);
diff --git a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ReflogTest.java b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ReflogTest.java
index 7330ee9..bf6bacb 100644
--- a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ReflogTest.java
+++ b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ReflogTest.java
@@ -80,4 +80,4 @@ public void testBranch() throws Exception {
 					"" }, execute("git reflog refs/heads/side"));
 		}
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ResetTest.java b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ResetTest.java
index 44a7630..81287c1 100644
--- a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ResetTest.java
+++ b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ResetTest.java
@@ -69,7 +69,7 @@ public void setUp() throws Exception {
 	public void testPathOptionHelp() throws Exception {
 		String[] result = execute("git reset -h");
 		assertTrue("Unexpected argument: " + result[1],
-				result[1].endsWith("[-- path ... ...]"));
+				result[1].endsWith("[-- path ...]"));
 	}
 
 	@Test
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/RmTest.java
similarity index 62%
copy from org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
copy to org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/RmTest.java
index 98a2a94..00a1a9a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
+++ b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/RmTest.java
@@ -1,6 +1,5 @@
 /*
- * Copyright (C) 2011, Google Inc.
- * and other copyright owners as documented in the project's IP log.
+ * Copyright (C) 2013 Robin Stocker <robin@nibor.org> and others.
  *
  * This program and the accompanying materials are made available
  * under the terms of the Eclipse Distribution License v1.0 which
@@ -40,21 +39,42 @@
  * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
  * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
+package org.eclipse.jgit.pgm;
 
-package org.eclipse.jgit.internal.storage.dfs;
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
 
-import java.util.concurrent.atomic.AtomicLong;
+import java.io.File;
 
-final class DfsPackKey {
-	final int hash;
+import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.dircache.DirCache;
+import org.eclipse.jgit.lib.CLIRepositoryTestCase;
+import org.junit.Before;
+import org.junit.Test;
 
-	final AtomicLong cachedSize;
+public class RmTest extends CLIRepositoryTestCase {
+	private Git git;
 
-	DfsPackKey() {
-		// Multiply by 31 here so we can more directly combine with another
-		// value without doing the multiply there.
-		//
-		hash = System.identityHashCode(this) * 31;
-		cachedSize = new AtomicLong();
+	@Override
+	@Before
+	public void setUp() throws Exception {
+		super.setUp();
+		git = new Git(db);
+	}
+
+	@Test
+	public void multiplePathsShouldBeRemoved() throws Exception {
+		File a = writeTrashFile("a", "Hello");
+		File b = writeTrashFile("b", "world!");
+		git.add().addFilepattern("a").addFilepattern("b").call();
+
+		String[] result = execute("git rm a b");
+		assertArrayEquals(new String[] { "" }, result);
+		DirCache cache = db.readDirCache();
+		assertNull(cache.getEntry("a"));
+		assertNull(cache.getEntry("b"));
+		assertFalse(a.exists());
+		assertFalse(b.exists());
 	}
 }
diff --git a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/StatusTest.java b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/StatusTest.java
index 368047c..cc68da2 100644
--- a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/StatusTest.java
+++ b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/StatusTest.java
@@ -60,7 +60,7 @@ public class StatusTest extends CLIRepositoryTestCase {
 	public void testPathOptionHelp() throws Exception {
 		String[] result = execute("git status -h");
 		assertTrue("Unexpected argument: " + result[1],
-				result[1].endsWith("[-- path ... ...]"));
+				result[1].endsWith("[-- path ...]"));
 	}
 
 	@Test
diff --git a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/TextBuiltinTest.java b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/TextBuiltinTest.java
new file mode 100644
index 0000000..256d2af
--- /dev/null
+++ b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/TextBuiltinTest.java
@@ -0,0 +1,110 @@
+/*
+ * Copyright (C) 2017, Ned Twigg <ned.twigg@diffplug.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.pgm;
+
+import static org.eclipse.jgit.junit.JGitTestUtil.check;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.lib.CLIRepositoryTestCase;
+import org.eclipse.jgit.pgm.opt.CmdLineParser;
+import org.eclipse.jgit.pgm.opt.SubcommandHandler;
+import org.junit.Test;
+import org.kohsuke.args4j.Argument;
+
+public class TextBuiltinTest extends CLIRepositoryTestCase {
+	public static class GitCliJGitWrapperParser {
+		@Argument(index = 0, metaVar = "metaVar_command", required = true, handler = SubcommandHandler.class)
+		TextBuiltin subcommand;
+
+		@Argument(index = 1, metaVar = "metaVar_arg")
+		List<String> arguments = new ArrayList<>();
+	}
+
+	private String[] runAndCaptureUsingInitRaw(String... args)
+			throws Exception {
+		CLIGitCommand.Result result = new CLIGitCommand.Result();
+
+		GitCliJGitWrapperParser bean = new GitCliJGitWrapperParser();
+		final CmdLineParser clp = new CmdLineParser(bean);
+		clp.parseArgument(args);
+
+		final TextBuiltin cmd = bean.subcommand;
+		cmd.initRaw(db, null, null, result.out, result.err);
+		cmd.execute(bean.arguments.toArray(new String[bean.arguments.size()]));
+		if (cmd.getOutputWriter() != null) {
+			cmd.getOutputWriter().flush();
+		}
+		if (cmd.getErrorWriter() != null) {
+			cmd.getErrorWriter().flush();
+		}
+		return result.outLines().toArray(new String[0]);
+	}
+
+	@Test
+	public void testCleanDeleteDirs() throws Exception {
+		try (Git git = new Git(db)) {
+			git.commit().setMessage("initial commit").call();
+
+			writeTrashFile("dir/file", "someData");
+			writeTrashFile("a", "someData");
+			writeTrashFile("b", "someData");
+
+			// all these files should be there
+			assertTrue(check(db, "a"));
+			assertTrue(check(db, "b"));
+			assertTrue(check(db, "dir/file"));
+
+			assertArrayOfLinesEquals(new String[] { "Removing a", "Removing b",
+					"Removing dir/" },
+					runAndCaptureUsingInitRaw("clean", "-d", "-f"));
+			assertFalse(check(db, "a"));
+			assertFalse(check(db, "b"));
+			assertFalse(check(db, "dir/file"));
+		}
+	}
+}
diff --git a/org.eclipse.jgit.pgm/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.pgm/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.pgm/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.pgm/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.pgm/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.pgm/.settings/org.eclipse.pde.api.tools.prefs
index cd148d9..c0030de 100644
--- a/org.eclipse.jgit.pgm/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.pgm/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,4 +1,4 @@
-#Tue Oct 18 00:52:01 CEST 2011
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -8,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -47,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -58,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -75,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -83,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF b/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF
index 5bde6a3..33ed801 100644
--- a/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.pgm
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
 Bundle-Localization: plugin
@@ -27,46 +27,49 @@
  org.eclipse.jetty.util.log;version="[9.4.5,10.0.0)",
  org.eclipse.jetty.util.security;version="[9.4.5,10.0.0)",
  org.eclipse.jetty.util.thread;version="[9.4.5,10.0.0)",
- org.eclipse.jgit.api;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.api.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.archive;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.awtui;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.blame;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.diff;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.dircache;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.gitrepo;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.ketch;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.file;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.pack;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.reftree;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs.server;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs.server.fs;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs.server.s3;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.merge;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.nls;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.notes;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revplot;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revwalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revwalk.filter;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.storage.file;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.storage.pack;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport.http.apache;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport.resolver;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.treewalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.treewalk.filter;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util.io;version="[4.8.1,4.9.0)",
- org.kohsuke.args4j;version="[2.0.12,2.1.0)",
- org.kohsuke.args4j.spi;version="[2.0.15,2.1.0)"
-Export-Package: org.eclipse.jgit.console;version="4.8.1";
+ org.eclipse.jgit.api;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.api.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.archive;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.awtui;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.blame;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.diff;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.dircache;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.gitrepo;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.ketch;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.dfs;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.file;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.io;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.pack;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.reftable;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.reftree;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs.server;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs.server.fs;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs.server.s3;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.merge;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.nls;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.notes;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revplot;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revwalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revwalk.filter;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.storage.file;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.storage.pack;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport.http.apache;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport.resolver;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.treewalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.treewalk.filter;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util.io;version="[4.9.6,4.10.0)",
+ org.kohsuke.args4j;version="[2.33.0,3.0.0)",
+ org.kohsuke.args4j.spi;version="[2.33.0,3.0.0)"
+Export-Package: org.eclipse.jgit.console;version="4.9.6";
   uses:="org.eclipse.jgit.transport,
    org.eclipse.jgit.util",
- org.eclipse.jgit.pgm;version="4.8.1";
+ org.eclipse.jgit.pgm;version="4.9.6";
   uses:="org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.pgm.opt,
@@ -77,11 +80,11 @@
    org.eclipse.jgit.treewalk,
    javax.swing,
    org.eclipse.jgit.transport",
- org.eclipse.jgit.pgm.debug;version="4.8.1";
+ org.eclipse.jgit.pgm.debug;version="4.9.6";
   uses:="org.eclipse.jgit.util.io,
    org.eclipse.jgit.pgm",
- org.eclipse.jgit.pgm.internal;version="4.8.1";x-friends:="org.eclipse.jgit.pgm.test,org.eclipse.jgit.test",
- org.eclipse.jgit.pgm.opt;version="4.8.1";
+ org.eclipse.jgit.pgm.internal;version="4.9.6";x-friends:="org.eclipse.jgit.pgm.test,org.eclipse.jgit.test",
+ org.eclipse.jgit.pgm.opt;version="4.9.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.revwalk,
    org.kohsuke.args4j.spi,
diff --git a/org.eclipse.jgit.pgm/META-INF/SOURCE-MANIFEST.MF b/org.eclipse.jgit.pgm/META-INF/SOURCE-MANIFEST.MF
index d5d71ee..55ea5e8 100644
--- a/org.eclipse.jgit.pgm/META-INF/SOURCE-MANIFEST.MF
+++ b/org.eclipse.jgit.pgm/META-INF/SOURCE-MANIFEST.MF
@@ -3,5 +3,5 @@
 Bundle-Name: org.eclipse.jgit.pgm - Sources
 Bundle-SymbolicName: org.eclipse.jgit.pgm.source
 Bundle-Vendor: Eclipse.org - JGit
-Bundle-Version: 4.8.1.qualifier
-Eclipse-SourceBundle: org.eclipse.jgit.pgm;version="4.8.1.qualifier";roots="."
+Bundle-Version: 4.9.6.qualifier
+Eclipse-SourceBundle: org.eclipse.jgit.pgm;version="4.9.6.qualifier";roots="."
diff --git a/org.eclipse.jgit.pgm/META-INF/services/org.eclipse.jgit.pgm.TextBuiltin b/org.eclipse.jgit.pgm/META-INF/services/org.eclipse.jgit.pgm.TextBuiltin
index 5495be6..9025473 100644
--- a/org.eclipse.jgit.pgm/META-INF/services/org.eclipse.jgit.pgm.TextBuiltin
+++ b/org.eclipse.jgit.pgm/META-INF/services/org.eclipse.jgit.pgm.TextBuiltin
@@ -38,10 +38,12 @@
 org.eclipse.jgit.pgm.UploadPack
 org.eclipse.jgit.pgm.Version
 
+org.eclipse.jgit.pgm.debug.BenchmarkReftable
 org.eclipse.jgit.pgm.debug.DiffAlgorithms
 org.eclipse.jgit.pgm.debug.LfsStore
 org.eclipse.jgit.pgm.debug.MakeCacheTree
 org.eclipse.jgit.pgm.debug.ReadDirCache
+org.eclipse.jgit.pgm.debug.ReadReftable
 org.eclipse.jgit.pgm.debug.RebuildCommitGraph
 org.eclipse.jgit.pgm.debug.RebuildRefTree
 org.eclipse.jgit.pgm.debug.ShowCacheTree
@@ -49,5 +51,6 @@
 org.eclipse.jgit.pgm.debug.ShowDirCache
 org.eclipse.jgit.pgm.debug.ShowPackDelta
 org.eclipse.jgit.pgm.debug.TextHashFunctions
-org.eclipse.jgit.pgm.debug.WriteDirCache
-
+org.eclipse.jgit.pgm.debug.VerifyReftable
+org.eclipse.jgit.pgm.debug.WriteReftable
+org.eclipse.jgit.pgm.debug.WriteReftable
diff --git a/org.eclipse.jgit.pgm/pom.xml b/org.eclipse.jgit.pgm/pom.xml
index 7d6ec1d..6d4b834 100644
--- a/org.eclipse.jgit.pgm/pom.xml
+++ b/org.eclipse.jgit.pgm/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.pgm</artifactId>
diff --git a/org.eclipse.jgit.pgm/resources/org/eclipse/jgit/pgm/internal/CLIText.properties b/org.eclipse.jgit.pgm/resources/org/eclipse/jgit/pgm/internal/CLIText.properties
index c3d7c68..cb0ea1b 100644
--- a/org.eclipse.jgit.pgm/resources/org/eclipse/jgit/pgm/internal/CLIText.properties
+++ b/org.eclipse.jgit.pgm/resources/org/eclipse/jgit/pgm/internal/CLIText.properties
@@ -75,6 +75,7 @@
 initializedEmptyGitRepositoryIn=Initialized empty Git repository in {0}
 invalidHttpProxyOnlyHttpSupported=Invalid http_proxy: {0}: Only http supported.
 invalidRecurseSubmodulesMode=Invalid recurse submodules mode: {0}
+invalidUntrackedFilesMode=Invalid untracked files mode ''{0}''
 jgitVersion=jgit version {0}
 lineFormat={0}
 listeningOn=Listening on {0}
@@ -129,6 +130,7 @@
 metaVar_pass=PASS
 metaVar_path=path
 metaVar_paths=path ...
+metaVar_pattern=pattern
 metaVar_port=PORT
 metaVar_ref=REF
 metaVar_refs=REFS
@@ -248,6 +250,7 @@
 usage_lsRemoteTags=Show only refs starting with refs/tags
 usage_LsTree=List the contents of a tree object
 usage_MakeCacheTree=Show the current cache tree structure
+usage_Match=Only consider tags matching the given glob(7) pattern or patterns, excluding the "refs/tags/" prefix.
 usage_MergeBase=Find as good common ancestors as possible for a merge
 usage_MergesTwoDevelopmentHistories=Merges two development histories
 usage_PreserveOldPacks=Preserve old pack files by moving them into the preserved subdirectory instead of deleting them after repacking
@@ -255,13 +258,16 @@
 usage_ReadDirCache= Read the DirCache 100 times
 usage_RebuildCommitGraph=Recreate a repository from another one's commit graph
 usage_RebuildRefTree=Copy references into a RefTree
-usage_RebuildRefTreeEnable=set extensions.refsStorage = reftree
+usage_RebuildRefTreeEnable=set extensions.refStorage = reftree
 usage_Remote=Manage set of tracked repositories
 usage_RepositoryToReadFrom=Repository to read from
 usage_RepositoryToReceiveInto=Repository to receive into
 usage_RevList=List commit objects in reverse chronological order
 usage_RevParse=Pick out and massage parameters
 usage_RevParseAll=Show all refs found in refs/
+usage_RevParseVerify=Verify that exactly one parameter is provided, and that it can be turned into \
+a raw 20-byte SHA-1 that can be used to access the object database. If so, emit it to the standard \
+output; otherwise, error out.
 usage_S3Bucket=S3 bucket name
 usage_S3Expiration=Authorization validity in seconds, default 60 sec
 usage_S3Region=S3 region (us-east-1 | us-west-1 | us-west-2 | eu-west-1 |\
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Checkout.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Checkout.java
index c2f3c46..2af1eca 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Checkout.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Checkout.java
@@ -77,7 +77,7 @@ class Checkout extends TextBuiltin {
 	@Argument(required = false, index = 0, metaVar = "metaVar_name", usage = "usage_checkout")
 	private String name;
 
-	@Option(name = "--", metaVar = "metaVar_paths", multiValued = true, handler = RestOfArgumentsHandler.class)
+	@Option(name = "--", metaVar = "metaVar_paths", handler = RestOfArgumentsHandler.class)
 	private List<String> paths = new ArrayList<>();
 
 	@Override
@@ -122,17 +122,21 @@ protected void run() throws Exception {
 							CLIText.get().switchedToBranch,
 							Repository.shortenRefName(ref.getName())));
 			} catch (RefNotFoundException e) {
-				outw.println(MessageFormat.format(
-						CLIText.get().pathspecDidNotMatch,
-						name));
+				throw die(MessageFormat
+						.format(CLIText.get().pathspecDidNotMatch, name), e);
 			} catch (RefAlreadyExistsException e) {
-				throw die(MessageFormat.format(CLIText.get().branchAlreadyExists,
-						name));
+				throw die(MessageFormat
+						.format(CLIText.get().branchAlreadyExists, name));
 			} catch (CheckoutConflictException e) {
-				outw.println(CLIText.get().checkoutConflict);
-				for (String path : e.getConflictingPaths())
-					outw.println(MessageFormat.format(
+				StringBuilder builder = new StringBuilder();
+				builder.append(CLIText.get().checkoutConflict);
+				builder.append(System.lineSeparator());
+				for (String path : e.getConflictingPaths()) {
+					builder.append(MessageFormat.format(
 							CLIText.get().checkoutConflictPathLine, path));
+					builder.append(System.lineSeparator());
+				}
+				throw die(builder.toString(), e);
 			}
 		}
 	}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java
index ca5205a..a8eb474 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java
@@ -101,6 +101,9 @@ protected void run() throws Exception {
 		if (localName == null) {
 			try {
 				localName = uri.getHumanishName();
+				if (isBare) {
+					localName = localName + Constants.DOT_GIT_EXT;
+				}
 				localNameF = new File(SystemReader.getInstance().getProperty(
 						Constants.OS_USER_DIR), localName);
 			} catch (IllegalArgumentException e) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CommandRef.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CommandRef.java
index 5222515..e5f8532 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CommandRef.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CommandRef.java
@@ -165,4 +165,12 @@ public TextBuiltin create() {
 		r.setCommandName(getName());
 		return r;
 	}
+
+	@SuppressWarnings("nls")
+	@Override
+	public String toString() {
+		return "CommandRef [impl=" + impl + ", name=" + name + ", usage="
+				+ CLIText.get().resourceBundle().getString(usage) + ", common="
+				+ common + "]";
+	}
 }
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Config.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Config.java
index faae13a..f5c3f9a 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Config.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Config.java
@@ -122,4 +122,4 @@ private void list(StoredConfig config) throws IOException,
 			}
 		}
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Daemon.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Daemon.java
index 1008593..51bb979 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Daemon.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Daemon.java
@@ -86,17 +86,17 @@ class Daemon extends TextBuiltin {
 	@Option(name = "--timeout", metaVar = "metaVar_seconds", usage = "usage_abortConnectionIfNoActivity")
 	int timeout = -1;
 
-	@Option(name = "--enable", metaVar = "metaVar_service", usage = "usage_enableTheServiceInAllRepositories", multiValued = true)
-	final List<String> enable = new ArrayList<>();
+	@Option(name = "--enable", metaVar = "metaVar_service", usage = "usage_enableTheServiceInAllRepositories")
+	List<String> enable = new ArrayList<>();
 
-	@Option(name = "--disable", metaVar = "metaVar_service", usage = "usage_disableTheServiceInAllRepositories", multiValued = true)
-	final List<String> disable = new ArrayList<>();
+	@Option(name = "--disable", metaVar = "metaVar_service", usage = "usage_disableTheServiceInAllRepositories")
+	List<String> disable = new ArrayList<>();
 
-	@Option(name = "--allow-override", metaVar = "metaVar_service", usage = "usage_configureTheServiceInDaemonServicename", multiValued = true)
-	final List<String> canOverride = new ArrayList<>();
+	@Option(name = "--allow-override", metaVar = "metaVar_service", usage = "usage_configureTheServiceInDaemonServicename")
+	List<String> canOverride = new ArrayList<>();
 
-	@Option(name = "--forbid-override", metaVar = "metaVar_service", usage = "usage_configureTheServiceInDaemonServicename", multiValued = true)
-	final List<String> forbidOverride = new ArrayList<>();
+	@Option(name = "--forbid-override", metaVar = "metaVar_service", usage = "usage_configureTheServiceInDaemonServicename")
+	List<String> forbidOverride = new ArrayList<>();
 
 	@Option(name = "--export-all", usage = "usage_exportWithoutGitDaemonExportOk")
 	boolean exportAll;
@@ -109,7 +109,7 @@ enum KetchServerType {
 	}
 
 	@Argument(required = true, metaVar = "metaVar_directory", usage = "usage_directoriesToExport")
-	final List<File> directory = new ArrayList<>();
+	List<File> directory = new ArrayList<>();
 
 	@Override
 	protected boolean requiresRepository() {
@@ -204,4 +204,4 @@ public ReceivePack create(DaemonClient req, Repository repo)
 			}
 		});
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Describe.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Describe.java
index ec000f3..03e2711 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Describe.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Describe.java
@@ -42,6 +42,9 @@
  */
 package org.eclipse.jgit.pgm;
 
+import java.util.ArrayList;
+import java.util.List;
+
 import org.eclipse.jgit.api.DescribeCommand;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.RefNotFoundException;
@@ -59,6 +62,9 @@ class Describe extends TextBuiltin {
 	@Option(name = "--long", usage = "usage_LongFormat")
 	private boolean longDesc;
 
+	@Option(name = "--match", usage = "usage_Match", metaVar = "metaVar_pattern")
+	private List<String> patterns = new ArrayList<>();
+
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
@@ -66,6 +72,7 @@ protected void run() throws Exception {
 			if (tree != null)
 				cmd.setTarget(tree);
 			cmd.setLong(longDesc);
+			cmd.setMatch(patterns.toArray(new String[patterns.size()]));
 			String result = null;
 			try {
 				result = cmd.call();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Diff.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Diff.java
index 61a385d..16284d5 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Diff.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Diff.java
@@ -89,7 +89,7 @@ class Diff extends TextBuiltin {
 	@Option(name = "--cached", usage = "usage_cached")
 	private boolean cached;
 
-	@Option(name = "--", metaVar = "metaVar_paths", multiValued = true, handler = PathTreeFilterHandler.class)
+	@Option(name = "--", metaVar = "metaVar_paths", handler = PathTreeFilterHandler.class)
 	private TreeFilter pathFilter = TreeFilter.ALL;
 
 	// BEGIN -- Options shared with Log
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/DiffTree.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/DiffTree.java
index 56b6241..4432405 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/DiffTree.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/DiffTree.java
@@ -67,9 +67,9 @@ void tree_0(final AbstractTreeIterator c) {
 	}
 
 	@Argument(index = 1, metaVar = "metaVar_treeish", required = true)
-	private final List<AbstractTreeIterator> trees = new ArrayList<>();
+	private List<AbstractTreeIterator> trees = new ArrayList<>();
 
-	@Option(name = "--", metaVar = "metaVar_path", multiValued = true, handler = PathTreeFilterHandler.class)
+	@Option(name = "--", metaVar = "metaVar_path", handler = PathTreeFilterHandler.class)
 	private TreeFilter pathFilter = TreeFilter.ALL;
 
 	@Override
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Fetch.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Fetch.java
index 5ed23b9..f4b7708 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Fetch.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Fetch.java
@@ -53,8 +53,8 @@
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.SubmoduleConfig.FetchRecurseSubmodulesMode;
-import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.lib.TextProgressMonitor;
+import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.transport.FetchResult;
 import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.transport.TagOpt;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsTree.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsTree.java
index 02d61e5..398d305 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsTree.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsTree.java
@@ -67,7 +67,7 @@ class LsTree extends TextBuiltin {
 	private AbstractTreeIterator tree;
 
 	@Argument(index = 1)
-	@Option(name = "--", metaVar = "metaVar_paths", multiValued = true, handler = StopOptionHandler.class)
+	@Option(name = "--", metaVar = "metaVar_paths", handler = StopOptionHandler.class)
 	private List<String> paths = new ArrayList<>();
 
 	@Override
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java
index c94ba0b..9d44dc0 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java
@@ -77,8 +77,8 @@
 import org.eclipse.jgit.util.CachedAuthenticator;
 import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.CmdLineException;
-import org.kohsuke.args4j.ExampleMode;
 import org.kohsuke.args4j.Option;
+import org.kohsuke.args4j.OptionHandlerFilter;
 
 /** Command line entry point. */
 public class Main {
@@ -231,7 +231,8 @@ private void execute(final String[] argv) throws Exception {
 		}
 
 		if (argv.length == 0 || help) {
-			final String ex = clp.printExample(ExampleMode.ALL, CLIText.get().resourceBundle());
+			final String ex = clp.printExample(OptionHandlerFilter.ALL,
+					CLIText.get().resourceBundle());
 			writer.println("jgit" + ex + " command [ARG ...]"); //$NON-NLS-1$ //$NON-NLS-2$
 			if (help) {
 				writer.println();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MergeBase.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MergeBase.java
index f8bae1d..975d5de 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MergeBase.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MergeBase.java
@@ -63,7 +63,7 @@ void commit_0(final RevCommit c) {
 	}
 
 	@Argument(index = 1, metaVar = "metaVar_commitish", required = true)
-	private final List<RevCommit> commits = new ArrayList<>();
+	private List<RevCommit> commits = new ArrayList<>();
 
 	@Override
 	protected void run() throws Exception {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Push.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Push.java
index 1b805d1..389708e 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Push.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Push.java
@@ -77,7 +77,7 @@ class Push extends TextBuiltin {
 	private String remote = Constants.DEFAULT_REMOTE_NAME;
 
 	@Argument(index = 1, metaVar = "metaVar_refspec")
-	private final List<RefSpec> refSpecs = new ArrayList<>();
+	private List<RefSpec> refSpecs = new ArrayList<>();
 
 	@Option(name = "--all")
 	private boolean all;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reset.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reset.java
index 9cee37b..4c19883 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reset.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reset.java
@@ -69,7 +69,7 @@ class Reset extends TextBuiltin {
 	private String commit;
 
 	@Argument(required = false, index = 1, metaVar = "metaVar_paths")
-	@Option(name = "--", metaVar = "metaVar_paths", multiValued = true, handler = RestOfArgumentsHandler.class)
+	@Option(name = "--", metaVar = "metaVar_paths", handler = RestOfArgumentsHandler.class)
 	private List<String> paths = new ArrayList<>();
 
 	@Override
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevParse.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevParse.java
index a66b7fa..2157034 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevParse.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevParse.java
@@ -68,7 +68,7 @@ class RevParse extends TextBuiltin {
 	boolean verify;
 
 	@Argument(index = 0, metaVar = "metaVar_commitish")
-	private final List<ObjectId> commits = new ArrayList<>();
+	private List<ObjectId> commits = new ArrayList<>();
 
 	@Override
 	protected void run() throws Exception {
@@ -86,7 +86,8 @@ protected void run() throws Exception {
 		} else {
 			if (verify && commits.size() > 1) {
 				final CmdLineParser clp = new CmdLineParser(this);
-				throw new CmdLineException(clp, CLIText.get().needSingleRevision);
+				throw new CmdLineException(clp,
+						CLIText.format(CLIText.get().needSingleRevision));
 			}
 
 			for (final ObjectId o : commits) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevWalkTextBuiltin.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevWalkTextBuiltin.java
index 74135e4..6b0744d 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevWalkTextBuiltin.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevWalkTextBuiltin.java
@@ -124,9 +124,9 @@ void enableBoundary(final boolean on) {
 	private String followPath;
 
 	@Argument(index = 0, metaVar = "metaVar_commitish")
-	private final List<RevCommit> commits = new ArrayList<>();
+	private List<RevCommit> commits = new ArrayList<>();
 
-	@Option(name = "--", metaVar = "metaVar_path", multiValued = true, handler = PathTreeFilterHandler.class)
+	@Option(name = "--", metaVar = "metaVar_path", handler = PathTreeFilterHandler.class)
 	protected TreeFilter pathFilter = TreeFilter.ALL;
 
 	private final List<RevFilter> revLimiter = new ArrayList<>();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Rm.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Rm.java
index 79c3f09..32a5631 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Rm.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Rm.java
@@ -55,12 +55,10 @@
 
 @Command(usage = "usage_StopTrackingAFile", common = true)
 class Rm extends TextBuiltin {
-	@Argument(metaVar = "metaVar_path", usage = "usage_path", multiValued = true, required = true)
-
+	@Argument(metaVar = "metaVar_path", usage = "usage_path", required = true)
 	@Option(name = "--", handler = StopOptionHandler.class)
 	private List<String> paths = new ArrayList<>();
 
-
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java
index 6892c99..5eda36f 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java
@@ -87,7 +87,7 @@ class Show extends TextBuiltin {
 	@Argument(index = 0, metaVar = "metaVar_object")
 	private String objectName;
 
-	@Option(name = "--", metaVar = "metaVar_path", multiValued = true, handler = PathTreeFilterHandler.class)
+	@Option(name = "--", metaVar = "metaVar_path", handler = PathTreeFilterHandler.class)
 	protected TreeFilter pathFilter = TreeFilter.ALL;
 
 	// BEGIN -- Options shared with Diff
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Status.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Status.java
index b7f5e58..adcfea4 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Status.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Status.java
@@ -83,7 +83,7 @@ class Status extends TextBuiltin {
 	protected String untrackedFilesMode = "all"; // default value //$NON-NLS-1$
 
 	@Argument(required = false, index = 0, metaVar = "metaVar_paths")
-	@Option(name = "--", metaVar = "metaVar_paths", multiValued = true, handler = RestOfArgumentsHandler.class)
+	@Option(name = "--", metaVar = "metaVar_paths", handler = RestOfArgumentsHandler.class)
 	protected List<String> filterPaths;
 
 	@Override
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java
index 0dc549c..c3b45e8 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java
@@ -139,6 +139,31 @@ protected boolean requiresRepository() {
 	}
 
 	/**
+	 * Initializes the command to work with a repository, including setting the
+	 * output and error streams.
+	 *
+	 * @param repository
+	 *            the opened repository that the command should work on.
+	 * @param gitDir
+	 *            value of the {@code --git-dir} command line option, if
+	 *            {@code repository} is null.
+	 * @param input
+	 *            input stream from which input will be read
+	 * @param output
+	 *            output stream to which output will be written
+	 * @param error
+	 *            error stream to which errors will be written
+	 * @since 4.9
+	 */
+	public void initRaw(final Repository repository, final String gitDir,
+			InputStream input, OutputStream output, OutputStream error) {
+		this.ins = input;
+		this.outs = output;
+		this.errs = error;
+		init(repository, gitDir);
+	}
+
+	/**
 	 * Initialize the command to work with a repository.
 	 *
 	 * @param repository
@@ -285,6 +310,14 @@ public ThrowingPrintWriter getErrorWriter() {
 	}
 
 	/**
+	 * @return output writer, typically this is standard output.
+	 * @since 4.9
+	 */
+	public ThrowingPrintWriter getOutputWriter() {
+		return outw;
+	}
+
+	/**
 	 * @return the resource bundle that will be passed to args4j for purpose of
 	 *         string localization
 	 */
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/BenchmarkReftable.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/BenchmarkReftable.java
new file mode 100644
index 0000000..71c8db8
--- /dev/null
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/BenchmarkReftable.java
@@ -0,0 +1,315 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.pgm.debug;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.eclipse.jgit.lib.Constants.HEAD;
+import static org.eclipse.jgit.lib.Constants.MASTER;
+import static org.eclipse.jgit.lib.Constants.R_HEADS;
+import static org.eclipse.jgit.lib.Ref.Storage.NEW;
+import static org.eclipse.jgit.lib.Ref.Storage.PACKED;
+
+import java.io.BufferedReader;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+import org.eclipse.jgit.internal.storage.io.BlockSource;
+import org.eclipse.jgit.internal.storage.reftable.RefCursor;
+import org.eclipse.jgit.internal.storage.reftable.ReftableReader;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectIdRef;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.SymbolicRef;
+import org.eclipse.jgit.pgm.Command;
+import org.eclipse.jgit.pgm.TextBuiltin;
+import org.eclipse.jgit.util.RefList;
+import org.kohsuke.args4j.Argument;
+import org.kohsuke.args4j.Option;
+
+@Command
+class BenchmarkReftable extends TextBuiltin {
+	enum Test {
+		SCAN,
+		SEEK_COLD, SEEK_HOT,
+		BY_ID_COLD, BY_ID_HOT;
+	}
+
+	@Option(name = "--tries")
+	private int tries = 10;
+
+	@Option(name = "--test")
+	private Test test = Test.SCAN;
+
+	@Option(name = "--ref")
+	private String ref;
+
+	@Option(name = "--object-id")
+	private String objectId;
+
+	@Argument(index = 0)
+	private String lsRemotePath;
+
+	@Argument(index = 1)
+	private String reftablePath;
+
+	@Override
+	protected void run() throws Exception {
+		switch (test) {
+		case SCAN:
+			scan();
+			break;
+
+		case SEEK_COLD:
+			seekCold(ref);
+			break;
+		case SEEK_HOT:
+			seekHot(ref);
+			break;
+
+		case BY_ID_COLD:
+			byIdCold(ObjectId.fromString(objectId));
+			break;
+		case BY_ID_HOT:
+			byIdHot(ObjectId.fromString(objectId));
+			break;
+		}
+	}
+
+	private void printf(String fmt, Object... args) throws IOException {
+		errw.println(String.format(fmt, args));
+	}
+
+	@SuppressWarnings({ "nls", "boxing" })
+	private void scan() throws Exception {
+		long start, tot;
+
+		start = System.currentTimeMillis();
+		for (int i = 0; i < tries; i++) {
+			readLsRemote();
+		}
+		tot = System.currentTimeMillis() - start;
+		printf("%12s %10d ms  %6d ms/run", "packed-refs", tot, tot / tries);
+
+		start = System.currentTimeMillis();
+		for (int i = 0; i < tries; i++) {
+			try (FileInputStream in = new FileInputStream(reftablePath);
+					BlockSource src = BlockSource.from(in);
+					ReftableReader reader = new ReftableReader(src)) {
+				try (RefCursor rc = reader.allRefs()) {
+					while (rc.next()) {
+						rc.getRef();
+					}
+				}
+			}
+		}
+		tot = System.currentTimeMillis() - start;
+		printf("%12s %10d ms  %6d ms/run", "reftable", tot, tot / tries);
+	}
+
+	private RefList<Ref> readLsRemote()
+			throws IOException, FileNotFoundException {
+		RefList.Builder<Ref> list = new RefList.Builder<>();
+		try (BufferedReader br = new BufferedReader(new InputStreamReader(
+				new FileInputStream(lsRemotePath), UTF_8))) {
+			Ref last = null;
+			String line;
+			while ((line = br.readLine()) != null) {
+				ObjectId id = ObjectId.fromString(line.substring(0, 40));
+				String name = line.substring(41, line.length());
+				if (last != null && name.endsWith("^{}")) { //$NON-NLS-1$
+					last = new ObjectIdRef.PeeledTag(PACKED, last.getName(),
+							last.getObjectId(), id);
+					list.set(list.size() - 1, last);
+					continue;
+				}
+
+				if (name.equals(HEAD)) {
+					last = new SymbolicRef(name, new ObjectIdRef.Unpeeled(NEW,
+							R_HEADS + MASTER, null));
+				} else {
+					last = new ObjectIdRef.PeeledNonTag(PACKED, name, id);
+				}
+				list.add(last);
+			}
+		}
+		list.sort();
+		return list.toRefList();
+	}
+
+	@SuppressWarnings({ "nls", "boxing" })
+	private void seekCold(String refName) throws Exception {
+		long start, tot;
+
+		int lsTries = Math.min(tries, 64);
+		start = System.nanoTime();
+		for (int i = 0; i < lsTries; i++) {
+			readLsRemote().get(refName);
+		}
+		tot = System.nanoTime() - start;
+		printf("%12s %10d usec  %9.1f usec/run  %5d runs", "packed-refs",
+				tot / 1000,
+				(((double) tot) / lsTries) / 1000,
+				lsTries);
+
+		start = System.nanoTime();
+		for (int i = 0; i < tries; i++) {
+			try (FileInputStream in = new FileInputStream(reftablePath);
+					BlockSource src = BlockSource.from(in);
+					ReftableReader reader = new ReftableReader(src)) {
+				try (RefCursor rc = reader.seekRef(refName)) {
+					while (rc.next()) {
+						rc.getRef();
+					}
+				}
+			}
+		}
+		tot = System.nanoTime() - start;
+		printf("%12s %10d usec  %9.1f usec/run  %5d runs", "reftable",
+				tot / 1000,
+				(((double) tot) / tries) / 1000,
+				tries);
+	}
+
+	@SuppressWarnings({ "nls", "boxing" })
+	private void seekHot(String refName) throws Exception {
+		long start, tot;
+
+		int lsTries = Math.min(tries, 64);
+		start = System.nanoTime();
+		RefList<Ref> lsRemote = readLsRemote();
+		for (int i = 0; i < lsTries; i++) {
+			lsRemote.get(refName);
+		}
+		tot = System.nanoTime() - start;
+		printf("%12s %10d usec  %9.1f usec/run  %5d runs", "packed-refs",
+				tot / 1000, (((double) tot) / lsTries) / 1000, lsTries);
+
+		start = System.nanoTime();
+		try (FileInputStream in = new FileInputStream(reftablePath);
+				BlockSource src = BlockSource.from(in);
+				ReftableReader reader = new ReftableReader(src)) {
+			for (int i = 0; i < tries; i++) {
+				try (RefCursor rc = reader.seekRef(refName)) {
+					while (rc.next()) {
+						rc.getRef();
+					}
+				}
+			}
+		}
+		tot = System.nanoTime() - start;
+		printf("%12s %10d usec  %9.1f usec/run  %5d runs", "reftable",
+				tot / 1000, (((double) tot) / tries) / 1000, tries);
+	}
+
+	@SuppressWarnings({ "nls", "boxing" })
+	private void byIdCold(ObjectId id) throws Exception {
+		long start, tot;
+
+		int lsTries = Math.min(tries, 64);
+		start = System.nanoTime();
+		for (int i = 0; i < lsTries; i++) {
+			for (Ref r : readLsRemote()) {
+				if (id.equals(r.getObjectId())) {
+					continue;
+				}
+			}
+		}
+		tot = System.nanoTime() - start;
+		printf("%12s %10d usec  %9.1f usec/run  %5d runs", "packed-refs",
+				tot / 1000, (((double) tot) / lsTries) / 1000, lsTries);
+
+		start = System.nanoTime();
+		for (int i = 0; i < tries; i++) {
+			try (FileInputStream in = new FileInputStream(reftablePath);
+					BlockSource src = BlockSource.from(in);
+					ReftableReader reader = new ReftableReader(src)) {
+				try (RefCursor rc = reader.byObjectId(id)) {
+					while (rc.next()) {
+						rc.getRef();
+					}
+				}
+			}
+		}
+		tot = System.nanoTime() - start;
+		printf("%12s %10d usec  %9.1f usec/run  %5d runs", "reftable",
+				tot / 1000, (((double) tot) / tries) / 1000, tries);
+	}
+
+	@SuppressWarnings({ "nls", "boxing" })
+	private void byIdHot(ObjectId id) throws Exception {
+		long start, tot;
+
+		int lsTries = Math.min(tries, 64);
+		start = System.nanoTime();
+		RefList<Ref> lsRemote = readLsRemote();
+		for (int i = 0; i < lsTries; i++) {
+			for (Ref r : lsRemote) {
+				if (id.equals(r.getObjectId())) {
+					continue;
+				}
+			}
+		}
+		tot = System.nanoTime() - start;
+		printf("%12s %10d usec  %9.1f usec/run  %5d runs", "packed-refs",
+				tot / 1000, (((double) tot) / lsTries) / 1000, lsTries);
+
+		start = System.nanoTime();
+		try (FileInputStream in = new FileInputStream(reftablePath);
+				BlockSource src = BlockSource.from(in);
+				ReftableReader reader = new ReftableReader(src)) {
+			for (int i = 0; i < tries; i++) {
+				try (RefCursor rc = reader.byObjectId(id)) {
+					while (rc.next()) {
+						rc.getRef();
+					}
+				}
+			}
+		}
+		tot = System.nanoTime() - start;
+		printf("%12s %10d usec  %9.1f usec/run  %5d runs", "reftable",
+				tot / 1000, (((double) tot) / tries) / 1000, tries);
+	}
+}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/DiffAlgorithms.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/DiffAlgorithms.java
index 44ec3f4..8de57e3 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/DiffAlgorithms.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/DiffAlgorithms.java
@@ -114,13 +114,13 @@ DiffAlgorithm create() {
 	//
 	//
 
-	@Option(name = "--algorithm", multiValued = true, metaVar = "NAME", usage = "Enable algorithm(s)")
+	@Option(name = "--algorithm", metaVar = "NAME", usage = "Enable algorithm(s)")
 	List<String> algorithms = new ArrayList<>();
 
 	@Option(name = "--text-limit", metaVar = "LIMIT", usage = "Maximum size in KiB to scan per file revision")
 	int textLimit = 15 * 1024; // 15 MiB as later we do * 1024.
 
-	@Option(name = "--repository", aliases = { "-r" }, multiValued = true, metaVar = "GIT_DIR", usage = "Repository to scan")
+	@Option(name = "--repository", aliases = { "-r" }, metaVar = "GIT_DIR", usage = "Repository to scan")
 	List<File> gitDirs = new ArrayList<>();
 
 	@Option(name = "--count", metaVar = "LIMIT", usage = "Number of file revisions to be compared")
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/LfsStore.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/LfsStore.java
index 5839f33..9dc4721 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/LfsStore.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/LfsStore.java
@@ -82,7 +82,7 @@ class LfsStore extends TextBuiltin {
 	/**
 	 * Tiny web application server for testing
 	 */
-	class AppServer {
+	static class AppServer {
 
 		private final Server server;
 
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ReadReftable.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ReadReftable.java
new file mode 100644
index 0000000..9b8db3e
--- /dev/null
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ReadReftable.java
@@ -0,0 +1,97 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.pgm.debug;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+
+import org.eclipse.jgit.internal.storage.io.BlockSource;
+import org.eclipse.jgit.internal.storage.reftable.RefCursor;
+import org.eclipse.jgit.internal.storage.reftable.ReftableReader;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.pgm.Command;
+import org.eclipse.jgit.pgm.TextBuiltin;
+import org.kohsuke.args4j.Argument;
+
+@Command
+class ReadReftable extends TextBuiltin {
+	@Argument(index = 0)
+	private String input;
+
+	@Argument(index = 1, required = false)
+	private String ref;
+
+	@Override
+	protected void run() throws Exception {
+		try (FileInputStream in = new FileInputStream(input);
+				BlockSource src = BlockSource.from(in);
+				ReftableReader reader = new ReftableReader(src)) {
+			try (RefCursor rc = ref != null
+					? reader.seekRef(ref)
+					: reader.allRefs()) {
+				while (rc.next()) {
+					write(rc.getRef());
+				}
+			}
+		}
+	}
+
+	private void write(Ref r) throws IOException {
+		if (r.isSymbolic()) {
+			outw.println(r.getTarget().getName() + '\t' + r.getName());
+			return;
+		}
+
+		ObjectId id1 = r.getObjectId();
+		if (id1 != null) {
+			outw.println(id1.name() + '\t' + r.getName());
+		}
+
+		ObjectId id2 = r.getPeeledObjectId();
+		if (id2 != null) {
+			outw.println('^' + id2.name());
+		}
+	}
+}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
index 57345e2..8cde513 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
@@ -133,7 +133,7 @@ protected void run() throws Exception {
 			if (enable && !(db.getRefDatabase() instanceof RefTreeDatabase)) {
 				StoredConfig cfg = db.getConfig();
 				cfg.setInt("core", null, "repositoryformatversion", 1); //$NON-NLS-1$ //$NON-NLS-2$
-				cfg.setString("extensions", null, "refsStorage", "reftree"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
+				cfg.setString("extensions", null, "refStorage", "reftree"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
 				cfg.save();
 				errw.println("Enabled reftree."); //$NON-NLS-1$
 				errw.flush();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java
index 0eb4e05..ce58201 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java
@@ -250,16 +250,16 @@ public int fold(int hash, int bits) {
 	//
 	//
 
-	@Option(name = "--hash", multiValued = true, metaVar = "NAME", usage = "Enable hash function(s)")
+	@Option(name = "--hash", metaVar = "NAME", usage = "Enable hash function(s)")
 	List<String> hashFunctions = new ArrayList<>();
 
-	@Option(name = "--fold", multiValued = true, metaVar = "NAME", usage = "Enable fold function(s)")
+	@Option(name = "--fold", metaVar = "NAME", usage = "Enable fold function(s)")
 	List<String> foldFunctions = new ArrayList<>();
 
 	@Option(name = "--text-limit", metaVar = "LIMIT", usage = "Maximum size in KiB to scan")
 	int textLimit = 15 * 1024; // 15 MiB as later we do * 1024.
 
-	@Option(name = "--repository", aliases = { "-r" }, multiValued = true, metaVar = "GIT_DIR", usage = "Repository to scan")
+	@Option(name = "--repository", aliases = { "-r" }, metaVar = "GIT_DIR", usage = "Repository to scan")
 	List<File> gitDirs = new ArrayList<>();
 
 	@Override
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/VerifyReftable.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/VerifyReftable.java
new file mode 100644
index 0000000..dffb579
--- /dev/null
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/VerifyReftable.java
@@ -0,0 +1,211 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.pgm.debug;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Random;
+
+import org.eclipse.jgit.internal.storage.io.BlockSource;
+import org.eclipse.jgit.internal.storage.reftable.RefCursor;
+import org.eclipse.jgit.internal.storage.reftable.ReftableReader;
+import org.eclipse.jgit.lib.AnyObjectId;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.RefComparator;
+import org.eclipse.jgit.lib.TextProgressMonitor;
+import org.eclipse.jgit.pgm.Command;
+import org.eclipse.jgit.pgm.TextBuiltin;
+import org.kohsuke.args4j.Argument;
+
+@Command
+class VerifyReftable extends TextBuiltin {
+	private static final long SEED1 = 0xaba8bb4de4caf86cL;
+	private static final long SEED2 = 0x28bb5c25ad43ecb5L;
+
+	@Argument(index = 0)
+	private String lsRemotePath;
+
+	@Argument(index = 1)
+	private String reftablePath;
+
+	@Override
+	protected void run() throws Exception {
+		List<Ref> refs = WriteReftable.readRefs(lsRemotePath);
+
+		try (FileInputStream in = new FileInputStream(reftablePath);
+				BlockSource src = BlockSource.from(in);
+				ReftableReader reader = new ReftableReader(src)) {
+			scan(refs, reader);
+			seek(refs, reader);
+			byId(refs, reader);
+		}
+	}
+
+	@SuppressWarnings("nls")
+	private void scan(List<Ref> refs, ReftableReader reader)
+			throws IOException {
+		errw.print(String.format("%-20s", "sequential scan..."));
+		errw.flush();
+		try (RefCursor rc = reader.allRefs()) {
+			for (Ref exp : refs) {
+				verify(exp, rc);
+			}
+			if (rc.next()) {
+				throw die("expected end of table");
+			}
+		}
+		errw.println(" OK");
+	}
+
+	@SuppressWarnings("nls")
+	private void seek(List<Ref> refs, ReftableReader reader)
+			throws IOException {
+		List<Ref> rnd = new ArrayList<>(refs);
+		Collections.shuffle(rnd, new Random(SEED1));
+
+		TextProgressMonitor pm = new TextProgressMonitor(errw);
+		pm.beginTask("random seek", rnd.size());
+		for (Ref exp : rnd) {
+			try (RefCursor rc = reader.seekRef(exp.getName())) {
+				verify(exp, rc);
+				if (rc.next()) {
+					throw die("should not have ref after " + exp.getName());
+				}
+			}
+			pm.update(1);
+		}
+		pm.endTask();
+	}
+
+	@SuppressWarnings("nls")
+	private void byId(List<Ref> refs, ReftableReader reader)
+			throws IOException {
+		Map<ObjectId, List<Ref>> want = groupById(refs);
+		List<List<Ref>> rnd = new ArrayList<>(want.values());
+		Collections.shuffle(rnd, new Random(SEED2));
+
+		TextProgressMonitor pm = new TextProgressMonitor(errw);
+		pm.beginTask("byObjectId", rnd.size());
+		for (List<Ref> exp : rnd) {
+			Collections.sort(exp, RefComparator.INSTANCE);
+			ObjectId id = exp.get(0).getObjectId();
+			try (RefCursor rc = reader.byObjectId(id)) {
+				for (Ref r : exp) {
+					verify(r, rc);
+				}
+			}
+			pm.update(1);
+		}
+		pm.endTask();
+	}
+
+	private static Map<ObjectId, List<Ref>> groupById(List<Ref> refs) {
+		Map<ObjectId, List<Ref>> m = new HashMap<>();
+		for (Ref r : refs) {
+			ObjectId id = r.getObjectId();
+			if (id != null) {
+				List<Ref> c = m.get(id);
+				if (c == null) {
+					c = new ArrayList<>(2);
+					m.put(id, c);
+				}
+				c.add(r);
+			}
+		}
+		return m;
+	}
+
+	@SuppressWarnings("nls")
+	private void verify(Ref exp, RefCursor rc) throws IOException {
+		if (!rc.next()) {
+			throw die("ended before " + exp.getName());
+		}
+
+		Ref act = rc.getRef();
+		if (!exp.getName().equals(act.getName())) {
+			throw die(String.format("expected %s, found %s",
+					exp.getName(),
+					act.getName()));
+		}
+
+		if (exp.isSymbolic()) {
+			if (!act.isSymbolic()) {
+				throw die("expected " + act.getName() + " to be symbolic");
+			}
+			if (!exp.getTarget().getName().equals(act.getTarget().getName())) {
+				throw die(String.format("expected %s to be %s, found %s",
+						exp.getName(),
+						exp.getLeaf().getName(),
+						act.getLeaf().getName()));
+			}
+			return;
+		}
+
+		if (!AnyObjectId.equals(exp.getObjectId(), act.getObjectId())) {
+			throw die(String.format("expected %s to be %s, found %s",
+					exp.getName(),
+					id(exp.getObjectId()),
+					id(act.getObjectId())));
+		}
+
+		if (exp.getPeeledObjectId() != null
+				&& !AnyObjectId.equals(exp.getPeeledObjectId(), act.getPeeledObjectId())) {
+			throw die(String.format("expected %s to be %s, found %s",
+					exp.getName(),
+					id(exp.getPeeledObjectId()),
+					id(act.getPeeledObjectId())));
+		}
+	}
+
+	@SuppressWarnings("nls")
+	private static String id(ObjectId id) {
+		return id != null ? id.name() : "<null>";
+	}
+}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteReftable.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteReftable.java
new file mode 100644
index 0000000..76ffa19
--- /dev/null
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteReftable.java
@@ -0,0 +1,301 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.pgm.debug;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.eclipse.jgit.lib.Constants.HEAD;
+import static org.eclipse.jgit.lib.Constants.MASTER;
+import static org.eclipse.jgit.lib.Constants.R_HEADS;
+import static org.eclipse.jgit.lib.Ref.Storage.NEW;
+import static org.eclipse.jgit.lib.Ref.Storage.PACKED;
+
+import java.io.BufferedReader;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.eclipse.jgit.internal.storage.reftable.ReftableConfig;
+import org.eclipse.jgit.internal.storage.reftable.ReftableWriter;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectIdRef;
+import org.eclipse.jgit.lib.PersonIdent;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.SymbolicRef;
+import org.eclipse.jgit.pgm.Command;
+import org.eclipse.jgit.pgm.TextBuiltin;
+import org.kohsuke.args4j.Argument;
+import org.kohsuke.args4j.Option;
+
+@Command
+class WriteReftable extends TextBuiltin {
+	private static final int KIB = 1 << 10;
+	private static final int MIB = 1 << 20;
+
+	@Option(name = "--block-size")
+	private int refBlockSize;
+
+	@Option(name = "--log-block-size")
+	private int logBlockSize;
+
+	@Option(name = "--restart-interval")
+	private int restartInterval;
+
+	@Option(name = "--index-levels")
+	private int indexLevels;
+
+	@Option(name = "--reflog-in")
+	private String reflogIn;
+
+	@Option(name = "--no-index-objects")
+	private boolean noIndexObjects;
+
+	@Argument(index = 0)
+	private String in;
+
+	@Argument(index = 1)
+	private String out;
+
+	@SuppressWarnings({ "nls", "boxing" })
+	@Override
+	protected void run() throws Exception {
+		List<Ref> refs = readRefs(in);
+		List<LogEntry> logs = readLog(reflogIn);
+
+		ReftableWriter.Stats stats;
+		try (OutputStream os = new FileOutputStream(out)) {
+			ReftableConfig cfg = new ReftableConfig();
+			cfg.setIndexObjects(!noIndexObjects);
+			if (refBlockSize > 0) {
+				cfg.setRefBlockSize(refBlockSize);
+			}
+			if (logBlockSize > 0) {
+				cfg.setLogBlockSize(logBlockSize);
+			}
+			if (restartInterval > 0) {
+				cfg.setRestartInterval(restartInterval);
+			}
+			if (indexLevels > 0) {
+				cfg.setMaxIndexLevels(indexLevels);
+			}
+
+			ReftableWriter w = new ReftableWriter(cfg);
+			w.setMinUpdateIndex(min(logs)).setMaxUpdateIndex(max(logs));
+			w.begin(os);
+			w.sortAndWriteRefs(refs);
+			for (LogEntry e : logs) {
+				w.writeLog(e.ref, e.updateIndex, e.who,
+						e.oldId, e.newId, e.message);
+			}
+			stats = w.finish().getStats();
+		}
+
+		double fileMiB = ((double) stats.totalBytes()) / MIB;
+		printf("Summary:");
+		printf("  file sz : %.1f MiB (%d bytes)", fileMiB, stats.totalBytes());
+		printf("  padding : %d KiB", stats.paddingBytes() / KIB);
+		errw.println();
+
+		printf("Refs:");
+		printf("  ref blk : %d", stats.refBlockSize());
+		printf("  restarts: %d", stats.restartInterval());
+		printf("  refs    : %d", stats.refCount());
+		if (stats.refIndexLevels() > 0) {
+			int idxSize = (int) Math.round(((double) stats.refIndexSize()) / KIB);
+			printf("  idx sz  : %d KiB", idxSize);
+			printf("  idx lvl : %d", stats.refIndexLevels());
+		}
+		printf("  avg ref : %d bytes", stats.refBytes() / refs.size());
+		errw.println();
+
+		if (stats.objCount() > 0) {
+			int objMiB = (int) Math.round(((double) stats.objBytes()) / MIB);
+			int idLen = stats.objIdLength();
+			printf("Objects:");
+			printf("  obj blk : %d", stats.refBlockSize());
+			printf("  restarts: %d", stats.restartInterval());
+			printf("  objects : %d", stats.objCount());
+			printf("  obj sz  : %d MiB (%d bytes)", objMiB, stats.objBytes());
+			if (stats.objIndexSize() > 0) {
+				int s = (int) Math.round(((double) stats.objIndexSize()) / KIB);
+				printf("  idx sz  : %d KiB", s);
+				printf("  idx lvl : %d", stats.objIndexLevels());
+			}
+			printf("  id len  : %d bytes (%d hex digits)", idLen, 2 * idLen);
+			printf("  avg obj : %d bytes", stats.objBytes() / stats.objCount());
+			errw.println();
+		}
+		if (stats.logCount() > 0) {
+			int logMiB = (int) Math.round(((double) stats.logBytes()) / MIB);
+			printf("Log:");
+			printf("  log blk : %d", stats.logBlockSize());
+			printf("  logs    : %d", stats.logCount());
+			printf("  log sz  : %d MiB (%d bytes)", logMiB, stats.logBytes());
+			printf("  avg log : %d bytes", stats.logBytes() / logs.size());
+			errw.println();
+		}
+	}
+
+	private void printf(String fmt, Object... args) throws IOException {
+		errw.println(String.format(fmt, args));
+	}
+
+	static List<Ref> readRefs(String inputFile) throws IOException {
+		List<Ref> refs = new ArrayList<>();
+		try (BufferedReader br = new BufferedReader(
+				new InputStreamReader(new FileInputStream(inputFile), UTF_8))) {
+			String line;
+			while ((line = br.readLine()) != null) {
+				ObjectId id = ObjectId.fromString(line.substring(0, 40));
+				String name = line.substring(41, line.length());
+				if (name.endsWith("^{}")) { //$NON-NLS-1$
+					int lastIdx = refs.size() - 1;
+					Ref last = refs.get(lastIdx);
+					refs.set(lastIdx, new ObjectIdRef.PeeledTag(PACKED,
+							last.getName(), last.getObjectId(), id));
+					continue;
+				}
+
+				Ref ref;
+				if (name.equals(HEAD)) {
+					ref = new SymbolicRef(name, new ObjectIdRef.Unpeeled(NEW,
+							R_HEADS + MASTER, null));
+				} else {
+					ref = new ObjectIdRef.PeeledNonTag(PACKED, name, id);
+				}
+				refs.add(ref);
+			}
+		}
+		Collections.sort(refs, (a, b) -> a.getName().compareTo(b.getName()));
+		return refs;
+	}
+
+	private static List<LogEntry> readLog(String logPath)
+			throws FileNotFoundException, IOException {
+		if (logPath == null) {
+			return Collections.emptyList();
+		}
+
+		List<LogEntry> log = new ArrayList<>();
+		try (BufferedReader br = new BufferedReader(
+				new InputStreamReader(new FileInputStream(logPath), UTF_8))) {
+			@SuppressWarnings("nls")
+			Pattern pattern = Pattern.compile("([^,]+)" // 1: ref
+					+ ",([0-9]+(?:[.][0-9]+)?)" // 2: time
+					+ ",([^,]+)" // 3: who
+					+ ",([^,]+)" // 4: old
+					+ ",([^,]+)" // 5: new
+					+ ",(.*)"); // 6: msg
+			String line;
+			while ((line = br.readLine()) != null) {
+				Matcher m = pattern.matcher(line);
+				if (!m.matches()) {
+					throw new IOException("unparsed line: " + line); //$NON-NLS-1$
+				}
+				String ref = m.group(1);
+				double t = Double.parseDouble(m.group(2));
+				long time = ((long) t) * 1000L;
+				long index = (long) (t * 1e6);
+				String user = m.group(3);
+				ObjectId oldId = parseId(m.group(4));
+				ObjectId newId = parseId(m.group(5));
+				String msg = m.group(6);
+				String email = user + "@gerrit"; //$NON-NLS-1$
+				PersonIdent who = new PersonIdent(user, email, time, -480);
+				log.add(new LogEntry(ref, index, who, oldId, newId, msg));
+			}
+		}
+		Collections.sort(log, LogEntry::compare);
+		return log;
+	}
+
+	private static long min(List<LogEntry> log) {
+		return log.stream().mapToLong(e -> e.updateIndex).min().orElse(0);
+	}
+
+	private static long max(List<LogEntry> log) {
+		return log.stream().mapToLong(e -> e.updateIndex).max().orElse(0);
+	}
+
+	private static ObjectId parseId(String s) {
+		if ("NULL".equals(s)) { //$NON-NLS-1$
+			return ObjectId.zeroId();
+		}
+		return ObjectId.fromString(s);
+	}
+
+	private static class LogEntry {
+		static int compare(LogEntry a, LogEntry b) {
+			int cmp = a.ref.compareTo(b.ref);
+			if (cmp == 0) {
+				cmp = Long.signum(b.updateIndex - a.updateIndex);
+			}
+			return cmp;
+		}
+
+		final String ref;
+		final long updateIndex;
+		final PersonIdent who;
+		final ObjectId oldId;
+		final ObjectId newId;
+		final String message;
+
+		LogEntry(String ref, long updateIndex, PersonIdent who,
+				ObjectId oldId, ObjectId newId, String message) {
+			this.ref = ref;
+			this.updateIndex = updateIndex;
+			this.who = who;
+			this.oldId = oldId;
+			this.newId = newId;
+			this.message = message;
+		}
+	}
+}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/CLIText.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/CLIText.java
index e012372..dfb489d 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/CLIText.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/CLIText.java
@@ -45,14 +45,47 @@
 package org.eclipse.jgit.pgm.internal;
 
 import java.text.MessageFormat;
+import java.util.Locale;
 
 import org.eclipse.jgit.nls.NLS;
 import org.eclipse.jgit.nls.TranslationBundle;
+import org.kohsuke.args4j.Localizable;
 
 /**
  * Translation bundle for JGit command line interface
  */
 public class CLIText extends TranslationBundle {
+	/**
+	 * Formats text strings using {@code Localizable}.
+	 *
+	 */
+	public static class Format implements Localizable {
+		final String text;
+
+		Format(String text) {
+			this.text = text;
+		}
+
+		@Override
+		public String formatWithLocale(Locale locale, Object... args) {
+			// we don't care about Locale for now
+			return format(args);
+		}
+
+		@Override
+		public String format(Object... args) {
+			return MessageFormat.format(text, args);
+		}
+	}
+
+	/**
+	 * @param text
+	 *            the text to format.
+	 * @return a new Format instance.
+	 */
+	public static Format format(String text) {
+		return new Format(text);
+	}
 
 	/**
 	 * @return an instance of this translation bundle
@@ -151,6 +184,7 @@ public static String fatalError(String message) {
 	/***/ public String initializedEmptyGitRepositoryIn;
 	/***/ public String invalidHttpProxyOnlyHttpSupported;
 	/***/ public String invalidRecurseSubmodulesMode;
+	/***/ public String invalidUntrackedFilesMode;
 	/***/ public String jgitVersion;
 	/***/ public String lfsNoAccessKey;
 	/***/ public String lfsNoSecretKey;
@@ -196,6 +230,7 @@ public static String fatalError(String message) {
 	/***/ public String metaVar_pass;
 	/***/ public String metaVar_path;
 	/***/ public String metaVar_paths;
+	/***/ public String metaVar_pattern;
 	/***/ public String metaVar_port;
 	/***/ public String metaVar_ref;
 	/***/ public String metaVar_refs;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/AbstractTreeIteratorHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/AbstractTreeIteratorHandler.java
index 8f56bda..587f98c 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/AbstractTreeIteratorHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/AbstractTreeIteratorHandler.java
@@ -119,20 +119,25 @@ public int parseArguments(final Parameters params) throws CmdLineException {
 		try {
 			id = clp.getRepository().resolve(name);
 		} catch (IOException e) {
-			throw new CmdLineException(clp, e.getMessage());
+			throw new CmdLineException(clp, CLIText.format(e.getMessage()));
 		}
 		if (id == null)
-			throw new CmdLineException(clp, MessageFormat.format(CLIText.get().notATree, name));
+			throw new CmdLineException(clp,
+					CLIText.format(CLIText.get().notATree), name);
 
 		final CanonicalTreeParser p = new CanonicalTreeParser();
 		try (ObjectReader curs = clp.getRepository().newObjectReader()) {
 			p.reset(curs, clp.getRevWalk().parseTree(id));
 		} catch (MissingObjectException e) {
-			throw new CmdLineException(clp, MessageFormat.format(CLIText.get().notATree, name));
+			throw new CmdLineException(clp,
+					CLIText.format(CLIText.get().notATree), name);
 		} catch (IncorrectObjectTypeException e) {
-			throw new CmdLineException(clp, MessageFormat.format(CLIText.get().notATree, name));
+			throw new CmdLineException(clp,
+					CLIText.format(CLIText.get().notATree), name);
 		} catch (IOException e) {
-			throw new CmdLineException(clp, MessageFormat.format(CLIText.get().cannotReadBecause, name, e.getMessage()));
+			throw new CmdLineException(clp,
+					CLIText.format(CLIText.get().cannotReadBecause), name,
+					e.getMessage());
 		}
 
 		setter.addValue(p);
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/CmdLineParser.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/CmdLineParser.java
index 020b625..3dcb2a3 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/CmdLineParser.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/CmdLineParser.java
@@ -47,7 +47,6 @@
 import java.io.Writer;
 import java.lang.reflect.Field;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 import java.util.ResourceBundle;
@@ -68,6 +67,7 @@
 import org.kohsuke.args4j.NamedOptionDef;
 import org.kohsuke.args4j.Option;
 import org.kohsuke.args4j.OptionDef;
+import org.kohsuke.args4j.OptionHandlerRegistry;
 import org.kohsuke.args4j.spi.OptionHandler;
 import org.kohsuke.args4j.spi.RestOfArgumentsHandler;
 import org.kohsuke.args4j.spi.Setter;
@@ -82,13 +82,14 @@
  */
 public class CmdLineParser extends org.kohsuke.args4j.CmdLineParser {
 	static {
-		registerHandler(AbstractTreeIterator.class,
+		OptionHandlerRegistry registry = OptionHandlerRegistry.getRegistry();
+		registry.registerHandler(AbstractTreeIterator.class,
 				AbstractTreeIteratorHandler.class);
-		registerHandler(ObjectId.class, ObjectIdHandler.class);
-		registerHandler(RefSpec.class, RefSpecHandler.class);
-		registerHandler(RevCommit.class, RevCommitHandler.class);
-		registerHandler(RevTree.class, RevTreeHandler.class);
-		registerHandler(List.class, OptionWithValuesListHandler.class);
+		registry.registerHandler(ObjectId.class, ObjectIdHandler.class);
+		registry.registerHandler(RefSpec.class, RefSpecHandler.class);
+		registry.registerHandler(RevCommit.class, RevCommitHandler.class);
+		registry.registerHandler(RevTree.class, RevTreeHandler.class);
+		registry.registerHandler(List.class, OptionWithValuesListHandler.class);
 	}
 
 	private final Repository db;
@@ -267,8 +268,8 @@ public RevWalk getRevWalkGently() {
 	class MyOptionDef extends OptionDef {
 
 		public MyOptionDef(OptionDef o) {
-			super(o.usage(), o.metaVar(), o.required(), o.handler(), o
-					.isMultiValued());
+			super(o.usage(), o.metaVar(), o.required(), o.help(), o.hidden(),
+					o.handler(), o.isMultiValued());
 		}
 
 		@Override
@@ -300,24 +301,6 @@ protected OptionHandler createOptionHandler(OptionDef o, Setter setter) {
 
 	}
 
-	@SuppressWarnings("unchecked")
-	private List<OptionHandler> getOptions() {
-		List<OptionHandler> options = null;
-		try {
-			Field field = org.kohsuke.args4j.CmdLineParser.class
-					.getDeclaredField("options"); //$NON-NLS-1$
-			field.setAccessible(true);
-			options = (List<OptionHandler>) field.get(this);
-		} catch (NoSuchFieldException | SecurityException
-				| IllegalArgumentException | IllegalAccessException e) {
-			// ignore
-		}
-		if (options == null) {
-			return Collections.emptyList();
-		}
-		return options;
-	}
-
 	@Override
 	public void printSingleLineUsage(Writer w, ResourceBundle rb) {
 		List<OptionHandler> options = getOptions();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/ObjectIdHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/ObjectIdHandler.java
index 75ca554..74bab2d 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/ObjectIdHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/ObjectIdHandler.java
@@ -45,7 +45,6 @@
 package org.eclipse.jgit.pgm.opt;
 
 import java.io.IOException;
-import java.text.MessageFormat;
 
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.pgm.internal.CLIText;
@@ -86,14 +85,15 @@ public int parseArguments(final Parameters params) throws CmdLineException {
 		try {
 			id = clp.getRepository().resolve(name);
 		} catch (IOException e) {
-			throw new CmdLineException(clp, e.getMessage());
+			throw new CmdLineException(clp, CLIText.format(e.getMessage()));
 		}
 		if (id != null) {
 			setter.addValue(id);
 			return 1;
 		}
 
-		throw new CmdLineException(clp, MessageFormat.format(CLIText.get().notAnObject, name));
+		throw new CmdLineException(clp,
+				CLIText.format(CLIText.get().notAnObject), name);
 	}
 
 	@Override
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevCommitHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevCommitHandler.java
index 7661774..27555e3 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevCommitHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevCommitHandler.java
@@ -45,7 +45,6 @@
 package org.eclipse.jgit.pgm.opt;
 
 import java.io.IOException;
-import java.text.MessageFormat;
 
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.MissingObjectException;
@@ -97,9 +96,8 @@ public int parseArguments(final Parameters params) throws CmdLineException {
 		if (dot2 != -1) {
 			if (!option.isMultiValued())
 				throw new CmdLineException(clp,
-						MessageFormat.format(
-								CLIText.get().onlyOneMetaVarExpectedIn,
-								option.metaVar(), name));
+						CLIText.format(CLIText.get().onlyOneMetaVarExpectedIn),
+						option.metaVar(), name);
 
 			final String left = name.substring(0, dot2);
 			final String right = name.substring(dot2 + 2);
@@ -118,20 +116,25 @@ private void addOne(final String name, final boolean interesting)
 		try {
 			id = clp.getRepository().resolve(name);
 		} catch (IOException e) {
-			throw new CmdLineException(clp, e.getMessage());
+			throw new CmdLineException(clp, CLIText.format(e.getMessage()));
 		}
 		if (id == null)
-			throw new CmdLineException(clp, MessageFormat.format(CLIText.get().notACommit, name));
+			throw new CmdLineException(clp,
+					CLIText.format(CLIText.get().notACommit), name);
 
 		final RevCommit c;
 		try {
 			c = clp.getRevWalk().parseCommit(id);
 		} catch (MissingObjectException e) {
-			throw new CmdLineException(clp, MessageFormat.format(CLIText.get().notACommit, name));
+			throw new CmdLineException(clp,
+					CLIText.format(CLIText.get().notACommit), name);
 		} catch (IncorrectObjectTypeException e) {
-			throw new CmdLineException(clp, MessageFormat.format(CLIText.get().notACommit, name));
+			throw new CmdLineException(clp,
+					CLIText.format(CLIText.get().notACommit), name);
 		} catch (IOException e) {
-			throw new CmdLineException(clp, MessageFormat.format(CLIText.get().cannotReadBecause, name, e.getMessage()));
+			throw new CmdLineException(clp,
+					CLIText.format(CLIText.get().cannotReadBecause), name,
+					e.getMessage());
 		}
 
 		if (interesting)
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevTreeHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevTreeHandler.java
index 9f1d21e..15ed589 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevTreeHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevTreeHandler.java
@@ -45,7 +45,6 @@
 package org.eclipse.jgit.pgm.opt;
 
 import java.io.IOException;
-import java.text.MessageFormat;
 
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.MissingObjectException;
@@ -89,20 +88,25 @@ public int parseArguments(final Parameters params) throws CmdLineException {
 		try {
 			id = clp.getRepository().resolve(name);
 		} catch (IOException e) {
-			throw new CmdLineException(clp, e.getMessage());
+			throw new CmdLineException(clp, CLIText.format(e.getMessage()));
 		}
 		if (id == null)
-			throw new CmdLineException(clp, MessageFormat.format(CLIText.get().notATree, name));
+			throw new CmdLineException(clp,
+					CLIText.format(CLIText.get().notATree), name);
 
 		final RevTree c;
 		try {
 			c = clp.getRevWalk().parseTree(id);
 		} catch (MissingObjectException e) {
-			throw new CmdLineException(clp, MessageFormat.format(CLIText.get().notATree, name));
+			throw new CmdLineException(clp,
+					CLIText.format(CLIText.get().notATree), name);
 		} catch (IncorrectObjectTypeException e) {
-			throw new CmdLineException(clp, MessageFormat.format(CLIText.get().notATree, name));
+			throw new CmdLineException(clp,
+					CLIText.format(CLIText.get().notATree), name);
 		} catch (IOException e) {
-			throw new CmdLineException(clp, MessageFormat.format(CLIText.get().cannotReadBecause, name, e.getMessage()));
+			throw new CmdLineException(clp,
+					CLIText.format(CLIText.get().cannotReadBecause), name,
+					e.getMessage());
 		}
 		setter.addValue(c);
 		return 1;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/SubcommandHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/SubcommandHandler.java
index 311597e..ae5263f 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/SubcommandHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/SubcommandHandler.java
@@ -43,8 +43,6 @@
 
 package org.eclipse.jgit.pgm.opt;
 
-import java.text.MessageFormat;
-
 import org.eclipse.jgit.pgm.CommandCatalog;
 import org.eclipse.jgit.pgm.CommandRef;
 import org.eclipse.jgit.pgm.TextBuiltin;
@@ -85,8 +83,8 @@ public int parseArguments(final Parameters params) throws CmdLineException {
 		final String name = params.getParameter(0);
 		final CommandRef cr = CommandCatalog.get(name);
 		if (cr == null)
-			throw new CmdLineException(clp, MessageFormat.format(
-					CLIText.get().notAJgitCommand, name));
+			throw new CmdLineException(clp,
+					CLIText.format(CLIText.get().notAJgitCommand), name);
 
 		// Force option parsing to stop. Everything after us should
 		// be arguments known only to this command and must not be
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/UntrackedFilesHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/UntrackedFilesHandler.java
index c4e8b05..e22b2e4 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/UntrackedFilesHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/UntrackedFilesHandler.java
@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.pgm.opt;
 
+import org.eclipse.jgit.pgm.internal.CLIText;
 import org.kohsuke.args4j.CmdLineException;
 import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.OptionDef;
@@ -102,8 +103,9 @@ public int parseArguments(Parameters params) throws CmdLineException {
 			if ("no".equals(mode) || "all".equals(mode)) { //$NON-NLS-1$ //$NON-NLS-2$
 				setter.addValue(mode);
 			} else {
-				throw new CmdLineException(owner, String.format(
-						"Invalid untracked files mode '%s'", mode)); //$NON-NLS-1$
+				throw new CmdLineException(owner,
+						CLIText.format(CLIText.get().invalidUntrackedFilesMode),
+						mode);
 			}
 			return 1;
 		} else {
@@ -111,4 +113,4 @@ public int parseArguments(Parameters params) throws CmdLineException {
 		}
 	}
 
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.test/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.test/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.test/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.test/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.test/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.test/.settings/org.eclipse.pde.api.tools.prefs
index cd148d9..c0030de 100644
--- a/org.eclipse.jgit.test/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.test/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,4 +1,4 @@
-#Tue Oct 18 00:52:01 CEST 2011
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -8,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -47,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -58,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -75,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -83,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
index 7bacb05..acf2b3c 100644
--- a/org.eclipse.jgit.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
@@ -2,54 +2,58 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.test
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: com.googlecode.javaewah;version="[1.1.6,2.0.0)",
- org.eclipse.jgit.api;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.api.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.attributes;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.awtui;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.blame;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.diff;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.dircache;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.events;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.fnmatch;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.gitrepo;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.hooks;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.ignore;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.ignore.internal;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.dfs;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.file;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.pack;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.internal.storage.reftree;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.junit;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lfs;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.merge;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.nls;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.notes;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.patch;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.pgm;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.pgm.internal;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revplot;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revwalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revwalk.filter;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.storage.file;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.storage.pack;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.submodule;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport.http;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport.resolver;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.treewalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.treewalk.filter;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util.io;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util.sha1;version="[4.8.1,4.9.0)",
+ com.jcraft.jsch;version="[0.1.54,0.2.0)",
+ org.eclipse.jgit.api;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.api.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.attributes;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.awtui;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.blame;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.diff;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.dircache;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.events;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.fnmatch;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.gitrepo;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.hooks;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.ignore;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.ignore.internal;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.fsck;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.dfs;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.file;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.io;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.pack;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.reftable;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.internal.storage.reftree;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.junit;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lfs;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.merge;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.nls;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.notes;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.patch;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.pgm;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.pgm.internal;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revplot;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revwalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revwalk.filter;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.storage.file;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.storage.pack;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.submodule;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport.http;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport.resolver;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.treewalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.treewalk.filter;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util.io;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util.sha1;version="[4.9.6,4.10.0)",
  org.junit;version="[4.4.0,5.0.0)",
  org.junit.experimental.theories;version="[4.4.0,5.0.0)",
  org.junit.rules;version="[4.11.0,5.0.0)",
diff --git a/org.eclipse.jgit.test/pom.xml b/org.eclipse.jgit.test/pom.xml
index c373112..07ef322 100644
--- a/org.eclipse.jgit.test/pom.xml
+++ b/org.eclipse.jgit.test/pom.xml
@@ -52,7 +52,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.test</artifactId>
@@ -66,7 +66,6 @@
     <dependency>
       <groupId>junit</groupId>
       <artifactId>junit</artifactId>
-      <scope>test</scope>
     </dependency>
 
     <!-- Optional security provider for encryption tests. -->
diff --git a/org.eclipse.jgit.test/src/org/eclipse/jgit/events/ChangeRecorder.java b/org.eclipse.jgit.test/src/org/eclipse/jgit/events/ChangeRecorder.java
new file mode 100644
index 0000000..c5582a8
--- /dev/null
+++ b/org.eclipse.jgit.test/src/org/eclipse/jgit/events/ChangeRecorder.java
@@ -0,0 +1,108 @@
+/*
+ * Copyright (C) 2017, Thomas Wolf <thomas.wolf@paranor.ch>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.events;
+
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ * A {@link WorkingTreeModifiedListener} that can be used in tests to check
+ * expected events.
+ */
+public class ChangeRecorder implements WorkingTreeModifiedListener {
+
+	public static final String[] EMPTY = new String[0];
+
+	private Set<String> modified = new HashSet<>();
+
+	private Set<String> deleted = new HashSet<>();
+
+	private int eventCount;
+
+	@Override
+	public void onWorkingTreeModified(WorkingTreeModifiedEvent event) {
+		eventCount++;
+		modified.removeAll(event.getDeleted());
+		deleted.removeAll(event.getModified());
+		modified.addAll(event.getModified());
+		deleted.addAll(event.getDeleted());
+	}
+
+	private String[] getModified() {
+		return modified.toArray(new String[modified.size()]);
+	}
+
+	private String[] getDeleted() {
+		return deleted.toArray(new String[deleted.size()]);
+	}
+
+	private void reset() {
+		eventCount = 0;
+		modified.clear();
+		deleted.clear();
+	}
+
+	public void assertNoEvent() {
+		assertEquals("Unexpected WorkingTreeModifiedEvent ", 0, eventCount);
+	}
+
+	public void assertEvent(String[] expectedModified,
+			String[] expectedDeleted) {
+		String[] actuallyModified = getModified();
+		String[] actuallyDeleted = getDeleted();
+		Arrays.sort(actuallyModified);
+		Arrays.sort(expectedModified);
+		Arrays.sort(actuallyDeleted);
+		Arrays.sort(expectedDeleted);
+		assertArrayEquals("Unexpected modifications reported", expectedModified,
+				actuallyModified);
+		assertArrayEquals("Unexpected deletions reported", expectedDeleted,
+				actuallyDeleted);
+		reset();
+	}
+}
diff --git a/org.eclipse.jgit.test/tests.bzl b/org.eclipse.jgit.test/tests.bzl
index 8ae0065..c75ab76 100644
--- a/org.eclipse.jgit.test/tests.bzl
+++ b/org.eclipse.jgit.test/tests.bzl
@@ -29,6 +29,14 @@
             additional_deps = [
                 "//org.eclipse.jgit:insecure_cipher_factory",
             ]
+        if src.endswith("OpenSshConfigTest.java"):
+            additional_deps = [
+                "//lib:jsch",
+            ]
+        if src.endswith("JschConfigSessionFactoryTest.java"):
+            additional_deps = [
+                "//lib:jsch",
+            ]
 
         junit_tests(
             name = name,
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/attributes/merge/disabled_checked.gif b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/attributes/merge/disabled_checked.gif
new file mode 100644
index 0000000..47b9e32
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/attributes/merge/disabled_checked.gif
Binary files differ
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/attributes/merge/enabled_checked.gif b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/attributes/merge/enabled_checked.gif
new file mode 100644
index 0000000..252f762
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/attributes/merge/enabled_checked.gif
Binary files differ
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
index ed3907e..aafda01 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
@@ -303,6 +303,21 @@ public void testAttributesWithTreeWalkFilter()
 	}
 
 	@Test
+	public void testAttributesConflictingMatch() throws Exception {
+		writeTrashFile(".gitattributes", "foo/** crlf=input\n*.jar binary");
+		writeTrashFile("foo/bar.jar", "\r\n");
+		// We end up with attributes [binary -diff -merge -text crlf=input].
+		// crlf should have no effect when -text is present.
+		try (Git git = new Git(db)) {
+			git.add().addFilepattern(".").call();
+			assertEquals(
+					"[.gitattributes, mode:100644, content:foo/** crlf=input\n*.jar binary]"
+							+ "[foo/bar.jar, mode:100644, content:\r\n]",
+					indexState(CONTENT));
+		}
+	}
+
+	@Test
 	public void testCleanFilterEnvironment()
 			throws IOException, GitAPIException {
 		writeTrashFile(".gitattributes", "*.txt filter=tstFilter");
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java
index 3c19672..1201d9f 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java
@@ -85,7 +85,6 @@
 import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
-import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.transport.RemoteConfig;
 import org.eclipse.jgit.transport.URIish;
 import org.eclipse.jgit.util.FileUtils;
@@ -431,8 +430,8 @@ private Repository createRepositoryWithRemote() throws IOException,
 			config.save();
 
 			// fetch from first repository
-			RefSpec spec = new RefSpec("+refs/heads/*:refs/remotes/origin/*");
-			git2.fetch().setRemote("origin").setRefSpecs(spec).call();
+			git2.fetch().setRemote("origin")
+					.setRefSpecs("+refs/heads/*:refs/remotes/origin/*").call();
 			return db2;
 		}
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
index ae0b8dd..e687a6c 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
@@ -76,6 +76,7 @@
 import org.eclipse.jgit.submodule.SubmoduleWalk;
 import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.transport.RemoteConfig;
+import org.eclipse.jgit.transport.URIish;
 import org.eclipse.jgit.util.SystemReader;
 import org.junit.Test;
 
@@ -145,16 +146,36 @@ public void testCloneRepositoryExplicitGitDir() throws IOException,
 		File directory = createTempDirectory("testCloneRepository");
 		CloneCommand command = Git.cloneRepository();
 		command.setDirectory(directory);
-		command.setGitDir(new File(directory, ".git"));
+		command.setGitDir(new File(directory, Constants.DOT_GIT));
 		command.setURI(fileUri());
 		Git git2 = command.call();
 		addRepoToClose(git2.getRepository());
 		assertEquals(directory, git2.getRepository().getWorkTree());
-		assertEquals(new File(directory, ".git"), git2.getRepository()
+		assertEquals(new File(directory, Constants.DOT_GIT), git2.getRepository()
 				.getDirectory());
 	}
 
 	@Test
+	public void testCloneRepositoryDefaultDirectory()
+			throws URISyntaxException, JGitInternalException {
+		CloneCommand command = Git.cloneRepository().setURI(fileUri());
+
+		command.verifyDirectories(new URIish(fileUri()));
+		File directory = command.getDirectory();
+		assertEquals(git.getRepository().getWorkTree().getName(), directory.getName());
+	}
+
+	@Test
+	public void testCloneBareRepositoryDefaultDirectory()
+			throws URISyntaxException, JGitInternalException {
+		CloneCommand command = Git.cloneRepository().setURI(fileUri()).setBare(true);
+
+		command.verifyDirectories(new URIish(fileUri()));
+		File directory = command.getDirectory();
+		assertEquals(git.getRepository().getWorkTree().getName() + Constants.DOT_GIT_EXT, directory.getName());
+	}
+
+	@Test
 	public void testCloneRepositoryExplicitGitDirNonStd() throws IOException,
 			JGitInternalException, GitAPIException {
 		File directory = createTempDirectory("testCloneRepository");
@@ -168,8 +189,8 @@ public void testCloneRepositoryExplicitGitDirNonStd() throws IOException,
 		assertEquals(directory, git2.getRepository().getWorkTree());
 		assertEquals(gDir, git2.getRepository()
 				.getDirectory());
-		assertTrue(new File(directory, ".git").isFile());
-		assertFalse(new File(gDir, ".git").exists());
+		assertTrue(new File(directory, Constants.DOT_GIT).isFile());
+		assertFalse(new File(gDir, Constants.DOT_GIT).exists());
 	}
 
 	@Test
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitCommandTest.java
index 37fee40..a0834e7 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitCommandTest.java
@@ -557,6 +557,11 @@ public void commitEmptyCommits() throws Exception {
 			} catch (EmtpyCommitException e) {
 				// expect this exception
 			}
+
+			// Allow empty commits also when setOnly was set
+			git.commit().setAuthor("New Author", "newauthor@example.org")
+					.setMessage("again no change").setOnly("file1")
+					.setAllowEmpty(true).call();
 		}
 	}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/DescribeCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/DescribeCommandTest.java
index 1e5d3bc..6a66783 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/DescribeCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/DescribeCommandTest.java
@@ -54,6 +54,7 @@
 
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.RefNotFoundException;
+import org.eclipse.jgit.errors.InvalidPatternException;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.ObjectId;
 import org.junit.Test;
@@ -92,26 +93,65 @@ public void testDescribe() throws Exception {
 		ObjectId c1 = modify("aaa");
 
 		ObjectId c2 = modify("bbb");
-		tag("t1");
+		tag("alice-t1");
 
 		ObjectId c3 = modify("ccc");
-		tag("t2");
+		tag("bob-t2");
 
 		ObjectId c4 = modify("ddd");
 
 		assertNull(describe(c1));
 		assertNull(describe(c1, true));
-		assertEquals("t1", describe(c2));
-		assertEquals("t2", describe(c3));
-		assertEquals("t2-0-g44579eb", describe(c3, true));
+		assertNull(describe(c1, "a*", "b*", "c*"));
+
+		assertEquals("alice-t1", describe(c2));
+		assertEquals("alice-t1", describe(c2, "alice*"));
+		assertNull(describe(c2, "bob*"));
+		assertNull(describe(c2, "?ob*"));
+		assertEquals("alice-t1", describe(c2, "a*", "b*", "c*"));
+
+		assertEquals("bob-t2", describe(c3));
+		assertEquals("bob-t2-0-g44579eb", describe(c3, true));
+		assertEquals("alice-t1-1-g44579eb", describe(c3, "alice*"));
+		assertEquals("alice-t1-1-g44579eb", describe(c3, "a??c?-t*"));
+		assertEquals("bob-t2", describe(c3, "bob*"));
+		assertEquals("bob-t2", describe(c3, "?ob*"));
+		assertEquals("bob-t2", describe(c3, "a*", "b*", "c*"));
 
 		assertNameStartsWith(c4, "3e563c5");
 		// the value verified with git-describe(1)
-		assertEquals("t2-1-g3e563c5", describe(c4));
-		assertEquals("t2-1-g3e563c5", describe(c4, true));
+		assertEquals("bob-t2-1-g3e563c5", describe(c4));
+		assertEquals("bob-t2-1-g3e563c5", describe(c4, true));
+		assertEquals("alice-t1-2-g3e563c5", describe(c4, "alice*"));
+		assertEquals("bob-t2-1-g3e563c5", describe(c4, "bob*"));
+		assertEquals("bob-t2-1-g3e563c5", describe(c4, "a*", "b*", "c*"));
 
 		// test default target
-		assertEquals("t2-1-g3e563c5", git.describe().call());
+		assertEquals("bob-t2-1-g3e563c5", git.describe().call());
+	}
+
+	@Test
+	public void testDescribeMultiMatch() throws Exception {
+		ObjectId c1 = modify("aaa");
+		tag("v1.0.0");
+		tag("v1.1.1");
+		ObjectId c2 = modify("bbb");
+
+		// Ensure that if we're interested in any tags, we get the first match as per Git behaviour
+		assertEquals("v1.0.0", describe(c1));
+		assertEquals("v1.0.0-1-g3747db3", describe(c2));
+
+		// Ensure that if we're only interested in one of multiple tags, we get the right match
+		assertEquals("v1.0.0", describe(c1, "v1.0*"));
+		assertEquals("v1.1.1", describe(c1, "v1.1*"));
+		assertEquals("v1.0.0-1-g3747db3", describe(c2, "v1.0*"));
+		assertEquals("v1.1.1-1-g3747db3", describe(c2, "v1.1*"));
+
+		// Ensure that ordering of match precedence is preserved as per Git behaviour
+		assertEquals("v1.0.0", describe(c1, "v1.0*", "v1.1*"));
+		assertEquals("v1.1.1", describe(c1, "v1.1*", "v1.0*"));
+		assertEquals("v1.0.0-1-g3747db3", describe(c2, "v1.0*", "v1.1*"));
+		assertEquals("v1.1.1-1-g3747db3", describe(c2, "v1.1*", "v1.0*"));
 	}
 
 	/**
@@ -271,6 +311,10 @@ private String describe(ObjectId c1) throws GitAPIException, IOException {
 		return describe(c1, false);
 	}
 
+	private String describe(ObjectId c1, String... patterns) throws GitAPIException, IOException, InvalidPatternException {
+		return git.describe().setTarget(c1).setMatch(patterns).call();
+	}
+
 	private static void assertNameStartsWith(ObjectId c4, String prefix) {
 		assertTrue(c4.name(), c4.name().startsWith(prefix));
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/FetchCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/FetchCommandTest.java
index a36f6c5..530fb1b 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/FetchCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/FetchCommandTest.java
@@ -45,7 +45,9 @@
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNull;
 
+import java.util.ArrayList;
 import java.util.Collection;
+import java.util.List;
 
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.Constants;
@@ -93,9 +95,8 @@ public void testFetch() throws Exception {
 		RevCommit commit = remoteGit.commit().setMessage("initial commit").call();
 		Ref tagRef = remoteGit.tag().setName("tag").call();
 
-		RefSpec spec = new RefSpec("refs/heads/master:refs/heads/x");
-		git.fetch().setRemote("test").setRefSpecs(spec)
-				.call();
+		git.fetch().setRemote("test")
+				.setRefSpecs("refs/heads/master:refs/heads/x").call();
 
 		assertEquals(commit.getId(),
 				db.resolve(commit.getId().getName() + "^{commit}"));
@@ -104,12 +105,97 @@ public void testFetch() throws Exception {
 	}
 
 	@Test
+	public void fetchAddsBranches() throws Exception {
+		final String branch1 = "b1";
+		final String branch2 = "b2";
+		final String remoteBranch1 = "test/" + branch1;
+		final String remoteBranch2 = "test/" + branch2;
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef1 = remoteGit.branchCreate().setName(branch1).call();
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef2 = remoteGit.branchCreate().setName(branch2).call();
+
+		String spec = "refs/heads/*:refs/remotes/test/*";
+		git.fetch().setRemote("test").setRefSpecs(spec).call();
+		assertEquals(branchRef1.getObjectId(), db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+	}
+
+	@Test
+	public void fetchDoesntDeleteBranches() throws Exception {
+		final String branch1 = "b1";
+		final String branch2 = "b2";
+		final String remoteBranch1 = "test/" + branch1;
+		final String remoteBranch2 = "test/" + branch2;
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef1 = remoteGit.branchCreate().setName(branch1).call();
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef2 = remoteGit.branchCreate().setName(branch2).call();
+
+		String spec = "refs/heads/*:refs/remotes/test/*";
+		git.fetch().setRemote("test").setRefSpecs(spec).call();
+		assertEquals(branchRef1.getObjectId(), db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+
+		remoteGit.branchDelete().setBranchNames(branch1).call();
+		git.fetch().setRemote("test").setRefSpecs(spec).call();
+		assertEquals(branchRef1.getObjectId(), db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+	}
+
+	@Test
+	public void fetchUpdatesBranches() throws Exception {
+		final String branch1 = "b1";
+		final String branch2 = "b2";
+		final String remoteBranch1 = "test/" + branch1;
+		final String remoteBranch2 = "test/" + branch2;
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef1 = remoteGit.branchCreate().setName(branch1).call();
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef2 = remoteGit.branchCreate().setName(branch2).call();
+
+		String spec = "refs/heads/*:refs/remotes/test/*";
+		git.fetch().setRemote("test").setRefSpecs(spec).call();
+		assertEquals(branchRef1.getObjectId(), db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+
+		remoteGit.commit().setMessage("commit").call();
+		branchRef2 = remoteGit.branchCreate().setName(branch2).setForce(true).call();
+		git.fetch().setRemote("test").setRefSpecs(spec).call();
+		assertEquals(branchRef1.getObjectId(), db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+	}
+
+	@Test
+	public void fetchPrunesBranches() throws Exception {
+		final String branch1 = "b1";
+		final String branch2 = "b2";
+		final String remoteBranch1 = "test/" + branch1;
+		final String remoteBranch2 = "test/" + branch2;
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef1 = remoteGit.branchCreate().setName(branch1).call();
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef2 = remoteGit.branchCreate().setName(branch2).call();
+
+		String spec = "refs/heads/*:refs/remotes/test/*";
+		git.fetch().setRemote("test").setRefSpecs(spec).call();
+		assertEquals(branchRef1.getObjectId(), db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+
+		remoteGit.branchDelete().setBranchNames(branch1).call();
+		git.fetch().setRemote("test").setRefSpecs(spec)
+				.setRemoveDeletedRefs(true).call();
+		assertNull(db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+	}
+
+	@Test
 	public void fetchShouldAutoFollowTag() throws Exception {
 		remoteGit.commit().setMessage("commit").call();
 		Ref tagRef = remoteGit.tag().setName("foo").call();
 
-		RefSpec spec = new RefSpec("refs/heads/*:refs/remotes/origin/*");
-		git.fetch().setRemote("test").setRefSpecs(spec)
+		git.fetch().setRemote("test")
+				.setRefSpecs("refs/heads/*:refs/remotes/origin/*")
 				.setTagOpt(TagOpt.AUTO_FOLLOW).call();
 
 		assertEquals(tagRef.getObjectId(), db.resolve("foo"));
@@ -120,8 +206,8 @@ public void fetchShouldAutoFollowTagForFetchedObjects() throws Exception {
 		remoteGit.commit().setMessage("commit").call();
 		Ref tagRef = remoteGit.tag().setName("foo").call();
 		remoteGit.commit().setMessage("commit2").call();
-		RefSpec spec = new RefSpec("refs/heads/*:refs/remotes/origin/*");
-		git.fetch().setRemote("test").setRefSpecs(spec)
+		git.fetch().setRemote("test")
+				.setRefSpecs("refs/heads/*:refs/remotes/origin/*")
 				.setTagOpt(TagOpt.AUTO_FOLLOW).call();
 		assertEquals(tagRef.getObjectId(), db.resolve("foo"));
 	}
@@ -132,9 +218,8 @@ public void fetchShouldNotFetchTagsFromOtherBranches() throws Exception {
 		remoteGit.checkout().setName("other").setCreateBranch(true).call();
 		remoteGit.commit().setMessage("commit2").call();
 		remoteGit.tag().setName("foo").call();
-		RefSpec spec = new RefSpec(
-				"refs/heads/master:refs/remotes/origin/master");
-		git.fetch().setRemote("test").setRefSpecs(spec)
+		git.fetch().setRemote("test")
+				.setRefSpecs("refs/heads/master:refs/remotes/origin/master")
 				.setTagOpt(TagOpt.AUTO_FOLLOW).call();
 		assertNull(db.resolve("foo"));
 	}
@@ -146,7 +231,7 @@ public void fetchWithUpdatedTagShouldNotTryToUpdateLocal() throws Exception {
 		Ref tagRef = remoteGit.tag().setName(tagName).call();
 		ObjectId originalId = tagRef.getObjectId();
 
-		RefSpec spec = new RefSpec("refs/heads/*:refs/remotes/origin/*");
+		String spec = "refs/heads/*:refs/remotes/origin/*";
 		git.fetch().setRemote("test").setRefSpecs(spec)
 				.setTagOpt(TagOpt.AUTO_FOLLOW).call();
 		assertEquals(originalId, db.resolve(tagName));
@@ -172,7 +257,7 @@ public void fetchWithExplicitTagsShouldUpdateLocal() throws Exception {
 		remoteGit.commit().setMessage("commit").call();
 		Ref tagRef1 = remoteGit.tag().setName(tagName).call();
 
-		RefSpec spec = new RefSpec("refs/heads/*:refs/remotes/origin/*");
+		String spec = "refs/heads/*:refs/remotes/origin/*";
 		git.fetch().setRemote("test").setRefSpecs(spec)
 				.setTagOpt(TagOpt.AUTO_FOLLOW).call();
 		assertEquals(tagRef1.getObjectId(), db.resolve(tagName));
@@ -188,4 +273,75 @@ public void fetchWithExplicitTagsShouldUpdateLocal() throws Exception {
 		assertEquals(RefUpdate.Result.FORCED, update.getResult());
 		assertEquals(tagRef2.getObjectId(), db.resolve(tagName));
 	}
+
+	@Test
+	public void fetchAddRefsWithDuplicateRefspec() throws Exception {
+		final String branchName = "branch";
+		final String remoteBranchName = "test/" + branchName;
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef = remoteGit.branchCreate().setName(branchName).call();
+
+		final String spec1 = "+refs/heads/*:refs/remotes/test/*";
+		final String spec2 = "refs/heads/*:refs/remotes/test/*";
+		final StoredConfig config = db.getConfig();
+		RemoteConfig remoteConfig = new RemoteConfig(config, "test");
+		remoteConfig.addFetchRefSpec(new RefSpec(spec1));
+		remoteConfig.addFetchRefSpec(new RefSpec(spec2));
+		remoteConfig.update(config);
+
+		git.fetch().setRemote("test").setRefSpecs(spec1).call();
+		assertEquals(branchRef.getObjectId(), db.resolve(remoteBranchName));
+	}
+
+	@Test
+	public void fetchPruneRefsWithDuplicateRefspec()
+			throws Exception {
+		final String branchName = "branch";
+		final String remoteBranchName = "test/" + branchName;
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef = remoteGit.branchCreate().setName(branchName).call();
+
+		final String spec1 = "+refs/heads/*:refs/remotes/test/*";
+		final String spec2 = "refs/heads/*:refs/remotes/test/*";
+		final StoredConfig config = db.getConfig();
+		RemoteConfig remoteConfig = new RemoteConfig(config, "test");
+		remoteConfig.addFetchRefSpec(new RefSpec(spec1));
+		remoteConfig.addFetchRefSpec(new RefSpec(spec2));
+		remoteConfig.update(config);
+
+		git.fetch().setRemote("test").setRefSpecs(spec1).call();
+		assertEquals(branchRef.getObjectId(), db.resolve(remoteBranchName));
+
+		remoteGit.branchDelete().setBranchNames(branchName).call();
+		git.fetch().setRemote("test").setRefSpecs(spec1)
+				.setRemoveDeletedRefs(true).call();
+		assertNull(db.resolve(remoteBranchName));
+	}
+
+	@Test
+	public void fetchUpdateRefsWithDuplicateRefspec() throws Exception {
+		final String tagName = "foo";
+		remoteGit.commit().setMessage("commit").call();
+		Ref tagRef1 = remoteGit.tag().setName(tagName).call();
+		List<RefSpec> refSpecs = new ArrayList<>();
+		refSpecs.add(new RefSpec("+refs/heads/*:refs/remotes/origin/*"));
+		refSpecs.add(new RefSpec("+refs/tags/*:refs/tags/*"));
+		// Updating tags via the RefSpecs and setting TagOpt.FETCH_TAGS (or
+		// AUTO_FOLLOW) will result internally in *two* updates for the same
+		// ref.
+		git.fetch().setRemote("test").setRefSpecs(refSpecs)
+				.setTagOpt(TagOpt.AUTO_FOLLOW).call();
+		assertEquals(tagRef1.getObjectId(), db.resolve(tagName));
+
+		remoteGit.commit().setMessage("commit 2").call();
+		Ref tagRef2 = remoteGit.tag().setName(tagName).setForceUpdate(true)
+				.call();
+		FetchResult result = git.fetch().setRemote("test").setRefSpecs(refSpecs)
+				.setTagOpt(TagOpt.FETCH_TAGS).call();
+		assertEquals(2, result.getTrackingRefUpdates().size());
+		TrackingRefUpdate update = result
+				.getTrackingRefUpdate(Constants.R_TAGS + tagName);
+		assertEquals(RefUpdate.Result.FORCED, update.getResult());
+		assertEquals(tagRef2.getObjectId(), db.resolve(tagName));
+	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/LogCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/LogCommandTest.java
index 38178bf..bd0efad 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/LogCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/LogCommandTest.java
@@ -289,4 +289,4 @@ private void setCommitsAndMerge() throws Exception {
 				.setMessage("merge s0 with m1").call();
 	}
 
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PullCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PullCommandTest.java
index 823516b..a341284 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PullCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PullCommandTest.java
@@ -620,4 +620,4 @@ private static void assertFileContentsEqual(File actFile, String string)
 				fis.close();
 		}
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PushCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PushCommandTest.java
index 8c613ec..e0c1499 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PushCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PushCommandTest.java
@@ -83,6 +83,11 @@ public void testPush() throws JGitInternalException, IOException,
 
 		// create other repository
 		Repository db2 = createWorkRepository();
+		final StoredConfig config2 = db2.getConfig();
+
+		// this tests that this config can be parsed properly
+		config2.setString("fsck", "", "missingEmail", "ignore");
+		config2.save();
 
 		// setup the first repository
 		final StoredConfig config = db.getConfig();
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/StashApplyCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/StashApplyCommandTest.java
index f2e4d5b..ad3ab7f 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/StashApplyCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/StashApplyCommandTest.java
@@ -55,12 +55,15 @@
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.NoHeadException;
 import org.eclipse.jgit.api.errors.StashApplyFailureException;
+import org.eclipse.jgit.events.ChangeRecorder;
+import org.eclipse.jgit.events.ListenerHandle;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.util.FileUtils;
+import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -77,15 +80,31 @@ public class StashApplyCommandTest extends RepositoryTestCase {
 
 	private File committedFile;
 
+	private ChangeRecorder recorder;
+
+	private ListenerHandle handle;
+
 	@Override
 	@Before
 	public void setUp() throws Exception {
 		super.setUp();
 		git = Git.wrap(db);
+		recorder = new ChangeRecorder();
+		handle = db.getListenerList().addWorkingTreeModifiedListener(recorder);
 		committedFile = writeTrashFile(PATH, "content");
 		git.add().addFilepattern(PATH).call();
 		head = git.commit().setMessage("add file").call();
 		assertNotNull(head);
+		recorder.assertNoEvent();
+	}
+
+	@Override
+	@After
+	public void tearDown() throws Exception {
+		if (handle != null) {
+			handle.remove();
+		}
+		super.tearDown();
 	}
 
 	@Test
@@ -95,10 +114,12 @@ public void workingDirectoryDelete() throws Exception {
 		RevCommit stashed = git.stashCreate().call();
 		assertNotNull(stashed);
 		assertEquals("content", read(committedFile));
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 
 		ObjectId unstashed = git.stashApply().call();
 		assertEquals(stashed, unstashed);
 		assertFalse(committedFile.exists());
+		recorder.assertEvent(ChangeRecorder.EMPTY, new String[] { PATH });
 
 		Status status = git.status().call();
 		assertTrue(status.getAdded().isEmpty());
@@ -121,11 +142,13 @@ public void indexAdd() throws Exception {
 		RevCommit stashed = git.stashCreate().call();
 		assertNotNull(stashed);
 		assertFalse(addedFile.exists());
+		recorder.assertEvent(ChangeRecorder.EMPTY, new String[] { addedPath });
 
 		ObjectId unstashed = git.stashApply().call();
 		assertEquals(stashed, unstashed);
 		assertTrue(addedFile.exists());
 		assertEquals("content2", read(addedFile));
+		recorder.assertEvent(new String[] { addedPath }, ChangeRecorder.EMPTY);
 
 		Status status = git.status().call();
 		assertTrue(status.getChanged().isEmpty());
@@ -142,14 +165,17 @@ public void indexAdd() throws Exception {
 	@Test
 	public void indexDelete() throws Exception {
 		git.rm().addFilepattern("file.txt").call();
+		recorder.assertEvent(ChangeRecorder.EMPTY, new String[] { "file.txt" });
 
 		RevCommit stashed = git.stashCreate().call();
 		assertNotNull(stashed);
 		assertEquals("content", read(committedFile));
+		recorder.assertEvent(new String[] { "file.txt" }, ChangeRecorder.EMPTY);
 
 		ObjectId unstashed = git.stashApply().call();
 		assertEquals(stashed, unstashed);
 		assertFalse(committedFile.exists());
+		recorder.assertEvent(ChangeRecorder.EMPTY, new String[] { "file.txt" });
 
 		Status status = git.status().call();
 		assertTrue(status.getAdded().isEmpty());
@@ -170,10 +196,12 @@ public void workingDirectoryModify() throws Exception {
 		RevCommit stashed = git.stashCreate().call();
 		assertNotNull(stashed);
 		assertEquals("content", read(committedFile));
+		recorder.assertEvent(new String[] { "file.txt" }, ChangeRecorder.EMPTY);
 
 		ObjectId unstashed = git.stashApply().call();
 		assertEquals(stashed, unstashed);
 		assertEquals("content2", read(committedFile));
+		recorder.assertEvent(new String[] { "file.txt" }, ChangeRecorder.EMPTY);
 
 		Status status = git.status().call();
 		assertTrue(status.getAdded().isEmpty());
@@ -193,16 +221,21 @@ public void workingDirectoryModifyInSubfolder() throws Exception {
 		File subfolderFile = writeTrashFile(path, "content");
 		git.add().addFilepattern(path).call();
 		head = git.commit().setMessage("add file").call();
+		recorder.assertNoEvent();
 
 		writeTrashFile(path, "content2");
 
 		RevCommit stashed = git.stashCreate().call();
 		assertNotNull(stashed);
 		assertEquals("content", read(subfolderFile));
+		recorder.assertEvent(new String[] { "d1/d2/f.txt" },
+				ChangeRecorder.EMPTY);
 
 		ObjectId unstashed = git.stashApply().call();
 		assertEquals(stashed, unstashed);
 		assertEquals("content2", read(subfolderFile));
+		recorder.assertEvent(new String[] { "d1/d2/f.txt", "d1/d2", "d1" },
+				ChangeRecorder.EMPTY);
 
 		Status status = git.status().call();
 		assertTrue(status.getAdded().isEmpty());
@@ -225,10 +258,12 @@ public void workingDirectoryModifyIndexChanged() throws Exception {
 		RevCommit stashed = git.stashCreate().call();
 		assertNotNull(stashed);
 		assertEquals("content", read(committedFile));
+		recorder.assertEvent(new String[] { "file.txt" }, ChangeRecorder.EMPTY);
 
 		ObjectId unstashed = git.stashApply().call();
 		assertEquals(stashed, unstashed);
 		assertEquals("content3", read(committedFile));
+		recorder.assertEvent(new String[] { "file.txt" }, ChangeRecorder.EMPTY);
 
 		Status status = git.status().call();
 		assertTrue(status.getAdded().isEmpty());
@@ -252,10 +287,12 @@ public void workingDirectoryCleanIndexModify() throws Exception {
 		RevCommit stashed = git.stashCreate().call();
 		assertNotNull(stashed);
 		assertEquals("content", read(committedFile));
+		recorder.assertEvent(new String[] { "file.txt" }, ChangeRecorder.EMPTY);
 
 		ObjectId unstashed = git.stashApply().call();
 		assertEquals(stashed, unstashed);
 		assertEquals("content2", read(committedFile));
+		recorder.assertEvent(new String[] { "file.txt" }, ChangeRecorder.EMPTY);
 
 		Status status = git.status().call();
 		assertTrue(status.getAdded().isEmpty());
@@ -281,10 +318,12 @@ public void workingDirectoryDeleteIndexAdd() throws Exception {
 		RevCommit stashed = git.stashCreate().call();
 		assertNotNull(stashed);
 		assertFalse(added.exists());
+		recorder.assertNoEvent();
 
 		ObjectId unstashed = git.stashApply().call();
 		assertEquals(stashed, unstashed);
 		assertEquals("content2", read(added));
+		recorder.assertEvent(new String[] { path }, ChangeRecorder.EMPTY);
 
 		Status status = git.status().call();
 		assertTrue(status.getChanged().isEmpty());
@@ -308,10 +347,12 @@ public void workingDirectoryDeleteIndexEdit() throws Exception {
 		RevCommit stashed = git.stashCreate().call();
 		assertNotNull(stashed);
 		assertEquals("content", read(committedFile));
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 
 		ObjectId unstashed = git.stashApply().call();
 		assertEquals(stashed, unstashed);
 		assertFalse(committedFile.exists());
+		recorder.assertEvent(ChangeRecorder.EMPTY, new String[] { PATH });
 
 		Status status = git.status().call();
 		assertTrue(status.getAdded().isEmpty());
@@ -337,9 +378,13 @@ public void multipleEdits() throws Exception {
 		assertNotNull(stashed);
 		assertTrue(committedFile.exists());
 		assertFalse(addedFile.exists());
+		recorder.assertEvent(new String[] { PATH },
+				new String[] { "file2.txt" });
 
 		ObjectId unstashed = git.stashApply().call();
 		assertEquals(stashed, unstashed);
+		recorder.assertEvent(new String[] { "file2.txt" },
+				new String[] { PATH });
 
 		Status status = git.status().call();
 		assertTrue(status.getChanged().isEmpty());
@@ -362,6 +407,7 @@ public void workingDirectoryContentConflict() throws Exception {
 		assertNotNull(stashed);
 		assertEquals("content", read(committedFile));
 		assertTrue(git.status().call().isClean());
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 
 		writeTrashFile(PATH, "content3");
 
@@ -372,6 +418,7 @@ public void workingDirectoryContentConflict() throws Exception {
 			// expected
  		}
 		assertEquals("content3", read(PATH));
+		recorder.assertNoEvent();
 	}
 
 	@Test
@@ -391,10 +438,12 @@ public void stashedContentMerge() throws Exception {
 		assertEquals("content\nhead change\nmore content\n",
 				read(committedFile));
 		assertTrue(git.status().call().isClean());
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 
 		writeTrashFile(PATH, "content\nmore content\ncommitted change\n");
 		git.add().addFilepattern(PATH).call();
 		git.commit().setMessage("committed change").call();
+		recorder.assertNoEvent();
 
 		try {
 			git.stashApply().call();
@@ -402,6 +451,7 @@ public void stashedContentMerge() throws Exception {
 		} catch (StashApplyFailureException e) {
 			// expected
 		}
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 		Status status = new StatusCommand(db).call();
 		assertEquals(1, status.getConflicting().size());
 		assertEquals(
@@ -426,12 +476,15 @@ public void stashedApplyOnOtherBranch() throws Exception {
 		writeTrashFile(PATH, "master content");
 		git.add().addFilepattern(PATH).call();
 		git.commit().setMessage("even content").call();
+		recorder.assertNoEvent();
 
 		git.checkout().setName(otherBranch).call();
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 
 		writeTrashFile(PATH, "otherBranch content");
 		git.add().addFilepattern(PATH).call();
 		git.commit().setMessage("even more content").call();
+		recorder.assertNoEvent();
 
 		writeTrashFile(path2, "content\nstashed change\nmore content\n");
 
@@ -442,12 +495,15 @@ public void stashedApplyOnOtherBranch() throws Exception {
 		assertEquals("otherBranch content",
 				read(committedFile));
 		assertTrue(git.status().call().isClean());
+		recorder.assertEvent(new String[] { path2 }, ChangeRecorder.EMPTY);
 
 		git.checkout().setName("master").call();
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 		git.stashApply().call();
 		assertEquals("content\nstashed change\nmore content\n", read(file2));
 		assertEquals("master content",
 				read(committedFile));
+		recorder.assertEvent(new String[] { path2 }, ChangeRecorder.EMPTY);
 	}
 
 	@Test
@@ -467,12 +523,15 @@ public void stashedApplyOnOtherBranchWithStagedChange() throws Exception {
 		writeTrashFile(PATH, "master content");
 		git.add().addFilepattern(PATH).call();
 		git.commit().setMessage("even content").call();
+		recorder.assertNoEvent();
 
 		git.checkout().setName(otherBranch).call();
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 
 		writeTrashFile(PATH, "otherBranch content");
 		git.add().addFilepattern(PATH).call();
 		git.commit().setMessage("even more content").call();
+		recorder.assertNoEvent();
 
 		writeTrashFile(path2,
 				"content\nstashed change in index\nmore content\n");
@@ -485,8 +544,10 @@ public void stashedApplyOnOtherBranchWithStagedChange() throws Exception {
 		assertEquals("content\nmore content\n", read(file2));
 		assertEquals("otherBranch content", read(committedFile));
 		assertTrue(git.status().call().isClean());
+		recorder.assertEvent(new String[] { path2 }, ChangeRecorder.EMPTY);
 
 		git.checkout().setName("master").call();
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 		git.stashApply().call();
 		assertEquals("content\nstashed change\nmore content\n", read(file2));
 		assertEquals(
@@ -494,6 +555,7 @@ public void stashedApplyOnOtherBranchWithStagedChange() throws Exception {
 						+ "[file2.txt, mode:100644, content:content\nstashed change in index\nmore content\n]",
 				indexState(CONTENT));
 		assertEquals("master content", read(committedFile));
+		recorder.assertEvent(new String[] { path2 }, ChangeRecorder.EMPTY);
 	}
 
 	@Test
@@ -501,6 +563,7 @@ public void workingDirectoryContentMerge() throws Exception {
 		writeTrashFile(PATH, "content\nmore content\n");
 		git.add().addFilepattern(PATH).call();
 		git.commit().setMessage("more content").call();
+		recorder.assertNoEvent();
 
 		writeTrashFile(PATH, "content\nstashed change\nmore content\n");
 
@@ -508,15 +571,18 @@ public void workingDirectoryContentMerge() throws Exception {
 		assertNotNull(stashed);
 		assertEquals("content\nmore content\n", read(committedFile));
 		assertTrue(git.status().call().isClean());
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 
 		writeTrashFile(PATH, "content\nmore content\ncommitted change\n");
 		git.add().addFilepattern(PATH).call();
 		git.commit().setMessage("committed change").call();
+		recorder.assertNoEvent();
 
 		git.stashApply().call();
 		assertEquals(
 				"content\nstashed change\nmore content\ncommitted change\n",
 				read(committedFile));
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 	}
 
 	@Test
@@ -527,6 +593,7 @@ public void indexContentConflict() throws Exception {
 		assertNotNull(stashed);
 		assertEquals("content", read(committedFile));
 		assertTrue(git.status().call().isClean());
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 
 		writeTrashFile(PATH, "content3");
 		git.add().addFilepattern(PATH).call();
@@ -538,6 +605,7 @@ public void indexContentConflict() throws Exception {
 		} catch (StashApplyFailureException e) {
 			// expected
 		}
+		recorder.assertNoEvent();
 		assertEquals("content2", read(PATH));
 	}
 
@@ -549,6 +617,7 @@ public void workingDirectoryEditPreCommit() throws Exception {
 		assertNotNull(stashed);
 		assertEquals("content", read(committedFile));
 		assertTrue(git.status().call().isClean());
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 
 		String path2 = "file2.txt";
 		writeTrashFile(path2, "content3");
@@ -557,6 +626,7 @@ public void workingDirectoryEditPreCommit() throws Exception {
 
 		ObjectId unstashed = git.stashApply().call();
 		assertEquals(stashed, unstashed);
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 
 		Status status = git.status().call();
 		assertTrue(status.getAdded().isEmpty());
@@ -583,12 +653,15 @@ public void stashChangeInANewSubdirectory() throws Exception {
 		RevCommit stashed = git.stashCreate().call();
 		assertNotNull(stashed);
 		assertTrue(git.status().call().isClean());
+		recorder.assertEvent(ChangeRecorder.EMPTY,
+				new String[] { subdir, path });
 
 		git.branchCreate().setName(otherBranch).call();
 		git.checkout().setName(otherBranch).call();
 
 		ObjectId unstashed = git.stashApply().call();
 		assertEquals(stashed, unstashed);
+		recorder.assertEvent(new String[] { path }, ChangeRecorder.EMPTY);
 
 		Status status = git.status().call();
 		assertTrue(status.getChanged().isEmpty());
@@ -643,12 +716,15 @@ public void testApplyStashWithDeletedFile() throws Exception {
 		git.commit().setMessage("x").call();
 		file.delete();
 		git.rm().addFilepattern("file").call();
+		recorder.assertNoEvent();
 		git.stashCreate().call();
+		recorder.assertEvent(new String[] { "file" }, ChangeRecorder.EMPTY);
 		file.delete();
 
 		git.stashApply().setStashRef("stash@{0}").call();
 
 		assertFalse(file.exists());
+		recorder.assertEvent(ChangeRecorder.EMPTY, new String[] { "file" });
 	}
 
 	@Test
@@ -660,9 +736,11 @@ public void untrackedFileNotIncluded() throws Exception {
 		git.add().addFilepattern(PATH).call();
 		git.stashCreate().call();
 		assertTrue(untrackedFile.exists());
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 
 		git.stashApply().setStashRef("stash@{0}").call();
 		assertTrue(untrackedFile.exists());
+		recorder.assertEvent(new String[] { PATH }, ChangeRecorder.EMPTY);
 
 		Status status = git.status().call();
 		assertEquals(1, status.getUntracked().size());
@@ -684,11 +762,14 @@ public void untrackedFileIncluded() throws Exception {
 				.call();
 		assertNotNull(stashedCommit);
 		assertFalse(untrackedFile.exists());
+		recorder.assertEvent(ChangeRecorder.EMPTY, new String[] { path });
+
 		deleteTrashFile("a/b"); // checkout should create parent dirs
 
 		git.stashApply().setStashRef("stash@{0}").call();
 		assertTrue(untrackedFile.exists());
 		assertEquals("content", read(path));
+		recorder.assertEvent(new String[] { path }, ChangeRecorder.EMPTY);
 
 		Status status = git.status().call();
 		assertEquals(1, status.getUntracked().size());
@@ -706,6 +787,7 @@ public void untrackedFileConflictsWithCommit() throws Exception {
 		String path = "untracked.txt";
 		writeTrashFile(path, "untracked");
 		git.stashCreate().setIncludeUntracked(true).call();
+		recorder.assertEvent(ChangeRecorder.EMPTY, new String[] { path });
 
 		writeTrashFile(path, "committed");
 		head = git.commit().setMessage("add file").call();
@@ -719,6 +801,7 @@ public void untrackedFileConflictsWithCommit() throws Exception {
 			assertEquals(e.getMessage(), JGitText.get().stashApplyConflict);
 		}
 		assertEquals("committed", read(path));
+		recorder.assertNoEvent();
 	}
 
 	@Test
@@ -727,6 +810,7 @@ public void untrackedFileConflictsWithWorkingDirectory()
 		String path = "untracked.txt";
 		writeTrashFile(path, "untracked");
 		git.stashCreate().setIncludeUntracked(true).call();
+		recorder.assertEvent(ChangeRecorder.EMPTY, new String[] { path });
 
 		writeTrashFile(path, "working-directory");
 		try {
@@ -736,6 +820,7 @@ public void untrackedFileConflictsWithWorkingDirectory()
 			assertEquals(e.getMessage(), JGitText.get().stashApplyConflict);
 		}
 		assertEquals("working-directory", read(path));
+		recorder.assertNoEvent();
 	}
 
 	@Test
@@ -747,11 +832,13 @@ public void untrackedAndTrackedChanges() throws Exception {
 		assertTrue(PATH + " should exist", check(PATH));
 		assertEquals(PATH + " should have been reset", "content", read(PATH));
 		assertFalse(path + " should not exist", check(path));
+		recorder.assertEvent(new String[] { PATH }, new String[] { path });
 		git.stashApply().setStashRef("stash@{0}").call();
 		assertTrue(PATH + " should exist", check(PATH));
 		assertEquals(PATH + " should have new content", "changed", read(PATH));
 		assertTrue(path + " should exist", check(path));
 		assertEquals(path + " should have new content", "untracked",
 				read(path));
+		recorder.assertEvent(new String[] { PATH, path }, ChangeRecorder.EMPTY);
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/StashListCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/StashListCommandTest.java
index a7e0ab9..d658a53 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/StashListCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/StashListCommandTest.java
@@ -51,6 +51,7 @@
 
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.RefUpdate;
 import org.eclipse.jgit.lib.RefUpdate.Result;
 import org.eclipse.jgit.revwalk.RevCommit;
@@ -94,9 +95,7 @@ public void singleStashedCommit() throws Exception {
 		git.add().addFilepattern("file.txt").call();
 		RevCommit commit = git.commit().setMessage("create file").call();
 
-		RefUpdate update = db.updateRef(Constants.R_STASH);
-		update.setNewObjectId(commit);
-		assertEquals(Result.NEW, update.update());
+		assertEquals(Result.NEW, newStashUpdate(commit).update());
 
 		StashListCommand command = git.stashList();
 		Collection<RevCommit> stashed = command.call();
@@ -117,13 +116,8 @@ public void multipleStashedCommits() throws Exception {
 		git.add().addFilepattern("file.txt").call();
 		RevCommit commit2 = git.commit().setMessage("edit file").call();
 
-		RefUpdate create = db.updateRef(Constants.R_STASH);
-		create.setNewObjectId(commit1);
-		assertEquals(Result.NEW, create.update());
-
-		RefUpdate update = db.updateRef(Constants.R_STASH);
-		update.setNewObjectId(commit2);
-		assertEquals(Result.FAST_FORWARD, update.update());
+		assertEquals(Result.NEW, newStashUpdate(commit1).update());
+		assertEquals(Result.FAST_FORWARD, newStashUpdate(commit2).update());
 
 		StashListCommand command = git.stashList();
 		Collection<RevCommit> stashed = command.call();
@@ -133,4 +127,11 @@ public void multipleStashedCommits() throws Exception {
 		assertEquals(commit2, iter.next());
 		assertEquals(commit1, iter.next());
 	}
+
+	private RefUpdate newStashUpdate(ObjectId newId) throws Exception {
+		RefUpdate ru = db.updateRef(Constants.R_STASH);
+		ru.setNewObjectId(newId);
+		ru.setForceRefLog(true);
+		return ru;
+	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesHandlerTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesHandlerTest.java
index ca456b3..5868482 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesHandlerTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesHandlerTest.java
@@ -1,4 +1,7 @@
 /*
+ * Copyright (C) 2015, 2017 Ivan Motsch <ivan.motsch@bsiag.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
  * This program and the accompanying materials are made available
  * under the terms of the Eclipse Distribution License v1.0 which
  * accompanies this distribution, is reproduced below, and is
@@ -254,6 +257,282 @@ public void testCyclicMacros() throws Exception {
 		endWalk();
 	}
 
+	@Test
+	public void testRelativePaths() throws Exception {
+		setupRepo("sub/ global", "sub/** init",
+				"sub/** top_sub\n*.txt top",
+				"sub/** subsub\nsub/ subsub2\n*.txt foo");
+		// The last sub/** is in sub/.gitattributes. It must not
+		// apply to any of the files here. It would match for a
+		// further subdirectory sub/sub. The sub/ rules must match
+		// only for directories.
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "sub", attrs("global"));
+		assertIteration(F, "sub/.gitattributes", attrs("init top_sub"));
+		assertIteration(F, "sub/a.txt", attrs("init foo top top_sub"));
+		endWalk();
+		// All right, let's see that they *do* apply in sub/sub:
+		writeTrashFile("sub/sub/b.txt", "b");
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "sub", attrs("global"));
+		assertIteration(F, "sub/.gitattributes", attrs("init top_sub"));
+		assertIteration(F, "sub/a.txt", attrs("init foo top top_sub"));
+		assertIteration(D, "sub/sub", attrs("init subsub2 top_sub global"));
+		assertIteration(F, "sub/sub/b.txt",
+				attrs("init foo subsub top top_sub"));
+		endWalk();
+	}
+
+	@Test
+	public void testNestedMatchNot() throws Exception {
+		setupRepo(null, null, "*.xml xml\n*.jar jar", null);
+		writeTrashFile("foo.xml/bar.jar", "b");
+		writeTrashFile("foo.xml/bar.xml", "bx");
+		writeTrashFile("sub/b.jar", "bj");
+		writeTrashFile("sub/b.xml", "bx");
+		// On foo.xml/bar.jar we must not have 'xml'
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "foo.xml", attrs("xml"));
+		assertIteration(F, "foo.xml/bar.jar", attrs("jar"));
+		assertIteration(F, "foo.xml/bar.xml", attrs("xml"));
+		assertIteration(D, "sub");
+		assertIteration(F, "sub/a.txt");
+		assertIteration(F, "sub/b.jar", attrs("jar"));
+		assertIteration(F, "sub/b.xml", attrs("xml"));
+		endWalk();
+	}
+
+	@Test
+	public void testNestedMatch() throws Exception {
+		// See also CGitAttributeTest.testNestedMatch()
+		setupRepo(null, null, "foo/ xml\nsub/foo/ sub\n*.jar jar", null);
+		writeTrashFile("foo/bar.jar", "b");
+		writeTrashFile("foo/bar.xml", "bx");
+		writeTrashFile("sub/b.jar", "bj");
+		writeTrashFile("sub/b.xml", "bx");
+		writeTrashFile("sub/foo/b.jar", "bf");
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "foo", attrs("xml"));
+		assertIteration(F, "foo/bar.jar", attrs("jar"));
+		assertIteration(F, "foo/bar.xml");
+		assertIteration(D, "sub");
+		assertIteration(F, "sub/a.txt");
+		assertIteration(F, "sub/b.jar", attrs("jar"));
+		assertIteration(F, "sub/b.xml");
+		assertIteration(D, "sub/foo", attrs("sub xml"));
+		assertIteration(F, "sub/foo/b.jar", attrs("jar"));
+		endWalk();
+	}
+
+	@Test
+	public void testNestedMatchRecursive() throws Exception {
+		setupRepo(null, null, "foo/** xml\n*.jar jar", null);
+		writeTrashFile("foo/bar.jar", "b");
+		writeTrashFile("foo/bar.xml", "bx");
+		writeTrashFile("sub/b.jar", "bj");
+		writeTrashFile("sub/b.xml", "bx");
+		writeTrashFile("sub/foo/b.jar", "bf");
+		// On foo.xml/bar.jar we must not have 'xml'
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "foo");
+		assertIteration(F, "foo/bar.jar", attrs("jar xml"));
+		assertIteration(F, "foo/bar.xml", attrs("xml"));
+		assertIteration(D, "sub");
+		assertIteration(F, "sub/a.txt");
+		assertIteration(F, "sub/b.jar", attrs("jar"));
+		assertIteration(F, "sub/b.xml");
+		assertIteration(D, "sub/foo");
+		assertIteration(F, "sub/foo/b.jar", attrs("jar"));
+		endWalk();
+	}
+
+	@Test
+	public void testStarMatchOnSlashNot() throws Exception {
+		setupRepo(null, null, "s*xt bar", null);
+		writeTrashFile("sub/a.txt", "1");
+		writeTrashFile("foo/sext", "2");
+		writeTrashFile("foo/s.txt", "3");
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "foo");
+		assertIteration(F, "foo/s.txt", attrs("bar"));
+		assertIteration(F, "foo/sext", attrs("bar"));
+		assertIteration(D, "sub");
+		assertIteration(F, "sub/a.txt");
+		endWalk();
+	}
+
+	@Test
+	public void testPrefixMatchNot() throws Exception {
+		setupRepo(null, null, "sub/new bar", null);
+		writeTrashFile("sub/new/foo.txt", "1");
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "sub");
+		assertIteration(F, "sub/a.txt");
+		assertIteration(D, "sub/new", attrs("bar"));
+		assertIteration(F, "sub/new/foo.txt");
+		endWalk();
+	}
+
+	@Test
+	public void testComplexPathMatch() throws Exception {
+		setupRepo(null, null, "s[t-v]b/n[de]w bar", null);
+		writeTrashFile("sub/new/foo.txt", "1");
+		writeTrashFile("sub/ndw", "2");
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "sub");
+		assertIteration(F, "sub/a.txt");
+		assertIteration(F, "sub/ndw", attrs("bar"));
+		assertIteration(D, "sub/new", attrs("bar"));
+		assertIteration(F, "sub/new/foo.txt");
+		endWalk();
+	}
+
+	@Test
+	public void testStarPathMatch() throws Exception {
+		setupRepo(null, null, "sub/new/* bar", null);
+		writeTrashFile("sub/new/foo.txt", "1");
+		writeTrashFile("sub/new/lower/foo.txt", "2");
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "sub");
+		assertIteration(F, "sub/a.txt");
+		assertIteration(D, "sub/new");
+		assertIteration(F, "sub/new/foo.txt", attrs("bar"));
+		assertIteration(D, "sub/new/lower", attrs("bar"));
+		assertIteration(F, "sub/new/lower/foo.txt");
+		endWalk();
+	}
+
+	@Test
+	public void testDirectoryMatchSubSimple() throws Exception {
+		setupRepo(null, null, "sub/new/ bar", null);
+		writeTrashFile("sub/new/foo.txt", "1");
+		writeTrashFile("foo/sub/new/foo.txt", "2");
+		writeTrashFile("sub/sub/new/foo.txt", "3");
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "foo");
+		assertIteration(D, "foo/sub");
+		assertIteration(D, "foo/sub/new");
+		assertIteration(F, "foo/sub/new/foo.txt");
+		assertIteration(D, "sub");
+		assertIteration(F, "sub/a.txt");
+		assertIteration(D, "sub/new", attrs("bar"));
+		assertIteration(F, "sub/new/foo.txt");
+		assertIteration(D, "sub/sub");
+		assertIteration(D, "sub/sub/new");
+		assertIteration(F, "sub/sub/new/foo.txt");
+		endWalk();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursive() throws Exception {
+		setupRepo(null, null, "**/sub/new/ bar", null);
+		writeTrashFile("sub/new/foo.txt", "1");
+		writeTrashFile("foo/sub/new/foo.txt", "2");
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "foo");
+		assertIteration(D, "foo/sub");
+		assertIteration(D, "foo/sub/new", attrs("bar"));
+		assertIteration(F, "foo/sub/new/foo.txt");
+		assertIteration(D, "sub");
+		assertIteration(F, "sub/a.txt");
+		assertIteration(D, "sub/new", attrs("bar"));
+		assertIteration(F, "sub/new/foo.txt");
+		endWalk();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursiveBacktrack() throws Exception {
+		setupRepo(null, null, "**/sub/new/ bar", null);
+		writeTrashFile("sub/new/foo.txt", "1");
+		writeTrashFile("foo/sub/new/foo.txt", "2");
+		writeTrashFile("sub/sub/new/foo.txt", "3");
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "foo");
+		assertIteration(D, "foo/sub");
+		assertIteration(D, "foo/sub/new", attrs("bar"));
+		assertIteration(F, "foo/sub/new/foo.txt");
+		assertIteration(D, "sub");
+		assertIteration(F, "sub/a.txt");
+		assertIteration(D, "sub/new", attrs("bar"));
+		assertIteration(F, "sub/new/foo.txt");
+		assertIteration(D, "sub/sub");
+		assertIteration(D, "sub/sub/new", attrs("bar"));
+		assertIteration(F, "sub/sub/new/foo.txt");
+		endWalk();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursiveBacktrack2() throws Exception {
+		setupRepo(null, null, "**/**/sub/new/ bar", null);
+		writeTrashFile("sub/new/foo.txt", "1");
+		writeTrashFile("foo/sub/new/foo.txt", "2");
+		writeTrashFile("sub/sub/new/foo.txt", "3");
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "foo");
+		assertIteration(D, "foo/sub");
+		assertIteration(D, "foo/sub/new", attrs("bar"));
+		assertIteration(F, "foo/sub/new/foo.txt");
+		assertIteration(D, "sub");
+		assertIteration(F, "sub/a.txt");
+		assertIteration(D, "sub/new", attrs("bar"));
+		assertIteration(F, "sub/new/foo.txt");
+		assertIteration(D, "sub/sub");
+		assertIteration(D, "sub/sub/new", attrs("bar"));
+		assertIteration(F, "sub/sub/new/foo.txt");
+		endWalk();
+	}
+
+	@Test
+	public void testDirectoryMatchSubComplex() throws Exception {
+		setupRepo(null, null, "s[uv]b/n*/ bar", null);
+		writeTrashFile("sub/new/foo.txt", "1");
+		writeTrashFile("foo/sub/new/foo.txt", "2");
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "foo");
+		assertIteration(D, "foo/sub");
+		assertIteration(D, "foo/sub/new");
+		assertIteration(F, "foo/sub/new/foo.txt");
+		assertIteration(D, "sub");
+		assertIteration(F, "sub/a.txt");
+		assertIteration(D, "sub/new", attrs("bar"));
+		assertIteration(F, "sub/new/foo.txt");
+		endWalk();
+	}
+
+	@Test
+	public void testDirectoryMatch() throws Exception {
+		setupRepo(null, null, "new/ bar", null);
+		writeTrashFile("sub/new/foo.txt", "1");
+		writeTrashFile("foo/sub/new/foo.txt", "2");
+		writeTrashFile("foo/new", "3");
+		walk = beginWalk();
+		assertIteration(F, ".gitattributes");
+		assertIteration(D, "foo");
+		assertIteration(F, "foo/new");
+		assertIteration(D, "foo/sub");
+		assertIteration(D, "foo/sub/new", attrs("bar"));
+		assertIteration(F, "foo/sub/new/foo.txt");
+		assertIteration(D, "sub");
+		assertIteration(F, "sub/a.txt");
+		assertIteration(D, "sub/new", attrs("bar"));
+		assertIteration(F, "sub/new/foo.txt");
+		endWalk();
+	}
+
 	private static Collection<Attribute> attrs(String s) {
 		return new AttributesRule("*", s).getAttributes();
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesMatcherTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesMatcherTest.java
index e8dd952..72cc1d1 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesMatcherTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesMatcherTest.java
@@ -109,16 +109,16 @@ public void testFileNameWildcards() {
 		pattern = "/src/ne?";
 		assertMatched(pattern, "/src/new/");
 		assertMatched(pattern, "/src/new");
-		assertMatched(pattern, "/src/new/a.c");
-		assertMatched(pattern, "/src/new/a/a.c");
+		assertNotMatched(pattern, "/src/new/a.c");
+		assertNotMatched(pattern, "/src/new/a/a.c");
 		assertNotMatched(pattern, "/src/new.c");
 
 		//Test name-only fnmatcher matches
 		pattern = "ne?";
 		assertMatched(pattern, "/src/new/");
 		assertMatched(pattern, "/src/new");
-		assertMatched(pattern, "/src/new/a.c");
-		assertMatched(pattern, "/src/new/a/a.c");
+		assertNotMatched(pattern, "/src/new/a.c");
+		assertNotMatched(pattern, "/src/new/a/a.c");
 		assertMatched(pattern, "/neb");
 		assertNotMatched(pattern, "/src/new.c");
 	}
@@ -169,16 +169,16 @@ public void testTargetWithoutLeadingSlash() {
 		pattern = "/src/ne?";
 		assertMatched(pattern, "src/new/");
 		assertMatched(pattern, "src/new");
-		assertMatched(pattern, "src/new/a.c");
-		assertMatched(pattern, "src/new/a/a.c");
+		assertNotMatched(pattern, "src/new/a.c");
+		assertNotMatched(pattern, "src/new/a/a.c");
 		assertNotMatched(pattern, "src/new.c");
 
 		//Test name-only fnmatcher matches
 		pattern = "ne?";
 		assertMatched(pattern, "src/new/");
 		assertMatched(pattern, "src/new");
-		assertMatched(pattern, "src/new/a.c");
-		assertMatched(pattern, "src/new/a/a.c");
+		assertNotMatched(pattern, "src/new/a.c");
+		assertNotMatched(pattern, "src/new/a/a.c");
 		assertMatched(pattern, "neb");
 		assertNotMatched(pattern, "src/new.c");
 	}
@@ -197,35 +197,50 @@ public void testParentDirectoryGitAttributes() {
 		pattern = "/src/new";
 		assertMatched(pattern, "/src/new/");
 		assertMatched(pattern, "/src/new");
-		assertMatched(pattern, "/src/new/a.c");
-		assertMatched(pattern, "/src/new/a/a.c");
+		assertNotMatched(pattern, "/src/new/a.c");
+		assertNotMatched(pattern, "/src/new/a/a.c");
 		assertNotMatched(pattern, "/src/new.c");
 
 		//Test child directory is matched, slash after name
 		pattern = "/src/new/";
 		assertMatched(pattern, "/src/new/");
-		assertMatched(pattern, "/src/new/a.c");
-		assertMatched(pattern, "/src/new/a/a.c");
+		assertNotMatched(pattern, "/src/new/a.c");
+		assertNotMatched(pattern, "/src/new/a/a.c");
 		assertNotMatched(pattern, "/src/new");
 		assertNotMatched(pattern, "/src/new.c");
 
 		//Test directory is matched by name only
 		pattern = "b1";
-		assertMatched(pattern, "/src/new/a/b1/a.c");
+		assertNotMatched(pattern, "/src/new/a/b1/a.c");
 		assertNotMatched(pattern, "/src/new/a/b2/file.c");
 		assertNotMatched(pattern, "/src/new/a/bb1/file.c");
 		assertNotMatched(pattern, "/src/new/a/file.c");
+		assertNotMatched(pattern, "/src/new/a/bb1");
+		assertMatched(pattern, "/src/new/a/b1");
 	}
 
 	@Test
 	public void testTrailingSlash() {
 		String pattern = "/src/";
 		assertMatched(pattern, "/src/");
-		assertMatched(pattern, "/src/new");
-		assertMatched(pattern, "/src/new/a.c");
-		assertMatched(pattern, "/src/a.c");
+		assertNotMatched(pattern, "/src/new");
+		assertNotMatched(pattern, "/src/new/a.c");
+		assertNotMatched(pattern, "/src/a.c");
 		assertNotMatched(pattern, "/src");
 		assertNotMatched(pattern, "/srcA/");
+
+		pattern = "src/";
+		assertMatched(pattern, "src/");
+		assertMatched(pattern, "/src/");
+		assertNotMatched(pattern, "src");
+		assertNotMatched(pattern, "/src/new");
+		assertNotMatched(pattern, "/src/new/a.c");
+		assertNotMatched(pattern, "/src/a.c");
+		assertNotMatched(pattern, "foo/src/a.c");
+		assertNotMatched(pattern, "foo/src/bar/a.c");
+		assertNotMatched(pattern, "foo/src/bar/src");
+		assertMatched(pattern, "foo/src/");
+		assertMatched(pattern, "foo/src/bar/src/");
 	}
 
 	@Test
@@ -239,51 +254,58 @@ public void testNameOnlyMatches() {
 		assertMatched(pattern, "/src/test.stp");
 		assertNotMatched(pattern, "/test.stp1");
 		assertNotMatched(pattern, "/test.astp");
+		assertNotMatched(pattern, "test.stp/foo.bar");
+		assertMatched(pattern, "test.stp");
+		assertMatched(pattern, "test.stp/");
+		assertMatched(pattern, "test.stp/test.stp");
 
 		//Test matches for name-only, applies to file name or folder name
 		pattern = "src";
 		assertMatched(pattern, "/src");
 		assertMatched(pattern, "/src/");
-		assertMatched(pattern, "/src/a.c");
-		assertMatched(pattern, "/src/new/a.c");
-		assertMatched(pattern, "/new/src/a.c");
+		assertNotMatched(pattern, "/src/a.c");
+		assertNotMatched(pattern, "/src/new/a.c");
+		assertNotMatched(pattern, "/new/src/a.c");
 		assertMatched(pattern, "/file/src");
 
 		//Test matches for name-only, applies only to folder names
 		pattern = "src/";
-		assertMatched(pattern, "/src/");
-		assertMatched(pattern, "/src/a.c");
-		assertMatched(pattern, "/src/new/a.c");
-		assertMatched(pattern, "/new/src/a.c");
+		assertNotMatched(pattern, "/src/a.c");
+		assertNotMatched(pattern, "/src/new/a.c");
+		assertNotMatched(pattern, "/new/src/a.c");
 		assertNotMatched(pattern, "/src");
 		assertNotMatched(pattern, "/file/src");
+		assertMatched(pattern, "/file/src/");
 
 		//Test matches for name-only, applies to file name or folder name
 		//With a small wildcard
 		pattern = "?rc";
-		assertMatched(pattern, "/src/a.c");
-		assertMatched(pattern, "/src/new/a.c");
-		assertMatched(pattern, "/new/src/a.c");
+		assertNotMatched(pattern, "/src/a.c");
+		assertNotMatched(pattern, "/src/new/a.c");
+		assertNotMatched(pattern, "/new/src/a.c");
+		assertMatched(pattern, "/new/src/");
 		assertMatched(pattern, "/file/src");
 		assertMatched(pattern, "/src/");
 
 		//Test matches for name-only, applies to file name or folder name
 		//With a small wildcard
 		pattern = "?r[a-c]";
-		assertMatched(pattern, "/src/a.c");
-		assertMatched(pattern, "/src/new/a.c");
-		assertMatched(pattern, "/new/src/a.c");
+		assertNotMatched(pattern, "/src/a.c");
+		assertNotMatched(pattern, "/src/new/a.c");
+		assertNotMatched(pattern, "/new/src/a.c");
 		assertMatched(pattern, "/file/src");
 		assertMatched(pattern, "/src/");
-		assertMatched(pattern, "/srb/a.c");
-		assertMatched(pattern, "/grb/new/a.c");
-		assertMatched(pattern, "/new/crb/a.c");
+		assertNotMatched(pattern, "/srb/a.c");
+		assertNotMatched(pattern, "/grb/new/a.c");
+		assertNotMatched(pattern, "/new/crb/a.c");
 		assertMatched(pattern, "/file/3rb");
 		assertMatched(pattern, "/xrb/");
-		assertMatched(pattern, "/3ra/a.c");
-		assertMatched(pattern, "/5ra/new/a.c");
-		assertMatched(pattern, "/new/1ra/a.c");
+		assertNotMatched(pattern, "/3ra/a.c");
+		assertNotMatched(pattern, "/5ra/new/a.c");
+		assertNotMatched(pattern, "/new/1ra/a.c");
+		assertNotMatched(pattern, "/new/1ra/a.c/");
 		assertMatched(pattern, "/file/dra");
+		assertMatched(pattern, "/file/dra/");
 		assertMatched(pattern, "/era/");
 		assertNotMatched(pattern, "/crg");
 		assertNotMatched(pattern, "/cr3");
@@ -360,6 +382,39 @@ public void testGetters() {
 		assertEquals(r.getAttributes().get(2).toString(), "attribute3=value");
 	}
 
+	@Test
+	public void testBracketsInGroup() {
+		//combinations of brackets in brackets, escaped and not
+
+		String[] patterns = new String[]{"[[\\]]", "[\\[\\]]"};
+		for (String pattern : patterns) {
+			assertNotMatched(pattern, "");
+			assertNotMatched(pattern, "[]");
+			assertNotMatched(pattern, "][");
+			assertNotMatched(pattern, "[\\[]");
+			assertNotMatched(pattern, "[[]");
+			assertNotMatched(pattern, "[[]]");
+			assertNotMatched(pattern, "[\\[\\]]");
+
+			assertMatched(pattern, "[");
+			assertMatched(pattern, "]");
+		}
+
+		patterns = new String[]{"[[]]", "[\\[]]"};
+		for (String pattern : patterns) {
+			assertNotMatched(pattern, "");
+			assertMatched(pattern, "[]");
+			assertNotMatched(pattern, "][");
+			assertNotMatched(pattern, "[\\[]");
+			assertNotMatched(pattern, "[[]");
+			assertNotMatched(pattern, "[[]]");
+			assertNotMatched(pattern, "[\\[\\]]");
+
+			assertNotMatched(pattern, "[");
+			assertNotMatched(pattern, "]");
+		}
+	}
+
 	/**
 	 * Check for a match. If target ends with "/", match will assume that the
 	 * target is meant to be a directory.
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesNodeTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesNodeTest.java
index ec2370e..f0d3c36 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesNodeTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesNodeTest.java
@@ -166,6 +166,25 @@ public void testTabSeparator() throws IOException {
 		assertAttribute("file.type3", node, asSet(A_UNSET_ATTR, B_SET_ATTR));
 	}
 
+	@Test
+	public void testDoubleAsteriskAtEnd() throws IOException {
+		String attributeFileContent = "dir/** \tA -B\tC=value";
+
+		is = new ByteArrayInputStream(attributeFileContent.getBytes());
+		AttributesNode node = new AttributesNode();
+		node.parse(is);
+		assertAttribute("dir", node,
+				asSet(new Attribute[]{}));
+		assertAttribute("dir/", node,
+				asSet(new Attribute[]{}));
+		assertAttribute("dir/file.type1", node,
+				asSet(A_SET_ATTR, B_UNSET_ATTR, C_VALUE_ATTR));
+		assertAttribute("dir/sub/", node,
+				asSet(A_SET_ATTR, B_UNSET_ATTR, C_VALUE_ATTR));
+		assertAttribute("dir/sub/file.type1", node,
+				asSet(A_SET_ATTR, B_UNSET_ATTR, C_VALUE_ATTR));
+	}
+
 	private void assertAttribute(String path, AttributesNode node,
 			Attributes attrs) throws IOException {
 		Attributes attributes = new Attributes();
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/CGitAttributesTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/CGitAttributesTest.java
new file mode 100644
index 0000000..3483813
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/CGitAttributesTest.java
@@ -0,0 +1,389 @@
+/*
+ * Copyright (C) 2017 Thomas Wolf <thomas.wolf@paranor.ch>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.attributes;
+
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.Set;
+
+import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.StoredConfig;
+import org.eclipse.jgit.treewalk.FileTreeIterator;
+import org.eclipse.jgit.treewalk.TreeWalk;
+import org.eclipse.jgit.treewalk.filter.NotIgnoredFilter;
+import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.util.FS.ExecutionResult;
+import org.eclipse.jgit.util.RawParseUtils;
+import org.eclipse.jgit.util.TemporaryBuffer;
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Tests that verify that the attributes of files in a repository are the same
+ * in JGit and in C-git.
+ */
+public class CGitAttributesTest extends RepositoryTestCase {
+
+	@Before
+	public void initRepo() throws IOException {
+		// Because we run C-git, we must ensure that global or user exclude
+		// files cannot influence the tests. So we set core.excludesFile to an
+		// empty file inside the repository.
+		StoredConfig config = db.getConfig();
+		File fakeUserGitignore = writeTrashFile(".fake_user_gitignore", "");
+		config.setString("core", null, "excludesFile",
+				fakeUserGitignore.getAbsolutePath());
+		// Disable case-insensitivity -- JGit doesn't handle that yet.
+		config.setBoolean("core", null, "ignoreCase", false);
+		// And try to switch off the global attributes file, too.
+		config.setString("core", null, "attributesFile",
+				fakeUserGitignore.getAbsolutePath());
+		config.save();
+	}
+
+	private void createFiles(String... paths) throws IOException {
+		for (String path : paths) {
+			writeTrashFile(path, "x");
+		}
+	}
+
+	private String toString(TemporaryBuffer b) throws IOException {
+		return RawParseUtils.decode(b.toByteArray());
+	}
+
+	private Attribute fromString(String key, String value) {
+		if ("set".equals(value)) {
+			return new Attribute(key, Attribute.State.SET);
+		}
+		if ("unset".equals(value)) {
+			return new Attribute(key, Attribute.State.UNSET);
+		}
+		if ("unspecified".equals(value)) {
+			return new Attribute(key, Attribute.State.UNSPECIFIED);
+		}
+		return new Attribute(key, value);
+	}
+
+	private LinkedHashMap<String, Attributes> cgitAttributes(
+			Set<String> allFiles) throws Exception {
+		FS fs = db.getFS();
+		StringBuilder input = new StringBuilder();
+		for (String filename : allFiles) {
+			input.append(filename).append('\n');
+		}
+		ProcessBuilder builder = fs.runInShell("git",
+				new String[] { "check-attr", "--stdin", "--all" });
+		builder.directory(db.getWorkTree());
+		builder.environment().put("HOME", fs.userHome().getAbsolutePath());
+		ExecutionResult result = fs.execute(builder, new ByteArrayInputStream(
+				input.toString().getBytes(Constants.CHARSET)));
+		String errorOut = toString(result.getStderr());
+		assertEquals("External git failed", "exit 0\n",
+				"exit " + result.getRc() + '\n' + errorOut);
+		LinkedHashMap<String, Attributes> map = new LinkedHashMap<>();
+		try (BufferedReader r = new BufferedReader(new InputStreamReader(
+				new BufferedInputStream(result.getStdout().openInputStream()),
+				Constants.CHARSET))) {
+			r.lines().forEach(line -> {
+				// Parse the line and add to result map
+				int start = 0;
+				int i = line.indexOf(':');
+				String path = line.substring(0, i).trim();
+				start = i + 1;
+				i = line.indexOf(':', start);
+				String key = line.substring(start, i).trim();
+				String value = line.substring(i + 1).trim();
+				Attribute attr = fromString(key, value);
+				Attributes attrs = map.get(path);
+				if (attrs == null) {
+					attrs = new Attributes(attr);
+					map.put(path, attrs);
+				} else {
+					attrs.put(attr);
+				}
+			});
+		}
+		return map;
+	}
+
+	private LinkedHashMap<String, Attributes> jgitAttributes()
+			throws IOException {
+		// Do a tree walk and return a list of all files and directories with
+		// their attributes
+		LinkedHashMap<String, Attributes> result = new LinkedHashMap<>();
+		try (TreeWalk walk = new TreeWalk(db)) {
+			walk.addTree(new FileTreeIterator(db));
+			walk.setFilter(new NotIgnoredFilter(0));
+			while (walk.next()) {
+				String path = walk.getPathString();
+				if (walk.isSubtree() && !path.endsWith("/")) {
+					// git check-attr expects directory paths to end with a
+					// slash
+					path += '/';
+				}
+				Attributes attrs = walk.getAttributes();
+				if (attrs != null && !attrs.isEmpty()) {
+					result.put(path, attrs);
+				} else {
+					result.put(path, null);
+				}
+				if (walk.isSubtree()) {
+					walk.enterSubtree();
+				}
+			}
+		}
+		return result;
+	}
+
+	private void assertSameAsCGit() throws Exception {
+		LinkedHashMap<String, Attributes> jgit = jgitAttributes();
+		LinkedHashMap<String, Attributes> cgit = cgitAttributes(jgit.keySet());
+		// remove all without attributes
+		Iterator<Map.Entry<String, Attributes>> iterator = jgit.entrySet()
+				.iterator();
+		while (iterator.hasNext()) {
+			Map.Entry<String, Attributes> entry = iterator.next();
+			if (entry.getValue() == null) {
+				iterator.remove();
+			}
+		}
+		assertArrayEquals("JGit attributes differ from C git",
+				cgit.entrySet().toArray(), jgit.entrySet().toArray());
+	}
+
+	@Test
+	public void testBug508568() throws Exception {
+		createFiles("foo.xml/bar.jar", "sub/foo.xml/bar.jar");
+		writeTrashFile(".gitattributes", "*.xml xml\n" + "*.jar jar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testRelativePath() throws Exception {
+		createFiles("sub/foo.txt");
+		writeTrashFile("sub/.gitattributes", "sub/** sub\n" + "*.txt txt\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testRelativePaths() throws Exception {
+		createFiles("sub/foo.txt", "sub/sub/bar", "foo/sub/a.txt",
+				"foo/sub/bar/a.tmp");
+		writeTrashFile(".gitattributes", "sub/** sub\n" + "*.txt txt\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testNestedMatchNot() throws Exception {
+		createFiles("foo.xml/bar.jar", "foo.xml/bar.xml", "sub/b.jar",
+				"sub/b.xml");
+		writeTrashFile("sub/.gitattributes", "*.xml xml\n" + "*.jar jar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testNestedMatch() throws Exception {
+		// This is an interesting test. At the time of this writing, the
+		// gitignore documentation says: "In other words, foo/ will match a
+		// directory foo AND PATHS UNDERNEATH IT, but will not match a regular
+		// file or a symbolic link foo". (Emphasis added.) And gitattributes is
+		// supposed to follow the same rules. But the documentation appears to
+		// lie: C-git will *not* apply the attribute "xml" to *any* files in
+		// any subfolder "foo" here. It will only apply the "jar" attribute
+		// to the three *.jar files.
+		//
+		// The point is probably that ignores are handled top-down, and once a
+		// directory "foo" is matched (here: on paths "foo" and "sub/foo" by
+		// pattern "foo/"), the directory is excluded and the gitignore
+		// documentation also says: "It is not possible to re-include a file if
+		// a parent directory of that file is excluded." So once the pattern
+		// "foo/" has matched, it appears as if everything beneath would also be
+		// matched.
+		//
+		// But not so for gitattributes! The foo/ rule only matches the
+		// directory itself, but not anything beneath.
+		createFiles("foo/bar.jar", "foo/bar.xml", "sub/b.jar", "sub/b.xml",
+				"sub/foo/b.jar");
+		writeTrashFile(".gitattributes",
+				"foo/ xml\n" + "sub/foo/ sub\n" + "*.jar jar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testNestedMatchWithWildcard() throws Exception {
+		// See above.
+		createFiles("foo/bar.jar", "foo/bar.xml", "sub/b.jar", "sub/b.xml",
+				"sub/foo/b.jar");
+		writeTrashFile(".gitattributes",
+				"**/foo/ xml\n" + "*/foo/ sub\n" + "*.jar jar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testNestedMatchRecursive() throws Exception {
+		createFiles("foo/bar.jar", "foo/bar.xml", "sub/b.jar", "sub/b.xml",
+				"sub/foo/b.jar");
+		writeTrashFile(".gitattributes", "foo/** xml\n" + "*.jar jar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testStarMatchOnSlashNot() throws Exception {
+		createFiles("sub/a.txt", "foo/sext", "foo/s.txt");
+		writeTrashFile(".gitattributes", "s*xt bar");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testPrefixMatchNot() throws Exception {
+		createFiles("src/new/foo.txt");
+		writeTrashFile(".gitattributes", "src/new bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testComplexPathMatchNot() throws Exception {
+		createFiles("src/new/foo.txt", "src/ndw");
+		writeTrashFile(".gitattributes", "s[p-s]c/n[de]w bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testStarPathMatchNot() throws Exception {
+		createFiles("src/new/foo.txt", "src/ndw");
+		writeTrashFile(".gitattributes", "src/* bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubSimple() throws Exception {
+		createFiles("src/new/foo.txt", "foo/src/new/foo.txt", "sub/src/new");
+		writeTrashFile(".gitattributes", "src/new/ bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursive() throws Exception {
+		createFiles("src/new/foo.txt", "foo/src/new/foo.txt", "sub/src/new");
+		writeTrashFile(".gitattributes", "**/src/new/ bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursiveBacktrack() throws Exception {
+		createFiles("src/new/foo.txt", "src/src/new/foo.txt");
+		writeTrashFile(".gitattributes", "**/src/new/ bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursiveBacktrack2() throws Exception {
+		createFiles("src/new/foo.txt", "src/src/new/foo.txt");
+		writeTrashFile(".gitattributes", "**/**/src/new/ bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursiveBacktrack3() throws Exception {
+		createFiles("src/new/src/new/foo.txt",
+				"foo/src/new/bar/src/new/foo.txt");
+		writeTrashFile(".gitattributes", "**/src/new/ bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursiveBacktrack4() throws Exception {
+		createFiles("src/src/src/new/foo.txt",
+				"foo/src/src/bar/src/new/foo.txt");
+		writeTrashFile(".gitattributes", "**/src/ bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursiveBacktrack5() throws Exception {
+		createFiles("x/a/a/b/foo.txt", "x/y/z/b/a/b/foo.txt",
+				"x/y/a/a/a/a/b/foo.txt", "x/y/a/a/a/a/b/a/b/foo.txt");
+		writeTrashFile(".gitattributes", "**/*/a/b bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursiveBacktrack6() throws Exception {
+		createFiles("x/a/a/b/foo.txt", "x/y/a/b/a/b/foo.txt");
+		writeTrashFile(".gitattributes", "**/*/**/a/b bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubComplex() throws Exception {
+		createFiles("src/new/foo.txt", "foo/src/new/foo.txt", "sub/src/new");
+		writeTrashFile(".gitattributes", "s[rs]c/n*/ bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatch() throws Exception {
+		createFiles("src/new/foo.txt", "foo/src/new/foo.txt", "sub/src/new");
+		writeTrashFile(".gitattributes", "new/ bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testBracketsInGroup() throws Exception {
+		createFiles("[", "]", "[]", "][", "[[]", "[]]", "[[]]");
+		writeTrashFile(".gitattributes", "[[]] bar1\n" + "[\\[]] bar2\n"
+				+ "[[\\]] bar3\n" + "[\\[\\]] bar4\n");
+		assertSameAsCGit();
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/merge/MergeGitAttributeTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/merge/MergeGitAttributeTest.java
new file mode 100644
index 0000000..a4f3d18
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/merge/MergeGitAttributeTest.java
@@ -0,0 +1,585 @@
+/*
+ * Copyright (C) 2017, Obeo (mathieu.cartaud@obeo.fr)
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.attributes.merge;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.util.function.Consumer;
+
+import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.api.MergeResult;
+import org.eclipse.jgit.api.MergeResult.MergeStatus;
+import org.eclipse.jgit.api.errors.CheckoutConflictException;
+import org.eclipse.jgit.api.errors.ConcurrentRefUpdateException;
+import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.api.errors.InvalidMergeHeadsException;
+import org.eclipse.jgit.api.errors.NoFilepatternException;
+import org.eclipse.jgit.api.errors.NoHeadException;
+import org.eclipse.jgit.api.errors.NoMessageException;
+import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
+import org.eclipse.jgit.attributes.Attribute;
+import org.eclipse.jgit.attributes.Attributes;
+import org.eclipse.jgit.errors.NoWorkTreeException;
+import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.treewalk.FileTreeIterator;
+import org.eclipse.jgit.treewalk.TreeWalk;
+import org.eclipse.jgit.treewalk.filter.PathFilter;
+import org.junit.Ignore;
+import org.junit.Test;
+
+public class MergeGitAttributeTest extends RepositoryTestCase {
+
+	private static final String REFS_HEADS_RIGHT = "refs/heads/right";
+
+	private static final String REFS_HEADS_MASTER = "refs/heads/master";
+
+	private static final String REFS_HEADS_LEFT = "refs/heads/left";
+
+	private static final String DISABLE_CHECK_BRANCH = "refs/heads/disabled_checked";
+
+	private static final String ENABLE_CHECKED_BRANCH = "refs/heads/enabled_checked";
+
+	private static final String ENABLED_CHECKED_GIF = "enabled_checked.gif";
+
+	public Git createRepositoryBinaryConflict(Consumer<Git> initialCommit,
+			Consumer<Git> leftCommit, Consumer<Git> rightCommit)
+			throws NoFilepatternException, GitAPIException, NoWorkTreeException,
+			IOException {
+		// Set up a git whith conflict commits on images
+		Git git = new Git(db);
+
+		// First commit
+		initialCommit.accept(git);
+		git.add().addFilepattern(".").call();
+		RevCommit firstCommit = git.commit().setAll(true)
+				.setMessage("initial commit adding git attribute file").call();
+
+		// Create branch and add an icon Checked_Boxe (enabled_checked)
+		createBranch(firstCommit, REFS_HEADS_LEFT);
+		checkoutBranch(REFS_HEADS_LEFT);
+		leftCommit.accept(git);
+		git.add().addFilepattern(".").call();
+		git.commit().setMessage("Left").call();
+
+		// Create a second branch from master Unchecked_Boxe
+		checkoutBranch(REFS_HEADS_MASTER);
+		createBranch(firstCommit, REFS_HEADS_RIGHT);
+		checkoutBranch(REFS_HEADS_RIGHT);
+		rightCommit.accept(git);
+		git.add().addFilepattern(".").call();
+		git.commit().setMessage("Right").call();
+
+		checkoutBranch(REFS_HEADS_LEFT);
+		return git;
+
+	}
+
+	@Test
+	public void mergeTextualFile_NoAttr() throws NoWorkTreeException,
+			NoFilepatternException, GitAPIException, IOException {
+		try (Git git = createRepositoryBinaryConflict(g -> {
+			try {
+				writeTrashFile("main.cat", "A\n" + "B\n" + "C\n" + "D\n");
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		}, g -> {
+			try {
+				writeTrashFile("main.cat", "A\n" + "B\n" + "C\n" + "F\n");
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		}, g -> {
+			try {
+				writeTrashFile("main.cat", "A\n" + "E\n" + "C\n" + "D\n");
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		})) {
+			checkoutBranch(REFS_HEADS_LEFT);
+			// Merge refs/heads/enabled_checked -> refs/heads/disabled_checked
+
+			MergeResult mergeResult = git.merge()
+					.include(git.getRepository().resolve(REFS_HEADS_RIGHT))
+					.call();
+			assertEquals(MergeStatus.MERGED, mergeResult.getMergeStatus());
+
+			assertNull(mergeResult.getConflicts());
+
+			// Check that the image was not modified (not conflict marker added)
+			String result = read(
+					writeTrashFile("res.cat", "A\n" + "E\n" + "C\n" + "F\n"));
+			assertEquals(result, read(git.getRepository().getWorkTree().toPath()
+					.resolve("main.cat").toFile()));
+		}
+	}
+
+	@Test
+	public void mergeTextualFile_UnsetMerge_Conflict()
+			throws NoWorkTreeException, NoFilepatternException, GitAPIException,
+			IOException {
+		try (Git git = createRepositoryBinaryConflict(g -> {
+			try {
+				writeTrashFile(".gitattributes", "*.cat -merge");
+				writeTrashFile("main.cat", "A\n" + "B\n" + "C\n" + "D\n");
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		}, g -> {
+			try {
+				writeTrashFile("main.cat", "A\n" + "B\n" + "C\n" + "F\n");
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		}, g -> {
+			try {
+				writeTrashFile("main.cat", "A\n" + "E\n" + "C\n" + "D\n");
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		})) {
+			// Check that the merge attribute is unset
+			assertAddMergeAttributeUnset(REFS_HEADS_LEFT, "main.cat");
+			assertAddMergeAttributeUnset(REFS_HEADS_RIGHT, "main.cat");
+
+			checkoutBranch(REFS_HEADS_LEFT);
+			// Merge refs/heads/enabled_checked -> refs/heads/disabled_checked
+
+			String catContent = read(git.getRepository().getWorkTree().toPath()
+					.resolve("main.cat").toFile());
+
+			MergeResult mergeResult = git.merge()
+					.include(git.getRepository().resolve(REFS_HEADS_RIGHT))
+					.call();
+			assertEquals(MergeStatus.CONFLICTING, mergeResult.getMergeStatus());
+
+			// Check that the image was not modified (not conflict marker added)
+			assertEquals(catContent, read(git.getRepository().getWorkTree()
+					.toPath().resolve("main.cat").toFile()));
+		}
+	}
+
+	@Test
+	public void mergeTextualFile_UnsetMerge_NoConflict()
+			throws NoWorkTreeException, NoFilepatternException, GitAPIException,
+			IOException {
+		try (Git git = createRepositoryBinaryConflict(g -> {
+			try {
+				writeTrashFile(".gitattributes", "*.txt -merge");
+				writeTrashFile("main.cat", "A\n" + "B\n" + "C\n" + "D\n");
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		}, g -> {
+			try {
+				writeTrashFile("main.cat", "A\n" + "B\n" + "C\n" + "F\n");
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		}, g -> {
+			try {
+				writeTrashFile("main.cat", "A\n" + "E\n" + "C\n" + "D\n");
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		})) {
+			// Check that the merge attribute is unset
+			assertAddMergeAttributeUndefined(REFS_HEADS_LEFT, "main.cat");
+			assertAddMergeAttributeUndefined(REFS_HEADS_RIGHT, "main.cat");
+
+			checkoutBranch(REFS_HEADS_LEFT);
+			// Merge refs/heads/enabled_checked -> refs/heads/disabled_checked
+
+			MergeResult mergeResult = git.merge()
+					.include(git.getRepository().resolve(REFS_HEADS_RIGHT))
+					.call();
+			assertEquals(MergeStatus.MERGED, mergeResult.getMergeStatus());
+
+			// Check that the image was not modified (not conflict marker added)
+			String result = read(
+					writeTrashFile("res.cat", "A\n" + "E\n" + "C\n" + "F\n"));
+			assertEquals(result, read(git.getRepository().getWorkTree()
+					.toPath().resolve("main.cat").toFile()));
+		}
+	}
+
+	@Test
+	public void mergeTextualFile_SetBinaryMerge_Conflict()
+			throws NoWorkTreeException, NoFilepatternException, GitAPIException,
+			IOException {
+		try (Git git = createRepositoryBinaryConflict(g -> {
+			try {
+				writeTrashFile(".gitattributes", "*.cat merge=binary");
+				writeTrashFile("main.cat", "A\n" + "B\n" + "C\n" + "D\n");
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		}, g -> {
+			try {
+				writeTrashFile("main.cat", "A\n" + "B\n" + "C\n" + "F\n");
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		}, g -> {
+			try {
+				writeTrashFile("main.cat", "A\n" + "E\n" + "C\n" + "D\n");
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		})) {
+			// Check that the merge attribute is set to binary
+			assertAddMergeAttributeCustom(REFS_HEADS_LEFT, "main.cat",
+					"binary");
+			assertAddMergeAttributeCustom(REFS_HEADS_RIGHT, "main.cat",
+					"binary");
+
+			checkoutBranch(REFS_HEADS_LEFT);
+			// Merge refs/heads/enabled_checked -> refs/heads/disabled_checked
+
+			String catContent = read(git.getRepository().getWorkTree().toPath()
+					.resolve("main.cat").toFile());
+
+			MergeResult mergeResult = git.merge()
+					.include(git.getRepository().resolve(REFS_HEADS_RIGHT))
+					.call();
+			assertEquals(MergeStatus.CONFLICTING, mergeResult.getMergeStatus());
+
+			// Check that the image was not modified (not conflict marker added)
+			assertEquals(catContent, read(git.getRepository().getWorkTree()
+					.toPath().resolve("main.cat").toFile()));
+		}
+	}
+
+	/*
+	 * This test is commented because JGit add conflict markers in binary files.
+	 * cf. https://www.eclipse.org/forums/index.php/t/1086511/
+	 */
+	@Test
+	@Ignore
+	public void mergeBinaryFile_NoAttr_Conflict() throws IllegalStateException,
+			IOException, NoHeadException, ConcurrentRefUpdateException,
+			CheckoutConflictException, InvalidMergeHeadsException,
+			WrongRepositoryStateException, NoMessageException, GitAPIException {
+
+		RevCommit disableCheckedCommit;
+		FileInputStream mergeResultFile = null;
+		// Set up a git with conflict commits on images
+		try (Git git = new Git(db)) {
+			// First commit
+			write(new File(db.getWorkTree(), ".gitattributes"), "");
+			git.add().addFilepattern(".gitattributes").call();
+			RevCommit firstCommit = git.commit()
+					.setMessage("initial commit adding git attribute file")
+					.call();
+
+			// Create branch and add an icon Checked_Boxe (enabled_checked)
+			createBranch(firstCommit, ENABLE_CHECKED_BRANCH);
+			checkoutBranch(ENABLE_CHECKED_BRANCH);
+			copy(ENABLED_CHECKED_GIF, ENABLED_CHECKED_GIF, "");
+			git.add().addFilepattern(ENABLED_CHECKED_GIF).call();
+			git.commit().setMessage("enabled_checked commit").call();
+
+			// Create a second branch from master Unchecked_Boxe
+			checkoutBranch(REFS_HEADS_MASTER);
+			createBranch(firstCommit, DISABLE_CHECK_BRANCH);
+			checkoutBranch(DISABLE_CHECK_BRANCH);
+			copy("disabled_checked.gif", ENABLED_CHECKED_GIF, "");
+			git.add().addFilepattern(ENABLED_CHECKED_GIF).call();
+			disableCheckedCommit = git.commit()
+					.setMessage("disabled_checked commit").call();
+
+			// Check that the merge attribute is unset
+			assertAddMergeAttributeUndefined(ENABLE_CHECKED_BRANCH,
+					ENABLED_CHECKED_GIF);
+			assertAddMergeAttributeUndefined(DISABLE_CHECK_BRANCH,
+					ENABLED_CHECKED_GIF);
+
+			checkoutBranch(ENABLE_CHECKED_BRANCH);
+			// Merge refs/heads/enabled_checked -> refs/heads/disabled_checked
+			MergeResult mergeResult = git.merge().include(disableCheckedCommit)
+					.call();
+			assertEquals(MergeStatus.CONFLICTING, mergeResult.getMergeStatus());
+
+			// Check that the image was not modified (no conflict marker added)
+			mergeResultFile = new FileInputStream(
+					db.getWorkTree().toPath().resolve(ENABLED_CHECKED_GIF)
+							.toFile());
+			assertTrue(contentEquals(
+					getClass().getResourceAsStream(ENABLED_CHECKED_GIF),
+					mergeResultFile));
+		} finally {
+			if (mergeResultFile != null) {
+				mergeResultFile.close();
+			}
+		}
+	}
+
+	@Test
+	public void mergeBinaryFile_UnsetMerge_Conflict()
+			throws IllegalStateException,
+			IOException, NoHeadException, ConcurrentRefUpdateException,
+			CheckoutConflictException, InvalidMergeHeadsException,
+			WrongRepositoryStateException, NoMessageException, GitAPIException {
+
+		RevCommit disableCheckedCommit;
+		FileInputStream mergeResultFile = null;
+		// Set up a git whith conflict commits on images
+		try (Git git = new Git(db)) {
+			// First commit
+			write(new File(db.getWorkTree(), ".gitattributes"), "*.gif -merge");
+			git.add().addFilepattern(".gitattributes").call();
+			RevCommit firstCommit = git.commit()
+					.setMessage("initial commit adding git attribute file")
+					.call();
+
+			// Create branch and add an icon Checked_Boxe (enabled_checked)
+			createBranch(firstCommit, ENABLE_CHECKED_BRANCH);
+			checkoutBranch(ENABLE_CHECKED_BRANCH);
+			copy(ENABLED_CHECKED_GIF, ENABLED_CHECKED_GIF, "");
+			git.add().addFilepattern(ENABLED_CHECKED_GIF).call();
+			git.commit().setMessage("enabled_checked commit").call();
+
+			// Create a second branch from master Unchecked_Boxe
+			checkoutBranch(REFS_HEADS_MASTER);
+			createBranch(firstCommit, DISABLE_CHECK_BRANCH);
+			checkoutBranch(DISABLE_CHECK_BRANCH);
+			copy("disabled_checked.gif", ENABLED_CHECKED_GIF, "");
+			git.add().addFilepattern(ENABLED_CHECKED_GIF).call();
+			disableCheckedCommit = git.commit()
+					.setMessage("disabled_checked commit").call();
+
+			// Check that the merge attribute is unset
+			assertAddMergeAttributeUnset(ENABLE_CHECKED_BRANCH,
+					ENABLED_CHECKED_GIF);
+			assertAddMergeAttributeUnset(DISABLE_CHECK_BRANCH,
+					ENABLED_CHECKED_GIF);
+
+			checkoutBranch(ENABLE_CHECKED_BRANCH);
+			// Merge refs/heads/enabled_checked -> refs/heads/disabled_checked
+			MergeResult mergeResult = git.merge().include(disableCheckedCommit)
+					.call();
+			assertEquals(MergeStatus.CONFLICTING, mergeResult.getMergeStatus());
+
+			// Check that the image was not modified (not conflict marker added)
+			mergeResultFile = new FileInputStream(db.getWorkTree().toPath()
+					.resolve(ENABLED_CHECKED_GIF).toFile());
+			assertTrue(contentEquals(
+					getClass().getResourceAsStream(ENABLED_CHECKED_GIF),
+					mergeResultFile));
+		} finally {
+			if (mergeResultFile != null) {
+				mergeResultFile.close();
+			}
+		}
+	}
+
+	@Test
+	public void mergeBinaryFile_SetMerge_Conflict()
+			throws IllegalStateException, IOException, NoHeadException,
+			ConcurrentRefUpdateException, CheckoutConflictException,
+			InvalidMergeHeadsException, WrongRepositoryStateException,
+			NoMessageException, GitAPIException {
+
+		RevCommit disableCheckedCommit;
+		FileInputStream mergeResultFile = null;
+		// Set up a git whith conflict commits on images
+		try (Git git = new Git(db)) {
+			// First commit
+			write(new File(db.getWorkTree(), ".gitattributes"), "*.gif merge");
+			git.add().addFilepattern(".gitattributes").call();
+			RevCommit firstCommit = git.commit()
+					.setMessage("initial commit adding git attribute file")
+					.call();
+
+			// Create branch and add an icon Checked_Boxe (enabled_checked)
+			createBranch(firstCommit, ENABLE_CHECKED_BRANCH);
+			checkoutBranch(ENABLE_CHECKED_BRANCH);
+			copy(ENABLED_CHECKED_GIF, ENABLED_CHECKED_GIF, "");
+			git.add().addFilepattern(ENABLED_CHECKED_GIF).call();
+			git.commit().setMessage("enabled_checked commit").call();
+
+			// Create a second branch from master Unchecked_Boxe
+			checkoutBranch(REFS_HEADS_MASTER);
+			createBranch(firstCommit, DISABLE_CHECK_BRANCH);
+			checkoutBranch(DISABLE_CHECK_BRANCH);
+			copy("disabled_checked.gif", ENABLED_CHECKED_GIF, "");
+			git.add().addFilepattern(ENABLED_CHECKED_GIF).call();
+			disableCheckedCommit = git.commit()
+					.setMessage("disabled_checked commit").call();
+
+			// Check that the merge attribute is set
+			assertAddMergeAttributeSet(ENABLE_CHECKED_BRANCH,
+					ENABLED_CHECKED_GIF);
+			assertAddMergeAttributeSet(DISABLE_CHECK_BRANCH,
+					ENABLED_CHECKED_GIF);
+
+			checkoutBranch(ENABLE_CHECKED_BRANCH);
+			// Merge refs/heads/enabled_checked -> refs/heads/disabled_checked
+			MergeResult mergeResult = git.merge().include(disableCheckedCommit)
+					.call();
+			assertEquals(MergeStatus.CONFLICTING, mergeResult.getMergeStatus());
+
+			// Check that the image was not modified (not conflict marker added)
+			mergeResultFile = new FileInputStream(db.getWorkTree().toPath()
+					.resolve(ENABLED_CHECKED_GIF).toFile());
+			assertFalse(contentEquals(
+					getClass().getResourceAsStream(ENABLED_CHECKED_GIF),
+					mergeResultFile));
+		} finally {
+			if (mergeResultFile != null) {
+				mergeResultFile.close();
+			}
+		}
+	}
+
+	/*
+	 * Copied from org.apache.commons.io.IOUtils
+	 */
+	private boolean contentEquals(InputStream input1, InputStream input2)
+			throws IOException {
+		if (input1 == input2) {
+			return true;
+		}
+		if (!(input1 instanceof BufferedInputStream)) {
+			input1 = new BufferedInputStream(input1);
+		}
+		if (!(input2 instanceof BufferedInputStream)) {
+			input2 = new BufferedInputStream(input2);
+		}
+
+		int ch = input1.read();
+		while (-1 != ch) {
+			final int ch2 = input2.read();
+			if (ch != ch2) {
+				return false;
+			}
+			ch = input1.read();
+		}
+
+		final int ch2 = input2.read();
+		return ch2 == -1;
+	}
+
+	private void assertAddMergeAttributeUnset(String branch, String fileName)
+			throws IllegalStateException, IOException {
+		checkoutBranch(branch);
+
+		try (TreeWalk treeWaklEnableChecked = new TreeWalk(db)) {
+			treeWaklEnableChecked.addTree(new FileTreeIterator(db));
+			treeWaklEnableChecked.setFilter(PathFilter.create(fileName));
+
+			assertTrue(treeWaklEnableChecked.next());
+			Attributes attributes = treeWaklEnableChecked.getAttributes();
+			Attribute mergeAttribute = attributes.get("merge");
+			assertNotNull(mergeAttribute);
+			assertEquals(Attribute.State.UNSET, mergeAttribute.getState());
+		}
+	}
+
+	private void assertAddMergeAttributeSet(String branch, String fileName)
+			throws IllegalStateException, IOException {
+		checkoutBranch(branch);
+
+		try (TreeWalk treeWaklEnableChecked = new TreeWalk(db)) {
+			treeWaklEnableChecked.addTree(new FileTreeIterator(db));
+			treeWaklEnableChecked.setFilter(PathFilter.create(fileName));
+
+			assertTrue(treeWaklEnableChecked.next());
+			Attributes attributes = treeWaklEnableChecked.getAttributes();
+			Attribute mergeAttribute = attributes.get("merge");
+			assertNotNull(mergeAttribute);
+			assertEquals(Attribute.State.SET, mergeAttribute.getState());
+		}
+	}
+
+	private void assertAddMergeAttributeUndefined(String branch,
+			String fileName) throws IllegalStateException, IOException {
+		checkoutBranch(branch);
+
+		try (TreeWalk treeWaklEnableChecked = new TreeWalk(db)) {
+			treeWaklEnableChecked.addTree(new FileTreeIterator(db));
+			treeWaklEnableChecked.setFilter(PathFilter.create(fileName));
+
+			assertTrue(treeWaklEnableChecked.next());
+			Attributes attributes = treeWaklEnableChecked.getAttributes();
+			Attribute mergeAttribute = attributes.get("merge");
+			assertNull(mergeAttribute);
+		}
+	}
+
+	private void assertAddMergeAttributeCustom(String branch, String fileName,
+			String value) throws IllegalStateException, IOException {
+		checkoutBranch(branch);
+
+		try (TreeWalk treeWaklEnableChecked = new TreeWalk(db)) {
+			treeWaklEnableChecked.addTree(new FileTreeIterator(db));
+			treeWaklEnableChecked.setFilter(PathFilter.create(fileName));
+
+			assertTrue(treeWaklEnableChecked.next());
+			Attributes attributes = treeWaklEnableChecked.getAttributes();
+			Attribute mergeAttribute = attributes.get("merge");
+			assertNotNull(mergeAttribute);
+			assertEquals(Attribute.State.CUSTOM, mergeAttribute.getState());
+			assertEquals(value, mergeAttribute.getValue());
+		}
+	}
+
+	private void copy(String resourcePath, String resourceNewName,
+			String pathInRepo) throws IOException {
+		InputStream input = getClass().getResourceAsStream(resourcePath);
+		Files.copy(input, db.getWorkTree().toPath().resolve(pathInRepo)
+				.resolve(resourceNewName));
+	}
+
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/gitrepo/RepoCommandSymlinkTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/gitrepo/RepoCommandSymlinkTest.java
index 12f4dcc..341cc4f 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/gitrepo/RepoCommandSymlinkTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/gitrepo/RepoCommandSymlinkTest.java
@@ -47,6 +47,7 @@
 import static org.junit.Assert.assertTrue;
 
 import java.io.File;
+
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.junit.JGitTestUtil;
 import org.eclipse.jgit.junit.RepositoryTestCase;
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/ignore/CGitIgnoreTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/ignore/CGitIgnoreTest.java
new file mode 100644
index 0000000..ee8191f
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/ignore/CGitIgnoreTest.java
@@ -0,0 +1,271 @@
+/*
+ * Copyright (C) 2017 Thomas Wolf <thomas.wolf@paranor.ch>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.ignore;
+
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.LinkedHashSet;
+import java.util.Set;
+
+import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.StoredConfig;
+import org.eclipse.jgit.treewalk.FileTreeIterator;
+import org.eclipse.jgit.treewalk.TreeWalk;
+import org.eclipse.jgit.treewalk.WorkingTreeIterator;
+import org.eclipse.jgit.treewalk.filter.NotIgnoredFilter;
+import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.util.FS.ExecutionResult;
+import org.eclipse.jgit.util.RawParseUtils;
+import org.eclipse.jgit.util.TemporaryBuffer;
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Tests that verify that the set of ignore files in a repository is the same in
+ * JGit and in C-git.
+ */
+public class CGitIgnoreTest extends RepositoryTestCase {
+
+	@Before
+	public void initRepo() throws IOException {
+		// These tests focus on .gitignore files inside the repository. Because
+		// we run C-git, we must ensure that global or user exclude files cannot
+		// influence the tests. So we set core.excludesFile to an empty file
+		// inside the repository.
+		File fakeUserGitignore = writeTrashFile(".fake_user_gitignore", "");
+		StoredConfig config = db.getConfig();
+		config.setString("core", null, "excludesFile",
+				fakeUserGitignore.getAbsolutePath());
+		// Disable case-insensitivity -- JGit doesn't handle that yet.
+		config.setBoolean("core", null, "ignoreCase", false);
+		config.save();
+	}
+
+	private void createFiles(String... paths) throws IOException {
+		for (String path : paths) {
+			writeTrashFile(path, "x");
+		}
+	}
+
+	private String toString(TemporaryBuffer b) throws IOException {
+		return RawParseUtils.decode(b.toByteArray());
+	}
+
+	private String[] cgitIgnored() throws Exception {
+		FS fs = db.getFS();
+		ProcessBuilder builder = fs.runInShell("git", new String[] { "ls-files",
+				"--ignored", "--exclude-standard", "-o" });
+		builder.directory(db.getWorkTree());
+		builder.environment().put("HOME", fs.userHome().getAbsolutePath());
+		ExecutionResult result = fs.execute(builder,
+				new ByteArrayInputStream(new byte[0]));
+		String errorOut = toString(result.getStderr());
+		assertEquals("External git failed", "exit 0\n",
+				"exit " + result.getRc() + '\n' + errorOut);
+		try (BufferedReader r = new BufferedReader(new InputStreamReader(
+				new BufferedInputStream(result.getStdout().openInputStream()),
+				Constants.CHARSET))) {
+			return r.lines().toArray(String[]::new);
+		}
+	}
+
+	private LinkedHashSet<String> jgitIgnored() throws IOException {
+		// Do a tree walk that does descend into ignored directories and return
+		// a list of all ignored files
+		LinkedHashSet<String> result = new LinkedHashSet<>();
+		try (TreeWalk walk = new TreeWalk(db)) {
+			walk.addTree(new FileTreeIterator(db));
+			walk.setRecursive(true);
+			while (walk.next()) {
+				if (walk.getTree(WorkingTreeIterator.class).isEntryIgnored()) {
+					result.add(walk.getPathString());
+				}
+			}
+		}
+		return result;
+	}
+
+	private void assertNoIgnoredVisited(Set<String> ignored) throws Exception {
+		// Do a recursive tree walk with a NotIgnoredFilter and verify that none
+		// of the files visited is in the ignored set
+		try (TreeWalk walk = new TreeWalk(db)) {
+			walk.addTree(new FileTreeIterator(db));
+			walk.setFilter(new NotIgnoredFilter(0));
+			walk.setRecursive(true);
+			while (walk.next()) {
+				String path = walk.getPathString();
+				assertFalse("File " + path + " is ignored, should not appear",
+						ignored.contains(path));
+			}
+		}
+	}
+
+	private void assertSameAsCGit(String... notIgnored) throws Exception {
+		LinkedHashSet<String> ignored = jgitIgnored();
+		String[] cgit = cgitIgnored();
+		assertArrayEquals(cgit, ignored.toArray());
+		for (String notExcluded : notIgnored) {
+			assertFalse("File " + notExcluded + " should not be ignored",
+					ignored.contains(notExcluded));
+		}
+		assertNoIgnoredVisited(ignored);
+	}
+
+	@Test
+	public void testSimpleIgnored() throws Exception {
+		createFiles("a.txt", "a.tmp", "src/sub/a.txt", "src/a.tmp",
+				"src/a.txt/b.tmp", "ignored/a.tmp", "ignored/not_ignored/a.tmp",
+				"ignored/other/a.tmp");
+		writeTrashFile(".gitignore",
+				"*.txt\n" + "/ignored/*\n" + "!/ignored/not_ignored");
+		assertSameAsCGit("ignored/not_ignored/a.tmp");
+	}
+
+	@Test
+	public void testDirOnlyMatch() throws Exception {
+		createFiles("a.txt", "src/foo/a.txt", "src/a.txt", "foo/a.txt");
+		writeTrashFile(".gitignore", "foo/");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirOnlyMatchDeep() throws Exception {
+		createFiles("a.txt", "src/foo/a.txt", "src/a.txt", "foo/a.txt");
+		writeTrashFile(".gitignore", "**/foo/");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testStarMatchOnSlashNot() throws Exception {
+		createFiles("sub/a.txt", "foo/sext", "foo/s.txt");
+		writeTrashFile(".gitignore", "s*xt");
+		assertSameAsCGit("sub/a.txt");
+	}
+
+	@Test
+	public void testPrefixMatch() throws Exception {
+		createFiles("src/new/foo.txt");
+		writeTrashFile(".gitignore", "src/new");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursive() throws Exception {
+		createFiles("src/new/foo.txt", "foo/src/new/foo.txt", "sub/src/new");
+		writeTrashFile(".gitignore", "**/src/new/");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursiveBacktrack() throws Exception {
+		createFiles("src/new/foo.txt", "src/src/new/foo.txt");
+		writeTrashFile(".gitignore", "**/src/new/");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursiveBacktrack2() throws Exception {
+		createFiles("src/new/foo.txt", "src/src/new/foo.txt");
+		writeTrashFile(".gitignore", "**/**/src/new/");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursiveBacktrack3() throws Exception {
+		createFiles("x/a/a/b/foo.txt");
+		writeTrashFile(".gitignore", "**/*/a/b/");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursiveBacktrack4() throws Exception {
+		createFiles("x/a/a/b/foo.txt", "x/y/z/b/a/b/foo.txt",
+				"x/y/a/a/a/a/b/foo.txt", "x/y/a/a/a/a/b/a/b/foo.txt");
+		writeTrashFile(".gitignore", "**/*/a/b bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testDirectoryMatchSubRecursiveBacktrack5() throws Exception {
+		createFiles("x/a/a/b/foo.txt", "x/y/a/b/a/b/foo.txt");
+		writeTrashFile(".gitignore", "**/*/**/a/b bar\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testUnescapedBracketsInGroup() throws Exception {
+		createFiles("[", "]", "[]", "][", "[[]", "[]]", "[[]]");
+		writeTrashFile(".gitignore", "[[]]\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testEscapedFirstBracketInGroup() throws Exception {
+		createFiles("[", "]", "[]", "][", "[[]", "[]]", "[[]]");
+		writeTrashFile(".gitignore", "[\\[]]\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testEscapedSecondBracketInGroup() throws Exception {
+		createFiles("[", "]", "[]", "][", "[[]", "[]]", "[[]]");
+		writeTrashFile(".gitignore", "[[\\]]\n");
+		assertSameAsCGit();
+	}
+
+	@Test
+	public void testEscapedBothBracketsInGroup() throws Exception {
+		createFiles("[", "]", "[]", "][", "[[]", "[]]", "[[]]");
+		writeTrashFile(".gitignore", "[\\[\\]]\n");
+		assertSameAsCGit();
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/ignore/FastIgnoreRuleTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/ignore/FastIgnoreRuleTest.java
index 1863b80..bcc8f7e 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/ignore/FastIgnoreRuleTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/ignore/FastIgnoreRuleTest.java
@@ -391,7 +391,6 @@ public void testWildmatch() {
 		assertMatched("/**/a/b", "c/d/a/b");
 		assertMatched("/**/**/a/b", "c/d/a/b");
 
-		assertMatched("a/b/**", "a/b");
 		assertMatched("a/b/**", "a/b/c");
 		assertMatched("a/b/**", "a/b/c/d/");
 		assertMatched("a/b/**/**", "a/b/c/d");
@@ -415,6 +414,12 @@ public void testWildmatch() {
 
 	@Test
 	public void testWildmatchDoNotMatch() {
+		assertNotMatched("a/**", "a/");
+		assertNotMatched("a/b/**", "a/b/");
+		assertNotMatched("a/**", "a");
+		assertNotMatched("a/b/**", "a/b");
+		assertNotMatched("a/b/**/", "a/b");
+		assertNotMatched("a/b/**/**", "a/b");
 		assertNotMatched("**/a/b", "a/c/b");
 		assertNotMatched("!/**/*.zip", "c/a/b.zip");
 		assertNotMatched("!**/*.zip", "c/a/b.zip");
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/ignore/internal/StringsTest.java
similarity index 69%
copy from org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
copy to org.eclipse.jgit.test/tst/org/eclipse/jgit/ignore/internal/StringsTest.java
index 98a2a94..468989f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/ignore/internal/StringsTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2011, Google Inc.
+ * Copyright (C) 2017, Thomas Wolf <thomas.wolf@paranor.ch>
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -40,21 +40,34 @@
  * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
  * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
+package org.eclipse.jgit.ignore.internal;
 
-package org.eclipse.jgit.internal.storage.dfs;
+import static org.junit.Assert.assertEquals;
 
-import java.util.concurrent.atomic.AtomicLong;
+import org.junit.Test;
 
-final class DfsPackKey {
-	final int hash;
+public class StringsTest {
 
-	final AtomicLong cachedSize;
+	private void testString(String string, int n, int m) {
+		assertEquals(string, n, Strings.count(string, '/', false));
+		assertEquals(string, m, Strings.count(string, '/', true));
+	}
 
-	DfsPackKey() {
-		// Multiply by 31 here so we can more directly combine with another
-		// value without doing the multiply there.
-		//
-		hash = System.identityHashCode(this) * 31;
-		cachedSize = new AtomicLong();
+	@Test
+	public void testCount() {
+		testString("", 0, 0);
+		testString("/", 1, 0);
+		testString("//", 2, 0);
+		testString("///", 3, 1);
+		testString("////", 4, 2);
+		testString("foo", 0, 0);
+		testString("/foo", 1, 0);
+		testString("foo/", 1, 0);
+		testString("/foo/", 2, 0);
+		testString("foo/bar", 1, 1);
+		testString("/foo/bar/", 3, 1);
+		testString("/foo/bar//", 4, 2);
+		testString("/foo//bar/", 4, 2);
+		testString(" /foo/ ", 2, 2);
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/indexdiff/IndexDiffWithSymlinkTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/indexdiff/IndexDiffWithSymlinkTest.java
index 4f3b601..4228c9d 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/indexdiff/IndexDiffWithSymlinkTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/indexdiff/IndexDiffWithSymlinkTest.java
@@ -142,7 +142,11 @@ private File restoreGitRepo(InputStream in, File testDir, String name)
 		String[] cmd = { "/bin/sh", "./" + name + ".sh" };
 		int exitCode;
 		String stdErr;
-		Process process = Runtime.getRuntime().exec(cmd, null, testDir);
+		ProcessBuilder builder = new ProcessBuilder(cmd);
+		builder.environment().put("HOME",
+				FS.DETECTED.userHome().getAbsolutePath());
+		builder.directory(testDir);
+		Process process = builder.start();
 		try (InputStream stdOutStream = process.getInputStream();
 				InputStream stdErrStream = process.getErrorStream();
 				OutputStream stdInStream = process.getOutputStream()) {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DeltaBaseCacheTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DeltaBaseCacheTest.java
index 5bef9fa..32d711f 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DeltaBaseCacheTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DeltaBaseCacheTest.java
@@ -57,13 +57,14 @@
 public class DeltaBaseCacheTest {
 	private static final int SZ = 512;
 
-	private DfsPackKey key;
+	private DfsStreamKey key;
 	private DeltaBaseCache cache;
 	private TestRng rng;
 
 	@Before
 	public void setUp() {
-		key = new DfsPackKey();
+		DfsRepositoryDescription repo = new DfsRepositoryDescription("test");
+		key = DfsStreamKey.of(repo, "test.key");
 		cache = new DeltaBaseCache(SZ);
 		rng = new TestRng(getClass().getSimpleName());
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsBlockCacheTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsBlockCacheTest.java
new file mode 100644
index 0000000..2e3ee45
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsBlockCacheTest.java
@@ -0,0 +1,144 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.dfs;
+
+import static org.eclipse.jgit.lib.Constants.OBJ_BLOB;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import org.eclipse.jgit.junit.TestRng;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectInserter;
+import org.eclipse.jgit.lib.ObjectReader;
+import org.junit.Before;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TestName;
+
+public class DfsBlockCacheTest {
+	@Rule
+	public TestName testName = new TestName();
+	private TestRng rng;
+	private DfsBlockCache cache;
+
+	@Before
+	public void setUp() {
+		rng = new TestRng(testName.getMethodName());
+		resetCache();
+	}
+
+	@SuppressWarnings("resource")
+	@Test
+	public void streamKeyReusesBlocks() throws Exception {
+		DfsRepositoryDescription repo = new DfsRepositoryDescription("test");
+		InMemoryRepository r1 = new InMemoryRepository(repo);
+		byte[] content = rng.nextBytes(424242);
+		ObjectId id;
+		try (ObjectInserter ins = r1.newObjectInserter()) {
+			id = ins.insert(OBJ_BLOB, content);
+			ins.flush();
+		}
+
+		long oldSize = cache.getCurrentSize();
+		assertTrue(oldSize > 2000);
+		assertEquals(0, cache.getHitCount());
+
+		List<DfsPackDescription> packs = r1.getObjectDatabase().listPacks();
+		InMemoryRepository r2 = new InMemoryRepository(repo);
+		r2.getObjectDatabase().commitPack(packs, Collections.emptyList());
+		try (ObjectReader rdr = r2.newObjectReader()) {
+			byte[] actual = rdr.open(id, OBJ_BLOB).getBytes();
+			assertTrue(Arrays.equals(content, actual));
+		}
+		assertEquals(0, cache.getMissCount());
+		assertEquals(oldSize, cache.getCurrentSize());
+	}
+
+	@SuppressWarnings("resource")
+	@Test
+	public void weirdBlockSize() throws Exception {
+		DfsRepositoryDescription repo = new DfsRepositoryDescription("test");
+		InMemoryRepository r1 = new InMemoryRepository(repo);
+
+		byte[] content1 = rng.nextBytes(4);
+		byte[] content2 = rng.nextBytes(424242);
+		ObjectId id1;
+		ObjectId id2;
+		try (ObjectInserter ins = r1.newObjectInserter()) {
+			id1 = ins.insert(OBJ_BLOB, content1);
+			id2 = ins.insert(OBJ_BLOB, content2);
+			ins.flush();
+		}
+
+		resetCache();
+		List<DfsPackDescription> packs = r1.getObjectDatabase().listPacks();
+
+		InMemoryRepository r2 = new InMemoryRepository(repo);
+		r2.getObjectDatabase().setReadableChannelBlockSizeForTest(500);
+		r2.getObjectDatabase().commitPack(packs, Collections.emptyList());
+		try (ObjectReader rdr = r2.newObjectReader()) {
+			byte[] actual = rdr.open(id1, OBJ_BLOB).getBytes();
+			assertTrue(Arrays.equals(content1, actual));
+		}
+
+		InMemoryRepository r3 = new InMemoryRepository(repo);
+		r3.getObjectDatabase().setReadableChannelBlockSizeForTest(500);
+		r3.getObjectDatabase().commitPack(packs, Collections.emptyList());
+		try (ObjectReader rdr = r3.newObjectReader()) {
+			byte[] actual = rdr.open(id2, OBJ_BLOB).getBytes();
+			assertTrue(Arrays.equals(content2, actual));
+		}
+	}
+
+	private void resetCache() {
+		DfsBlockCache.reconfigure(new DfsBlockCacheConfig()
+				.setBlockSize(512)
+				.setBlockLimit(1 << 20));
+		cache = DfsBlockCache.getInstance();
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsFsckTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsFsckTest.java
new file mode 100644
index 0000000..804d744
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsFsckTest.java
@@ -0,0 +1,269 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.dfs;
+
+import static org.eclipse.jgit.junit.JGitTestUtil.concat;
+import static org.eclipse.jgit.lib.Constants.OBJECT_ID_LENGTH;
+import static org.eclipse.jgit.lib.Constants.encodeASCII;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+
+import org.eclipse.jgit.internal.fsck.FsckError;
+import org.eclipse.jgit.internal.fsck.FsckError.CorruptObject;
+import org.eclipse.jgit.junit.TestRepository;
+import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.ObjectChecker.ErrorType;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectInserter;
+import org.eclipse.jgit.revwalk.RevCommit;
+import org.junit.Before;
+import org.junit.Test;
+
+public class DfsFsckTest {
+	private TestRepository<InMemoryRepository> git;
+
+	private InMemoryRepository repo;
+
+	private ObjectInserter ins;
+
+	@Before
+	public void setUp() throws IOException {
+		DfsRepositoryDescription desc = new DfsRepositoryDescription("test");
+		git = new TestRepository<>(new InMemoryRepository(desc));
+		repo = git.getRepository();
+		ins = repo.newObjectInserter();
+	}
+
+	@Test
+	public void testHealthyRepo() throws Exception {
+		RevCommit commit0 = git.commit().message("0").create();
+		RevCommit commit1 = git.commit().message("1").parent(commit0).create();
+		git.update("master", commit1);
+
+		DfsFsck fsck = new DfsFsck(repo);
+		FsckError errors = fsck.check(null);
+
+		assertEquals(errors.getCorruptObjects().size(), 0);
+		assertEquals(errors.getMissingObjects().size(), 0);
+		assertEquals(errors.getCorruptIndices().size(), 0);
+	}
+
+	@Test
+	public void testCommitWithCorruptAuthor() throws Exception {
+		StringBuilder b = new StringBuilder();
+		b.append("tree be9bfa841874ccc9f2ef7c48d0c76226f89b7189\n");
+		b.append("author b <b@c> <b@c> 0 +0000\n");
+		b.append("committer <> 0 +0000\n");
+		byte[] data = encodeASCII(b.toString());
+		ObjectId id = ins.insert(Constants.OBJ_COMMIT, data);
+		ins.flush();
+
+		DfsFsck fsck = new DfsFsck(repo);
+		FsckError errors = fsck.check(null);
+
+		assertEquals(errors.getCorruptObjects().size(), 1);
+		CorruptObject o = errors.getCorruptObjects().iterator().next();
+		assertTrue(o.getId().equals(id));
+		assertEquals(o.getErrorType(), ErrorType.BAD_DATE);
+	}
+
+	@Test
+	public void testCommitWithoutTree() throws Exception {
+		StringBuilder b = new StringBuilder();
+		b.append("parent ");
+		b.append("be9bfa841874ccc9f2ef7c48d0c76226f89b7189");
+		b.append('\n');
+		byte[] data = encodeASCII(b.toString());
+		ObjectId id = ins.insert(Constants.OBJ_COMMIT, data);
+		ins.flush();
+
+		DfsFsck fsck = new DfsFsck(repo);
+		FsckError errors = fsck.check(null);
+
+		assertEquals(errors.getCorruptObjects().size(), 1);
+		CorruptObject o = errors.getCorruptObjects().iterator().next();
+		assertTrue(o.getId().equals(id));
+		assertEquals(o.getErrorType(), ErrorType.MISSING_TREE);
+	}
+
+	@Test
+	public void testTagWithoutObject() throws Exception {
+		StringBuilder b = new StringBuilder();
+		b.append("type commit\n");
+		b.append("tag test-tag\n");
+		b.append("tagger A. U. Thor <author@localhost> 1 +0000\n");
+		byte[] data = encodeASCII(b.toString());
+		ObjectId id = ins.insert(Constants.OBJ_TAG, data);
+		ins.flush();
+
+		DfsFsck fsck = new DfsFsck(repo);
+		FsckError errors = fsck.check(null);
+
+		assertEquals(errors.getCorruptObjects().size(), 1);
+		CorruptObject o = errors.getCorruptObjects().iterator().next();
+		assertTrue(o.getId().equals(id));
+		assertEquals(o.getErrorType(), ErrorType.MISSING_OBJECT);
+	}
+
+	@Test
+	public void testTreeWithNullSha() throws Exception {
+		byte[] data = concat(encodeASCII("100644 A"), new byte[] { '\0' },
+				new byte[OBJECT_ID_LENGTH]);
+		ObjectId id = ins.insert(Constants.OBJ_TREE, data);
+		ins.flush();
+
+		DfsFsck fsck = new DfsFsck(repo);
+		FsckError errors = fsck.check(null);
+
+		assertEquals(errors.getCorruptObjects().size(), 1);
+		CorruptObject o = errors.getCorruptObjects().iterator().next();
+		assertTrue(o.getId().equals(id));
+		assertEquals(o.getErrorType(), ErrorType.NULL_SHA1);
+	}
+
+	@Test
+	public void testMultipleInvalidObjects() throws Exception {
+		StringBuilder b = new StringBuilder();
+		b.append("tree ");
+		b.append("be9bfa841874ccc9f2ef7c48d0c76226f89b7189");
+		b.append('\n');
+		b.append("parent ");
+		b.append("\n");
+		byte[] data = encodeASCII(b.toString());
+		ObjectId id1 = ins.insert(Constants.OBJ_COMMIT, data);
+
+		b = new StringBuilder();
+		b.append("100644");
+		data = encodeASCII(b.toString());
+		ObjectId id2 = ins.insert(Constants.OBJ_TREE, data);
+
+		ins.flush();
+
+		DfsFsck fsck = new DfsFsck(repo);
+		FsckError errors = fsck.check(null);
+
+		assertEquals(errors.getCorruptObjects().size(), 2);
+		for (CorruptObject o : errors.getCorruptObjects()) {
+			if (o.getId().equals(id1)) {
+				assertEquals(o.getErrorType(), ErrorType.BAD_PARENT_SHA1);
+			} else if (o.getId().equals(id2)) {
+				assertNull(o.getErrorType());
+			} else {
+				fail();
+			}
+		}
+	}
+
+	@Test
+	public void testValidConnectivity() throws Exception {
+		ObjectId blobId = ins
+				.insert(Constants.OBJ_BLOB, Constants.encode("foo"));
+
+		byte[] blobIdBytes = new byte[OBJECT_ID_LENGTH];
+		blobId.copyRawTo(blobIdBytes, 0);
+		byte[] data = concat(encodeASCII("100644 regular-file\0"), blobIdBytes);
+		ObjectId treeId = ins.insert(Constants.OBJ_TREE, data);
+		ins.flush();
+
+		RevCommit commit = git.commit().message("0").setTopLevelTree(treeId)
+				.create();
+
+		git.update("master", commit);
+
+		DfsFsck fsck = new DfsFsck(repo);
+		FsckError errors = fsck.check(null);
+		assertEquals(errors.getMissingObjects().size(), 0);
+	}
+
+	@Test
+	public void testMissingObject() throws Exception {
+		ObjectId blobId = ObjectId
+				.fromString("19102815663d23f8b75a47e7a01965dcdc96468c");
+		byte[] blobIdBytes = new byte[OBJECT_ID_LENGTH];
+		blobId.copyRawTo(blobIdBytes, 0);
+		byte[] data = concat(encodeASCII("100644 regular-file\0"), blobIdBytes);
+		ObjectId treeId = ins.insert(Constants.OBJ_TREE, data);
+		ins.flush();
+
+		RevCommit commit = git.commit().message("0").setTopLevelTree(treeId)
+				.create();
+
+		git.update("master", commit);
+
+		DfsFsck fsck = new DfsFsck(repo);
+		FsckError errors = fsck.check(null);
+		assertEquals(errors.getMissingObjects().size(), 1);
+		assertEquals(errors.getMissingObjects().iterator().next(), blobId);
+	}
+
+	@Test
+	public void testNonCommitHead() throws Exception {
+		RevCommit commit0 = git.commit().message("0").create();
+		StringBuilder b = new StringBuilder();
+		b.append("object ");
+		b.append(commit0.getName());
+		b.append('\n');
+		b.append("type commit\n");
+		b.append("tag test-tag\n");
+		b.append("tagger A. U. Thor <author@localhost> 1 +0000\n");
+
+		byte[] data = encodeASCII(b.toString());
+		ObjectId tagId = ins.insert(Constants.OBJ_TAG, data);
+		ins.flush();
+
+		git.update("master", tagId);
+
+		DfsFsck fsck = new DfsFsck(repo);
+		FsckError errors = fsck.check(null);
+		assertEquals(errors.getCorruptObjects().size(), 0);
+		assertEquals(errors.getNonCommitHeads().size(), 1);
+		assertEquals(errors.getNonCommitHeads().iterator().next(),
+				"refs/heads/master");
+	}
+
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java
index 17c1835..55a5f72 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java
@@ -5,6 +5,7 @@
 import static org.eclipse.jgit.internal.storage.dfs.DfsObjDatabase.PackSource.INSERT;
 import static org.eclipse.jgit.internal.storage.dfs.DfsObjDatabase.PackSource.UNREACHABLE_GARBAGE;
 import static org.eclipse.jgit.internal.storage.pack.PackExt.PACK;
+import static org.eclipse.jgit.internal.storage.pack.PackExt.REFTABLE;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
@@ -13,24 +14,35 @@
 import static org.junit.Assert.fail;
 
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 import java.util.Collections;
 import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.internal.storage.dfs.DfsObjDatabase.PackSource;
+import org.eclipse.jgit.internal.storage.reftable.RefCursor;
+import org.eclipse.jgit.internal.storage.reftable.ReftableConfig;
+import org.eclipse.jgit.internal.storage.reftable.ReftableReader;
+import org.eclipse.jgit.internal.storage.reftable.ReftableWriter;
 import org.eclipse.jgit.junit.MockSystemReader;
 import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.lib.AnyObjectId;
+import org.eclipse.jgit.lib.BatchRefUpdate;
+import org.eclipse.jgit.lib.NullProgressMonitor;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectIdRef;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.RevBlob;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.storage.pack.PackConfig;
+import org.eclipse.jgit.transport.ReceiveCommand;
 import org.eclipse.jgit.util.SystemReader;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 
+/** Tests for pack creation and garbage expiration. */
 public class DfsGarbageCollectorTest {
 	private TestRepository<InMemoryRepository> git;
 	private InMemoryRepository repo;
@@ -632,6 +644,205 @@ public void testEstimateUnreachableGarbagePackSize() throws Exception {
 		}
 	}
 
+	@Test
+	public void testSinglePackForAllRefs() throws Exception {
+		RevCommit commit0 = commit().message("0").create();
+		git.update("head", commit0);
+		RevCommit commit1 = commit().message("1").parent(commit0).create();
+		git.update("refs/notes/note1", commit1);
+
+		DfsGarbageCollector gc = new DfsGarbageCollector(repo);
+		gc.setGarbageTtl(0, TimeUnit.MILLISECONDS);
+		gc.getPackConfig().setSinglePack(true);
+		run(gc);
+		assertEquals(1, odb.getPacks().length);
+
+		gc = new DfsGarbageCollector(repo);
+		gc.setGarbageTtl(0, TimeUnit.MILLISECONDS);
+		gc.getPackConfig().setSinglePack(false);
+		run(gc);
+		assertEquals(2, odb.getPacks().length);
+	}
+
+	@SuppressWarnings("boxing")
+	@Test
+	public void producesNewReftable() throws Exception {
+		String master = "refs/heads/master";
+		RevCommit commit0 = commit().message("0").create();
+		RevCommit commit1 = commit().message("1").parent(commit0).create();
+
+		BatchRefUpdate bru = git.getRepository().getRefDatabase()
+				.newBatchUpdate();
+		bru.addCommand(new ReceiveCommand(ObjectId.zeroId(), commit1, master));
+		for (int i = 1; i <= 5100; i++) {
+			bru.addCommand(new ReceiveCommand(ObjectId.zeroId(), commit0,
+					String.format("refs/pulls/%04d", i)));
+		}
+		try (RevWalk rw = new RevWalk(git.getRepository())) {
+			bru.execute(rw, NullProgressMonitor.INSTANCE);
+		}
+
+		DfsGarbageCollector gc = new DfsGarbageCollector(repo);
+		gc.setReftableConfig(new ReftableConfig());
+		run(gc);
+
+		// Single GC pack present with all objects.
+		assertEquals(1, odb.getPacks().length);
+		DfsPackFile pack = odb.getPacks()[0];
+		DfsPackDescription desc = pack.getPackDescription();
+		assertEquals(GC, desc.getPackSource());
+		assertTrue("commit0 in pack", isObjectInPack(commit0, pack));
+		assertTrue("commit1 in pack", isObjectInPack(commit1, pack));
+
+		// Sibling REFTABLE is also present.
+		assertTrue(desc.hasFileExt(REFTABLE));
+		ReftableWriter.Stats stats = desc.getReftableStats();
+		assertNotNull(stats);
+		assertTrue(stats.totalBytes() > 0);
+		assertEquals(5101, stats.refCount());
+		assertEquals(1, stats.minUpdateIndex());
+		assertEquals(1, stats.maxUpdateIndex());
+
+		DfsReftable table = new DfsReftable(DfsBlockCache.getInstance(), desc);
+		try (DfsReader ctx = odb.newReader();
+				ReftableReader rr = table.open(ctx);
+				RefCursor rc = rr.seekRef("refs/pulls/5100")) {
+			assertTrue(rc.next());
+			assertEquals(commit0, rc.getRef().getObjectId());
+			assertFalse(rc.next());
+		}
+	}
+
+	@Test
+	public void leavesNonGcReftablesIfNotConfigured() throws Exception {
+		String master = "refs/heads/master";
+		RevCommit commit0 = commit().message("0").create();
+		RevCommit commit1 = commit().message("1").parent(commit0).create();
+		git.update(master, commit1);
+
+		DfsPackDescription t1 = odb.newPack(INSERT);
+		try (DfsOutputStream out = odb.writeFile(t1, REFTABLE)) {
+			out.write("ignored".getBytes(StandardCharsets.UTF_8));
+			t1.addFileExt(REFTABLE);
+		}
+		odb.commitPack(Collections.singleton(t1), null);
+
+		DfsGarbageCollector gc = new DfsGarbageCollector(repo);
+		gc.setReftableConfig(null);
+		run(gc);
+
+		// Single GC pack present with all objects.
+		assertEquals(1, odb.getPacks().length);
+		DfsPackFile pack = odb.getPacks()[0];
+		DfsPackDescription desc = pack.getPackDescription();
+		assertEquals(GC, desc.getPackSource());
+		assertTrue("commit0 in pack", isObjectInPack(commit0, pack));
+		assertTrue("commit1 in pack", isObjectInPack(commit1, pack));
+
+		// Only INSERT REFTABLE above is present.
+		DfsReftable[] tables = odb.getReftables();
+		assertEquals(1, tables.length);
+		assertEquals(t1, tables[0].getPackDescription());
+	}
+
+	@Test
+	public void prunesNonGcReftables() throws Exception {
+		String master = "refs/heads/master";
+		RevCommit commit0 = commit().message("0").create();
+		RevCommit commit1 = commit().message("1").parent(commit0).create();
+		git.update(master, commit1);
+
+		DfsPackDescription t1 = odb.newPack(INSERT);
+		try (DfsOutputStream out = odb.writeFile(t1, REFTABLE)) {
+			out.write("ignored".getBytes(StandardCharsets.UTF_8));
+			t1.addFileExt(REFTABLE);
+		}
+		odb.commitPack(Collections.singleton(t1), null);
+		odb.clearCache();
+
+		DfsGarbageCollector gc = new DfsGarbageCollector(repo);
+		gc.setReftableConfig(new ReftableConfig());
+		run(gc);
+
+		// Single GC pack present with all objects.
+		assertEquals(1, odb.getPacks().length);
+		DfsPackFile pack = odb.getPacks()[0];
+		DfsPackDescription desc = pack.getPackDescription();
+		assertEquals(GC, desc.getPackSource());
+		assertTrue("commit0 in pack", isObjectInPack(commit0, pack));
+		assertTrue("commit1 in pack", isObjectInPack(commit1, pack));
+
+		// Only sibling GC REFTABLE is present.
+		DfsReftable[] tables = odb.getReftables();
+		assertEquals(1, tables.length);
+		assertEquals(desc, tables[0].getPackDescription());
+		assertTrue(desc.hasFileExt(REFTABLE));
+	}
+
+	@Test
+	public void compactsReftables() throws Exception {
+		String master = "refs/heads/master";
+		RevCommit commit0 = commit().message("0").create();
+		RevCommit commit1 = commit().message("1").parent(commit0).create();
+		git.update(master, commit1);
+
+		DfsGarbageCollector gc = new DfsGarbageCollector(repo);
+		gc.setReftableConfig(new ReftableConfig());
+		run(gc);
+
+		DfsPackDescription t1 = odb.newPack(INSERT);
+		Ref next = new ObjectIdRef.PeeledNonTag(Ref.Storage.LOOSE,
+				"refs/heads/next", commit0.copy());
+		try (DfsOutputStream out = odb.writeFile(t1, REFTABLE)) {
+			ReftableWriter w = new ReftableWriter();
+			w.setMinUpdateIndex(42);
+			w.setMaxUpdateIndex(42);
+			w.begin(out);
+			w.sortAndWriteRefs(Collections.singleton(next));
+			w.finish();
+			t1.addFileExt(REFTABLE);
+			t1.setReftableStats(w.getStats());
+		}
+		odb.commitPack(Collections.singleton(t1), null);
+
+		gc = new DfsGarbageCollector(repo);
+		gc.setReftableConfig(new ReftableConfig());
+		run(gc);
+
+		// Single GC pack present with all objects.
+		assertEquals(1, odb.getPacks().length);
+		DfsPackFile pack = odb.getPacks()[0];
+		DfsPackDescription desc = pack.getPackDescription();
+		assertEquals(GC, desc.getPackSource());
+		assertTrue("commit0 in pack", isObjectInPack(commit0, pack));
+		assertTrue("commit1 in pack", isObjectInPack(commit1, pack));
+
+		// Only sibling GC REFTABLE is present.
+		DfsReftable[] tables = odb.getReftables();
+		assertEquals(1, tables.length);
+		assertEquals(desc, tables[0].getPackDescription());
+		assertTrue(desc.hasFileExt(REFTABLE));
+
+		// GC reftable contains the compaction.
+		DfsReftable table = new DfsReftable(DfsBlockCache.getInstance(), desc);
+		try (DfsReader ctx = odb.newReader();
+				ReftableReader rr = table.open(ctx);
+				RefCursor rc = rr.allRefs()) {
+			assertEquals(1, rr.minUpdateIndex());
+			assertEquals(42, rr.maxUpdateIndex());
+
+			assertTrue(rc.next());
+			assertEquals(master, rc.getRef().getName());
+			assertEquals(commit1, rc.getRef().getObjectId());
+
+			assertTrue(rc.next());
+			assertEquals(next.getName(), rc.getRef().getName());
+			assertEquals(commit0, rc.getRef().getObjectId());
+
+			assertFalse(rc.next());
+		}
+	}
+
 	private TestRepository<InMemoryRepository>.CommitBuilder commit() {
 		return git.commit();
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/BatchRefUpdateTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/BatchRefUpdateTest.java
new file mode 100644
index 0000000..3c4b8cf
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/BatchRefUpdateTest.java
@@ -0,0 +1,1054 @@
+/*
+ * Copyright (C) 2017 Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.file;
+
+import static java.util.concurrent.TimeUnit.NANOSECONDS;
+import static java.util.concurrent.TimeUnit.SECONDS;
+import static org.eclipse.jgit.internal.storage.file.BatchRefUpdateTest.Result.LOCK_FAILURE;
+import static org.eclipse.jgit.internal.storage.file.BatchRefUpdateTest.Result.OK;
+import static org.eclipse.jgit.internal.storage.file.BatchRefUpdateTest.Result.REJECTED_MISSING_OBJECT;
+import static org.eclipse.jgit.internal.storage.file.BatchRefUpdateTest.Result.REJECTED_NONFASTFORWARD;
+import static org.eclipse.jgit.internal.storage.file.BatchRefUpdateTest.Result.TRANSACTION_ABORTED;
+import static org.eclipse.jgit.lib.ObjectId.zeroId;
+import static org.eclipse.jgit.transport.ReceiveCommand.Type.CREATE;
+import static org.eclipse.jgit.transport.ReceiveCommand.Type.DELETE;
+import static org.eclipse.jgit.transport.ReceiveCommand.Type.UPDATE;
+import static org.eclipse.jgit.transport.ReceiveCommand.Type.UPDATE_NONFASTFORWARD;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assume.assumeTrue;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.locks.ReentrantLock;
+import java.util.function.Predicate;
+
+import org.eclipse.jgit.events.ListenerHandle;
+import org.eclipse.jgit.events.RefsChangedListener;
+import org.eclipse.jgit.junit.LocalDiskRepositoryTestCase;
+import org.eclipse.jgit.junit.StrictWorkMonitor;
+import org.eclipse.jgit.junit.TestRepository;
+import org.eclipse.jgit.lib.AnyObjectId;
+import org.eclipse.jgit.lib.BatchRefUpdate;
+import org.eclipse.jgit.lib.CheckoutEntry;
+import org.eclipse.jgit.lib.ConfigConstants;
+import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.NullProgressMonitor;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.PersonIdent;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.RefDatabase;
+import org.eclipse.jgit.lib.RefUpdate;
+import org.eclipse.jgit.lib.ReflogEntry;
+import org.eclipse.jgit.lib.ReflogReader;
+import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.StoredConfig;
+import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.revwalk.RevWalk;
+import org.eclipse.jgit.transport.ReceiveCommand;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameter;
+import org.junit.runners.Parameterized.Parameters;
+
+@SuppressWarnings("boxing")
+@RunWith(Parameterized.class)
+public class BatchRefUpdateTest extends LocalDiskRepositoryTestCase {
+	@Parameter
+	public boolean atomic;
+
+	@Parameters(name = "atomic={0}")
+	public static Collection<Object[]> data() {
+		return Arrays.asList(new Object[][]{ {Boolean.FALSE}, {Boolean.TRUE} });
+	}
+
+	private Repository diskRepo;
+	private TestRepository<Repository> repo;
+	private RefDirectory refdir;
+	private RevCommit A;
+	private RevCommit B;
+
+	/**
+	 * When asserting the number of RefsChangedEvents you must account for one
+	 * additional event due to the initial ref setup via a number of calls to
+	 * {@link #writeLooseRef(String, AnyObjectId)} (will be fired in execute()
+	 * when it is detected that the on-disk loose refs have changed), or for one
+	 * additional event per {@link #writeRef(String, AnyObjectId)}.
+	 */
+	private int refsChangedEvents;
+
+	private ListenerHandle handle;
+
+	private RefsChangedListener refsChangedListener = event -> {
+		refsChangedEvents++;
+	};
+
+	@Override
+	@Before
+	public void setUp() throws Exception {
+		super.setUp();
+
+		diskRepo = createBareRepository();
+		setLogAllRefUpdates(true);
+
+		refdir = (RefDirectory) diskRepo.getRefDatabase();
+		refdir.setRetrySleepMs(Arrays.asList(0, 0));
+
+		repo = new TestRepository<>(diskRepo);
+		A = repo.commit().create();
+		B = repo.commit(repo.getRevWalk().parseCommit(A));
+		refsChangedEvents = 0;
+		handle = diskRepo.getListenerList()
+				.addRefsChangedListener(refsChangedListener);
+	}
+
+	@After
+	public void removeListener() {
+		handle.remove();
+		refsChangedEvents = 0;
+	}
+
+	@Test
+	public void simpleNoForce() throws IOException {
+		writeLooseRef("refs/heads/master", A);
+		writeLooseRef("refs/heads/masters", B);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(B, A, "refs/heads/masters", UPDATE_NONFASTFORWARD));
+		execute(newBatchUpdate(cmds));
+
+		if (atomic) {
+			assertResults(cmds, TRANSACTION_ABORTED, REJECTED_NONFASTFORWARD);
+			assertRefs(
+					"refs/heads/master", A,
+					"refs/heads/masters", B);
+			assertEquals(1, refsChangedEvents);
+		} else {
+			assertResults(cmds, OK, REJECTED_NONFASTFORWARD);
+			assertRefs(
+					"refs/heads/master", B,
+					"refs/heads/masters", B);
+			assertEquals(2, refsChangedEvents);
+		}
+	}
+
+	@Test
+	public void simpleForce() throws IOException {
+		writeLooseRef("refs/heads/master", A);
+		writeLooseRef("refs/heads/masters", B);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(B, A, "refs/heads/masters", UPDATE_NONFASTFORWARD));
+		execute(newBatchUpdate(cmds).setAllowNonFastForwards(true));
+
+		assertResults(cmds, OK, OK);
+		assertRefs(
+				"refs/heads/master", B,
+				"refs/heads/masters", A);
+		assertEquals(atomic ? 2 : 3, refsChangedEvents);
+	}
+
+	@Test
+	public void nonFastForwardDoesNotDoExpensiveMergeCheck() throws IOException {
+		writeLooseRef("refs/heads/master", B);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(B, A, "refs/heads/master", UPDATE_NONFASTFORWARD));
+		try (RevWalk rw = new RevWalk(diskRepo) {
+					@Override
+					public boolean isMergedInto(RevCommit base, RevCommit tip) {
+						throw new AssertionError("isMergedInto() should not be called");
+					}
+				}) {
+			newBatchUpdate(cmds)
+					.setAllowNonFastForwards(true)
+					.execute(rw, new StrictWorkMonitor());
+		}
+
+		assertResults(cmds, OK);
+		assertRefs("refs/heads/master", A);
+		assertEquals(2, refsChangedEvents);
+	}
+
+	@Test
+	public void fileDirectoryConflict() throws IOException {
+		writeLooseRef("refs/heads/master", A);
+		writeLooseRef("refs/heads/masters", B);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), A, "refs/heads/master/x", CREATE),
+				new ReceiveCommand(zeroId(), A, "refs/heads", CREATE));
+		execute(newBatchUpdate(cmds).setAllowNonFastForwards(true), false);
+
+		if (atomic) {
+			// Atomic update sees that master and master/x are conflicting, then marks
+			// the first one in the list as LOCK_FAILURE and aborts the rest.
+			assertResults(cmds,
+					LOCK_FAILURE, TRANSACTION_ABORTED, TRANSACTION_ABORTED);
+			assertRefs(
+					"refs/heads/master", A,
+					"refs/heads/masters", B);
+			assertEquals(1, refsChangedEvents);
+		} else {
+			// Non-atomic updates are applied in order: master succeeds, then master/x
+			// fails due to conflict.
+			assertResults(cmds, OK, LOCK_FAILURE, LOCK_FAILURE);
+			assertRefs(
+					"refs/heads/master", B,
+					"refs/heads/masters", B);
+			assertEquals(2, refsChangedEvents);
+		}
+	}
+
+	@Test
+	public void conflictThanksToDelete() throws IOException {
+		writeLooseRef("refs/heads/master", A);
+		writeLooseRef("refs/heads/masters", B);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), A, "refs/heads/masters/x", CREATE),
+				new ReceiveCommand(B, zeroId(), "refs/heads/masters", DELETE));
+		execute(newBatchUpdate(cmds).setAllowNonFastForwards(true));
+
+		assertResults(cmds, OK, OK, OK);
+		assertRefs(
+				"refs/heads/master", B,
+				"refs/heads/masters/x", A);
+		if (atomic) {
+			assertEquals(2, refsChangedEvents);
+		} else {
+			// The non-atomic case actually produces 5 events, but that's an
+			// implementation detail. We expect at least 4 events, one for the
+			// initial read due to writeLooseRef(), and then one for each
+			// successful ref update.
+			assertTrue(refsChangedEvents >= 4);
+		}
+	}
+
+	@Test
+	public void updateToMissingObject() throws IOException {
+		writeLooseRef("refs/heads/master", A);
+
+		ObjectId bad =
+				ObjectId.fromString("deadbeefdeadbeefdeadbeefdeadbeefdeadbeef");
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, bad, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), B, "refs/heads/foo2", CREATE));
+		execute(newBatchUpdate(cmds).setAllowNonFastForwards(true), false);
+
+		if (atomic) {
+			assertResults(cmds, REJECTED_MISSING_OBJECT, TRANSACTION_ABORTED);
+			assertRefs("refs/heads/master", A);
+			assertEquals(1, refsChangedEvents);
+		} else {
+			assertResults(cmds, REJECTED_MISSING_OBJECT, OK);
+			assertRefs(
+					"refs/heads/master", A,
+					"refs/heads/foo2", B);
+			assertEquals(2, refsChangedEvents);
+		}
+	}
+
+	@Test
+	public void addMissingObject() throws IOException {
+		writeLooseRef("refs/heads/master", A);
+
+		ObjectId bad =
+				ObjectId.fromString("deadbeefdeadbeefdeadbeefdeadbeefdeadbeef");
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), bad, "refs/heads/foo2", CREATE));
+		execute(newBatchUpdate(cmds).setAllowNonFastForwards(true), false);
+
+		if (atomic) {
+			assertResults(cmds, TRANSACTION_ABORTED, REJECTED_MISSING_OBJECT);
+			assertRefs("refs/heads/master", A);
+			assertEquals(1, refsChangedEvents);
+		} else {
+			assertResults(cmds, OK, REJECTED_MISSING_OBJECT);
+			assertRefs("refs/heads/master", B);
+			assertEquals(2, refsChangedEvents);
+		}
+	}
+
+	@Test
+	public void oneNonExistentRef() throws IOException {
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/foo1", UPDATE),
+				new ReceiveCommand(zeroId(), B, "refs/heads/foo2", CREATE));
+		execute(newBatchUpdate(cmds).setAllowNonFastForwards(true));
+
+		if (atomic) {
+			assertResults(cmds, LOCK_FAILURE, TRANSACTION_ABORTED);
+			assertRefs();
+			assertEquals(0, refsChangedEvents);
+		} else {
+			assertResults(cmds, LOCK_FAILURE, OK);
+			assertRefs("refs/heads/foo2", B);
+			assertEquals(1, refsChangedEvents);
+		}
+	}
+
+	@Test
+	public void oneRefWrongOldValue() throws IOException {
+		writeLooseRef("refs/heads/master", A);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(B, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), B, "refs/heads/foo2", CREATE));
+		execute(newBatchUpdate(cmds).setAllowNonFastForwards(true));
+
+		if (atomic) {
+			assertResults(cmds, LOCK_FAILURE, TRANSACTION_ABORTED);
+			assertRefs("refs/heads/master", A);
+			assertEquals(1, refsChangedEvents);
+		} else {
+			assertResults(cmds, LOCK_FAILURE, OK);
+			assertRefs(
+					"refs/heads/master", A,
+					"refs/heads/foo2", B);
+			assertEquals(2, refsChangedEvents);
+		}
+	}
+
+	@Test
+	public void nonExistentRef() throws IOException {
+		writeLooseRef("refs/heads/master", A);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(A, zeroId(), "refs/heads/foo2", DELETE));
+		execute(newBatchUpdate(cmds).setAllowNonFastForwards(true));
+
+		if (atomic) {
+			assertResults(cmds, TRANSACTION_ABORTED, LOCK_FAILURE);
+			assertRefs("refs/heads/master", A);
+			assertEquals(1, refsChangedEvents);
+		} else {
+			assertResults(cmds, OK, LOCK_FAILURE);
+			assertRefs("refs/heads/master", B);
+			assertEquals(2, refsChangedEvents);
+		}
+	}
+
+	@Test
+	public void noRefLog() throws IOException {
+		writeRef("refs/heads/master", A);
+
+		Map<String, ReflogEntry> oldLogs =
+				getLastReflogs("refs/heads/master", "refs/heads/branch");
+		assertEquals(Collections.singleton("refs/heads/master"), oldLogs.keySet());
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), B, "refs/heads/branch", CREATE));
+		execute(newBatchUpdate(cmds).setAllowNonFastForwards(true));
+
+		assertResults(cmds, OK, OK);
+		assertRefs(
+				"refs/heads/master", B,
+				"refs/heads/branch", B);
+		assertEquals(atomic ? 2 : 3, refsChangedEvents);
+		assertReflogUnchanged(oldLogs, "refs/heads/master");
+		assertReflogUnchanged(oldLogs, "refs/heads/branch");
+	}
+
+	@Test
+	public void reflogDefaultIdent() throws IOException {
+		writeRef("refs/heads/master", A);
+		writeRef("refs/heads/branch2", A);
+
+		Map<String, ReflogEntry> oldLogs = getLastReflogs(
+				"refs/heads/master", "refs/heads/branch1", "refs/heads/branch2");
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), B, "refs/heads/branch1", CREATE));
+		execute(
+				newBatchUpdate(cmds)
+						.setAllowNonFastForwards(true)
+						.setRefLogMessage("a reflog", false));
+
+		assertResults(cmds, OK, OK);
+		assertRefs(
+				"refs/heads/master", B,
+				"refs/heads/branch1", B,
+				"refs/heads/branch2", A);
+		assertEquals(atomic ? 3 : 4, refsChangedEvents);
+		assertReflogEquals(
+				reflog(A, B, new PersonIdent(diskRepo), "a reflog"),
+				getLastReflog("refs/heads/master"));
+		assertReflogEquals(
+				reflog(zeroId(), B, new PersonIdent(diskRepo), "a reflog"),
+				getLastReflog("refs/heads/branch1"));
+		assertReflogUnchanged(oldLogs, "refs/heads/branch2");
+	}
+
+	@Test
+	public void reflogAppendStatusNoMessage() throws IOException {
+		writeRef("refs/heads/master", A);
+		writeRef("refs/heads/branch1", B);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(B, A, "refs/heads/branch1", UPDATE_NONFASTFORWARD),
+				new ReceiveCommand(zeroId(), A, "refs/heads/branch2", CREATE));
+		execute(
+				newBatchUpdate(cmds)
+						.setAllowNonFastForwards(true)
+						.setRefLogMessage(null, true));
+
+		assertResults(cmds, OK, OK, OK);
+		assertRefs(
+				"refs/heads/master", B,
+				"refs/heads/branch1", A,
+				"refs/heads/branch2", A);
+		assertEquals(atomic ? 3 : 5, refsChangedEvents);
+		assertReflogEquals(
+				// Always forced; setAllowNonFastForwards(true) bypasses the check.
+				reflog(A, B, new PersonIdent(diskRepo), "forced-update"),
+				getLastReflog("refs/heads/master"));
+		assertReflogEquals(
+				reflog(B, A, new PersonIdent(diskRepo), "forced-update"),
+				getLastReflog("refs/heads/branch1"));
+		assertReflogEquals(
+				reflog(zeroId(), A, new PersonIdent(diskRepo), "created"),
+				getLastReflog("refs/heads/branch2"));
+	}
+
+	@Test
+	public void reflogAppendStatusFastForward() throws IOException {
+		writeRef("refs/heads/master", A);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE));
+		execute(newBatchUpdate(cmds).setRefLogMessage(null, true));
+
+		assertResults(cmds, OK);
+		assertRefs("refs/heads/master", B);
+		assertEquals(2, refsChangedEvents);
+		assertReflogEquals(
+				reflog(A, B, new PersonIdent(diskRepo), "fast-forward"),
+				getLastReflog("refs/heads/master"));
+	}
+
+	@Test
+	public void reflogAppendStatusWithMessage() throws IOException {
+		writeRef("refs/heads/master", A);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), A, "refs/heads/branch", CREATE));
+		execute(newBatchUpdate(cmds).setRefLogMessage("a reflog", true));
+
+		assertResults(cmds, OK, OK);
+		assertRefs(
+				"refs/heads/master", B,
+				"refs/heads/branch", A);
+		assertEquals(atomic ? 2 : 3, refsChangedEvents);
+		assertReflogEquals(
+				reflog(A, B, new PersonIdent(diskRepo), "a reflog: fast-forward"),
+				getLastReflog("refs/heads/master"));
+		assertReflogEquals(
+				reflog(zeroId(), A, new PersonIdent(diskRepo), "a reflog: created"),
+				getLastReflog("refs/heads/branch"));
+	}
+
+	@Test
+	public void reflogCustomIdent() throws IOException {
+		writeRef("refs/heads/master", A);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), B, "refs/heads/branch", CREATE));
+		PersonIdent ident = new PersonIdent("A Reflog User", "reflog@example.com");
+		execute(
+				newBatchUpdate(cmds)
+						.setRefLogMessage("a reflog", false)
+						.setRefLogIdent(ident));
+
+		assertResults(cmds, OK, OK);
+		assertEquals(atomic ? 2 : 3, refsChangedEvents);
+		assertRefs(
+				"refs/heads/master", B,
+				"refs/heads/branch", B);
+		assertReflogEquals(
+				reflog(A, B, ident, "a reflog"),
+				getLastReflog("refs/heads/master"),
+				true);
+		assertReflogEquals(
+				reflog(zeroId(), B, ident, "a reflog"),
+				getLastReflog("refs/heads/branch"),
+				true);
+	}
+
+	@Test
+	public void reflogDelete() throws IOException {
+		writeRef("refs/heads/master", A);
+		writeRef("refs/heads/branch", A);
+		assertEquals(
+				2, getLastReflogs("refs/heads/master", "refs/heads/branch").size());
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, zeroId(), "refs/heads/master", DELETE),
+				new ReceiveCommand(A, B, "refs/heads/branch", UPDATE));
+		execute(newBatchUpdate(cmds).setRefLogMessage("a reflog", false));
+
+		assertResults(cmds, OK, OK);
+		assertRefs("refs/heads/branch", B);
+		assertEquals(atomic ? 3 : 4, refsChangedEvents);
+		assertNull(getLastReflog("refs/heads/master"));
+		assertReflogEquals(
+				reflog(A, B, new PersonIdent(diskRepo), "a reflog"),
+				getLastReflog("refs/heads/branch"));
+	}
+
+	@Test
+	public void reflogFileDirectoryConflict() throws IOException {
+		writeRef("refs/heads/master", A);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, zeroId(), "refs/heads/master", DELETE),
+				new ReceiveCommand(zeroId(), A, "refs/heads/master/x", CREATE));
+		execute(newBatchUpdate(cmds).setRefLogMessage("a reflog", false));
+
+		assertResults(cmds, OK, OK);
+		assertRefs("refs/heads/master/x", A);
+		assertEquals(atomic ? 2 : 3, refsChangedEvents);
+		assertNull(getLastReflog("refs/heads/master"));
+		assertReflogEquals(
+				reflog(zeroId(), A, new PersonIdent(diskRepo), "a reflog"),
+				getLastReflog("refs/heads/master/x"));
+	}
+
+	@Test
+	public void reflogOnLockFailure() throws IOException {
+		writeRef("refs/heads/master", A);
+
+		Map<String, ReflogEntry> oldLogs =
+				getLastReflogs("refs/heads/master", "refs/heads/branch");
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(A, B, "refs/heads/branch", UPDATE));
+		execute(newBatchUpdate(cmds).setRefLogMessage("a reflog", false));
+
+		if (atomic) {
+			assertResults(cmds, TRANSACTION_ABORTED, LOCK_FAILURE);
+			assertEquals(1, refsChangedEvents);
+			assertReflogUnchanged(oldLogs, "refs/heads/master");
+			assertReflogUnchanged(oldLogs, "refs/heads/branch");
+		} else {
+			assertResults(cmds, OK, LOCK_FAILURE);
+			assertEquals(2, refsChangedEvents);
+			assertReflogEquals(
+					reflog(A, B, new PersonIdent(diskRepo), "a reflog"),
+					getLastReflog("refs/heads/master"));
+			assertReflogUnchanged(oldLogs, "refs/heads/branch");
+		}
+	}
+
+	@Test
+	public void overrideRefLogMessage() throws Exception {
+		writeRef("refs/heads/master", A);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), B, "refs/heads/branch", CREATE));
+		cmds.get(0).setRefLogMessage("custom log", false);
+		PersonIdent ident = new PersonIdent(diskRepo);
+		execute(
+				newBatchUpdate(cmds)
+						.setRefLogIdent(ident)
+						.setRefLogMessage("a reflog", true));
+
+		assertResults(cmds, OK, OK);
+		assertEquals(atomic ? 2 : 3, refsChangedEvents);
+		assertReflogEquals(
+				reflog(A, B, ident, "custom log"),
+				getLastReflog("refs/heads/master"),
+				true);
+		assertReflogEquals(
+				reflog(zeroId(), B, ident, "a reflog: created"),
+				getLastReflog("refs/heads/branch"),
+				true);
+	}
+
+	@Test
+	public void overrideDisableRefLog() throws Exception {
+		writeRef("refs/heads/master", A);
+
+		Map<String, ReflogEntry> oldLogs =
+				getLastReflogs("refs/heads/master", "refs/heads/branch");
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), B, "refs/heads/branch", CREATE));
+		cmds.get(0).disableRefLog();
+		execute(newBatchUpdate(cmds).setRefLogMessage("a reflog", true));
+
+		assertResults(cmds, OK, OK);
+		assertEquals(atomic ? 2 : 3, refsChangedEvents);
+		assertReflogUnchanged(oldLogs, "refs/heads/master");
+		assertReflogEquals(
+				reflog(zeroId(), B, new PersonIdent(diskRepo), "a reflog: created"),
+				getLastReflog("refs/heads/branch"));
+	}
+
+	@Test
+	public void refLogNotWrittenWithoutConfigOption() throws Exception {
+		setLogAllRefUpdates(false);
+		writeRef("refs/heads/master", A);
+
+		Map<String, ReflogEntry> oldLogs =
+				getLastReflogs("refs/heads/master", "refs/heads/branch");
+		assertTrue(oldLogs.isEmpty());
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), B, "refs/heads/branch", CREATE));
+		execute(newBatchUpdate(cmds).setRefLogMessage("a reflog", false));
+
+		assertResults(cmds, OK, OK);
+		assertReflogUnchanged(oldLogs, "refs/heads/master");
+		assertReflogUnchanged(oldLogs, "refs/heads/branch");
+	}
+
+	@Test
+	public void forceRefLogInUpdate() throws Exception {
+		setLogAllRefUpdates(false);
+		writeRef("refs/heads/master", A);
+		assertTrue(
+				getLastReflogs("refs/heads/master", "refs/heads/branch").isEmpty());
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), B, "refs/heads/branch", CREATE));
+		execute(
+				newBatchUpdate(cmds)
+						.setRefLogMessage("a reflog", false)
+						.setForceRefLog(true));
+
+		assertResults(cmds, OK, OK);
+		assertReflogEquals(
+				reflog(A, B, new PersonIdent(diskRepo), "a reflog"),
+				getLastReflog("refs/heads/master"));
+		assertReflogEquals(
+				reflog(zeroId(), B, new PersonIdent(diskRepo), "a reflog"),
+				getLastReflog("refs/heads/branch"));
+	}
+
+	@Test
+	public void forceRefLogInCommand() throws Exception {
+		setLogAllRefUpdates(false);
+		writeRef("refs/heads/master", A);
+
+		Map<String, ReflogEntry> oldLogs =
+				getLastReflogs("refs/heads/master", "refs/heads/branch");
+		assertTrue(oldLogs.isEmpty());
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), B, "refs/heads/branch", CREATE));
+		cmds.get(1).setForceRefLog(true);
+		execute(newBatchUpdate(cmds).setRefLogMessage("a reflog", false));
+
+		assertResults(cmds, OK, OK);
+		assertReflogUnchanged(oldLogs, "refs/heads/master");
+		assertReflogEquals(
+				reflog(zeroId(), B, new PersonIdent(diskRepo), "a reflog"),
+				getLastReflog("refs/heads/branch"));
+	}
+
+	@Test
+	public void packedRefsLockFailure() throws Exception {
+		writeLooseRef("refs/heads/master", A);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), B, "refs/heads/branch", CREATE));
+
+		LockFile myLock = refdir.lockPackedRefs();
+		try {
+			execute(newBatchUpdate(cmds).setAllowNonFastForwards(true));
+
+			assertFalse(getLockFile("refs/heads/master").exists());
+			assertFalse(getLockFile("refs/heads/branch").exists());
+
+			if (atomic) {
+				assertResults(cmds, LOCK_FAILURE, TRANSACTION_ABORTED);
+				assertRefs("refs/heads/master", A);
+				assertEquals(1, refsChangedEvents);
+			} else {
+				// Only operates on loose refs, doesn't care that packed-refs is locked.
+				assertResults(cmds, OK, OK);
+				assertRefs(
+						"refs/heads/master", B,
+						"refs/heads/branch", B);
+				assertEquals(3, refsChangedEvents);
+			}
+		} finally {
+			myLock.unlock();
+		}
+	}
+
+	@Test
+	public void oneRefLockFailure() throws Exception {
+		writeLooseRef("refs/heads/master", A);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(zeroId(), B, "refs/heads/branch", CREATE),
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE));
+
+		LockFile myLock = new LockFile(refdir.fileFor("refs/heads/master"));
+		assertTrue(myLock.lock());
+		try {
+			execute(newBatchUpdate(cmds).setAllowNonFastForwards(true));
+
+			assertFalse(LockFile.getLockFile(refdir.packedRefsFile).exists());
+			assertFalse(getLockFile("refs/heads/branch").exists());
+
+			if (atomic) {
+				assertResults(cmds, TRANSACTION_ABORTED, LOCK_FAILURE);
+				assertRefs("refs/heads/master", A);
+				assertEquals(1, refsChangedEvents);
+			} else {
+				assertResults(cmds, OK, LOCK_FAILURE);
+				assertRefs(
+						"refs/heads/branch", B,
+						"refs/heads/master", A);
+				assertEquals(2, refsChangedEvents);
+			}
+		} finally {
+			myLock.unlock();
+		}
+	}
+
+	@Test
+	public void singleRefUpdateDoesNotRequirePackedRefsLock() throws Exception {
+		writeLooseRef("refs/heads/master", A);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE));
+
+		LockFile myLock = refdir.lockPackedRefs();
+		try {
+			execute(newBatchUpdate(cmds).setAllowNonFastForwards(true));
+
+			assertFalse(getLockFile("refs/heads/master").exists());
+			assertResults(cmds, OK);
+			assertEquals(2, refsChangedEvents);
+			assertRefs("refs/heads/master", B);
+		} finally {
+			myLock.unlock();
+		}
+	}
+
+	@Test
+	public void atomicUpdateRespectsInProcessLock() throws Exception {
+		assumeTrue(atomic);
+
+		writeLooseRef("refs/heads/master", A);
+
+		List<ReceiveCommand> cmds = Arrays.asList(
+				new ReceiveCommand(A, B, "refs/heads/master", UPDATE),
+				new ReceiveCommand(zeroId(), B, "refs/heads/branch", CREATE));
+
+		Thread t = new Thread(() -> {
+			try {
+				execute(newBatchUpdate(cmds).setAllowNonFastForwards(true));
+			} catch (Exception e) {
+				throw new RuntimeException(e);
+			}
+		});
+
+		ReentrantLock l = refdir.inProcessPackedRefsLock;
+		l.lock();
+		try {
+			t.start();
+			long timeoutSecs = 10;
+			long startNanos = System.nanoTime();
+
+			// Hold onto the lock until we observe the worker thread has attempted to
+			// acquire it.
+			while (l.getQueueLength() == 0) {
+				long elapsedNanos = System.nanoTime() - startNanos;
+				assertTrue(
+						"timed out waiting for work thread to attempt to acquire lock",
+						NANOSECONDS.toSeconds(elapsedNanos) < timeoutSecs);
+				Thread.sleep(3);
+			}
+
+			// Once we unlock, the worker thread should finish the update promptly.
+			l.unlock();
+			t.join(SECONDS.toMillis(timeoutSecs));
+			assertFalse(t.isAlive());
+		} finally {
+			if (l.isHeldByCurrentThread()) {
+				l.unlock();
+			}
+		}
+
+		assertResults(cmds, OK, OK);
+		assertEquals(2, refsChangedEvents);
+		assertRefs(
+				"refs/heads/master", B,
+				"refs/heads/branch", B);
+	}
+
+	private void setLogAllRefUpdates(boolean enable) throws Exception {
+		StoredConfig cfg = diskRepo.getConfig();
+		cfg.load();
+		cfg.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
+				ConfigConstants.CONFIG_KEY_LOGALLREFUPDATES, enable);
+		cfg.save();
+	}
+
+	private void writeLooseRef(String name, AnyObjectId id) throws IOException {
+		write(new File(diskRepo.getDirectory(), name), id.name() + "\n");
+	}
+
+	private void writeRef(String name, AnyObjectId id) throws IOException {
+		RefUpdate u = diskRepo.updateRef(name);
+		u.setRefLogMessage(getClass().getSimpleName(), false);
+		u.setForceUpdate(true);
+		u.setNewObjectId(id);
+		RefUpdate.Result r = u.update();
+		switch (r) {
+			case NEW:
+			case FORCED:
+				return;
+			default:
+				throw new IOException("Got " + r + " while updating " + name);
+		}
+	}
+
+	private BatchRefUpdate newBatchUpdate(List<ReceiveCommand> cmds) {
+		BatchRefUpdate u = refdir.newBatchUpdate();
+		if (atomic) {
+			assertTrue(u.isAtomic());
+		} else {
+			u.setAtomic(false);
+		}
+		u.addCommand(cmds);
+		return u;
+	}
+
+	private void execute(BatchRefUpdate u) throws IOException {
+		execute(u, false);
+	}
+
+	private void execute(BatchRefUpdate u, boolean strictWork) throws IOException {
+		try (RevWalk rw = new RevWalk(diskRepo)) {
+			u.execute(rw,
+					strictWork ? new StrictWorkMonitor() : NullProgressMonitor.INSTANCE);
+		}
+	}
+
+	private void assertRefs(Object... args) throws IOException {
+		if (args.length % 2 != 0) {
+			throw new IllegalArgumentException(
+					"expected even number of args: " + Arrays.toString(args));
+		}
+
+		Map<String, AnyObjectId> expected = new LinkedHashMap<>();
+		for (int i = 0; i < args.length; i += 2) {
+			expected.put((String) args[i], (AnyObjectId) args[i + 1]);
+		}
+
+		Map<String, Ref> refs = refdir.getRefs(RefDatabase.ALL);
+		Ref actualHead = refs.remove(Constants.HEAD);
+		if (actualHead != null) {
+			String actualLeafName = actualHead.getLeaf().getName();
+			assertEquals(
+					"expected HEAD to point to refs/heads/master, got: " + actualLeafName,
+					"refs/heads/master", actualLeafName);
+			AnyObjectId expectedMaster = expected.get("refs/heads/master");
+			assertNotNull("expected master ref since HEAD exists", expectedMaster);
+			assertEquals(expectedMaster, actualHead.getObjectId());
+		}
+
+		Map<String, AnyObjectId> actual = new LinkedHashMap<>();
+		refs.forEach((n, r) -> actual.put(n, r.getObjectId()));
+
+		assertEquals(expected.keySet(), actual.keySet());
+		actual.forEach((n, a) -> assertEquals(n, expected.get(n), a));
+	}
+
+	enum Result {
+		OK(ReceiveCommand.Result.OK),
+		LOCK_FAILURE(ReceiveCommand.Result.LOCK_FAILURE),
+		REJECTED_NONFASTFORWARD(ReceiveCommand.Result.REJECTED_NONFASTFORWARD),
+		REJECTED_MISSING_OBJECT(ReceiveCommand.Result.REJECTED_MISSING_OBJECT),
+		TRANSACTION_ABORTED(ReceiveCommand::isTransactionAborted);
+
+		final Predicate<? super ReceiveCommand> p;
+
+		private Result(Predicate<? super ReceiveCommand> p) {
+			this.p = p;
+		}
+
+		private Result(ReceiveCommand.Result result) {
+			this(c -> c.getResult() == result);
+		}
+	}
+
+	private void assertResults(
+			List<ReceiveCommand> cmds, Result... expected) {
+		if (expected.length != cmds.size()) {
+			throw new IllegalArgumentException(
+					"expected " + cmds.size() + " result args");
+		}
+		for (int i = 0; i < cmds.size(); i++) {
+			ReceiveCommand c = cmds.get(i);
+			Result r = expected[i];
+			assertTrue(
+					String.format(
+							"result of command (%d) should be %s: %s %s%s",
+							Integer.valueOf(i), r, c,
+							c.getResult(),
+							c.getMessage() != null ? " (" + c.getMessage() + ")" : ""),
+					r.p.test(c));
+		}
+	}
+
+	private Map<String, ReflogEntry> getLastReflogs(String... names)
+			throws IOException {
+		Map<String, ReflogEntry> result = new LinkedHashMap<>();
+		for (String name : names) {
+			ReflogEntry e = getLastReflog(name);
+			if (e != null) {
+				result.put(name, e);
+			}
+		}
+		return result;
+	}
+
+	private ReflogEntry getLastReflog(String name) throws IOException {
+		ReflogReader r = diskRepo.getReflogReader(name);
+		if (r == null) {
+			return null;
+		}
+		return r.getLastEntry();
+	}
+
+	private File getLockFile(String refName) {
+		return LockFile.getLockFile(refdir.fileFor(refName));
+	}
+
+	private void assertReflogUnchanged(
+			Map<String, ReflogEntry> old, String name) throws IOException {
+		assertReflogEquals(old.get(name), getLastReflog(name), true);
+	}
+
+	private static void assertReflogEquals(
+			ReflogEntry expected, ReflogEntry actual) {
+		assertReflogEquals(expected, actual, false);
+	}
+
+	private static void assertReflogEquals(
+			ReflogEntry expected, ReflogEntry actual, boolean strictTime) {
+		if (expected == null) {
+			assertNull(actual);
+			return;
+		}
+		assertNotNull(actual);
+		assertEquals(expected.getOldId(), actual.getOldId());
+		assertEquals(expected.getNewId(), actual.getNewId());
+		if (strictTime) {
+			assertEquals(expected.getWho(), actual.getWho());
+		} else {
+			assertEquals(expected.getWho().getName(), actual.getWho().getName());
+			assertEquals(
+					expected.getWho().getEmailAddress(),
+					actual.getWho().getEmailAddress());
+		}
+		assertEquals(expected.getComment(), actual.getComment());
+	}
+
+	private static ReflogEntry reflog(ObjectId oldId, ObjectId newId,
+			PersonIdent who, String comment) {
+		return new ReflogEntry() {
+			@Override
+			public ObjectId getOldId() {
+				return oldId;
+			}
+
+			@Override
+			public ObjectId getNewId() {
+				return newId;
+			}
+
+			@Override
+			public PersonIdent getWho() {
+				return who;
+			}
+
+			@Override
+			public String getComment() {
+				return comment;
+			}
+
+			@Override
+			public CheckoutEntry parseCheckout() {
+				throw new UnsupportedOperationException();
+			}
+		};
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPackRefsTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPackRefsTest.java
index 11a2a22..c43bdbd 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPackRefsTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPackRefsTest.java
@@ -43,12 +43,13 @@
 
 package org.eclipse.jgit.internal.storage.file;
 
-import static java.lang.Integer.valueOf;
+import static org.hamcrest.Matchers.lessThanOrEqualTo;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertThat;
 
 import java.io.File;
 import java.io.IOException;
@@ -74,6 +75,7 @@
 import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.junit.Test;
 
+@SuppressWarnings("boxing")
 public class GcPackRefsTest extends GcTestCase {
 	@Test
 	public void looseRefPacked() throws Exception {
@@ -100,27 +102,23 @@ public void concurrentOnlyOneWritesPackedRefs() throws Exception {
 		RevBlob a = tr.blob("a");
 		tr.lightweightTag("t", a);
 
-		final CyclicBarrier syncPoint = new CyclicBarrier(2);
+		CyclicBarrier syncPoint = new CyclicBarrier(2);
 
-		Callable<Integer> packRefs = new Callable<Integer>() {
-
-			/** @return 0 for success, 1 in case of error when writing pack */
-			@Override
-			public Integer call() throws Exception {
-				syncPoint.await();
-				try {
-					gc.packRefs();
-					return valueOf(0);
-				} catch (IOException e) {
-					return valueOf(1);
-				}
+		// Returns 0 for success, 1 in case of error when writing pack.
+		Callable<Integer> packRefs = () -> {
+			syncPoint.await();
+			try {
+				gc.packRefs();
+				return 0;
+			} catch (IOException e) {
+				return 1;
 			}
 		};
 		ExecutorService pool = Executors.newFixedThreadPool(2);
 		try {
 			Future<Integer> p1 = pool.submit(packRefs);
 			Future<Integer> p2 = pool.submit(packRefs);
-			assertEquals(1, p1.get().intValue() + p2.get().intValue());
+			assertThat(p1.get() + p2.get(), lessThanOrEqualTo(1));
 		} finally {
 			pool.shutdown();
 			pool.awaitTermination(Long.MAX_VALUE, TimeUnit.SECONDS);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcTemporaryFilesTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcTemporaryFilesTest.java
new file mode 100644
index 0000000..59d544e
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcTemporaryFilesTest.java
@@ -0,0 +1,106 @@
+/*
+ * Copyright (C) 2017 Ericsson
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.file;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+import java.nio.file.Paths;
+import java.time.Instant;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class GcTemporaryFilesTest extends GcTestCase {
+	private static final String TEMP_IDX = "gc_1234567890.idx_tmp";
+
+	private static final String TEMP_PACK = "gc_1234567890.pack_tmp";
+
+	private File packDir;
+
+	@Override
+	@Before
+	public void setUp() throws Exception {
+		super.setUp();
+		packDir = Paths.get(repo.getObjectsDirectory().getAbsolutePath(),
+				"pack").toFile(); //$NON-NLS-1$
+	}
+
+	@Test
+	public void oldTempPacksAndIdxAreDeleted() throws Exception {
+		File tempIndex = new File(packDir, TEMP_IDX);
+		File tempPack = new File(packDir, TEMP_PACK);
+		if (!packDir.exists() || !packDir.isDirectory()) {
+			assertTrue(packDir.mkdirs());
+		}
+		assertTrue(tempPack.createNewFile());
+		assertTrue(tempIndex.createNewFile());
+		assertTrue(tempIndex.exists());
+		assertTrue(tempPack.exists());
+		long _24HoursBefore = Instant.now().toEpochMilli()
+				- 24 * 60 * 62 * 1000;
+		tempIndex.setLastModified(_24HoursBefore);
+		tempPack.setLastModified(_24HoursBefore);
+		gc.gc();
+		assertFalse(tempIndex.exists());
+		assertFalse(tempPack.exists());
+	}
+
+	@Test
+	public void recentTempPacksAndIdxAreNotDeleted() throws Exception {
+		File tempIndex = new File(packDir, TEMP_IDX);
+		File tempPack = new File(packDir, TEMP_PACK);
+		if (!packDir.exists() || !packDir.isDirectory()) {
+			assertTrue(packDir.mkdirs());
+		}
+		assertTrue(tempPack.createNewFile());
+		assertTrue(tempIndex.createNewFile());
+		assertTrue(tempIndex.exists());
+		assertTrue(tempPack.exists());
+		gc.gc();
+		assertTrue(tempIndex.exists());
+		assertTrue(tempPack.exists());
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackInserterTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackInserterTest.java
new file mode 100644
index 0000000..8596f74
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackInserterTest.java
@@ -0,0 +1,585 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *	 notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *	 copyright notice, this list of conditions and the following
+ *	 disclaimer in the documentation and/or other materials provided
+ *	 with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *	 names of its contributors may be used to endorse or promote
+ *	 products derived from this software without specific prior
+ *	 written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.file;
+
+import static java.util.Comparator.comparing;
+import static java.util.stream.Collectors.toList;
+
+import static org.eclipse.jgit.lib.Constants.OBJ_BLOB;
+import static org.eclipse.jgit.lib.Constants.OBJ_COMMIT;
+import static org.hamcrest.Matchers.greaterThan;
+import static org.hamcrest.Matchers.lessThan;
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.FileVisitResult;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.SimpleFileVisitor;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Random;
+import java.util.function.Predicate;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.eclipse.jgit.dircache.DirCache;
+import org.eclipse.jgit.dircache.DirCacheBuilder;
+import org.eclipse.jgit.dircache.DirCacheEntry;
+import org.eclipse.jgit.errors.MissingObjectException;
+import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.lib.CommitBuilder;
+import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.FileMode;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectLoader;
+import org.eclipse.jgit.lib.ObjectReader;
+import org.eclipse.jgit.lib.ObjectStream;
+import org.eclipse.jgit.storage.file.WindowCacheConfig;
+import org.eclipse.jgit.treewalk.CanonicalTreeParser;
+import org.eclipse.jgit.util.IO;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+@SuppressWarnings("boxing")
+public class PackInserterTest extends RepositoryTestCase {
+	private WindowCacheConfig origWindowCacheConfig;
+
+	@Before
+	public void setWindowCacheConfig() {
+		origWindowCacheConfig = new WindowCacheConfig();
+		origWindowCacheConfig.install();
+	}
+
+	@After
+	public void resetWindowCacheConfig() {
+		origWindowCacheConfig.install();
+	}
+
+	@Before
+	public void emptyAtSetUp() throws Exception {
+		assertEquals(0, listPacks().size());
+		assertNoObjects();
+	}
+
+	@Test
+	public void noFlush() throws Exception {
+		try (PackInserter ins = newInserter()) {
+			ins.insert(OBJ_BLOB, Constants.encode("foo contents"));
+			// No flush.
+		}
+		assertNoObjects();
+	}
+
+	@Test
+	public void flushEmptyPack() throws Exception {
+		try (PackInserter ins = newInserter()) {
+			ins.flush();
+		}
+		assertNoObjects();
+	}
+
+	@Test
+	public void singlePack() throws Exception {
+		ObjectId blobId;
+		byte[] blob = Constants.encode("foo contents");
+		ObjectId treeId;
+		ObjectId commitId;
+		byte[] commit;
+		try (PackInserter ins = newInserter()) {
+			blobId = ins.insert(OBJ_BLOB, blob);
+
+			DirCache dc = DirCache.newInCore();
+			DirCacheBuilder b = dc.builder();
+			DirCacheEntry dce = new DirCacheEntry("foo");
+			dce.setFileMode(FileMode.REGULAR_FILE);
+			dce.setObjectId(blobId);
+			b.add(dce);
+			b.finish();
+			treeId = dc.writeTree(ins);
+
+			CommitBuilder cb = new CommitBuilder();
+			cb.setTreeId(treeId);
+			cb.setAuthor(author);
+			cb.setCommitter(committer);
+			cb.setMessage("Commit message");
+			commit = cb.toByteArray();
+			commitId = ins.insert(cb);
+			ins.flush();
+		}
+
+		assertPacksOnly();
+		List<PackFile> packs = listPacks();
+		assertEquals(1, packs.size());
+		assertEquals(3, packs.get(0).getObjectCount());
+
+		try (ObjectReader reader = db.newObjectReader()) {
+			assertBlob(reader, blobId, blob);
+
+			CanonicalTreeParser treeParser =
+					new CanonicalTreeParser(null, reader, treeId);
+			assertEquals("foo", treeParser.getEntryPathString());
+			assertEquals(blobId, treeParser.getEntryObjectId());
+
+			ObjectLoader commitLoader = reader.open(commitId);
+			assertEquals(OBJ_COMMIT, commitLoader.getType());
+			assertArrayEquals(commit, commitLoader.getBytes());
+		}
+	}
+
+	@Test
+	public void multiplePacks() throws Exception {
+		ObjectId blobId1;
+		ObjectId blobId2;
+		byte[] blob1 = Constants.encode("blob1");
+		byte[] blob2 = Constants.encode("blob2");
+
+		try (PackInserter ins = newInserter()) {
+			blobId1 = ins.insert(OBJ_BLOB, blob1);
+			ins.flush();
+			blobId2 = ins.insert(OBJ_BLOB, blob2);
+			ins.flush();
+		}
+
+		assertPacksOnly();
+		List<PackFile> packs = listPacks();
+		assertEquals(2, packs.size());
+		assertEquals(1, packs.get(0).getObjectCount());
+		assertEquals(1, packs.get(1).getObjectCount());
+
+		try (ObjectReader reader = db.newObjectReader()) {
+			assertBlob(reader, blobId1, blob1);
+			assertBlob(reader, blobId2, blob2);
+		}
+	}
+
+	@Test
+	public void largeBlob() throws Exception {
+		ObjectId blobId;
+		byte[] blob = newLargeBlob();
+		try (PackInserter ins = newInserter()) {
+			assertThat(blob.length, greaterThan(ins.getBufferSize()));
+			blobId =
+					ins.insert(OBJ_BLOB, blob.length, new ByteArrayInputStream(blob));
+			ins.flush();
+		}
+
+		assertPacksOnly();
+		Collection<PackFile> packs = listPacks();
+		assertEquals(1, packs.size());
+		PackFile p = packs.iterator().next();
+		assertEquals(1, p.getObjectCount());
+
+		try (ObjectReader reader = db.newObjectReader()) {
+			assertBlob(reader, blobId, blob);
+		}
+	}
+
+	@Test
+	public void overwriteExistingPack() throws Exception {
+		ObjectId blobId;
+		byte[] blob = Constants.encode("foo contents");
+
+		try (PackInserter ins = newInserter()) {
+			blobId = ins.insert(OBJ_BLOB, blob);
+			ins.flush();
+		}
+
+		assertPacksOnly();
+		List<PackFile> packs = listPacks();
+		assertEquals(1, packs.size());
+		PackFile pack = packs.get(0);
+		assertEquals(1, pack.getObjectCount());
+
+		String inode = getInode(pack.getPackFile());
+
+		try (PackInserter ins = newInserter()) {
+			ins.checkExisting(false);
+			assertEquals(blobId, ins.insert(OBJ_BLOB, blob));
+			ins.flush();
+		}
+
+		assertPacksOnly();
+		packs = listPacks();
+		assertEquals(1, packs.size());
+		pack = packs.get(0);
+		assertEquals(1, pack.getObjectCount());
+
+		if (inode != null) {
+			// Old file was overwritten with new file, although objects were
+			// equivalent.
+			assertNotEquals(inode, getInode(pack.getPackFile()));
+		}
+	}
+
+	@Test
+	public void checkExisting() throws Exception {
+		ObjectId blobId;
+		byte[] blob = Constants.encode("foo contents");
+
+		try (PackInserter ins = newInserter()) {
+			blobId = ins.insert(OBJ_BLOB, blob);
+			ins.insert(OBJ_BLOB, Constants.encode("another blob"));
+			ins.flush();
+		}
+
+		assertPacksOnly();
+		assertEquals(1, listPacks().size());
+
+		try (PackInserter ins = newInserter()) {
+			assertEquals(blobId, ins.insert(OBJ_BLOB, blob));
+			ins.flush();
+		}
+
+		assertPacksOnly();
+		assertEquals(1, listPacks().size());
+
+		try (PackInserter ins = newInserter()) {
+			ins.checkExisting(false);
+			assertEquals(blobId, ins.insert(OBJ_BLOB, blob));
+			ins.flush();
+		}
+
+		assertPacksOnly();
+		assertEquals(2, listPacks().size());
+
+		try (ObjectReader reader = db.newObjectReader()) {
+			assertBlob(reader, blobId, blob);
+		}
+	}
+
+	@Test
+	public void insertSmallInputStreamRespectsCheckExisting() throws Exception {
+		ObjectId blobId;
+		byte[] blob = Constants.encode("foo contents");
+		try (PackInserter ins = newInserter()) {
+			assertThat(blob.length, lessThan(ins.getBufferSize()));
+			blobId = ins.insert(OBJ_BLOB, blob);
+			ins.insert(OBJ_BLOB, Constants.encode("another blob"));
+			ins.flush();
+		}
+
+		assertPacksOnly();
+		assertEquals(1, listPacks().size());
+
+		try (PackInserter ins = newInserter()) {
+			assertEquals(blobId,
+					ins.insert(OBJ_BLOB, blob.length, new ByteArrayInputStream(blob)));
+			ins.flush();
+		}
+
+		assertPacksOnly();
+		assertEquals(1, listPacks().size());
+	}
+
+	@Test
+	public void insertLargeInputStreamBypassesCheckExisting() throws Exception {
+		ObjectId blobId;
+		byte[] blob = newLargeBlob();
+
+		try (PackInserter ins = newInserter()) {
+			assertThat(blob.length, greaterThan(ins.getBufferSize()));
+			blobId = ins.insert(OBJ_BLOB, blob);
+			ins.insert(OBJ_BLOB, Constants.encode("another blob"));
+			ins.flush();
+		}
+
+		assertPacksOnly();
+		assertEquals(1, listPacks().size());
+
+		try (PackInserter ins = newInserter()) {
+			assertEquals(blobId,
+					ins.insert(OBJ_BLOB, blob.length, new ByteArrayInputStream(blob)));
+			ins.flush();
+		}
+
+		assertPacksOnly();
+		assertEquals(2, listPacks().size());
+	}
+
+	@Test
+	public void readBackSmallFiles() throws Exception {
+		ObjectId blobId1;
+		ObjectId blobId2;
+		ObjectId blobId3;
+		byte[] blob1 = Constants.encode("blob1");
+		byte[] blob2 = Constants.encode("blob2");
+		byte[] blob3 = Constants.encode("blob3");
+		try (PackInserter ins = newInserter()) {
+			assertThat(blob1.length, lessThan(ins.getBufferSize()));
+			blobId1 = ins.insert(OBJ_BLOB, blob1);
+
+			try (ObjectReader reader = ins.newReader()) {
+				assertBlob(reader, blobId1, blob1);
+			}
+
+			// Read-back should not mess up the file pointer.
+			blobId2 = ins.insert(OBJ_BLOB, blob2);
+			ins.flush();
+
+			blobId3 = ins.insert(OBJ_BLOB, blob3);
+		}
+
+		assertPacksOnly();
+		List<PackFile> packs = listPacks();
+		assertEquals(1, packs.size());
+		assertEquals(2, packs.get(0).getObjectCount());
+
+		try (ObjectReader reader = db.newObjectReader()) {
+			assertBlob(reader, blobId1, blob1);
+			assertBlob(reader, blobId2, blob2);
+
+			try {
+				reader.open(blobId3);
+				fail("Expected MissingObjectException");
+			} catch (MissingObjectException expected) {
+				// Expected.
+			}
+		}
+	}
+
+	@Test
+	public void readBackLargeFile() throws Exception {
+		ObjectId blobId;
+		byte[] blob = newLargeBlob();
+
+		WindowCacheConfig wcc = new WindowCacheConfig();
+		wcc.setStreamFileThreshold(1024);
+		wcc.install();
+		try (ObjectReader reader = db.newObjectReader()) {
+			assertThat(blob.length, greaterThan(reader.getStreamFileThreshold()));
+		}
+
+		try (PackInserter ins = newInserter()) {
+			blobId = ins.insert(OBJ_BLOB, blob);
+
+			try (ObjectReader reader = ins.newReader()) {
+				// Double-check threshold is propagated.
+				assertThat(blob.length, greaterThan(reader.getStreamFileThreshold()));
+				assertBlob(reader, blobId, blob);
+			}
+		}
+
+		assertPacksOnly();
+		// Pack was streamed out to disk and read back from the temp file, but
+		// ultimately rolled back and deleted.
+		assertEquals(0, listPacks().size());
+
+		try (ObjectReader reader = db.newObjectReader()) {
+			try {
+				reader.open(blobId);
+				fail("Expected MissingObjectException");
+			} catch (MissingObjectException expected) {
+				// Expected.
+			}
+		}
+	}
+
+	@Test
+	public void readBackFallsBackToRepo() throws Exception {
+		ObjectId blobId;
+		byte[] blob = Constants.encode("foo contents");
+		try (PackInserter ins = newInserter()) {
+			assertThat(blob.length, lessThan(ins.getBufferSize()));
+			blobId = ins.insert(OBJ_BLOB, blob);
+			ins.flush();
+		}
+
+		try (PackInserter ins = newInserter();
+				ObjectReader reader = ins.newReader()) {
+			assertBlob(reader, blobId, blob);
+		}
+	}
+
+	@Test
+	public void readBackSmallObjectBeforeLargeObject() throws Exception {
+		WindowCacheConfig wcc = new WindowCacheConfig();
+		wcc.setStreamFileThreshold(1024);
+		wcc.install();
+
+		ObjectId blobId1;
+		ObjectId blobId2;
+		ObjectId largeId;
+		byte[] blob1 = Constants.encode("blob1");
+		byte[] blob2 = Constants.encode("blob2");
+		byte[] largeBlob = newLargeBlob();
+		try (PackInserter ins = newInserter()) {
+			assertThat(blob1.length, lessThan(ins.getBufferSize()));
+			assertThat(largeBlob.length, greaterThan(ins.getBufferSize()));
+
+			blobId1 = ins.insert(OBJ_BLOB, blob1);
+			largeId = ins.insert(OBJ_BLOB, largeBlob);
+
+			try (ObjectReader reader = ins.newReader()) {
+				// A previous bug did not reset the file pointer to EOF after reading
+				// back. We need to seek to something further back than a full buffer,
+				// since the read-back code eagerly reads a full buffer's worth of data
+				// from the file to pass to the inflater. If we seeked back just a small
+				// amount, this step would consume the rest of the file, so the file
+				// pointer would coincidentally end up back at EOF, hiding the bug.
+				assertBlob(reader, blobId1, blob1);
+			}
+
+			blobId2 = ins.insert(OBJ_BLOB, blob2);
+
+			try (ObjectReader reader = ins.newReader()) {
+				assertBlob(reader, blobId1, blob1);
+				assertBlob(reader, blobId2, blob2);
+				assertBlob(reader, largeId, largeBlob);
+			}
+
+			ins.flush();
+		}
+
+		try (ObjectReader reader = db.newObjectReader()) {
+				assertBlob(reader, blobId1, blob1);
+				assertBlob(reader, blobId2, blob2);
+				assertBlob(reader, largeId, largeBlob);
+		}
+	}
+
+	private List<PackFile> listPacks() throws Exception {
+		List<PackFile> fromOpenDb = listPacks(db);
+		List<PackFile> reopened;
+		try (FileRepository db2 = new FileRepository(db.getDirectory())) {
+			reopened = listPacks(db2);
+		}
+		assertEquals(fromOpenDb.size(), reopened.size());
+		for (int i = 0 ; i < fromOpenDb.size(); i++) {
+			PackFile a = fromOpenDb.get(i);
+			PackFile b = reopened.get(i);
+			assertEquals(a.getPackName(), b.getPackName());
+			assertEquals(
+					a.getPackFile().getAbsolutePath(), b.getPackFile().getAbsolutePath());
+			assertEquals(a.getObjectCount(), b.getObjectCount());
+			a.getObjectCount();
+		}
+		return fromOpenDb;
+	}
+
+	private static List<PackFile> listPacks(FileRepository db) throws Exception {
+		return db.getObjectDatabase().getPacks().stream()
+				.sorted(comparing(PackFile::getPackName)).collect(toList());
+	}
+
+	private PackInserter newInserter() {
+		return db.getObjectDatabase().newPackInserter();
+	}
+
+	private static byte[] newLargeBlob() {
+		byte[] blob = new byte[10240];
+		new Random(0).nextBytes(blob);
+		return blob;
+	}
+
+	private static String getInode(File f) throws Exception {
+		BasicFileAttributes attrs = Files.readAttributes(
+				f.toPath(), BasicFileAttributes.class);
+		Object k = attrs.fileKey();
+		if (k == null) {
+			return null;
+		}
+		Pattern p = Pattern.compile("^\\(dev=[^,]*,ino=(\\d+)\\)$");
+		Matcher m = p.matcher(k.toString());
+		return m.matches() ? m.group(1) : null;
+	}
+
+	private static void assertBlob(ObjectReader reader, ObjectId id,
+			byte[] expected) throws Exception {
+		ObjectLoader loader = reader.open(id);
+		assertEquals(OBJ_BLOB, loader.getType());
+		assertEquals(expected.length, loader.getSize());
+		try (ObjectStream s = loader.openStream()) {
+			int n = (int) s.getSize();
+			byte[] actual = new byte[n];
+			assertEquals(n, IO.readFully(s, actual, 0));
+			assertArrayEquals(expected, actual);
+		}
+	}
+
+	private void assertPacksOnly() throws Exception {
+		new BadFileCollector(f -> !f.endsWith(".pack") && !f.endsWith(".idx"))
+				.assertNoBadFiles(db.getObjectDatabase().getDirectory());
+	}
+
+	private void assertNoObjects() throws Exception {
+		new BadFileCollector(f -> true)
+				.assertNoBadFiles(db.getObjectDatabase().getDirectory());
+	}
+
+	private static class BadFileCollector extends SimpleFileVisitor<Path> {
+		private final Predicate<String> badName;
+		private List<String> bad;
+
+		BadFileCollector(Predicate<String> badName) {
+			this.badName = badName;
+		}
+
+		void assertNoBadFiles(File f) throws IOException {
+			bad = new ArrayList<>();
+			Files.walkFileTree(f.toPath(), this);
+			if (!bad.isEmpty()) {
+				fail("unexpected files in object directory: " + bad);
+			}
+		}
+
+		@Override
+		public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) {
+			String name = file.getFileName().toString();
+			if (!attrs.isDirectory() && badName.test(name)) {
+				bad.add(name);
+			}
+			return FileVisitResult.CONTINUE;
+		}
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefDirectoryTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefDirectoryTest.java
index 53db123..fefccf3 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefDirectoryTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefDirectoryTest.java
@@ -61,32 +61,27 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.List;
 import java.util.Map;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.concurrent.atomic.AtomicReference;
 
+import org.eclipse.jgit.errors.LockFailedException;
 import org.eclipse.jgit.events.ListenerHandle;
 import org.eclipse.jgit.events.RefsChangedEvent;
 import org.eclipse.jgit.events.RefsChangedListener;
 import org.eclipse.jgit.junit.LocalDiskRepositoryTestCase;
 import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.lib.AnyObjectId;
-import org.eclipse.jgit.lib.BatchRefUpdate;
-import org.eclipse.jgit.lib.NullProgressMonitor;
-import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Ref.Storage;
 import org.eclipse.jgit.lib.RefDatabase;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevTag;
-import org.eclipse.jgit.revwalk.RevWalk;
-import org.eclipse.jgit.transport.ReceiveCommand;
-import org.eclipse.jgit.transport.ReceiveCommand.Type;
 import org.junit.Before;
 import org.junit.Test;
 
+@SuppressWarnings("boxing")
 public class RefDirectoryTest extends LocalDiskRepositoryTestCase {
 	private Repository diskRepo;
 
@@ -1293,125 +1288,20 @@ public void onRefsChanged(RefsChangedEvent event) {
 	}
 
 	@Test
-	public void testBatchRefUpdateSimpleNoForce() throws IOException {
+	public void testPackedRefsLockFailure() throws Exception {
 		writeLooseRef("refs/heads/master", A);
-		writeLooseRef("refs/heads/masters", B);
-		List<ReceiveCommand> commands = Arrays.asList(
-				newCommand(A, B, "refs/heads/master",
-						ReceiveCommand.Type.UPDATE),
-				newCommand(B, A, "refs/heads/masters",
-						ReceiveCommand.Type.UPDATE_NONFASTFORWARD));
-		BatchRefUpdate batchUpdate = refdir.newBatchUpdate();
-		batchUpdate.addCommand(commands);
-		batchUpdate.execute(new RevWalk(diskRepo), new StrictWorkMonitor());
-		Map<String, Ref> refs = refdir.getRefs(RefDatabase.ALL);
-		assertEquals(ReceiveCommand.Result.OK, commands.get(0).getResult());
-		assertEquals(ReceiveCommand.Result.REJECTED_NONFASTFORWARD, commands
-				.get(1).getResult());
-		assertEquals("[HEAD, refs/heads/master, refs/heads/masters]", refs
-				.keySet().toString());
-		assertEquals(B.getId(), refs.get("refs/heads/master").getObjectId());
-		assertEquals(B.getId(), refs.get("refs/heads/masters").getObjectId());
-	}
-
-	@Test
-	public void testBatchRefUpdateSimpleForce() throws IOException {
-		writeLooseRef("refs/heads/master", A);
-		writeLooseRef("refs/heads/masters", B);
-		List<ReceiveCommand> commands = Arrays.asList(
-				newCommand(A, B, "refs/heads/master",
-						ReceiveCommand.Type.UPDATE),
-				newCommand(B, A, "refs/heads/masters",
-						ReceiveCommand.Type.UPDATE_NONFASTFORWARD));
-		BatchRefUpdate batchUpdate = refdir.newBatchUpdate();
-		batchUpdate.setAllowNonFastForwards(true);
-		batchUpdate.addCommand(commands);
-		batchUpdate.execute(new RevWalk(diskRepo), new StrictWorkMonitor());
-		Map<String, Ref> refs = refdir.getRefs(RefDatabase.ALL);
-		assertEquals(ReceiveCommand.Result.OK, commands.get(0).getResult());
-		assertEquals(ReceiveCommand.Result.OK, commands.get(1).getResult());
-		assertEquals("[HEAD, refs/heads/master, refs/heads/masters]", refs
-				.keySet().toString());
-		assertEquals(B.getId(), refs.get("refs/heads/master").getObjectId());
-		assertEquals(A.getId(), refs.get("refs/heads/masters").getObjectId());
-	}
-
-	@Test
-	public void testBatchRefUpdateNonFastForwardDoesNotDoExpensiveMergeCheck()
-			throws IOException {
-		writeLooseRef("refs/heads/master", B);
-		List<ReceiveCommand> commands = Arrays.asList(
-				newCommand(B, A, "refs/heads/master",
-						ReceiveCommand.Type.UPDATE_NONFASTFORWARD));
-		BatchRefUpdate batchUpdate = refdir.newBatchUpdate();
-		batchUpdate.setAllowNonFastForwards(true);
-		batchUpdate.addCommand(commands);
-		batchUpdate.execute(new RevWalk(diskRepo) {
-			@Override
-			public boolean isMergedInto(RevCommit base, RevCommit tip) {
-				throw new AssertionError("isMergedInto() should not be called");
-			}
-		}, new StrictWorkMonitor());
-		Map<String, Ref> refs = refdir.getRefs(RefDatabase.ALL);
-		assertEquals(ReceiveCommand.Result.OK, commands.get(0).getResult());
-		assertEquals(A.getId(), refs.get("refs/heads/master").getObjectId());
-	}
-
-	@Test
-	public void testBatchRefUpdateConflict() throws IOException {
-		writeLooseRef("refs/heads/master", A);
-		writeLooseRef("refs/heads/masters", B);
-		List<ReceiveCommand> commands = Arrays.asList(
-				newCommand(A, B, "refs/heads/master",
-						ReceiveCommand.Type.UPDATE),
-				newCommand(null, A, "refs/heads/master/x",
-						ReceiveCommand.Type.CREATE),
-				newCommand(null, A, "refs/heads", ReceiveCommand.Type.CREATE));
-		BatchRefUpdate batchUpdate = refdir.newBatchUpdate();
-		batchUpdate.setAllowNonFastForwards(true);
-		batchUpdate.addCommand(commands);
-		batchUpdate
-				.execute(new RevWalk(diskRepo), NullProgressMonitor.INSTANCE);
-		Map<String, Ref> refs = refdir.getRefs(RefDatabase.ALL);
-		assertEquals(ReceiveCommand.Result.OK, commands.get(0).getResult());
-		assertEquals(ReceiveCommand.Result.LOCK_FAILURE, commands.get(1)
-				.getResult());
-		assertEquals(ReceiveCommand.Result.LOCK_FAILURE, commands.get(2)
-				.getResult());
-		assertEquals("[HEAD, refs/heads/master, refs/heads/masters]", refs
-				.keySet().toString());
-		assertEquals(B.getId(), refs.get("refs/heads/master").getObjectId());
-		assertEquals(B.getId(), refs.get("refs/heads/masters").getObjectId());
-	}
-
-	@Test
-	public void testBatchRefUpdateConflictThanksToDelete() throws IOException {
-		writeLooseRef("refs/heads/master", A);
-		writeLooseRef("refs/heads/masters", B);
-		List<ReceiveCommand> commands = Arrays.asList(
-				newCommand(A, B, "refs/heads/master",
-						ReceiveCommand.Type.UPDATE),
-				newCommand(null, A, "refs/heads/masters/x",
-						ReceiveCommand.Type.CREATE),
-				newCommand(B, null, "refs/heads/masters",
-						ReceiveCommand.Type.DELETE));
-		BatchRefUpdate batchUpdate = refdir.newBatchUpdate();
-		batchUpdate.setAllowNonFastForwards(true);
-		batchUpdate.addCommand(commands);
-		batchUpdate.execute(new RevWalk(diskRepo), new StrictWorkMonitor());
-		Map<String, Ref> refs = refdir.getRefs(RefDatabase.ALL);
-		assertEquals(ReceiveCommand.Result.OK, commands.get(0).getResult());
-		assertEquals(ReceiveCommand.Result.OK, commands.get(1).getResult());
-		assertEquals(ReceiveCommand.Result.OK, commands.get(2).getResult());
-		assertEquals("[HEAD, refs/heads/master, refs/heads/masters/x]", refs
-				.keySet().toString());
-		assertEquals(A.getId(), refs.get("refs/heads/masters/x").getObjectId());
-	}
-
-	private static ReceiveCommand newCommand(RevCommit a, RevCommit b,
-			String string, Type update) {
-		return new ReceiveCommand(a != null ? a.getId() : null,
-				b != null ? b.getId() : null, string, update);
+		refdir.setRetrySleepMs(Arrays.asList(0, 0));
+		LockFile myLock = refdir.lockPackedRefs();
+		try {
+			refdir.pack(Arrays.asList("refs/heads/master"));
+			fail("expected LockFailedException");
+		} catch (LockFailedException e) {
+			assertEquals(refdir.packedRefsFile.getPath(), e.getFile().getPath());
+		} finally {
+			myLock.unlock();
+		}
+		Ref ref = refdir.getRef("refs/heads/master");
+		assertEquals(Storage.LOOSE, ref.getStorage());
 	}
 
 	private void writeLooseRef(String name, AnyObjectId id) throws IOException {
@@ -1439,34 +1329,4 @@ private void deleteLooseRef(String name) {
 		File path = new File(diskRepo.getDirectory(), name);
 		assertTrue("deleted " + name, path.delete());
 	}
-
-	private static final class StrictWorkMonitor implements ProgressMonitor {
-		private int lastWork, totalWork;
-
-		@Override
-		public void start(int totalTasks) {
-			// empty
-		}
-
-		@Override
-		public void beginTask(String title, int total) {
-			this.totalWork = total;
-			lastWork = 0;
-		}
-
-		@Override
-		public void update(int completed) {
-			lastWork += completed;
-		}
-
-		@Override
-		public void endTask() {
-			assertEquals("Units of work recorded", totalWork, lastWork);
-		}
-
-		@Override
-		public boolean isCancelled() {
-			return false;
-		}
-	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefUpdateTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefUpdateTest.java
index 0f26b0f..d8d45a8 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefUpdateTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefUpdateTest.java
@@ -45,6 +45,7 @@
 
 package org.eclipse.jgit.internal.storage.file;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.junit.Assert.assertEquals;
 import static org.eclipse.jgit.lib.Constants.LOCK_SUFFIX;
 import static org.junit.Assert.assertEquals;
@@ -65,6 +66,7 @@
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectInserter;
 import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.RefRename;
@@ -241,14 +243,73 @@ public void testDeleteHead() throws IOException {
 	@Test
 	public void testDeleteHeadInBareRepo() throws IOException {
 		Repository bareRepo = createBareRepository();
+		String master = "refs/heads/master";
+		Ref head = bareRepo.exactRef(Constants.HEAD);
+		assertNotNull(head);
+		assertTrue(head.isSymbolic());
+		assertEquals(master, head.getLeaf().getName());
+		assertNull(head.getObjectId());
+		assertNull(bareRepo.exactRef(master));
+
+		ObjectId blobId;
+		try (ObjectInserter ins = bareRepo.newObjectInserter()) {
+			blobId = ins.insert(Constants.OBJ_BLOB, "contents".getBytes(UTF_8));
+			ins.flush();
+		}
+
+		// Create master via HEAD, so we delete it.
 		RefUpdate ref = bareRepo.updateRef(Constants.HEAD);
-		ref.setNewObjectId(ObjectId
-				.fromString("0123456789012345678901234567890123456789"));
-		// Create the HEAD ref so we can delete it.
+		ref.setNewObjectId(blobId);
 		assertEquals(Result.NEW, ref.update());
+
+		head = bareRepo.exactRef(Constants.HEAD);
+		assertTrue(head.isSymbolic());
+		assertEquals(master, head.getLeaf().getName());
+		assertEquals(blobId, head.getLeaf().getObjectId());
+		assertEquals(blobId, bareRepo.exactRef(master).getObjectId());
+
+		// Unlike in a non-bare repo, deleting the HEAD is allowed, and leaves HEAD
+		// back in a dangling state.
 		ref = bareRepo.updateRef(Constants.HEAD);
-		delete(bareRepo, ref, Result.NO_CHANGE, true, true);
+		ref.setExpectedOldObjectId(blobId);
+		ref.setForceUpdate(true);
+		delete(bareRepo, ref, Result.FORCED, true, true);
+
+		head = bareRepo.exactRef(Constants.HEAD);
+		assertNotNull(head);
+		assertTrue(head.isSymbolic());
+		assertEquals(master, head.getLeaf().getName());
+		assertNull(head.getObjectId());
+		assertNull(bareRepo.exactRef(master));
 	}
+
+	@Test
+	public void testDeleteSymref() throws IOException {
+		RefUpdate dst = updateRef("refs/heads/abc");
+		assertEquals(Result.NEW, dst.update());
+		ObjectId id = dst.getNewObjectId();
+
+		RefUpdate u = db.updateRef("refs/symref");
+		assertEquals(Result.NEW, u.link(dst.getName()));
+
+		Ref ref = db.exactRef(u.getName());
+		assertNotNull(ref);
+		assertTrue(ref.isSymbolic());
+		assertEquals(dst.getName(), ref.getLeaf().getName());
+		assertEquals(id, ref.getLeaf().getObjectId());
+
+		u = db.updateRef(u.getName());
+		u.setDetachingSymbolicRef();
+		u.setForceUpdate(true);
+		assertEquals(Result.FORCED, u.delete());
+
+		assertNull(db.exactRef(u.getName()));
+		ref = db.exactRef(dst.getName());
+		assertNotNull(ref);
+		assertFalse(ref.isSymbolic());
+		assertEquals(id, ref.getObjectId());
+	}
+
 	/**
 	 * Delete a loose ref and make sure the directory in refs is deleted too,
 	 * and the reflog dir too
@@ -899,12 +960,66 @@ public void testRenameRefNameColission2avoided() throws IOException {
 				"HEAD").getReverseEntries().get(0).getComment());
 	}
 
+	@Test
+	public void testCreateMissingObject() throws IOException {
+		String name = "refs/heads/abc";
+		ObjectId bad =
+				ObjectId.fromString("deadbeefdeadbeefdeadbeefdeadbeefdeadbeef");
+		RefUpdate ru = db.updateRef(name);
+		ru.setNewObjectId(bad);
+		Result update = ru.update();
+		assertEquals(Result.REJECTED_MISSING_OBJECT, update);
+
+		Ref ref = db.exactRef(name);
+		assertNull(ref);
+	}
+
+	@Test
+	public void testUpdateMissingObject() throws IOException {
+		String name = "refs/heads/abc";
+		RefUpdate ru = updateRef(name);
+		Result update = ru.update();
+		assertEquals(Result.NEW, update);
+		ObjectId oldId = ru.getNewObjectId();
+
+		ObjectId bad =
+				ObjectId.fromString("deadbeefdeadbeefdeadbeefdeadbeefdeadbeef");
+		ru = db.updateRef(name);
+		ru.setNewObjectId(bad);
+		update = ru.update();
+		assertEquals(Result.REJECTED_MISSING_OBJECT, update);
+
+		Ref ref = db.exactRef(name);
+		assertNotNull(ref);
+		assertEquals(oldId, ref.getObjectId());
+	}
+
+	@Test
+	public void testForceUpdateMissingObject() throws IOException {
+		String name = "refs/heads/abc";
+		RefUpdate ru = updateRef(name);
+		Result update = ru.update();
+		assertEquals(Result.NEW, update);
+		ObjectId oldId = ru.getNewObjectId();
+
+		ObjectId bad =
+				ObjectId.fromString("deadbeefdeadbeefdeadbeefdeadbeefdeadbeef");
+		ru = db.updateRef(name);
+		ru.setNewObjectId(bad);
+		update = ru.forceUpdate();
+		assertEquals(Result.REJECTED_MISSING_OBJECT, update);
+
+		Ref ref = db.exactRef(name);
+		assertNotNull(ref);
+		assertEquals(oldId, ref.getObjectId());
+	}
+
 	private static void writeReflog(Repository db, ObjectId newId, String msg,
 			String refName) throws IOException {
 		RefDirectory refs = (RefDirectory) db.getRefDatabase();
 		RefDirectoryUpdate update = refs.newUpdate(refName, true);
 		update.setNewObjectId(newId);
-		refs.log(update, msg, true);
+		refs.log(false, update, msg, true);
 	}
 
 	private static class SubclassedId extends ObjectId {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogWriterTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogWriterTest.java
index 89b969e..7f40bae 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogWriterTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogWriterTest.java
@@ -61,7 +61,8 @@ public class ReflogWriterTest extends SampleDataRepositoryTestCase {
 
 	@Test
 	public void shouldFilterLineFeedFromMessage() throws Exception {
-		ReflogWriter writer = new ReflogWriter(db);
+		ReflogWriter writer =
+				new ReflogWriter((RefDirectory) db.getRefDatabase());
 		PersonIdent ident = new PersonIdent("John Doe", "john@doe.com",
 				1243028200000L, 120);
 		ObjectId oldId = ObjectId
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/T0003_BasicTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/T0003_BasicTest.java
index ae1e531..9d23d83 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/T0003_BasicTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/T0003_BasicTest.java
@@ -661,33 +661,39 @@ public void test027_UnpackedRefHigherPriorityThanPacked()
 
 	@Test
 	public void test028_LockPackedRef() throws IOException {
+		ObjectId id1;
+		ObjectId id2;
+		try (ObjectInserter ins = db.newObjectInserter()) {
+			id1 = ins.insert(
+					Constants.OBJ_BLOB, "contents1".getBytes(Constants.CHARSET));
+			id2 = ins.insert(
+					Constants.OBJ_BLOB, "contents2".getBytes(Constants.CHARSET));
+			ins.flush();
+		}
+
 		writeTrashFile(".git/packed-refs",
-				"7f822839a2fe9760f386cbbbcb3f92c5fe81def7 refs/heads/foobar");
+				id1.name() + " refs/heads/foobar");
 		writeTrashFile(".git/HEAD", "ref: refs/heads/foobar\n");
 		BUG_WorkAroundRacyGitIssues("packed-refs");
 		BUG_WorkAroundRacyGitIssues("HEAD");
 
 		ObjectId resolve = db.resolve("HEAD");
-		assertEquals("7f822839a2fe9760f386cbbbcb3f92c5fe81def7", resolve.name());
+		assertEquals(id1, resolve);
 
 		RefUpdate lockRef = db.updateRef("HEAD");
-		ObjectId newId = ObjectId
-				.fromString("07f822839a2fe9760f386cbbbcb3f92c5fe81def");
-		lockRef.setNewObjectId(newId);
+		lockRef.setNewObjectId(id2);
 		assertEquals(RefUpdate.Result.FORCED, lockRef.forceUpdate());
 
 		assertTrue(new File(db.getDirectory(), "refs/heads/foobar").exists());
-		assertEquals(newId, db.resolve("refs/heads/foobar"));
+		assertEquals(id2, db.resolve("refs/heads/foobar"));
 
 		// Again. The ref already exists
 		RefUpdate lockRef2 = db.updateRef("HEAD");
-		ObjectId newId2 = ObjectId
-				.fromString("7f822839a2fe9760f386cbbbcb3f92c5fe81def7");
-		lockRef2.setNewObjectId(newId2);
+		lockRef2.setNewObjectId(id1);
 		assertEquals(RefUpdate.Result.FORCED, lockRef2.forceUpdate());
 
 		assertTrue(new File(db.getDirectory(), "refs/heads/foobar").exists());
-		assertEquals(newId2, db.resolve("refs/heads/foobar"));
+		assertEquals(id1, db.resolve("refs/heads/foobar"));
 	}
 
 	@Test
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/MergedReftableTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/MergedReftableTest.java
new file mode 100644
index 0000000..adba048
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/MergedReftableTest.java
@@ -0,0 +1,392 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.reftable;
+
+import static org.eclipse.jgit.lib.Constants.HEAD;
+import static org.eclipse.jgit.lib.Constants.OBJECT_ID_LENGTH;
+import static org.eclipse.jgit.lib.Constants.R_HEADS;
+import static org.eclipse.jgit.lib.Ref.Storage.NEW;
+import static org.eclipse.jgit.lib.Ref.Storage.PACKED;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.eclipse.jgit.internal.storage.io.BlockSource;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectIdRef;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.RefComparator;
+import org.junit.Test;
+
+public class MergedReftableTest {
+	@Test
+	public void noTables() throws IOException {
+		MergedReftable mr = merge(new byte[0][]);
+		try (RefCursor rc = mr.allRefs()) {
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = mr.seekRef(HEAD)) {
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = mr.seekRef(R_HEADS)) {
+			assertFalse(rc.next());
+		}
+	}
+
+	@Test
+	public void oneEmptyTable() throws IOException {
+		MergedReftable mr = merge(write());
+		try (RefCursor rc = mr.allRefs()) {
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = mr.seekRef(HEAD)) {
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = mr.seekRef(R_HEADS)) {
+			assertFalse(rc.next());
+		}
+	}
+
+	@Test
+	public void twoEmptyTables() throws IOException {
+		MergedReftable mr = merge(write(), write());
+		try (RefCursor rc = mr.allRefs()) {
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = mr.seekRef(HEAD)) {
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = mr.seekRef(R_HEADS)) {
+			assertFalse(rc.next());
+		}
+	}
+
+	@SuppressWarnings("boxing")
+	@Test
+	public void oneTableScan() throws IOException {
+		List<Ref> refs = new ArrayList<>();
+		for (int i = 1; i <= 567; i++) {
+			refs.add(ref(String.format("refs/heads/%03d", i), i));
+		}
+
+		MergedReftable mr = merge(write(refs));
+		try (RefCursor rc = mr.allRefs()) {
+			for (Ref exp : refs) {
+				assertTrue("has " + exp.getName(), rc.next());
+				Ref act = rc.getRef();
+				assertEquals(exp.getName(), act.getName());
+				assertEquals(exp.getObjectId(), act.getObjectId());
+			}
+			assertFalse(rc.next());
+		}
+	}
+
+	@Test
+	public void deleteIsHidden() throws IOException {
+		List<Ref> delta1 = Arrays.asList(
+				ref("refs/heads/apple", 1),
+				ref("refs/heads/master", 2));
+		List<Ref> delta2 = Arrays.asList(delete("refs/heads/apple"));
+
+		MergedReftable mr = merge(write(delta1), write(delta2));
+		try (RefCursor rc = mr.allRefs()) {
+			assertTrue(rc.next());
+			assertEquals("refs/heads/master", rc.getRef().getName());
+			assertEquals(id(2), rc.getRef().getObjectId());
+			assertFalse(rc.next());
+		}
+	}
+
+	@Test
+	public void twoTableSeek() throws IOException {
+		List<Ref> delta1 = Arrays.asList(
+				ref("refs/heads/apple", 1),
+				ref("refs/heads/master", 2));
+		List<Ref> delta2 = Arrays.asList(ref("refs/heads/banana", 3));
+
+		MergedReftable mr = merge(write(delta1), write(delta2));
+		try (RefCursor rc = mr.seekRef("refs/heads/master")) {
+			assertTrue(rc.next());
+			assertEquals("refs/heads/master", rc.getRef().getName());
+			assertEquals(id(2), rc.getRef().getObjectId());
+			assertFalse(rc.next());
+		}
+	}
+
+	@Test
+	public void twoTableById() throws IOException {
+		List<Ref> delta1 = Arrays.asList(
+				ref("refs/heads/apple", 1),
+				ref("refs/heads/master", 2));
+		List<Ref> delta2 = Arrays.asList(ref("refs/heads/banana", 3));
+
+		MergedReftable mr = merge(write(delta1), write(delta2));
+		try (RefCursor rc = mr.byObjectId(id(2))) {
+			assertTrue(rc.next());
+			assertEquals("refs/heads/master", rc.getRef().getName());
+			assertEquals(id(2), rc.getRef().getObjectId());
+			assertFalse(rc.next());
+		}
+	}
+
+	@SuppressWarnings("boxing")
+	@Test
+	public void fourTableScan() throws IOException {
+		List<Ref> base = new ArrayList<>();
+		for (int i = 1; i <= 567; i++) {
+			base.add(ref(String.format("refs/heads/%03d", i), i));
+		}
+
+		List<Ref> delta1 = Arrays.asList(
+				ref("refs/heads/next", 4),
+				ref(String.format("refs/heads/%03d", 55), 4096));
+		List<Ref> delta2 = Arrays.asList(
+				delete("refs/heads/next"),
+				ref(String.format("refs/heads/%03d", 55), 8192));
+		List<Ref> delta3 = Arrays.asList(
+				ref("refs/heads/master", 4242),
+				ref(String.format("refs/heads/%03d", 42), 5120),
+				ref(String.format("refs/heads/%03d", 98), 6120));
+
+		List<Ref> expected = merge(base, delta1, delta2, delta3);
+		MergedReftable mr = merge(
+				write(base),
+				write(delta1),
+				write(delta2),
+				write(delta3));
+		try (RefCursor rc = mr.allRefs()) {
+			for (Ref exp : expected) {
+				assertTrue("has " + exp.getName(), rc.next());
+				Ref act = rc.getRef();
+				assertEquals(exp.getName(), act.getName());
+				assertEquals(exp.getObjectId(), act.getObjectId());
+			}
+			assertFalse(rc.next());
+		}
+	}
+
+	@Test
+	public void scanIncludeDeletes() throws IOException {
+		List<Ref> delta1 = Arrays.asList(ref("refs/heads/next", 4));
+		List<Ref> delta2 = Arrays.asList(delete("refs/heads/next"));
+		List<Ref> delta3 = Arrays.asList(ref("refs/heads/master", 8));
+
+		MergedReftable mr = merge(write(delta1), write(delta2), write(delta3));
+		mr.setIncludeDeletes(true);
+		try (RefCursor rc = mr.allRefs()) {
+			assertTrue(rc.next());
+			Ref r = rc.getRef();
+			assertEquals("refs/heads/master", r.getName());
+			assertEquals(id(8), r.getObjectId());
+
+			assertTrue(rc.next());
+			r = rc.getRef();
+			assertEquals("refs/heads/next", r.getName());
+			assertEquals(NEW, r.getStorage());
+			assertNull(r.getObjectId());
+
+			assertFalse(rc.next());
+		}
+	}
+
+	@SuppressWarnings("boxing")
+	@Test
+	public void oneTableSeek() throws IOException {
+		List<Ref> refs = new ArrayList<>();
+		for (int i = 1; i <= 567; i++) {
+			refs.add(ref(String.format("refs/heads/%03d", i), i));
+		}
+
+		MergedReftable mr = merge(write(refs));
+		for (Ref exp : refs) {
+			try (RefCursor rc = mr.seekRef(exp.getName())) {
+				assertTrue("has " + exp.getName(), rc.next());
+				Ref act = rc.getRef();
+				assertEquals(exp.getName(), act.getName());
+				assertEquals(exp.getObjectId(), act.getObjectId());
+				assertFalse(rc.next());
+			}
+		}
+	}
+
+	@Test
+	public void missedUpdate() throws IOException {
+		ByteArrayOutputStream buf = new ByteArrayOutputStream();
+		ReftableWriter writer = new ReftableWriter()
+				.setMinUpdateIndex(1)
+				.setMaxUpdateIndex(3)
+				.begin(buf);
+		writer.writeRef(ref("refs/heads/a", 1), 1);
+		writer.writeRef(ref("refs/heads/c", 3), 3);
+		writer.finish();
+		byte[] base = buf.toByteArray();
+
+		byte[] delta = write(Arrays.asList(
+				ref("refs/heads/b", 2),
+				ref("refs/heads/c", 4)),
+				2);
+		MergedReftable mr = merge(base, delta);
+		try (RefCursor rc = mr.allRefs()) {
+			assertTrue(rc.next());
+			assertEquals("refs/heads/a", rc.getRef().getName());
+			assertEquals(id(1), rc.getRef().getObjectId());
+			assertEquals(1, rc.getUpdateIndex());
+
+			assertTrue(rc.next());
+			assertEquals("refs/heads/b", rc.getRef().getName());
+			assertEquals(id(2), rc.getRef().getObjectId());
+			assertEquals(2, rc.getUpdateIndex());
+
+			assertTrue(rc.next());
+			assertEquals("refs/heads/c", rc.getRef().getName());
+			assertEquals(id(3), rc.getRef().getObjectId());
+			assertEquals(3, rc.getUpdateIndex());
+		}
+	}
+
+	@Test
+	public void compaction() throws IOException {
+		List<Ref> delta1 = Arrays.asList(
+				ref("refs/heads/next", 4),
+				ref("refs/heads/master", 1));
+		List<Ref> delta2 = Arrays.asList(delete("refs/heads/next"));
+		List<Ref> delta3 = Arrays.asList(ref("refs/heads/master", 8));
+
+		ReftableCompactor compactor = new ReftableCompactor();
+		compactor.addAll(Arrays.asList(
+				read(write(delta1)),
+				read(write(delta2)),
+				read(write(delta3))));
+		ByteArrayOutputStream out = new ByteArrayOutputStream();
+		compactor.compact(out);
+		byte[] table = out.toByteArray();
+
+		ReftableReader reader = read(table);
+		try (RefCursor rc = reader.allRefs()) {
+			assertTrue(rc.next());
+			Ref r = rc.getRef();
+			assertEquals("refs/heads/master", r.getName());
+			assertEquals(id(8), r.getObjectId());
+			assertFalse(rc.next());
+		}
+	}
+
+	private static MergedReftable merge(byte[]... table) {
+		List<Reftable> stack = new ArrayList<>(table.length);
+		for (byte[] b : table) {
+			stack.add(read(b));
+		}
+		return new MergedReftable(stack);
+	}
+
+	private static ReftableReader read(byte[] table) {
+		return new ReftableReader(BlockSource.from(table));
+	}
+
+	private static Ref ref(String name, int id) {
+		return new ObjectIdRef.PeeledNonTag(PACKED, name, id(id));
+	}
+
+	private static Ref delete(String name) {
+		return new ObjectIdRef.Unpeeled(NEW, name, null);
+	}
+
+	private static ObjectId id(int i) {
+		byte[] buf = new byte[OBJECT_ID_LENGTH];
+		buf[0] = (byte) (i & 0xff);
+		buf[1] = (byte) ((i >>> 8) & 0xff);
+		buf[2] = (byte) ((i >>> 16) & 0xff);
+		buf[3] = (byte) (i >>> 24);
+		return ObjectId.fromRaw(buf);
+	}
+
+	private byte[] write(Ref... refs) throws IOException {
+		return write(Arrays.asList(refs));
+	}
+
+	private byte[] write(Collection<Ref> refs) throws IOException {
+		return write(refs, 1);
+	}
+
+	private byte[] write(Collection<Ref> refs, long updateIndex)
+			throws IOException {
+		ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+		new ReftableWriter()
+				.setMinUpdateIndex(updateIndex)
+				.setMaxUpdateIndex(updateIndex)
+				.begin(buffer)
+				.sortAndWriteRefs(refs)
+				.finish();
+		return buffer.toByteArray();
+	}
+
+	@SafeVarargs
+	private static List<Ref> merge(List<Ref>... tables) {
+		Map<String, Ref> expect = new HashMap<>();
+		for (List<Ref> t : tables) {
+			for (Ref r : t) {
+				if (r.getStorage() == NEW && r.getObjectId() == null) {
+					expect.remove(r.getName());
+				} else {
+					expect.put(r.getName(), r);
+				}
+			}
+		}
+
+		List<Ref> expected = new ArrayList<>(expect.values());
+		Collections.sort(expected, RefComparator.INSTANCE);
+		return expected;
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/ReftableTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/ReftableTest.java
new file mode 100644
index 0000000..3ea3061
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/ReftableTest.java
@@ -0,0 +1,726 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.reftable;
+
+import static org.eclipse.jgit.lib.Constants.HEAD;
+import static org.eclipse.jgit.lib.Constants.OBJECT_ID_LENGTH;
+import static org.eclipse.jgit.lib.Constants.R_HEADS;
+import static org.eclipse.jgit.lib.Ref.Storage.NEW;
+import static org.eclipse.jgit.lib.Ref.Storage.PACKED;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.internal.storage.io.BlockSource;
+import org.eclipse.jgit.internal.storage.reftable.ReftableWriter.Stats;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectIdRef;
+import org.eclipse.jgit.lib.PersonIdent;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.ReflogEntry;
+import org.eclipse.jgit.lib.SymbolicRef;
+import org.junit.Test;
+
+public class ReftableTest {
+	private static final String MASTER = "refs/heads/master";
+	private static final String NEXT = "refs/heads/next";
+	private static final String V1_0 = "refs/tags/v1.0";
+
+	private Stats stats;
+
+	@Test
+	public void emptyTable() throws IOException {
+		byte[] table = write();
+		assertEquals(92 /* header, footer */, table.length);
+		assertEquals('R', table[0]);
+		assertEquals('E', table[1]);
+		assertEquals('F', table[2]);
+		assertEquals('T', table[3]);
+		assertEquals(0x01, table[4]);
+		assertTrue(ReftableConstants.isFileHeaderMagic(table, 0, 8));
+		assertTrue(ReftableConstants.isFileHeaderMagic(table, 24, 92));
+
+		Reftable t = read(table);
+		try (RefCursor rc = t.allRefs()) {
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = t.seekRef(HEAD)) {
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = t.seekRef(R_HEADS)) {
+			assertFalse(rc.next());
+		}
+		try (LogCursor rc = t.allLogs()) {
+			assertFalse(rc.next());
+		}
+	}
+
+	@Test
+	public void emptyVirtualTableFromRefs() throws IOException {
+		Reftable t = Reftable.from(Collections.emptyList());
+		try (RefCursor rc = t.allRefs()) {
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = t.seekRef(HEAD)) {
+			assertFalse(rc.next());
+		}
+		try (LogCursor rc = t.allLogs()) {
+			assertFalse(rc.next());
+		}
+	}
+
+	@Test
+	public void estimateCurrentBytesOneRef() throws IOException {
+		Ref exp = ref(MASTER, 1);
+		int expBytes = 24 + 4 + 5 + 4 + MASTER.length() + 20 + 68;
+
+		byte[] table;
+		ReftableConfig cfg = new ReftableConfig();
+		cfg.setIndexObjects(false);
+		ReftableWriter writer = new ReftableWriter().setConfig(cfg);
+		try (ByteArrayOutputStream buf = new ByteArrayOutputStream()) {
+			writer.begin(buf);
+			assertEquals(92, writer.estimateTotalBytes());
+			writer.writeRef(exp);
+			assertEquals(expBytes, writer.estimateTotalBytes());
+			writer.finish();
+			table = buf.toByteArray();
+		}
+		assertEquals(expBytes, table.length);
+	}
+
+	@SuppressWarnings("boxing")
+	@Test
+	public void estimateCurrentBytesWithIndex() throws IOException {
+		List<Ref> refs = new ArrayList<>();
+		for (int i = 1; i <= 5670; i++) {
+			refs.add(ref(String.format("refs/heads/%04d", i), i));
+		}
+
+		ReftableConfig cfg = new ReftableConfig();
+		cfg.setIndexObjects(false);
+		cfg.setMaxIndexLevels(1);
+
+		int expBytes = 147860;
+		byte[] table;
+		ReftableWriter writer = new ReftableWriter().setConfig(cfg);
+		try (ByteArrayOutputStream buf = new ByteArrayOutputStream()) {
+			writer.begin(buf);
+			writer.sortAndWriteRefs(refs);
+			assertEquals(expBytes, writer.estimateTotalBytes());
+			writer.finish();
+			stats = writer.getStats();
+			table = buf.toByteArray();
+		}
+		assertEquals(1, stats.refIndexLevels());
+		assertEquals(expBytes, table.length);
+	}
+
+	@Test
+	public void oneIdRef() throws IOException {
+		Ref exp = ref(MASTER, 1);
+		byte[] table = write(exp);
+		assertEquals(24 + 4 + 5 + 4 + MASTER.length() + 20 + 68, table.length);
+
+		ReftableReader t = read(table);
+		try (RefCursor rc = t.allRefs()) {
+			assertTrue(rc.next());
+			Ref act = rc.getRef();
+			assertNotNull(act);
+			assertEquals(PACKED, act.getStorage());
+			assertTrue(act.isPeeled());
+			assertFalse(act.isSymbolic());
+			assertEquals(exp.getName(), act.getName());
+			assertEquals(exp.getObjectId(), act.getObjectId());
+			assertNull(act.getPeeledObjectId());
+			assertFalse(rc.wasDeleted());
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = t.seekRef(MASTER)) {
+			assertTrue(rc.next());
+			Ref act = rc.getRef();
+			assertNotNull(act);
+			assertEquals(exp.getName(), act.getName());
+			assertFalse(rc.next());
+		}
+	}
+
+	@Test
+	public void oneTagRef() throws IOException {
+		Ref exp = tag(V1_0, 1, 2);
+		byte[] table = write(exp);
+		assertEquals(24 + 4 + 5 + 3 + V1_0.length() + 40 + 68, table.length);
+
+		ReftableReader t = read(table);
+		try (RefCursor rc = t.allRefs()) {
+			assertTrue(rc.next());
+			Ref act = rc.getRef();
+			assertNotNull(act);
+			assertEquals(PACKED, act.getStorage());
+			assertTrue(act.isPeeled());
+			assertFalse(act.isSymbolic());
+			assertEquals(exp.getName(), act.getName());
+			assertEquals(exp.getObjectId(), act.getObjectId());
+			assertEquals(exp.getPeeledObjectId(), act.getPeeledObjectId());
+		}
+	}
+
+	@Test
+	public void oneSymbolicRef() throws IOException {
+		Ref exp = sym(HEAD, MASTER);
+		byte[] table = write(exp);
+		assertEquals(
+				24 + 4 + 5 + 2 + HEAD.length() + 2 + MASTER.length() + 68,
+				table.length);
+
+		ReftableReader t = read(table);
+		try (RefCursor rc = t.allRefs()) {
+			assertTrue(rc.next());
+			Ref act = rc.getRef();
+			assertNotNull(act);
+			assertTrue(act.isSymbolic());
+			assertEquals(exp.getName(), act.getName());
+			assertNotNull(act.getLeaf());
+			assertEquals(MASTER, act.getTarget().getName());
+			assertNull(act.getObjectId());
+		}
+	}
+
+	@Test
+	public void resolveSymbolicRef() throws IOException {
+		Reftable t = read(write(
+				sym(HEAD, "refs/heads/tmp"),
+				sym("refs/heads/tmp", MASTER),
+				ref(MASTER, 1)));
+
+		Ref head = t.exactRef(HEAD);
+		assertNull(head.getObjectId());
+		assertEquals("refs/heads/tmp", head.getTarget().getName());
+
+		head = t.resolve(head);
+		assertNotNull(head);
+		assertEquals(id(1), head.getObjectId());
+
+		Ref master = t.exactRef(MASTER);
+		assertNotNull(master);
+		assertSame(master, t.resolve(master));
+	}
+
+	@Test
+	public void failDeepChainOfSymbolicRef() throws IOException {
+		Reftable t = read(write(
+				sym(HEAD, "refs/heads/1"),
+				sym("refs/heads/1", "refs/heads/2"),
+				sym("refs/heads/2", "refs/heads/3"),
+				sym("refs/heads/3", "refs/heads/4"),
+				sym("refs/heads/4", "refs/heads/5"),
+				sym("refs/heads/5", MASTER),
+				ref(MASTER, 1)));
+
+		Ref head = t.exactRef(HEAD);
+		assertNull(head.getObjectId());
+		assertNull(t.resolve(head));
+	}
+
+	@Test
+	public void oneDeletedRef() throws IOException {
+		String name = "refs/heads/gone";
+		Ref exp = newRef(name);
+		byte[] table = write(exp);
+		assertEquals(24 + 4 + 5 + 3 + name.length() + 68, table.length);
+
+		ReftableReader t = read(table);
+		try (RefCursor rc = t.allRefs()) {
+			assertFalse(rc.next());
+		}
+
+		t.setIncludeDeletes(true);
+		try (RefCursor rc = t.allRefs()) {
+			assertTrue(rc.next());
+			Ref act = rc.getRef();
+			assertNotNull(act);
+			assertFalse(act.isSymbolic());
+			assertEquals(name, act.getName());
+			assertEquals(NEW, act.getStorage());
+			assertNull(act.getObjectId());
+			assertTrue(rc.wasDeleted());
+		}
+	}
+
+	@Test
+	public void seekNotFound() throws IOException {
+		Ref exp = ref(MASTER, 1);
+		ReftableReader t = read(write(exp));
+		try (RefCursor rc = t.seekRef("refs/heads/a")) {
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = t.seekRef("refs/heads/n")) {
+			assertFalse(rc.next());
+		}
+	}
+
+	@Test
+	public void namespaceNotFound() throws IOException {
+		Ref exp = ref(MASTER, 1);
+		ReftableReader t = read(write(exp));
+		try (RefCursor rc = t.seekRef("refs/changes/")) {
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = t.seekRef("refs/tags/")) {
+			assertFalse(rc.next());
+		}
+	}
+
+	@Test
+	public void namespaceHeads() throws IOException {
+		Ref master = ref(MASTER, 1);
+		Ref next = ref(NEXT, 2);
+		Ref v1 = tag(V1_0, 3, 4);
+
+		ReftableReader t = read(write(master, next, v1));
+		try (RefCursor rc = t.seekRef("refs/tags/")) {
+			assertTrue(rc.next());
+			assertEquals(V1_0, rc.getRef().getName());
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = t.seekRef("refs/heads/")) {
+			assertTrue(rc.next());
+			assertEquals(MASTER, rc.getRef().getName());
+
+			assertTrue(rc.next());
+			assertEquals(NEXT, rc.getRef().getName());
+
+			assertFalse(rc.next());
+		}
+	}
+
+	@SuppressWarnings("boxing")
+	@Test
+	public void indexScan() throws IOException {
+		List<Ref> refs = new ArrayList<>();
+		for (int i = 1; i <= 5670; i++) {
+			refs.add(ref(String.format("refs/heads/%04d", i), i));
+		}
+
+		byte[] table = write(refs);
+		assertTrue(stats.refIndexLevels() > 0);
+		assertTrue(stats.refIndexSize() > 0);
+		assertScan(refs, read(table));
+	}
+
+	@SuppressWarnings("boxing")
+	@Test
+	public void indexSeek() throws IOException {
+		List<Ref> refs = new ArrayList<>();
+		for (int i = 1; i <= 5670; i++) {
+			refs.add(ref(String.format("refs/heads/%04d", i), i));
+		}
+
+		byte[] table = write(refs);
+		assertTrue(stats.refIndexLevels() > 0);
+		assertTrue(stats.refIndexSize() > 0);
+		assertSeek(refs, read(table));
+	}
+
+	@SuppressWarnings("boxing")
+	@Test
+	public void noIndexScan() throws IOException {
+		List<Ref> refs = new ArrayList<>();
+		for (int i = 1; i <= 567; i++) {
+			refs.add(ref(String.format("refs/heads/%03d", i), i));
+		}
+
+		byte[] table = write(refs);
+		assertEquals(0, stats.refIndexLevels());
+		assertEquals(0, stats.refIndexSize());
+		assertEquals(table.length, stats.totalBytes());
+		assertScan(refs, read(table));
+	}
+
+	@SuppressWarnings("boxing")
+	@Test
+	public void noIndexSeek() throws IOException {
+		List<Ref> refs = new ArrayList<>();
+		for (int i = 1; i <= 567; i++) {
+			refs.add(ref(String.format("refs/heads/%03d", i), i));
+		}
+
+		byte[] table = write(refs);
+		assertEquals(0, stats.refIndexLevels());
+		assertSeek(refs, read(table));
+	}
+
+	@Test
+	public void withReflog() throws IOException {
+		Ref master = ref(MASTER, 1);
+		Ref next = ref(NEXT, 2);
+		PersonIdent who = new PersonIdent("Log", "Ger", 1500079709, -8 * 60);
+		String msg = "test";
+
+		ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+		ReftableWriter writer = new ReftableWriter()
+				.setMinUpdateIndex(1)
+				.setMaxUpdateIndex(1)
+				.begin(buffer);
+
+		writer.writeRef(master);
+		writer.writeRef(next);
+
+		writer.writeLog(MASTER, 1, who, ObjectId.zeroId(), id(1), msg);
+		writer.writeLog(NEXT, 1, who, ObjectId.zeroId(), id(2), msg);
+
+		writer.finish();
+		byte[] table = buffer.toByteArray();
+		assertEquals(247, table.length);
+
+		ReftableReader t = read(table);
+		try (RefCursor rc = t.allRefs()) {
+			assertTrue(rc.next());
+			assertEquals(MASTER, rc.getRef().getName());
+			assertEquals(id(1), rc.getRef().getObjectId());
+			assertEquals(1, rc.getUpdateIndex());
+
+			assertTrue(rc.next());
+			assertEquals(NEXT, rc.getRef().getName());
+			assertEquals(id(2), rc.getRef().getObjectId());
+			assertFalse(rc.next());
+		}
+		try (LogCursor lc = t.allLogs()) {
+			assertTrue(lc.next());
+			assertEquals(MASTER, lc.getRefName());
+			assertEquals(1, lc.getUpdateIndex());
+			assertEquals(ObjectId.zeroId(), lc.getReflogEntry().getOldId());
+			assertEquals(id(1), lc.getReflogEntry().getNewId());
+			assertEquals(who, lc.getReflogEntry().getWho());
+			assertEquals(msg, lc.getReflogEntry().getComment());
+
+			assertTrue(lc.next());
+			assertEquals(NEXT, lc.getRefName());
+			assertEquals(1, lc.getUpdateIndex());
+			assertEquals(ObjectId.zeroId(), lc.getReflogEntry().getOldId());
+			assertEquals(id(2), lc.getReflogEntry().getNewId());
+			assertEquals(who, lc.getReflogEntry().getWho());
+			assertEquals(msg, lc.getReflogEntry().getComment());
+
+			assertFalse(lc.next());
+		}
+	}
+
+	@Test
+	public void onlyReflog() throws IOException {
+		PersonIdent who = new PersonIdent("Log", "Ger", 1500079709, -8 * 60);
+		String msg = "test";
+
+		ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+		ReftableWriter writer = new ReftableWriter()
+				.setMinUpdateIndex(1)
+				.setMaxUpdateIndex(1)
+				.begin(buffer);
+		writer.writeLog(MASTER, 1, who, ObjectId.zeroId(), id(1), msg);
+		writer.writeLog(NEXT, 1, who, ObjectId.zeroId(), id(2), msg);
+		writer.finish();
+		byte[] table = buffer.toByteArray();
+		stats = writer.getStats();
+		assertEquals(170, table.length);
+		assertEquals(0, stats.refCount());
+		assertEquals(0, stats.refBytes());
+		assertEquals(0, stats.refIndexLevels());
+
+		ReftableReader t = read(table);
+		try (RefCursor rc = t.allRefs()) {
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = t.seekRef("refs/heads/")) {
+			assertFalse(rc.next());
+		}
+		try (LogCursor lc = t.allLogs()) {
+			assertTrue(lc.next());
+			assertEquals(MASTER, lc.getRefName());
+			assertEquals(1, lc.getUpdateIndex());
+			assertEquals(ObjectId.zeroId(), lc.getReflogEntry().getOldId());
+			assertEquals(id(1), lc.getReflogEntry().getNewId());
+			assertEquals(who, lc.getReflogEntry().getWho());
+			assertEquals(msg, lc.getReflogEntry().getComment());
+
+			assertTrue(lc.next());
+			assertEquals(NEXT, lc.getRefName());
+			assertEquals(1, lc.getUpdateIndex());
+			assertEquals(ObjectId.zeroId(), lc.getReflogEntry().getOldId());
+			assertEquals(id(2), lc.getReflogEntry().getNewId());
+			assertEquals(who, lc.getReflogEntry().getWho());
+			assertEquals(msg, lc.getReflogEntry().getComment());
+
+			assertFalse(lc.next());
+		}
+	}
+
+	@SuppressWarnings("boxing")
+	@Test
+	public void logScan() throws IOException {
+		ReftableConfig cfg = new ReftableConfig();
+		cfg.setRefBlockSize(256);
+		cfg.setLogBlockSize(2048);
+
+		ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+		ReftableWriter writer = new ReftableWriter(cfg);
+		writer.setMinUpdateIndex(1).setMaxUpdateIndex(1).begin(buffer);
+
+		List<Ref> refs = new ArrayList<>();
+		for (int i = 1; i <= 5670; i++) {
+			Ref ref = ref(String.format("refs/heads/%03d", i), i);
+			refs.add(ref);
+			writer.writeRef(ref);
+		}
+
+		PersonIdent who = new PersonIdent("Log", "Ger", 1500079709, -8 * 60);
+		for (Ref ref : refs) {
+			writer.writeLog(ref.getName(), 1, who,
+					ObjectId.zeroId(), ref.getObjectId(),
+					"create " + ref.getName());
+		}
+		writer.finish();
+		stats = writer.getStats();
+		assertTrue(stats.logBytes() > 4096);
+		byte[] table = buffer.toByteArray();
+
+		ReftableReader t = read(table);
+		try (LogCursor lc = t.allLogs()) {
+			for (Ref exp : refs) {
+				assertTrue("has " + exp.getName(), lc.next());
+				assertEquals(exp.getName(), lc.getRefName());
+				ReflogEntry entry = lc.getReflogEntry();
+				assertNotNull(entry);
+				assertEquals(who, entry.getWho());
+				assertEquals(ObjectId.zeroId(), entry.getOldId());
+				assertEquals(exp.getObjectId(), entry.getNewId());
+				assertEquals("create " + exp.getName(), entry.getComment());
+			}
+			assertFalse(lc.next());
+		}
+	}
+
+	@SuppressWarnings("boxing")
+	@Test
+	public void byObjectIdOneRefNoIndex() throws IOException {
+		List<Ref> refs = new ArrayList<>();
+		for (int i = 1; i <= 200; i++) {
+			refs.add(ref(String.format("refs/heads/%02d", i), i));
+		}
+		refs.add(ref("refs/heads/master", 100));
+
+		ReftableReader t = read(write(refs));
+		assertEquals(0, stats.objIndexSize());
+
+		try (RefCursor rc = t.byObjectId(id(42))) {
+			assertTrue("has 42", rc.next());
+			assertEquals("refs/heads/42", rc.getRef().getName());
+			assertEquals(id(42), rc.getRef().getObjectId());
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = t.byObjectId(id(100))) {
+			assertTrue("has 100", rc.next());
+			assertEquals("refs/heads/100", rc.getRef().getName());
+			assertEquals(id(100), rc.getRef().getObjectId());
+
+			assertTrue("has master", rc.next());
+			assertEquals("refs/heads/master", rc.getRef().getName());
+			assertEquals(id(100), rc.getRef().getObjectId());
+
+			assertFalse(rc.next());
+		}
+	}
+
+	@SuppressWarnings("boxing")
+	@Test
+	public void byObjectIdOneRefWithIndex() throws IOException {
+		List<Ref> refs = new ArrayList<>();
+		for (int i = 1; i <= 5200; i++) {
+			refs.add(ref(String.format("refs/heads/%02d", i), i));
+		}
+		refs.add(ref("refs/heads/master", 100));
+
+		ReftableReader t = read(write(refs));
+		assertTrue(stats.objIndexSize() > 0);
+
+		try (RefCursor rc = t.byObjectId(id(42))) {
+			assertTrue("has 42", rc.next());
+			assertEquals("refs/heads/42", rc.getRef().getName());
+			assertEquals(id(42), rc.getRef().getObjectId());
+			assertFalse(rc.next());
+		}
+		try (RefCursor rc = t.byObjectId(id(100))) {
+			assertTrue("has 100", rc.next());
+			assertEquals("refs/heads/100", rc.getRef().getName());
+			assertEquals(id(100), rc.getRef().getObjectId());
+
+			assertTrue("has master", rc.next());
+			assertEquals("refs/heads/master", rc.getRef().getName());
+			assertEquals(id(100), rc.getRef().getObjectId());
+
+			assertFalse(rc.next());
+		}
+	}
+
+	@Test
+	public void unpeeledDoesNotWrite() {
+		try {
+			write(new ObjectIdRef.Unpeeled(PACKED, MASTER, id(1)));
+			fail("expected IOException");
+		} catch (IOException e) {
+			assertEquals(JGitText.get().peeledRefIsRequired, e.getMessage());
+		}
+	}
+
+	@Test
+	public void nameTooLongDoesNotWrite() throws IOException {
+		try {
+			ReftableConfig cfg = new ReftableConfig();
+			cfg.setRefBlockSize(64);
+
+			ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+			ReftableWriter writer = new ReftableWriter(cfg).begin(buffer);
+			writer.writeRef(ref("refs/heads/i-am-not-a-teapot", 1));
+			writer.finish();
+			fail("expected BlockSizeTooSmallException");
+		} catch (BlockSizeTooSmallException e) {
+			assertEquals(85, e.getMinimumBlockSize());
+		}
+	}
+
+	@Test
+	public void badCrc32() throws IOException {
+		byte[] table = write();
+		table[table.length - 1] = 0x42;
+
+		try {
+			read(table).seekRef(HEAD);
+			fail("expected IOException");
+		} catch (IOException e) {
+			assertEquals(JGitText.get().invalidReftableCRC, e.getMessage());
+		}
+	}
+
+
+	private static void assertScan(List<Ref> refs, Reftable t)
+			throws IOException {
+		try (RefCursor rc = t.allRefs()) {
+			for (Ref exp : refs) {
+				assertTrue("has " + exp.getName(), rc.next());
+				Ref act = rc.getRef();
+				assertEquals(exp.getName(), act.getName());
+				assertEquals(exp.getObjectId(), act.getObjectId());
+			}
+			assertFalse(rc.next());
+		}
+	}
+
+	private static void assertSeek(List<Ref> refs, Reftable t)
+			throws IOException {
+		for (Ref exp : refs) {
+			try (RefCursor rc = t.seekRef(exp.getName())) {
+				assertTrue("has " + exp.getName(), rc.next());
+				Ref act = rc.getRef();
+				assertEquals(exp.getName(), act.getName());
+				assertEquals(exp.getObjectId(), act.getObjectId());
+				assertFalse(rc.next());
+			}
+		}
+	}
+
+	private static Ref ref(String name, int id) {
+		return new ObjectIdRef.PeeledNonTag(PACKED, name, id(id));
+	}
+
+	private static Ref tag(String name, int id1, int id2) {
+		return new ObjectIdRef.PeeledTag(PACKED, name, id(id1), id(id2));
+	}
+
+	private static Ref sym(String name, String target) {
+		return new SymbolicRef(name, newRef(target));
+	}
+
+	private static Ref newRef(String name) {
+		return new ObjectIdRef.Unpeeled(NEW, name, null);
+	}
+
+	private static ObjectId id(int i) {
+		byte[] buf = new byte[OBJECT_ID_LENGTH];
+		buf[0] = (byte) (i & 0xff);
+		buf[1] = (byte) ((i >>> 8) & 0xff);
+		buf[2] = (byte) ((i >>> 16) & 0xff);
+		buf[3] = (byte) (i >>> 24);
+		return ObjectId.fromRaw(buf);
+	}
+
+	private static ReftableReader read(byte[] table) {
+		return new ReftableReader(BlockSource.from(table));
+	}
+
+	private byte[] write(Ref... refs) throws IOException {
+		return write(Arrays.asList(refs));
+	}
+
+	private byte[] write(Collection<Ref> refs) throws IOException {
+		ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+		stats = new ReftableWriter()
+				.begin(buffer)
+				.sortAndWriteRefs(refs)
+				.finish()
+				.getStats();
+		return buffer.toByteArray();
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/LocalDiskRefTreeDatabaseTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/LocalDiskRefTreeDatabaseTest.java
index 67a7819..d5a07e0 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/LocalDiskRefTreeDatabaseTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/LocalDiskRefTreeDatabaseTest.java
@@ -83,7 +83,7 @@ public void setUp() throws Exception {
 		FileRepository init = createWorkRepository();
 		FileBasedConfig cfg = init.getConfig();
 		cfg.setInt("core", null, "repositoryformatversion", 1);
-		cfg.setString("extensions", null, "refsStorage", "reftree");
+		cfg.setString("extensions", null, "refStorage", "reftree");
 		cfg.save();
 
 		repo = (FileRepository) new FileRepositoryBuilder()
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/AbbreviatedObjectIdTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/AbbreviatedObjectIdTest.java
index 6529d9e..30a9626 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/AbbreviatedObjectIdTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/AbbreviatedObjectIdTest.java
@@ -86,7 +86,6 @@ public void testFull_FromByteArray() {
 		final ObjectId f = i.toObjectId();
 		assertNotNull(f);
 		assertEquals(ObjectId.fromString(s), f);
-		assertEquals(f.hashCode(), i.hashCode());
 	}
 
 	@Test
@@ -101,7 +100,6 @@ public void testFull_FromString() {
 		final ObjectId f = i.toObjectId();
 		assertNotNull(f);
 		assertEquals(ObjectId.fromString(s), f);
-		assertEquals(f.hashCode(), i.hashCode());
 	}
 
 	@Test
@@ -215,7 +213,7 @@ public void test17_FromString() {
 	}
 
 	@Test
-	public void testEquals_Short() {
+	public void testEquals_Short8() {
 		final String s = "7b6e8067";
 		final AbbreviatedObjectId a = AbbreviatedObjectId.fromString(s);
 		final AbbreviatedObjectId b = AbbreviatedObjectId.fromString(s);
@@ -226,6 +224,18 @@ public void testEquals_Short() {
 	}
 
 	@Test
+	public void testEquals_Short4() {
+		final String s = "7b6e";
+		final AbbreviatedObjectId a = AbbreviatedObjectId.fromString(s);
+		final AbbreviatedObjectId b = AbbreviatedObjectId.fromString(s);
+		assertNotSame(a, b);
+		assertTrue(a.hashCode() != 0);
+		assertTrue(a.hashCode() == b.hashCode());
+		assertEquals(b, a);
+		assertEquals(a, b);
+	}
+
+	@Test
 	public void testEquals_Full() {
 		final String s = "7b6e8067ec96acef9a4184b43210d583b6d2f99a";
 		final AbbreviatedObjectId a = AbbreviatedObjectId.fromString(s);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java
index e9505f6..a12831a 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java
@@ -80,6 +80,7 @@
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.SystemReader;
 import org.junit.After;
+import org.junit.Ignore;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
@@ -766,6 +767,7 @@ public void testReadMultipleValuesForName() throws ConfigInvalidException {
 	}
 
 	@Test
+	@Ignore
 	public void testIncludeInvalidName() throws ConfigInvalidException {
 		expectedEx.expect(ConfigInvalidException.class);
 		expectedEx.expectMessage(JGitText.get().invalidLineInConfigFile);
@@ -773,6 +775,7 @@ public void testIncludeInvalidName() throws ConfigInvalidException {
 	}
 
 	@Test
+	@Ignore
 	public void testIncludeNoValue() throws ConfigInvalidException {
 		expectedEx.expect(ConfigInvalidException.class);
 		expectedEx.expectMessage(JGitText.get().invalidLineInConfigFile);
@@ -780,6 +783,7 @@ public void testIncludeNoValue() throws ConfigInvalidException {
 	}
 
 	@Test
+	@Ignore
 	public void testIncludeEmptyValue() throws ConfigInvalidException {
 		expectedEx.expect(ConfigInvalidException.class);
 		expectedEx.expectMessage(JGitText.get().invalidLineInConfigFile);
@@ -816,6 +820,7 @@ public void testIncludeValuePathRelative() throws ConfigInvalidException {
 	}
 
 	@Test
+	@Ignore
 	public void testIncludeTooManyRecursions() throws IOException {
 		File config = tmp.newFile("config");
 		String include = "[include]\npath=" + config.toPath() + "\n";
@@ -832,27 +837,14 @@ public void testIncludeTooManyRecursions() throws IOException {
 	}
 
 	@Test
-	public void testInclude() throws IOException, ConfigInvalidException {
+	public void testIncludeIsNoop() throws IOException, ConfigInvalidException {
 		File config = tmp.newFile("config");
-		File more = tmp.newFile("config.more");
-		File other = tmp.newFile("config.other");
 
 		String fooBar = "[foo]\nbar=true\n";
-		String includeMore = "[include]\npath=" + more.toPath() + "\n";
-		String includeOther = "path=" + other.toPath() + "\n";
-		String fooPlus = fooBar + includeMore + includeOther;
-		Files.write(config.toPath(), fooPlus.getBytes());
-
-		String fooMore = "[foo]\nmore=bar\n";
-		Files.write(more.toPath(), fooMore.getBytes());
-
-		String otherMore = "[other]\nmore=bar\n";
-		Files.write(other.toPath(), otherMore.getBytes());
+		Files.write(config.toPath(), fooBar.getBytes());
 
 		Config parsed = parse("[include]\npath=" + config.toPath() + "\n");
-		assertTrue(parsed.getBoolean("foo", "bar", false));
-		assertEquals("bar", parsed.getString("foo", null, "more"));
-		assertEquals("bar", parsed.getString("other", null, "more"));
+		assertFalse(parsed.getBoolean("foo", "bar", false));
 	}
 
 	private static void assertReadLong(long exp) throws ConfigInvalidException {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutTest.java
index f8c2d45..05573b9 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutTest.java
@@ -72,6 +72,8 @@
 import org.eclipse.jgit.errors.CheckoutConflictException;
 import org.eclipse.jgit.errors.CorruptObjectException;
 import org.eclipse.jgit.errors.NoWorkTreeException;
+import org.eclipse.jgit.events.ChangeRecorder;
+import org.eclipse.jgit.events.ListenerHandle;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.junit.TestRepository.BranchBuilder;
@@ -141,14 +143,19 @@ private static HashMap<String, String> mkmap(String... args) {
 	@Test
 	public void testResetHard() throws IOException, NoFilepatternException,
 			GitAPIException {
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
 		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
 			writeTrashFile("f", "f()");
 			writeTrashFile("D/g", "g()");
 			git.add().addFilepattern(".").call();
 			git.commit().setMessage("inital").call();
 			assertIndex(mkmap("f", "f()", "D/g", "g()"));
-
+			recorder.assertNoEvent();
 			git.branchCreate().setName("topic").call();
+			recorder.assertNoEvent();
 
 			writeTrashFile("f", "f()\nmaster");
 			writeTrashFile("D/g", "g()\ng2()");
@@ -156,9 +163,12 @@ public void testResetHard() throws IOException, NoFilepatternException,
 			git.add().addFilepattern(".").call();
 			RevCommit master = git.commit().setMessage("master-1").call();
 			assertIndex(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h", "h()"));
+			recorder.assertNoEvent();
 
 			checkoutBranch("refs/heads/topic");
 			assertIndex(mkmap("f", "f()", "D/g", "g()"));
+			recorder.assertEvent(new String[] { "f", "D/g" },
+					new String[] { "E/h" });
 
 			writeTrashFile("f", "f()\nside");
 			assertTrue(new File(db.getWorkTree(), "D/g").delete());
@@ -167,26 +177,41 @@ public void testResetHard() throws IOException, NoFilepatternException,
 			git.add().addFilepattern(".").setUpdate(true).call();
 			RevCommit topic = git.commit().setMessage("topic-1").call();
 			assertIndex(mkmap("f", "f()\nside", "G/i", "i()"));
+			recorder.assertNoEvent();
 
 			writeTrashFile("untracked", "untracked");
 
 			resetHard(master);
 			assertIndex(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h", "h()"));
+			recorder.assertEvent(new String[] { "f", "D/g", "E/h" },
+					new String[] { "G", "G/i" });
+
 			resetHard(topic);
 			assertIndex(mkmap("f", "f()\nside", "G/i", "i()"));
 			assertWorkDir(mkmap("f", "f()\nside", "G/i", "i()", "untracked",
 					"untracked"));
+			recorder.assertEvent(new String[] { "f", "G/i" },
+					new String[] { "D", "D/g", "E", "E/h" });
 
 			assertEquals(MergeStatus.CONFLICTING, git.merge().include(master)
 					.call().getMergeStatus());
 			assertEquals(
 					"[D/g, mode:100644, stage:1][D/g, mode:100644, stage:3][E/h, mode:100644][G/i, mode:100644][f, mode:100644, stage:1][f, mode:100644, stage:2][f, mode:100644, stage:3]",
 					indexState(0));
+			recorder.assertEvent(new String[] { "f", "D/g", "E/h" },
+					ChangeRecorder.EMPTY);
 
 			resetHard(master);
 			assertIndex(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h", "h()"));
 			assertWorkDir(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h",
 					"h()", "untracked", "untracked"));
+			recorder.assertEvent(new String[] { "f", "D/g" },
+					new String[] { "G", "G/i" });
+
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
 		}
 	}
 
@@ -202,13 +227,18 @@ public void testResetHard() throws IOException, NoFilepatternException,
 	@Test
 	public void testResetHardFromIndexEntryWithoutFileToTreeWithoutFile()
 			throws Exception {
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
 		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
 			writeTrashFile("x", "x");
 			git.add().addFilepattern("x").call();
 			RevCommit id1 = git.commit().setMessage("c1").call();
 
 			writeTrashFile("f/g", "f/g");
 			git.rm().addFilepattern("x").call();
+			recorder.assertEvent(ChangeRecorder.EMPTY, new String[] { "x" });
 			git.add().addFilepattern("f/g").call();
 			git.commit().setMessage("c2").call();
 			deleteTrashFile("f/g");
@@ -217,6 +247,11 @@ public void testResetHardFromIndexEntryWithoutFileToTreeWithoutFile()
 			// The actual test
 			git.reset().setMode(ResetType.HARD).setRef(id1.getName()).call();
 			assertIndex(mkmap("x", "x"));
+			recorder.assertEvent(new String[] { "x" }, ChangeRecorder.EMPTY);
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
 		}
 	}
 
@@ -227,13 +262,22 @@ public void testResetHardFromIndexEntryWithoutFileToTreeWithoutFile()
 	 */
 	@Test
 	public void testInitialCheckout() throws Exception {
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
 		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
 			TestRepository<Repository> db_t = new TestRepository<>(db);
 			BranchBuilder master = db_t.branch("master");
 			master.commit().add("f", "1").message("m0").create();
 			assertFalse(new File(db.getWorkTree(), "f").exists());
 			git.checkout().setName("master").call();
 			assertTrue(new File(db.getWorkTree(), "f").exists());
+			recorder.assertEvent(new String[] { "f" }, ChangeRecorder.EMPTY);
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
 		}
 	}
 
@@ -930,120 +974,154 @@ public void testCheckoutOutChanges() throws IOException {
 	public void testCheckoutChangeLinkToEmptyDir() throws Exception {
 		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
 		String fname = "was_file";
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add a file
+			writeTrashFile(fname, "a");
+			git.add().addFilepattern(fname).call();
 
-		// Add a file
-		writeTrashFile(fname, "a");
-		git.add().addFilepattern(fname).call();
+			// Add a link to file
+			String linkName = "link";
+			File link = writeLink(linkName, fname).toFile();
+			git.add().addFilepattern(linkName).call();
+			git.commit().setMessage("Added file and link").call();
 
-		// Add a link to file
-		String linkName = "link";
-		File link = writeLink(linkName, fname).toFile();
-		git.add().addFilepattern(linkName).call();
-		git.commit().setMessage("Added file and link").call();
+			assertWorkDir(mkmap(linkName, "a", fname, "a"));
 
-		assertWorkDir(mkmap(linkName, "a", fname, "a"));
+			// replace link with empty directory
+			FileUtils.delete(link);
+			FileUtils.mkdir(link);
+			assertTrue("Link must be a directory now", link.isDirectory());
 
-		// replace link with empty directory
-		FileUtils.delete(link);
-		FileUtils.mkdir(link);
-		assertTrue("Link must be a directory now", link.isDirectory());
+			// modify file
+			writeTrashFile(fname, "b");
+			assertWorkDir(mkmap(fname, "b", linkName, "/"));
+			recorder.assertNoEvent();
 
-		// modify file
-		writeTrashFile(fname, "b");
-		assertWorkDir(mkmap(fname, "b", linkName, "/"));
+			// revert both paths to HEAD state
+			git.checkout().setStartPoint(Constants.HEAD).addPath(fname)
+					.addPath(linkName).call();
 
-		// revert both paths to HEAD state
-		git.checkout().setStartPoint(Constants.HEAD)
-				.addPath(fname).addPath(linkName).call();
+			assertWorkDir(mkmap(fname, "a", linkName, "a"));
+			recorder.assertEvent(new String[] { fname, linkName },
+					ChangeRecorder.EMPTY);
 
-		assertWorkDir(mkmap(fname, "a", linkName, "a"));
-
-		Status st = git.status().call();
-		assertTrue(st.isClean());
+			Status st = git.status().call();
+			assertTrue(st.isClean());
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
+		}
 	}
 
 	@Test
 	public void testCheckoutChangeLinkToEmptyDirs() throws Exception {
 		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
 		String fname = "was_file";
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add a file
+			writeTrashFile(fname, "a");
+			git.add().addFilepattern(fname).call();
 
-		// Add a file
-		writeTrashFile(fname, "a");
-		git.add().addFilepattern(fname).call();
+			// Add a link to file
+			String linkName = "link";
+			File link = writeLink(linkName, fname).toFile();
+			git.add().addFilepattern(linkName).call();
+			git.commit().setMessage("Added file and link").call();
 
-		// Add a link to file
-		String linkName = "link";
-		File link = writeLink(linkName, fname).toFile();
-		git.add().addFilepattern(linkName).call();
-		git.commit().setMessage("Added file and link").call();
+			assertWorkDir(mkmap(linkName, "a", fname, "a"));
 
-		assertWorkDir(mkmap(linkName, "a", fname, "a"));
+			// replace link with directory containing only directories, no files
+			FileUtils.delete(link);
+			FileUtils.mkdirs(new File(link, "dummyDir"));
+			assertTrue("Link must be a directory now", link.isDirectory());
 
-		// replace link with directory containing only directories, no files
-		FileUtils.delete(link);
-		FileUtils.mkdirs(new File(link, "dummyDir"));
-		assertTrue("Link must be a directory now", link.isDirectory());
+			assertFalse("Must not delete non empty directory", link.delete());
 
-		assertFalse("Must not delete non empty directory", link.delete());
+			// modify file
+			writeTrashFile(fname, "b");
+			assertWorkDir(mkmap(fname, "b", linkName + "/dummyDir", "/"));
+			recorder.assertNoEvent();
 
-		// modify file
-		writeTrashFile(fname, "b");
-		assertWorkDir(mkmap(fname, "b", linkName + "/dummyDir", "/"));
+			// revert both paths to HEAD state
+			git.checkout().setStartPoint(Constants.HEAD).addPath(fname)
+					.addPath(linkName).call();
 
-		// revert both paths to HEAD state
-		git.checkout().setStartPoint(Constants.HEAD)
-				.addPath(fname).addPath(linkName).call();
+			assertWorkDir(mkmap(fname, "a", linkName, "a"));
+			recorder.assertEvent(new String[] { fname, linkName },
+					ChangeRecorder.EMPTY);
 
-		assertWorkDir(mkmap(fname, "a", linkName, "a"));
-
-		Status st = git.status().call();
-		assertTrue(st.isClean());
+			Status st = git.status().call();
+			assertTrue(st.isClean());
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
+		}
 	}
 
 	@Test
 	public void testCheckoutChangeLinkToNonEmptyDirs() throws Exception {
 		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
 		String fname = "file";
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add a file
+			writeTrashFile(fname, "a");
+			git.add().addFilepattern(fname).call();
 
-		// Add a file
-		writeTrashFile(fname, "a");
-		git.add().addFilepattern(fname).call();
+			// Add a link to file
+			String linkName = "link";
+			File link = writeLink(linkName, fname).toFile();
+			git.add().addFilepattern(linkName).call();
+			git.commit().setMessage("Added file and link").call();
 
-		// Add a link to file
-		String linkName = "link";
-		File link = writeLink(linkName, fname).toFile();
-		git.add().addFilepattern(linkName).call();
-		git.commit().setMessage("Added file and link").call();
+			assertWorkDir(mkmap(linkName, "a", fname, "a"));
 
-		assertWorkDir(mkmap(linkName, "a", fname, "a"));
+			// replace link with directory containing only directories, no files
+			FileUtils.delete(link);
 
-		// replace link with directory containing only directories, no files
-		FileUtils.delete(link);
+			// create but do not add a file in the new directory to the index
+			writeTrashFile(linkName + "/dir1", "file1", "c");
 
-		// create but do not add a file in the new directory to the index
-		writeTrashFile(linkName + "/dir1", "file1", "c");
+			// create but do not add a file in the new directory to the index
+			writeTrashFile(linkName + "/dir2", "file2", "d");
 
-		// create but do not add a file in the new directory to the index
-		writeTrashFile(linkName + "/dir2", "file2", "d");
+			assertTrue("File must be a directory now", link.isDirectory());
+			assertFalse("Must not delete non empty directory", link.delete());
 
-		assertTrue("File must be a directory now", link.isDirectory());
-		assertFalse("Must not delete non empty directory", link.delete());
+			// 2 extra files are created
+			assertWorkDir(mkmap(fname, "a", linkName + "/dir1/file1", "c",
+					linkName + "/dir2/file2", "d"));
+			recorder.assertNoEvent();
 
-		// 2 extra files are created
-		assertWorkDir(mkmap(fname, "a", linkName + "/dir1/file1", "c",
-				linkName + "/dir2/file2", "d"));
+			// revert path to HEAD state
+			git.checkout().setStartPoint(Constants.HEAD).addPath(linkName)
+					.call();
 
-		// revert path to HEAD state
-		git.checkout().setStartPoint(Constants.HEAD).addPath(linkName).call();
+			// expect only the one added to the index
+			assertWorkDir(mkmap(linkName, "a", fname, "a"));
+			recorder.assertEvent(new String[] { linkName },
+					ChangeRecorder.EMPTY);
 
-		// expect only the one added to the index
-		assertWorkDir(mkmap(linkName, "a", fname, "a"));
-
-		Status st = git.status().call();
-		assertTrue(st.isClean());
+			Status st = git.status().call();
+			assertTrue(st.isClean());
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
+		}
 	}
 
 	@Test
@@ -1051,174 +1129,222 @@ public void testCheckoutChangeLinkToNonEmptyDirsAndNewIndexEntry()
 			throws Exception {
 		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
 		String fname = "file";
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add a file
+			writeTrashFile(fname, "a");
+			git.add().addFilepattern(fname).call();
 
-		// Add a file
-		writeTrashFile(fname, "a");
-		git.add().addFilepattern(fname).call();
+			// Add a link to file
+			String linkName = "link";
+			File link = writeLink(linkName, fname).toFile();
+			git.add().addFilepattern(linkName).call();
+			git.commit().setMessage("Added file and link").call();
 
-		// Add a link to file
-		String linkName = "link";
-		File link = writeLink(linkName, fname).toFile();
-		git.add().addFilepattern(linkName).call();
-		git.commit().setMessage("Added file and link").call();
+			assertWorkDir(mkmap(linkName, "a", fname, "a"));
 
-		assertWorkDir(mkmap(linkName, "a", fname, "a"));
+			// replace link with directory containing only directories, no files
+			FileUtils.delete(link);
 
-		// replace link with directory containing only directories, no files
-		FileUtils.delete(link);
+			// create and add a file in the new directory to the index
+			writeTrashFile(linkName + "/dir1", "file1", "c");
+			git.add().addFilepattern(linkName + "/dir1/file1").call();
 
-		// create and add a file in the new directory to the index
-		writeTrashFile(linkName + "/dir1", "file1", "c");
-		git.add().addFilepattern(linkName + "/dir1/file1").call();
+			// create but do not add a file in the new directory to the index
+			writeTrashFile(linkName + "/dir2", "file2", "d");
 
-		// create but do not add a file in the new directory to the index
-		writeTrashFile(linkName + "/dir2", "file2", "d");
+			assertTrue("File must be a directory now", link.isDirectory());
+			assertFalse("Must not delete non empty directory", link.delete());
 
-		assertTrue("File must be a directory now", link.isDirectory());
-		assertFalse("Must not delete non empty directory", link.delete());
+			// 2 extra files are created
+			assertWorkDir(mkmap(fname, "a", linkName + "/dir1/file1", "c",
+					linkName + "/dir2/file2", "d"));
+			recorder.assertNoEvent();
 
-		// 2 extra files are created
-		assertWorkDir(mkmap(fname, "a", linkName + "/dir1/file1", "c",
-				linkName + "/dir2/file2", "d"));
+			// revert path to HEAD state
+			git.checkout().setStartPoint(Constants.HEAD).addPath(linkName)
+					.call();
 
-		// revert path to HEAD state
-		git.checkout().setStartPoint(Constants.HEAD).addPath(linkName).call();
+			// original file and link
+			assertWorkDir(mkmap(linkName, "a", fname, "a"));
+			recorder.assertEvent(new String[] { linkName },
+					ChangeRecorder.EMPTY);
 
-		// original file and link
-		assertWorkDir(mkmap(linkName, "a", fname, "a"));
-
-		Status st = git.status().call();
-		assertTrue(st.isClean());
+			Status st = git.status().call();
+			assertTrue(st.isClean());
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
+		}
 	}
 
 	@Test
 	public void testCheckoutChangeFileToEmptyDir() throws Exception {
 		String fname = "was_file";
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add a file
+			File file = writeTrashFile(fname, "a");
+			git.add().addFilepattern(fname).call();
+			git.commit().setMessage("Added file").call();
 
-		// Add a file
-		File file = writeTrashFile(fname, "a");
-		git.add().addFilepattern(fname).call();
-		git.commit().setMessage("Added file").call();
+			// replace file with empty directory
+			FileUtils.delete(file);
+			FileUtils.mkdir(file);
+			assertTrue("File must be a directory now", file.isDirectory());
+			assertWorkDir(mkmap(fname, "/"));
+			recorder.assertNoEvent();
 
-		// replace file with empty directory
-		FileUtils.delete(file);
-		FileUtils.mkdir(file);
-		assertTrue("File must be a directory now", file.isDirectory());
+			// revert path to HEAD state
+			git.checkout().setStartPoint(Constants.HEAD).addPath(fname).call();
+			assertWorkDir(mkmap(fname, "a"));
+			recorder.assertEvent(new String[] { fname }, ChangeRecorder.EMPTY);
 
-		assertWorkDir(mkmap(fname, "/"));
-
-		// revert path to HEAD state
-		git.checkout().setStartPoint(Constants.HEAD).addPath(fname).call();
-
-		assertWorkDir(mkmap(fname, "a"));
-
-		Status st = git.status().call();
-		assertTrue(st.isClean());
+			Status st = git.status().call();
+			assertTrue(st.isClean());
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
+		}
 	}
 
 	@Test
 	public void testCheckoutChangeFileToEmptyDirs() throws Exception {
 		String fname = "was_file";
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add a file
+			File file = writeTrashFile(fname, "a");
+			git.add().addFilepattern(fname).call();
+			git.commit().setMessage("Added file").call();
 
-		// Add a file
-		File file = writeTrashFile(fname, "a");
-		git.add().addFilepattern(fname).call();
-		git.commit().setMessage("Added file").call();
+			// replace file with directory containing only directories, no files
+			FileUtils.delete(file);
+			FileUtils.mkdirs(new File(file, "dummyDir"));
+			assertTrue("File must be a directory now", file.isDirectory());
+			assertFalse("Must not delete non empty directory", file.delete());
 
-		// replace file with directory containing only directories, no files
-		FileUtils.delete(file);
-		FileUtils.mkdirs(new File(file, "dummyDir"));
-		assertTrue("File must be a directory now", file.isDirectory());
-		assertFalse("Must not delete non empty directory", file.delete());
+			assertWorkDir(mkmap(fname + "/dummyDir", "/"));
+			recorder.assertNoEvent();
 
-		assertWorkDir(mkmap(fname + "/dummyDir", "/"));
+			// revert path to HEAD state
+			git.checkout().setStartPoint(Constants.HEAD).addPath(fname).call();
+			assertWorkDir(mkmap(fname, "a"));
+			recorder.assertEvent(new String[] { fname }, ChangeRecorder.EMPTY);
 
-		// revert path to HEAD state
-		git.checkout().setStartPoint(Constants.HEAD).addPath(fname).call();
-
-		assertWorkDir(mkmap(fname, "a"));
-
-		Status st = git.status().call();
-		assertTrue(st.isClean());
+			Status st = git.status().call();
+			assertTrue(st.isClean());
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
+		}
 	}
 
 	@Test
 	public void testCheckoutChangeFileToNonEmptyDirs() throws Exception {
 		String fname = "was_file";
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add a file
+			File file = writeTrashFile(fname, "a");
+			git.add().addFilepattern(fname).call();
+			git.commit().setMessage("Added file").call();
 
-		// Add a file
-		File file = writeTrashFile(fname, "a");
-		git.add().addFilepattern(fname).call();
-		git.commit().setMessage("Added file").call();
+			assertWorkDir(mkmap(fname, "a"));
 
-		assertWorkDir(mkmap(fname, "a"));
+			// replace file with directory containing only directories, no files
+			FileUtils.delete(file);
 
-		// replace file with directory containing only directories, no files
-		FileUtils.delete(file);
+			// create but do not add a file in the new directory to the index
+			writeTrashFile(fname + "/dir1", "file1", "c");
 
-		// create but do not add a file in the new directory to the index
-		writeTrashFile(fname + "/dir1", "file1", "c");
+			// create but do not add a file in the new directory to the index
+			writeTrashFile(fname + "/dir2", "file2", "d");
 
-		// create but do not add a file in the new directory to the index
-		writeTrashFile(fname + "/dir2", "file2", "d");
+			assertTrue("File must be a directory now", file.isDirectory());
+			assertFalse("Must not delete non empty directory", file.delete());
 
-		assertTrue("File must be a directory now", file.isDirectory());
-		assertFalse("Must not delete non empty directory", file.delete());
+			// 2 extra files are created
+			assertWorkDir(mkmap(fname + "/dir1/file1", "c",
+					fname + "/dir2/file2", "d"));
+			recorder.assertNoEvent();
 
-		// 2 extra files are created
-		assertWorkDir(
-				mkmap(fname + "/dir1/file1", "c", fname + "/dir2/file2", "d"));
+			// revert path to HEAD state
+			git.checkout().setStartPoint(Constants.HEAD).addPath(fname).call();
 
-		// revert path to HEAD state
-		git.checkout().setStartPoint(Constants.HEAD).addPath(fname).call();
+			// expect only the one added to the index
+			assertWorkDir(mkmap(fname, "a"));
+			recorder.assertEvent(new String[] { fname }, ChangeRecorder.EMPTY);
 
-		// expect only the one added to the index
-		assertWorkDir(mkmap(fname, "a"));
-
-		Status st = git.status().call();
-		assertTrue(st.isClean());
+			Status st = git.status().call();
+			assertTrue(st.isClean());
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
+		}
 	}
 
 	@Test
 	public void testCheckoutChangeFileToNonEmptyDirsAndNewIndexEntry()
 			throws Exception {
 		String fname = "was_file";
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add a file
+			File file = writeTrashFile(fname, "a");
+			git.add().addFilepattern(fname).call();
+			git.commit().setMessage("Added file").call();
 
-		// Add a file
-		File file = writeTrashFile(fname, "a");
-		git.add().addFilepattern(fname).call();
-		git.commit().setMessage("Added file").call();
+			assertWorkDir(mkmap(fname, "a"));
 
-		assertWorkDir(mkmap(fname, "a"));
+			// replace file with directory containing only directories, no files
+			FileUtils.delete(file);
 
-		// replace file with directory containing only directories, no files
-		FileUtils.delete(file);
+			// create and add a file in the new directory to the index
+			writeTrashFile(fname + "/dir", "file1", "c");
+			git.add().addFilepattern(fname + "/dir/file1").call();
 
-		// create and add a file in the new directory to the index
-		writeTrashFile(fname + "/dir", "file1", "c");
-		git.add().addFilepattern(fname + "/dir/file1").call();
+			// create but do not add a file in the new directory to the index
+			writeTrashFile(fname + "/dir", "file2", "d");
 
-		// create but do not add a file in the new directory to the index
-		writeTrashFile(fname + "/dir", "file2", "d");
+			assertTrue("File must be a directory now", file.isDirectory());
+			assertFalse("Must not delete non empty directory", file.delete());
 
-		assertTrue("File must be a directory now", file.isDirectory());
-		assertFalse("Must not delete non empty directory", file.delete());
+			// 2 extra files are created
+			assertWorkDir(mkmap(fname + "/dir/file1", "c", fname + "/dir/file2",
+					"d"));
+			recorder.assertNoEvent();
 
-		// 2 extra files are created
-		assertWorkDir(
-				mkmap(fname + "/dir/file1", "c", fname + "/dir/file2", "d"));
-
-		// revert path to HEAD state
-		git.checkout().setStartPoint(Constants.HEAD).addPath(fname).call();
-		assertWorkDir(mkmap(fname, "a"));
-
-		Status st = git.status().call();
-		assertTrue(st.isClean());
+			// revert path to HEAD state
+			git.checkout().setStartPoint(Constants.HEAD).addPath(fname).call();
+			assertWorkDir(mkmap(fname, "a"));
+			recorder.assertEvent(new String[] { fname }, ChangeRecorder.EMPTY);
+			Status st = git.status().call();
+			assertTrue(st.isClean());
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
+		}
 	}
 
 	@Test
@@ -1293,76 +1419,100 @@ public void testDontOverwriteEmptyFolder() throws IOException {
 	public void testOverwriteUntrackedIgnoredFile() throws IOException,
 			GitAPIException {
 		String fname="file.txt";
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add a file
+			writeTrashFile(fname, "a");
+			git.add().addFilepattern(fname).call();
+			git.commit().setMessage("create file").call();
 
-		// Add a file
-		writeTrashFile(fname, "a");
-		git.add().addFilepattern(fname).call();
-		git.commit().setMessage("create file").call();
+			// Create branch
+			git.branchCreate().setName("side").call();
 
-		// Create branch
-		git.branchCreate().setName("side").call();
+			// Modify file
+			writeTrashFile(fname, "b");
+			git.add().addFilepattern(fname).call();
+			git.commit().setMessage("modify file").call();
+			recorder.assertNoEvent();
 
-		// Modify file
-		writeTrashFile(fname, "b");
-		git.add().addFilepattern(fname).call();
-		git.commit().setMessage("modify file").call();
+			// Switch branches
+			git.checkout().setName("side").call();
+			recorder.assertEvent(new String[] { fname }, ChangeRecorder.EMPTY);
+			git.rm().addFilepattern(fname).call();
+			recorder.assertEvent(ChangeRecorder.EMPTY, new String[] { fname });
+			writeTrashFile(".gitignore", fname);
+			git.add().addFilepattern(".gitignore").call();
+			git.commit().setMessage("delete and ignore file").call();
 
-		// Switch branches
-		git.checkout().setName("side").call();
-		git.rm().addFilepattern(fname).call();
-		writeTrashFile(".gitignore", fname);
-		git.add().addFilepattern(".gitignore").call();
-		git.commit().setMessage("delete and ignore file").call();
-
-		writeTrashFile(fname, "Something different");
-		git.checkout().setName("master").call();
-		assertWorkDir(mkmap(fname, "b"));
-		assertTrue(git.status().call().isClean());
+			writeTrashFile(fname, "Something different");
+			recorder.assertNoEvent();
+			git.checkout().setName("master").call();
+			assertWorkDir(mkmap(fname, "b"));
+			recorder.assertEvent(new String[] { fname },
+					new String[] { ".gitignore" });
+			assertTrue(git.status().call().isClean());
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
+		}
 	}
 
 	@Test
 	public void testOverwriteUntrackedFileModeChange()
 			throws IOException, GitAPIException {
 		String fname = "file.txt";
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add a file
+			File file = writeTrashFile(fname, "a");
+			git.add().addFilepattern(fname).call();
+			git.commit().setMessage("create file").call();
+			assertWorkDir(mkmap(fname, "a"));
 
-		// Add a file
-		File file = writeTrashFile(fname, "a");
-		git.add().addFilepattern(fname).call();
-		git.commit().setMessage("create file").call();
-		assertWorkDir(mkmap(fname, "a"));
+			// Create branch
+			git.branchCreate().setName("side").call();
 
-		// Create branch
-		git.branchCreate().setName("side").call();
+			// Switch branches
+			git.checkout().setName("side").call();
+			recorder.assertNoEvent();
 
-		// Switch branches
-		git.checkout().setName("side").call();
+			// replace file with directory containing files
+			FileUtils.delete(file);
 
-		// replace file with directory containing files
-		FileUtils.delete(file);
+			// create and add a file in the new directory to the index
+			writeTrashFile(fname + "/dir1", "file1", "c");
+			git.add().addFilepattern(fname + "/dir1/file1").call();
 
-		// create and add a file in the new directory to the index
-		writeTrashFile(fname + "/dir1", "file1", "c");
-		git.add().addFilepattern(fname + "/dir1/file1").call();
+			// create but do not add a file in the new directory to the index
+			writeTrashFile(fname + "/dir2", "file2", "d");
 
-		// create but do not add a file in the new directory to the index
-		writeTrashFile(fname + "/dir2", "file2", "d");
+			assertTrue("File must be a directory now", file.isDirectory());
+			assertFalse("Must not delete non empty directory", file.delete());
 
-		assertTrue("File must be a directory now", file.isDirectory());
-		assertFalse("Must not delete non empty directory", file.delete());
-
-		// 2 extra files are created
-		assertWorkDir(
-				mkmap(fname + "/dir1/file1", "c", fname + "/dir2/file2", "d"));
-
-		try {
-			git.checkout().setName("master").call();
-			fail("did not throw exception");
-		} catch (Exception e) {
-			// 2 extra files are still there
+			// 2 extra files are created
 			assertWorkDir(mkmap(fname + "/dir1/file1", "c",
 					fname + "/dir2/file2", "d"));
+
+			try {
+				git.checkout().setName("master").call();
+				fail("did not throw exception");
+			} catch (Exception e) {
+				// 2 extra files are still there
+				assertWorkDir(mkmap(fname + "/dir1/file1", "c",
+						fname + "/dir2/file2", "d"));
+			}
+			recorder.assertNoEvent();
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
 		}
 	}
 
@@ -1371,50 +1521,60 @@ public void testOverwriteUntrackedLinkModeChange()
 			throws Exception {
 		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
 		String fname = "file.txt";
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add a file
+			writeTrashFile(fname, "a");
+			git.add().addFilepattern(fname).call();
 
-		// Add a file
-		writeTrashFile(fname, "a");
-		git.add().addFilepattern(fname).call();
+			// Add a link to file
+			String linkName = "link";
+			File link = writeLink(linkName, fname).toFile();
+			git.add().addFilepattern(linkName).call();
+			git.commit().setMessage("Added file and link").call();
 
-		// Add a link to file
-		String linkName = "link";
-		File link = writeLink(linkName, fname).toFile();
-		git.add().addFilepattern(linkName).call();
-		git.commit().setMessage("Added file and link").call();
+			assertWorkDir(mkmap(linkName, "a", fname, "a"));
 
-		assertWorkDir(mkmap(linkName, "a", fname, "a"));
+			// Create branch
+			git.branchCreate().setName("side").call();
 
-		// Create branch
-		git.branchCreate().setName("side").call();
+			// Switch branches
+			git.checkout().setName("side").call();
+			recorder.assertNoEvent();
 
-		// Switch branches
-		git.checkout().setName("side").call();
+			// replace link with directory containing files
+			FileUtils.delete(link);
 
-		// replace link with directory containing files
-		FileUtils.delete(link);
+			// create and add a file in the new directory to the index
+			writeTrashFile(linkName + "/dir1", "file1", "c");
+			git.add().addFilepattern(linkName + "/dir1/file1").call();
 
-		// create and add a file in the new directory to the index
-		writeTrashFile(linkName + "/dir1", "file1", "c");
-		git.add().addFilepattern(linkName + "/dir1/file1").call();
+			// create but do not add a file in the new directory to the index
+			writeTrashFile(linkName + "/dir2", "file2", "d");
 
-		// create but do not add a file in the new directory to the index
-		writeTrashFile(linkName + "/dir2", "file2", "d");
+			assertTrue("Link must be a directory now", link.isDirectory());
+			assertFalse("Must not delete non empty directory", link.delete());
 
-		assertTrue("Link must be a directory now", link.isDirectory());
-		assertFalse("Must not delete non empty directory", link.delete());
-
-		// 2 extra files are created
-		assertWorkDir(mkmap(fname, "a", linkName + "/dir1/file1", "c",
-				linkName + "/dir2/file2", "d"));
-
-		try {
-			git.checkout().setName("master").call();
-			fail("did not throw exception");
-		} catch (Exception e) {
-			// 2 extra files are still there
+			// 2 extra files are created
 			assertWorkDir(mkmap(fname, "a", linkName + "/dir1/file1", "c",
 					linkName + "/dir2/file2", "d"));
+
+			try {
+				git.checkout().setName("master").call();
+				fail("did not throw exception");
+			} catch (Exception e) {
+				// 2 extra files are still there
+				assertWorkDir(mkmap(fname, "a", linkName + "/dir1/file1", "c",
+						linkName + "/dir2/file2", "d"));
+			}
+			recorder.assertNoEvent();
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
 		}
 	}
 
@@ -1423,36 +1583,47 @@ public void testFileModeChangeWithNoContentChangeUpdate() throws Exception {
 		if (!FS.DETECTED.supportsExecute())
 			return;
 
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add non-executable file
+			File file = writeTrashFile("file.txt", "a");
+			git.add().addFilepattern("file.txt").call();
+			git.commit().setMessage("commit1").call();
+			assertFalse(db.getFS().canExecute(file));
 
-		// Add non-executable file
-		File file = writeTrashFile("file.txt", "a");
-		git.add().addFilepattern("file.txt").call();
-		git.commit().setMessage("commit1").call();
-		assertFalse(db.getFS().canExecute(file));
+			// Create branch
+			git.branchCreate().setName("b1").call();
 
-		// Create branch
-		git.branchCreate().setName("b1").call();
+			// Make file executable
+			db.getFS().setExecute(file, true);
+			git.add().addFilepattern("file.txt").call();
+			git.commit().setMessage("commit2").call();
+			recorder.assertNoEvent();
 
-		// Make file executable
-		db.getFS().setExecute(file, true);
-		git.add().addFilepattern("file.txt").call();
-		git.commit().setMessage("commit2").call();
+			// Verify executable and working directory is clean
+			Status status = git.status().call();
+			assertTrue(status.getModified().isEmpty());
+			assertTrue(status.getChanged().isEmpty());
+			assertTrue(db.getFS().canExecute(file));
 
-		// Verify executable and working directory is clean
-		Status status = git.status().call();
-		assertTrue(status.getModified().isEmpty());
-		assertTrue(status.getChanged().isEmpty());
-		assertTrue(db.getFS().canExecute(file));
+			// Switch branches
+			git.checkout().setName("b1").call();
 
-		// Switch branches
-		git.checkout().setName("b1").call();
-
-		// Verify not executable and working directory is clean
-		status = git.status().call();
-		assertTrue(status.getModified().isEmpty());
-		assertTrue(status.getChanged().isEmpty());
-		assertFalse(db.getFS().canExecute(file));
+			// Verify not executable and working directory is clean
+			status = git.status().call();
+			assertTrue(status.getModified().isEmpty());
+			assertTrue(status.getChanged().isEmpty());
+			assertFalse(db.getFS().canExecute(file));
+			recorder.assertEvent(new String[] { "file.txt" },
+					ChangeRecorder.EMPTY);
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
+		}
 	}
 
 	@Test
@@ -1460,41 +1631,50 @@ public void testFileModeChangeAndContentChangeConflict() throws Exception {
 		if (!FS.DETECTED.supportsExecute())
 			return;
 
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add non-executable file
+			File file = writeTrashFile("file.txt", "a");
+			git.add().addFilepattern("file.txt").call();
+			git.commit().setMessage("commit1").call();
+			assertFalse(db.getFS().canExecute(file));
 
-		// Add non-executable file
-		File file = writeTrashFile("file.txt", "a");
-		git.add().addFilepattern("file.txt").call();
-		git.commit().setMessage("commit1").call();
-		assertFalse(db.getFS().canExecute(file));
+			// Create branch
+			git.branchCreate().setName("b1").call();
 
-		// Create branch
-		git.branchCreate().setName("b1").call();
+			// Make file executable
+			db.getFS().setExecute(file, true);
+			git.add().addFilepattern("file.txt").call();
+			git.commit().setMessage("commit2").call();
 
-		// Make file executable
-		db.getFS().setExecute(file, true);
-		git.add().addFilepattern("file.txt").call();
-		git.commit().setMessage("commit2").call();
+			// Verify executable and working directory is clean
+			Status status = git.status().call();
+			assertTrue(status.getModified().isEmpty());
+			assertTrue(status.getChanged().isEmpty());
+			assertTrue(db.getFS().canExecute(file));
 
-		// Verify executable and working directory is clean
-		Status status = git.status().call();
-		assertTrue(status.getModified().isEmpty());
-		assertTrue(status.getChanged().isEmpty());
-		assertTrue(db.getFS().canExecute(file));
+			writeTrashFile("file.txt", "b");
 
-		writeTrashFile("file.txt", "b");
-
-		// Switch branches
-		CheckoutCommand checkout = git.checkout().setName("b1");
-		try {
-			checkout.call();
-			fail("Checkout exception not thrown");
-		} catch (org.eclipse.jgit.api.errors.CheckoutConflictException e) {
-			CheckoutResult result = checkout.getResult();
-			assertNotNull(result);
-			assertNotNull(result.getConflictList());
-			assertEquals(1, result.getConflictList().size());
-			assertTrue(result.getConflictList().contains("file.txt"));
+			// Switch branches
+			CheckoutCommand checkout = git.checkout().setName("b1");
+			try {
+				checkout.call();
+				fail("Checkout exception not thrown");
+			} catch (org.eclipse.jgit.api.errors.CheckoutConflictException e) {
+				CheckoutResult result = checkout.getResult();
+				assertNotNull(result);
+				assertNotNull(result.getConflictList());
+				assertEquals(1, result.getConflictList().size());
+				assertTrue(result.getConflictList().contains("file.txt"));
+			}
+			recorder.assertNoEvent();
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
 		}
 	}
 
@@ -1504,40 +1684,52 @@ public void testDirtyFileModeEqualHeadMerge()
 		if (!FS.DETECTED.supportsExecute())
 			return;
 
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add non-executable file
+			File file = writeTrashFile("file.txt", "a");
+			git.add().addFilepattern("file.txt").call();
+			git.commit().setMessage("commit1").call();
+			assertFalse(db.getFS().canExecute(file));
 
-		// Add non-executable file
-		File file = writeTrashFile("file.txt", "a");
-		git.add().addFilepattern("file.txt").call();
-		git.commit().setMessage("commit1").call();
-		assertFalse(db.getFS().canExecute(file));
+			// Create branch
+			git.branchCreate().setName("b1").call();
 
-		// Create branch
-		git.branchCreate().setName("b1").call();
+			// Create second commit and don't touch file
+			writeTrashFile("file2.txt", "");
+			git.add().addFilepattern("file2.txt").call();
+			git.commit().setMessage("commit2").call();
 
-		// Create second commit and don't touch file
-		writeTrashFile("file2.txt", "");
-		git.add().addFilepattern("file2.txt").call();
-		git.commit().setMessage("commit2").call();
+			// stage a mode change
+			writeTrashFile("file.txt", "a");
+			db.getFS().setExecute(file, true);
+			git.add().addFilepattern("file.txt").call();
 
-		// stage a mode change
-		writeTrashFile("file.txt", "a");
-		db.getFS().setExecute(file, true);
-		git.add().addFilepattern("file.txt").call();
+			// dirty the file
+			writeTrashFile("file.txt", "b");
 
-		// dirty the file
-		writeTrashFile("file.txt", "b");
+			assertEquals(
+					"[file.txt, mode:100755, content:a][file2.txt, mode:100644, content:]",
+					indexState(CONTENT));
+			assertWorkDir(mkmap("file.txt", "b", "file2.txt", ""));
+			recorder.assertNoEvent();
 
-		assertEquals(
-				"[file.txt, mode:100755, content:a][file2.txt, mode:100644, content:]",
-				indexState(CONTENT));
-		assertWorkDir(mkmap("file.txt", "b", "file2.txt", ""));
-
-		// Switch branches and check that the dirty file survived in worktree
-		// and index
-		git.checkout().setName("b1").call();
-		assertEquals("[file.txt, mode:100755, content:a]", indexState(CONTENT));
-		assertWorkDir(mkmap("file.txt", "b"));
+			// Switch branches and check that the dirty file survived in
+			// worktree and index
+			git.checkout().setName("b1").call();
+			assertEquals("[file.txt, mode:100755, content:a]",
+					indexState(CONTENT));
+			assertWorkDir(mkmap("file.txt", "b"));
+			recorder.assertEvent(ChangeRecorder.EMPTY,
+					new String[] { "file2.txt" });
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
+		}
 	}
 
 	@Test
@@ -1546,40 +1738,53 @@ public void testDirtyFileModeEqualIndexMerge()
 		if (!FS.DETECTED.supportsExecute())
 			return;
 
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add non-executable file
+			File file = writeTrashFile("file.txt", "a");
+			git.add().addFilepattern("file.txt").call();
+			git.commit().setMessage("commit1").call();
+			assertFalse(db.getFS().canExecute(file));
 
-		// Add non-executable file
-		File file = writeTrashFile("file.txt", "a");
-		git.add().addFilepattern("file.txt").call();
-		git.commit().setMessage("commit1").call();
-		assertFalse(db.getFS().canExecute(file));
+			// Create branch
+			git.branchCreate().setName("b1").call();
 
-		// Create branch
-		git.branchCreate().setName("b1").call();
+			// Create second commit with executable file
+			file = writeTrashFile("file.txt", "b");
+			db.getFS().setExecute(file, true);
+			git.add().addFilepattern("file.txt").call();
+			git.commit().setMessage("commit2").call();
 
-		// Create second commit with executable file
-		file = writeTrashFile("file.txt", "b");
-		db.getFS().setExecute(file, true);
-		git.add().addFilepattern("file.txt").call();
-		git.commit().setMessage("commit2").call();
+			// stage the same content as in the branch we want to switch to
+			writeTrashFile("file.txt", "a");
+			db.getFS().setExecute(file, false);
+			git.add().addFilepattern("file.txt").call();
 
-		// stage the same content as in the branch we want to switch to
-		writeTrashFile("file.txt", "a");
-		db.getFS().setExecute(file, false);
-		git.add().addFilepattern("file.txt").call();
+			// dirty the file
+			writeTrashFile("file.txt", "c");
+			db.getFS().setExecute(file, true);
 
-		// dirty the file
-		writeTrashFile("file.txt", "c");
-		db.getFS().setExecute(file, true);
+			assertEquals("[file.txt, mode:100644, content:a]",
+					indexState(CONTENT));
+			assertWorkDir(mkmap("file.txt", "c"));
+			recorder.assertNoEvent();
 
-		assertEquals("[file.txt, mode:100644, content:a]", indexState(CONTENT));
-		assertWorkDir(mkmap("file.txt", "c"));
-
-		// Switch branches and check that the dirty file survived in worktree
-		// and index
-		git.checkout().setName("b1").call();
-		assertEquals("[file.txt, mode:100644, content:a]", indexState(CONTENT));
-		assertWorkDir(mkmap("file.txt", "c"));
+			// Switch branches and check that the dirty file survived in
+			// worktree
+			// and index
+			git.checkout().setName("b1").call();
+			assertEquals("[file.txt, mode:100644, content:a]",
+					indexState(CONTENT));
+			assertWorkDir(mkmap("file.txt", "c"));
+			recorder.assertNoEvent();
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
+		}
 	}
 
 	@Test
@@ -1587,31 +1792,44 @@ public void testFileModeChangeAndContentChangeNoConflict() throws Exception {
 		if (!FS.DETECTED.supportsExecute())
 			return;
 
-		Git git = Git.wrap(db);
+		ChangeRecorder recorder = new ChangeRecorder();
+		ListenerHandle handle = null;
+		try (Git git = new Git(db)) {
+			handle = db.getListenerList()
+					.addWorkingTreeModifiedListener(recorder);
+			// Add first file
+			File file1 = writeTrashFile("file1.txt", "a");
+			git.add().addFilepattern("file1.txt").call();
+			git.commit().setMessage("commit1").call();
+			assertFalse(db.getFS().canExecute(file1));
 
-		// Add first file
-		File file1 = writeTrashFile("file1.txt", "a");
-		git.add().addFilepattern("file1.txt").call();
-		git.commit().setMessage("commit1").call();
-		assertFalse(db.getFS().canExecute(file1));
+			// Add second file
+			File file2 = writeTrashFile("file2.txt", "b");
+			git.add().addFilepattern("file2.txt").call();
+			git.commit().setMessage("commit2").call();
+			assertFalse(db.getFS().canExecute(file2));
+			recorder.assertNoEvent();
 
-		// Add second file
-		File file2 = writeTrashFile("file2.txt", "b");
-		git.add().addFilepattern("file2.txt").call();
-		git.commit().setMessage("commit2").call();
-		assertFalse(db.getFS().canExecute(file2));
+			// Create branch from first commit
+			assertNotNull(git.checkout().setCreateBranch(true).setName("b1")
+					.setStartPoint(Constants.HEAD + "~1").call());
+			recorder.assertEvent(ChangeRecorder.EMPTY,
+					new String[] { "file2.txt" });
 
-		// Create branch from first commit
-		assertNotNull(git.checkout().setCreateBranch(true).setName("b1")
-				.setStartPoint(Constants.HEAD + "~1").call());
+			// Change content and file mode in working directory and index
+			file1 = writeTrashFile("file1.txt", "c");
+			db.getFS().setExecute(file1, true);
+			git.add().addFilepattern("file1.txt").call();
 
-		// Change content and file mode in working directory and index
-		file1 = writeTrashFile("file1.txt", "c");
-		db.getFS().setExecute(file1, true);
-		git.add().addFilepattern("file1.txt").call();
-
-		// Switch back to 'master'
-		assertNotNull(git.checkout().setName(Constants.MASTER).call());
+			// Switch back to 'master'
+			assertNotNull(git.checkout().setName(Constants.MASTER).call());
+			recorder.assertEvent(new String[] { "file2.txt" },
+					ChangeRecorder.EMPTY);
+		} finally {
+			if (handle != null) {
+				handle.remove();
+			}
+		}
 	}
 
 	@Test(expected = CheckoutConflictException.class)
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffSubmoduleTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffSubmoduleTest.java
index 0111b94..d89aabe 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffSubmoduleTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffSubmoduleTest.java
@@ -43,11 +43,13 @@
 
 package org.eclipse.jgit.lib;
 
+import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.Set;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.GitAPIException;
@@ -118,6 +120,31 @@ public void testDirtyRootWorktree(IgnoreSubmoduleMode mode)
 		assertTrue(indexDiff.diff());
 	}
 
+	private void assertDiff(IndexDiff indexDiff, IgnoreSubmoduleMode mode,
+			IgnoreSubmoduleMode... expectedEmptyModes) throws IOException {
+		boolean diffResult = indexDiff.diff();
+		Set<String> submodulePaths = indexDiff
+				.getPathsWithIndexMode(FileMode.GITLINK);
+		boolean emptyExpected = false;
+		for (IgnoreSubmoduleMode empty : expectedEmptyModes) {
+			if (mode.equals(empty)) {
+				emptyExpected = true;
+				break;
+			}
+		}
+		if (emptyExpected) {
+			assertFalse("diff should be false with mode=" + mode,
+					diffResult);
+			assertEquals("should have no paths with FileMode.GITLINK", 0,
+					submodulePaths.size());
+		} else {
+			assertTrue("diff should be true with mode=" + mode,
+					diffResult);
+			assertTrue("submodule path should have FileMode.GITLINK",
+					submodulePaths.contains("modules/submodule"));
+		}
+	}
+
 	@Theory
 	public void testDirtySubmoduleWorktree(IgnoreSubmoduleMode mode)
 			throws IOException {
@@ -125,13 +152,8 @@ public void testDirtySubmoduleWorktree(IgnoreSubmoduleMode mode)
 		IndexDiff indexDiff = new IndexDiff(db, Constants.HEAD,
 				new FileTreeIterator(db));
 		indexDiff.setIgnoreSubmoduleMode(mode);
-		if (mode.equals(IgnoreSubmoduleMode.ALL)
-				|| mode.equals(IgnoreSubmoduleMode.DIRTY))
-			assertFalse("diff should be false with mode=" + mode,
-					indexDiff.diff());
-		else
-			assertTrue("diff should be true with mode=" + mode,
-					indexDiff.diff());
+		assertDiff(indexDiff, mode, IgnoreSubmoduleMode.ALL,
+				IgnoreSubmoduleMode.DIRTY);
 	}
 
 	@Theory
@@ -145,12 +167,7 @@ public void testDirtySubmoduleHEAD(IgnoreSubmoduleMode mode)
 		IndexDiff indexDiff = new IndexDiff(db, Constants.HEAD,
 				new FileTreeIterator(db));
 		indexDiff.setIgnoreSubmoduleMode(mode);
-		if (mode.equals(IgnoreSubmoduleMode.ALL))
-			assertFalse("diff should be false with mode=" + mode,
-					indexDiff.diff());
-		else
-			assertTrue("diff should be true with mode=" + mode,
-					indexDiff.diff());
+		assertDiff(indexDiff, mode, IgnoreSubmoduleMode.ALL);
 	}
 
 	@Theory
@@ -163,13 +180,8 @@ public void testDirtySubmoduleIndex(IgnoreSubmoduleMode mode)
 		IndexDiff indexDiff = new IndexDiff(db, Constants.HEAD,
 				new FileTreeIterator(db));
 		indexDiff.setIgnoreSubmoduleMode(mode);
-		if (mode.equals(IgnoreSubmoduleMode.ALL)
-				|| mode.equals(IgnoreSubmoduleMode.DIRTY))
-			assertFalse("diff should be false with mode=" + mode,
-					indexDiff.diff());
-		else
-			assertTrue("diff should be true with mode=" + mode,
-					indexDiff.diff());
+		assertDiff(indexDiff, mode, IgnoreSubmoduleMode.ALL,
+				IgnoreSubmoduleMode.DIRTY);
 	}
 
 	@Theory
@@ -183,13 +195,8 @@ public void testDirtySubmoduleIndexAndWorktree(IgnoreSubmoduleMode mode)
 		IndexDiff indexDiff = new IndexDiff(db, Constants.HEAD,
 				new FileTreeIterator(db));
 		indexDiff.setIgnoreSubmoduleMode(mode);
-		if (mode.equals(IgnoreSubmoduleMode.ALL)
-				|| mode.equals(IgnoreSubmoduleMode.DIRTY))
-			assertFalse("diff should be false with mode=" + mode,
-					indexDiff.diff());
-		else
-			assertTrue("diff should be true with mode=" + mode,
-					indexDiff.diff());
+		assertDiff(indexDiff, mode, IgnoreSubmoduleMode.ALL,
+				IgnoreSubmoduleMode.DIRTY);
 	}
 
 	@Theory
@@ -200,13 +207,7 @@ public void testDirtySubmoduleWorktreeUntracked(IgnoreSubmoduleMode mode)
 		IndexDiff indexDiff = new IndexDiff(db, Constants.HEAD,
 				new FileTreeIterator(db));
 		indexDiff.setIgnoreSubmoduleMode(mode);
-		if (mode.equals(IgnoreSubmoduleMode.ALL)
-				|| mode.equals(IgnoreSubmoduleMode.DIRTY)
-				|| mode.equals(IgnoreSubmoduleMode.UNTRACKED))
-			assertFalse("diff should be false with mode=" + mode,
-					indexDiff.diff());
-		else
-			assertTrue("diff should be true with mode=" + mode,
-					indexDiff.diff());
+		assertDiff(indexDiff, mode, IgnoreSubmoduleMode.ALL,
+				IgnoreSubmoduleMode.DIRTY, IgnoreSubmoduleMode.UNTRACKED);
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ObjectCheckerTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ObjectCheckerTest.java
index 43160fb..7475d69 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ObjectCheckerTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ObjectCheckerTest.java
@@ -45,6 +45,7 @@
 package org.eclipse.jgit.lib;
 
 import static java.lang.Integer.valueOf;
+import static org.eclipse.jgit.junit.JGitTestUtil.concat;
 import static org.eclipse.jgit.lib.Constants.OBJECT_ID_LENGTH;
 import static org.eclipse.jgit.lib.Constants.OBJ_BAD;
 import static org.eclipse.jgit.lib.Constants.OBJ_BLOB;
@@ -62,6 +63,7 @@
 import static org.eclipse.jgit.lib.ObjectChecker.ErrorType.NULL_SHA1;
 import static org.eclipse.jgit.lib.ObjectChecker.ErrorType.TREE_NOT_SORTED;
 import static org.eclipse.jgit.lib.ObjectChecker.ErrorType.ZERO_PADDED_FILEMODE;
+import static org.eclipse.jgit.util.RawParseUtils.decode;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertSame;
 import static org.junit.Assert.fail;
@@ -72,11 +74,52 @@
 import org.eclipse.jgit.errors.CorruptObjectException;
 import org.eclipse.jgit.internal.JGitText;
 import org.junit.Before;
+import org.junit.Rule;
 import org.junit.Test;
+import org.junit.rules.ExpectedException;
 
 public class ObjectCheckerTest {
+	private static final ObjectChecker SECRET_KEY_CHECKER = new ObjectChecker() {
+		@Override
+		public void checkBlob(byte[] raw) throws CorruptObjectException {
+			String in = decode(raw);
+			if (in.contains("secret_key")) {
+				throw new CorruptObjectException("don't add a secret key");
+			}
+		}
+	};
+
+	private static final ObjectChecker SECRET_KEY_BLOB_CHECKER = new ObjectChecker() {
+		@Override
+		public BlobObjectChecker newBlobObjectChecker() {
+			return new BlobObjectChecker() {
+				private boolean containSecretKey;
+
+				@Override
+				public void update(byte[] in, int offset, int len) {
+					String str = decode(in, offset, offset + len);
+					if (str.contains("secret_key")) {
+						containSecretKey = true;
+					}
+				}
+
+				@Override
+				public void endBlob(AnyObjectId id)
+						throws CorruptObjectException {
+					if (containSecretKey) {
+						throw new CorruptObjectException(
+								"don't add a secret key");
+					}
+				}
+			};
+		}
+	};
+
 	private ObjectChecker checker;
 
+	@Rule
+	public final ExpectedException thrown = ExpectedException.none();
+
 	@Before
 	public void setUp() throws Exception {
 		checker = new ObjectChecker();
@@ -101,6 +144,32 @@ public void testCheckBlob() throws CorruptObjectException {
 	}
 
 	@Test
+	public void testCheckBlobNotCorrupt() throws CorruptObjectException {
+		SECRET_KEY_CHECKER.check(OBJ_BLOB, encodeASCII("key = \"public_key\""));
+	}
+
+	@Test
+	public void testCheckBlobCorrupt() throws CorruptObjectException {
+		thrown.expect(CorruptObjectException.class);
+		SECRET_KEY_CHECKER.check(OBJ_BLOB, encodeASCII("key = \"secret_key\""));
+	}
+
+	@Test
+	public void testCheckBlobWithBlobObjectCheckerNotCorrupt()
+			throws CorruptObjectException {
+		SECRET_KEY_BLOB_CHECKER.check(OBJ_BLOB,
+				encodeASCII("key = \"public_key\""));
+	}
+
+	@Test
+	public void testCheckBlobWithBlobObjectCheckerCorrupt()
+			throws CorruptObjectException {
+		thrown.expect(CorruptObjectException.class);
+		SECRET_KEY_BLOB_CHECKER.check(OBJ_BLOB,
+				encodeASCII("key = \"secret_key\""));
+	}
+
+	@Test
 	public void testValidCommitNoParent() throws CorruptObjectException {
 		StringBuilder b = new StringBuilder();
 
@@ -1054,20 +1123,7 @@ public void testInvalidTreeNameIsMacHFSGit3()
 		checker.checkTree(data);
 	}
 
-	private static byte[] concat(byte[]... b) {
-		int n = 0;
-		for (byte[] a : b) {
-			n += a.length;
-		}
 
-		byte[] data = new byte[n];
-		n = 0;
-		for (byte[] a : b) {
-			System.arraycopy(a, 0, data, n, a.length);
-			n += a.length;
-		}
-		return data;
-	}
 
 	@Test
 	public void testInvalidTreeNameIsMacHFSGitCorruptUTF8AtEnd()
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ReflogResolveTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ReflogResolveTest.java
index 7db9f60..15f28af 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ReflogResolveTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ReflogResolveTest.java
@@ -179,4 +179,4 @@ public void resolveDate() throws Exception {
 			}
 		}
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/SubmoduleConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/SubmoduleConfigTest.java
new file mode 100644
index 0000000..fb8dec5
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/SubmoduleConfigTest.java
@@ -0,0 +1,93 @@
+/*
+ * Copyright (C) 2017, David Pursehouse <david.pursehouse@gmail.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.lib;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import org.eclipse.jgit.lib.SubmoduleConfig.FetchRecurseSubmodulesMode;
+import org.junit.Test;
+
+public class SubmoduleConfigTest {
+	@Test
+	public void fetchRecurseMatch() throws Exception {
+		assertTrue(FetchRecurseSubmodulesMode.YES.matchConfigValue("yes"));
+		assertTrue(FetchRecurseSubmodulesMode.YES.matchConfigValue("YES"));
+		assertTrue(FetchRecurseSubmodulesMode.YES.matchConfigValue("true"));
+		assertTrue(FetchRecurseSubmodulesMode.YES.matchConfigValue("TRUE"));
+
+		assertTrue(FetchRecurseSubmodulesMode.ON_DEMAND
+				.matchConfigValue("on-demand"));
+		assertTrue(FetchRecurseSubmodulesMode.ON_DEMAND
+				.matchConfigValue("ON-DEMAND"));
+		assertTrue(FetchRecurseSubmodulesMode.ON_DEMAND
+				.matchConfigValue("on_demand"));
+		assertTrue(FetchRecurseSubmodulesMode.ON_DEMAND
+				.matchConfigValue("ON_DEMAND"));
+
+		assertTrue(FetchRecurseSubmodulesMode.NO.matchConfigValue("no"));
+		assertTrue(FetchRecurseSubmodulesMode.NO.matchConfigValue("NO"));
+		assertTrue(FetchRecurseSubmodulesMode.NO.matchConfigValue("false"));
+		assertTrue(FetchRecurseSubmodulesMode.NO.matchConfigValue("FALSE"));
+	}
+
+	@Test
+	public void fetchRecurseNoMatch() throws Exception {
+		assertFalse(FetchRecurseSubmodulesMode.YES.matchConfigValue("Y"));
+		assertFalse(FetchRecurseSubmodulesMode.NO.matchConfigValue("N"));
+		assertFalse(FetchRecurseSubmodulesMode.ON_DEMAND
+				.matchConfigValue("ONDEMAND"));
+		assertFalse(FetchRecurseSubmodulesMode.YES.matchConfigValue(""));
+		assertFalse(FetchRecurseSubmodulesMode.YES.matchConfigValue(null));
+	}
+
+	@Test
+	public void fetchRecurseToConfigValue() {
+		assertEquals("on-demand",
+				FetchRecurseSubmodulesMode.ON_DEMAND.toConfigValue());
+		assertEquals("true", FetchRecurseSubmodulesMode.YES.toConfigValue());
+		assertEquals("false", FetchRecurseSubmodulesMode.NO.toConfigValue());
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkMergeBaseTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkMergeBaseTest.java
index 2451c50..077645e 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkMergeBaseTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkMergeBaseTest.java
@@ -171,4 +171,4 @@ public void testInconsistentCommitTimes() throws Exception {
 		assertNull(rw.next());
 	}
 
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/SkipRevFilterTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/SkipRevFilterTest.java
index 353a487..cf02aa8 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/SkipRevFilterTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/SkipRevFilterTest.java
@@ -81,4 +81,4 @@ public void testSkipRevFilter0() throws Exception {
 	public void testSkipRevFilterNegative() throws Exception {
 		SkipRevFilter.create(-1);
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleAddTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleAddTest.java
index 5c46659..f42dd02 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleAddTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleAddTest.java
@@ -269,4 +269,4 @@ public void addSubmoduleWithExistingSubmoduleDefined() throws Exception {
 					ConfigConstants.CONFIG_KEY_URL));
 		}
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleStatusTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleStatusTest.java
index 61df9d9..5832518 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleStatusTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleStatusTest.java
@@ -59,11 +59,11 @@
 import org.eclipse.jgit.dircache.DirCacheEditor.PathEdit;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
-import org.eclipse.jgit.lib.RefUpdate;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
@@ -256,11 +256,16 @@ public void apply(DirCacheEntry ent) {
 	}
 
 	@Test
-	public void repositoryWithInitializedSubmodule() throws IOException,
-			GitAPIException {
-		final ObjectId id = ObjectId
-				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
-		final String path = "sub";
+	public void repositoryWithInitializedSubmodule() throws Exception {
+		String path = "sub";
+		Repository subRepo = Git.init().setBare(false)
+				.setDirectory(new File(db.getWorkTree(), path)).call()
+				.getRepository();
+		assertNotNull(subRepo);
+
+		TestRepository<?> subTr = new TestRepository<>(subRepo);
+		ObjectId id = subTr.branch(Constants.HEAD).commit().create().copy();
+
 		DirCache cache = db.lockDirCache();
 		DirCacheEditor editor = cache.editor();
 		editor.add(new PathEdit(path) {
@@ -287,15 +292,6 @@ public void apply(DirCacheEntry ent) {
 				ConfigConstants.CONFIG_KEY_URL, url);
 		modulesConfig.save();
 
-		Repository subRepo = Git.init().setBare(false)
-				.setDirectory(new File(db.getWorkTree(), path)).call()
-				.getRepository();
-		assertNotNull(subRepo);
-
-		RefUpdate update = subRepo.updateRef(Constants.HEAD, true);
-		update.setNewObjectId(id);
-		update.forceUpdate();
-
 		SubmoduleStatusCommand command = new SubmoduleStatusCommand(db);
 		Map<String, SubmoduleStatus> statuses = command.call();
 		assertNotNull(statuses);
@@ -312,11 +308,16 @@ public void apply(DirCacheEntry ent) {
 	}
 
 	@Test
-	public void repositoryWithDifferentRevCheckedOutSubmodule()
-			throws IOException, GitAPIException {
-		final ObjectId id = ObjectId
-				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
-		final String path = "sub";
+	public void repositoryWithDifferentRevCheckedOutSubmodule() throws Exception {
+		String path = "sub";
+		Repository subRepo = Git.init().setBare(false)
+				.setDirectory(new File(db.getWorkTree(), path)).call()
+				.getRepository();
+		assertNotNull(subRepo);
+
+		TestRepository<?> subTr = new TestRepository<>(subRepo);
+		ObjectId id = subTr.branch(Constants.HEAD).commit().create().copy();
+
 		DirCache cache = db.lockDirCache();
 		DirCacheEditor editor = cache.editor();
 		editor.add(new PathEdit(path) {
@@ -343,15 +344,7 @@ public void apply(DirCacheEntry ent) {
 				ConfigConstants.CONFIG_KEY_URL, url);
 		modulesConfig.save();
 
-		Repository subRepo = Git.init().setBare(false)
-				.setDirectory(new File(db.getWorkTree(), path)).call()
-				.getRepository();
-		assertNotNull(subRepo);
-
-		RefUpdate update = subRepo.updateRef(Constants.HEAD, true);
-		update.setNewObjectId(ObjectId
-				.fromString("aaaa0000aaaa0000aaaa0000aaaa0000aaaa0000"));
-		update.forceUpdate();
+		ObjectId newId = subTr.branch(Constants.HEAD).commit().create().copy();
 
 		SubmoduleStatusCommand command = new SubmoduleStatusCommand(db);
 		Map<String, SubmoduleStatus> statuses = command.call();
@@ -365,7 +358,7 @@ public void apply(DirCacheEntry ent) {
 		assertNotNull(status);
 		assertEquals(path, status.getPath());
 		assertEquals(id, status.getIndexId());
-		assertEquals(update.getNewObjectId(), status.getHeadId());
+		assertEquals(newId, status.getHeadId());
 		assertEquals(SubmoduleStatusType.REV_CHECKED_OUT, status.getType());
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleWalkTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleWalkTest.java
index 8998a85..fed22c0 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleWalkTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleWalkTest.java
@@ -444,4 +444,44 @@ public void apply(DirCacheEntry ent) {
 		assertNull(gen.getRepository());
 		assertFalse(gen.next());
 	}
+
+	@Test
+	public void testTreeIteratorWithGitmodulesNameNotPath() throws Exception {
+		final ObjectId subId = ObjectId
+				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
+		final String path = "sub";
+		final String arbitraryName = "x";
+
+		final Config gitmodules = new Config();
+		gitmodules.setString(CONFIG_SUBMODULE_SECTION, arbitraryName,
+				CONFIG_KEY_PATH, "sub");
+		gitmodules.setString(CONFIG_SUBMODULE_SECTION, arbitraryName,
+				CONFIG_KEY_URL, "git://example.com/sub");
+
+		RevCommit commit = testDb.getRevWalk()
+				.parseCommit(testDb.commit().noParents()
+						.add(DOT_GIT_MODULES, gitmodules.toText())
+						.edit(new PathEdit(path) {
+
+							@Override
+							public void apply(DirCacheEntry ent) {
+								ent.setFileMode(FileMode.GITLINK);
+								ent.setObjectId(subId);
+							}
+						}).create());
+
+		final CanonicalTreeParser p = new CanonicalTreeParser();
+		p.reset(testDb.getRevWalk().getObjectReader(), commit.getTree());
+		SubmoduleWalk gen = SubmoduleWalk.forPath(db, p, "sub");
+		assertEquals(path, gen.getPath());
+		assertEquals(subId, gen.getObjectId());
+		assertEquals(new File(db.getWorkTree(), path), gen.getDirectory());
+		assertNull(gen.getConfigUpdate());
+		assertNull(gen.getConfigUrl());
+		assertEquals("sub", gen.getModulesPath());
+		assertNull(gen.getModulesUpdate());
+		assertEquals("git://example.com/sub", gen.getModulesUrl());
+		assertNull(gen.getRepository());
+		assertFalse(gen.next());
+	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/DaemonTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/DaemonTest.java
new file mode 100644
index 0000000..a5e5441
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/DaemonTest.java
@@ -0,0 +1,96 @@
+/*
+ * Copyright (C) 2017 Thomas Wolf <thomas.wolf@paranor.ch>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.transport;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.net.InetSocketAddress;
+
+import org.junit.Test;
+
+/**
+ * Daemon tests.
+ */
+public class DaemonTest {
+
+	@Test
+	public void testDaemonStop() throws Exception {
+		Daemon d = new Daemon();
+		d.start();
+		InetSocketAddress address = d.getAddress();
+		assertTrue("Port should be allocated", address.getPort() > 0);
+		assertTrue("Daemon should be running", d.isRunning());
+		Thread.sleep(1000); // Give it time to enter accept()
+		d.stopAndWait();
+		// Try to start a new Daemon again on the same port
+		d = new Daemon(address);
+		d.start();
+		InetSocketAddress newAddress = d.getAddress();
+		assertEquals("New daemon should run on the same port", address,
+				newAddress);
+		assertTrue("Daemon should be running", d.isRunning());
+		Thread.sleep(1000);
+		d.stopAndWait();
+	}
+
+	@Test
+	public void testDaemonRestart() throws Exception {
+		Daemon d = new Daemon();
+		d.start();
+		InetSocketAddress address = d.getAddress();
+		assertTrue("Port should be allocated", address.getPort() > 0);
+		assertTrue("Daemon should be running", d.isRunning());
+		Thread.sleep(1000);
+		d.stopAndWait();
+		// Re-start the same daemon
+		d.start();
+		InetSocketAddress newAddress = d.getAddress();
+		assertEquals("Daemon should again run on the same port", address,
+				newAddress);
+		assertTrue("Daemon should be running", d.isRunning());
+		Thread.sleep(1000);
+		d.stopAndWait();
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/HttpConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/HttpConfigTest.java
new file mode 100644
index 0000000..c6b016a
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/HttpConfigTest.java
@@ -0,0 +1,210 @@
+/*
+ * Copyright (C) 2017, Thomas Wolf <thomas.wolf@paranor.ch>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.transport;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.eclipse.jgit.lib.Config;
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Tests for correctly resolving URIs when reading http.* values from a
+ * {@link Config}.
+ */
+public class HttpConfigTest {
+
+	private static final String DEFAULT = "[http]\n" + "\tpostBuffer = 1\n"
+			+ "\tsslVerify= true\n" + "\tfollowRedirects = true\n"
+			+ "\tmaxRedirects = 5\n\n";
+
+	private Config config;
+
+	@Before
+	public void setUp() {
+		config = new Config();
+	}
+
+	@Test
+	public void testDefault() throws Exception {
+		HttpConfig http = new HttpConfig(config,
+				new URIish("http://example.com/path/repo.git"));
+		assertEquals(1024 * 1024, http.getPostBuffer());
+		assertTrue(http.isSslVerify());
+		assertEquals(HttpConfig.HttpRedirectMode.INITIAL,
+				http.getFollowRedirects());
+	}
+
+	@Test
+	public void testMatchSuccess() throws Exception {
+		config.fromText(DEFAULT + "[http \"http://example.com\"]\n"
+				+ "\tpostBuffer = 1024\n");
+		HttpConfig http = new HttpConfig(config,
+				new URIish("http://example.com/path/repo.git"));
+		assertEquals(1024, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("https://example.com/path/repo.git"));
+		assertEquals(1, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("http://example.org/path/repo.git"));
+		assertEquals(1, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("http://example.com:80/path/repo.git"));
+		assertEquals(1024, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("http://example.com:8080/path/repo.git"));
+		assertEquals(1, http.getPostBuffer());
+	}
+
+	@Test
+	public void testMatchWithOnlySchemeInConfig() throws Exception {
+		config.fromText(
+				DEFAULT + "[http \"http://\"]\n" + "\tpostBuffer = 1024\n");
+		HttpConfig http = new HttpConfig(config,
+				new URIish("http://example.com/path/repo.git"));
+		assertEquals(1, http.getPostBuffer());
+	}
+
+	@Test
+	public void testMatchWithPrefixUriInConfig() throws Exception {
+		config.fromText(DEFAULT + "[http \"http://example\"]\n"
+				+ "\tpostBuffer = 1024\n");
+		HttpConfig http = new HttpConfig(config,
+				new URIish("http://example.com/path/repo.git"));
+		assertEquals(1, http.getPostBuffer());
+	}
+
+	@Test
+	public void testMatchCaseSensitivity() throws Exception {
+		config.fromText(DEFAULT + "[http \"http://exAMPle.com\"]\n"
+				+ "\tpostBuffer = 1024\n");
+		HttpConfig http = new HttpConfig(config,
+				new URIish("http://example.com/path/repo.git"));
+		assertEquals(1024, http.getPostBuffer());
+	}
+
+	@Test
+	public void testMatchWithInvalidUriInConfig() throws Exception {
+		config.fromText(
+				DEFAULT + "[http \"///\"]\n" + "\tpostBuffer = 1024\n");
+		HttpConfig http = new HttpConfig(config,
+				new URIish("http://example.com/path/repo.git"));
+		assertEquals(1, http.getPostBuffer());
+	}
+
+	@Test
+	public void testMatchWithInvalidAndValidUriInConfig() throws Exception {
+		config.fromText(DEFAULT + "[http \"///\"]\n" + "\tpostBuffer = 1024\n"
+				+ "[http \"http://example.com\"]\n" + "\tpostBuffer = 2048\n");
+		HttpConfig http = new HttpConfig(config,
+				new URIish("http://example.com/path/repo.git"));
+		assertEquals(2048, http.getPostBuffer());
+	}
+
+	@Test
+	public void testMatchWithHostEndingInSlash() throws Exception {
+		config.fromText(DEFAULT + "[http \"http://example.com/\"]\n"
+				+ "\tpostBuffer = 1024\n");
+		HttpConfig http = new HttpConfig(config,
+				new URIish("http://example.com/path/repo.git"));
+		assertEquals(1024, http.getPostBuffer());
+	}
+
+	@Test
+	public void testMatchWithUser() throws Exception {
+		config.fromText(DEFAULT + "[http \"http://example.com/path\"]\n"
+				+ "\tpostBuffer = 1024\n"
+				+ "[http \"http://example.com/path/repo\"]\n"
+				+ "\tpostBuffer = 2048\n"
+				+ "[http \"http://user@example.com/path\"]\n"
+				+ "\tpostBuffer = 4096\n");
+		HttpConfig http = new HttpConfig(config,
+				new URIish("http://example.com/path/repo.git"));
+		assertEquals(1024, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("http://user@example.com/path/repo.git"));
+		assertEquals(4096, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("http://user@example.com/path/repo/foo.git"));
+		assertEquals(2048, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("http://user@example.com/path/foo.git"));
+		assertEquals(4096, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("http://example.com/path/foo.git"));
+		assertEquals(1024, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("http://User@example.com/path/repo/foo.git"));
+		assertEquals(2048, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("http://User@example.com/path/foo.git"));
+		assertEquals(1024, http.getPostBuffer());
+	}
+
+	@Test
+	public void testMatchLonger() throws Exception {
+		config.fromText(DEFAULT + "[http \"http://example.com/path\"]\n"
+				+ "\tpostBuffer = 1024\n"
+				+ "[http \"http://example.com/path/repo\"]\n"
+				+ "\tpostBuffer = 2048\n");
+		HttpConfig http = new HttpConfig(config,
+				new URIish("http://example.com/path/repo.git"));
+		assertEquals(1024, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("http://example.com/foo/repo.git"));
+		assertEquals(1, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("https://example.com/path/repo.git"));
+		assertEquals(1, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("http://example.com/path/repo/.git"));
+		assertEquals(2048, http.getPostBuffer());
+		http = new HttpConfig(config, new URIish("http://example.com/path"));
+		assertEquals(1024, http.getPostBuffer());
+		http = new HttpConfig(config,
+				new URIish("http://user@example.com/path"));
+		assertEquals(1024, http.getPostBuffer());
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/HttpConfigUriPathTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/HttpConfigUriPathTest.java
new file mode 100644
index 0000000..94de2f2
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/HttpConfigUriPathTest.java
@@ -0,0 +1,222 @@
+/*
+ * Copyright (C) 2017, Thomas Wolf <thomas.wolf@paranor.ch>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.transport;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import org.junit.Test;
+
+/**
+ * Basic URI path prefix match tests for {@link HttpConfig}.
+ */
+public class HttpConfigUriPathTest {
+
+	@Test
+	public void testNormalizationEmptyPaths() {
+		assertEquals("/", HttpConfig.normalize(""));
+		assertEquals("/", HttpConfig.normalize("/"));
+	}
+
+	@Test
+	public void testNormalization() {
+		assertEquals("/f", HttpConfig.normalize("f"));
+		assertEquals("/f", HttpConfig.normalize("/f"));
+		assertEquals("/f/", HttpConfig.normalize("/f/"));
+		assertEquals("/foo", HttpConfig.normalize("foo"));
+		assertEquals("/foo", HttpConfig.normalize("/foo"));
+		assertEquals("/foo/", HttpConfig.normalize("/foo/"));
+		assertEquals("/foo/bar", HttpConfig.normalize("foo/bar"));
+		assertEquals("/foo/bar", HttpConfig.normalize("/foo/bar"));
+		assertEquals("/foo/bar/", HttpConfig.normalize("/foo/bar/"));
+	}
+
+	@Test
+	public void testNormalizationWithDot() {
+		assertEquals("/", HttpConfig.normalize("."));
+		assertEquals("/", HttpConfig.normalize("/."));
+		assertEquals("/", HttpConfig.normalize("/./"));
+		assertEquals("/foo", HttpConfig.normalize("foo/."));
+		assertEquals("/foo/bar", HttpConfig.normalize("/foo/./bar"));
+		assertEquals("/foo/bar", HttpConfig.normalize("/foo/bar/."));
+		assertEquals("/foo/bar/", HttpConfig.normalize("/foo/bar/./"));
+		assertEquals("/foo/bar", HttpConfig.normalize("/foo/./././bar"));
+		assertEquals("/foo/bar/", HttpConfig.normalize("/foo/./././bar/"));
+		assertEquals("/foo/bar", HttpConfig.normalize("/foo/bar/././."));
+		assertEquals("/foo/bar/", HttpConfig.normalize("/foo/bar/./././"));
+		assertEquals("/foo/bar/.baz/bam",
+				HttpConfig.normalize("/foo/bar/.baz/bam"));
+		assertEquals("/foo/bar/.baz/bam/",
+				HttpConfig.normalize("/foo/bar/.baz/bam/"));
+	}
+
+	@Test
+	public void testNormalizationWithDotDot() {
+		assertEquals("/", HttpConfig.normalize("foo/.."));
+		assertEquals("/", HttpConfig.normalize("/foo/.."));
+		assertEquals("/", HttpConfig.normalize("/foo/../bar/.."));
+		assertEquals("/", HttpConfig.normalize("/foo/.././bar/.."));
+		assertEquals("/bar", HttpConfig.normalize("foo/../bar"));
+		assertEquals("/bar", HttpConfig.normalize("/foo/../bar"));
+		assertEquals("/bar", HttpConfig.normalize("/foo/./.././bar"));
+		assertEquals("/bar/", HttpConfig.normalize("/foo/../bar/"));
+		assertEquals("/bar/", HttpConfig.normalize("/foo/./.././bar/"));
+		assertEquals("/foo/bar", HttpConfig.normalize("/foo/bar/baz/.."));
+		assertEquals("/foo/bar/", HttpConfig.normalize("/foo/bar/baz/../"));
+		assertEquals("/foo", HttpConfig.normalize("/foo/bar/baz/../.."));
+		assertEquals("/foo", HttpConfig.normalize("/foo/bar/baz/../.."));
+		assertEquals("/foo", HttpConfig.normalize("/foo/bar/baz/.././.."));
+		assertEquals("/foo", HttpConfig.normalize("/foo/bar/baz/../././.."));
+		assertEquals("/foo/baz", HttpConfig.normalize("/foo/bar/../baz"));
+		assertEquals("/foo/baz/", HttpConfig.normalize("/foo/bar/../baz/"));
+		assertEquals("/foo/baz", HttpConfig.normalize("/foo/bar/../baz/."));
+		assertEquals("/foo/baz/", HttpConfig.normalize("/foo/bar/../baz/./"));
+		assertEquals("/foo", HttpConfig.normalize("/foo/bar/../baz/.."));
+		assertEquals("/foo/", HttpConfig.normalize("/foo/bar/../baz/../"));
+		assertEquals("/baz", HttpConfig.normalize("/foo/bar/../../baz"));
+		assertEquals("/baz/", HttpConfig.normalize("/foo/bar/../../baz/"));
+		assertEquals("/foo/.b/bar", HttpConfig.normalize("/foo/.b/bar"));
+		assertEquals("/.f/foo/.b/bar/", HttpConfig.normalize(".f/foo/.b/bar/"));
+		assertEquals("/foo/bar/..baz/bam",
+				HttpConfig.normalize("/foo/bar/..baz/bam"));
+		assertEquals("/foo/bar/..baz/bam/",
+				HttpConfig.normalize("/foo/bar/..baz/bam/"));
+		assertEquals("/foo/bar/.../baz/bam",
+				HttpConfig.normalize("/foo/bar/.../baz/bam"));
+		assertEquals("/foo/bar/.../baz/bam/",
+				HttpConfig.normalize("/foo/bar/.../baz/bam/"));
+	}
+
+	@Test
+	public void testNormalizationWithDoubleSlash() {
+		assertEquals("/", HttpConfig.normalize("//"));
+		assertEquals("/foo/", HttpConfig.normalize("///foo//"));
+		assertEquals("/foo", HttpConfig.normalize("///foo//."));
+		assertEquals("/foo/", HttpConfig.normalize("///foo//.////"));
+		assertEquals("/foo/bar", HttpConfig.normalize("/foo//bar"));
+		assertEquals("/foo/bar", HttpConfig.normalize("/foo//bar//."));
+		assertEquals("/foo/bar/", HttpConfig.normalize("/foo//bar//./"));
+	}
+
+	@Test
+	public void testNormalizationWithDotDotFailing() {
+		assertNull(HttpConfig.normalize(".."));
+		assertNull(HttpConfig.normalize("/.."));
+		assertNull(HttpConfig.normalize("/../"));
+		assertNull(HttpConfig.normalize("/../foo"));
+		assertNull(HttpConfig.normalize("./../foo"));
+		assertNull(HttpConfig.normalize("/./../foo"));
+		assertNull(HttpConfig.normalize("/foo/./.././.."));
+		assertNull(HttpConfig.normalize("/foo/../bar/../.."));
+		assertNull(HttpConfig.normalize("/foo/../bar/../../baz"));
+	}
+
+	@Test
+	public void testSegmentCompare() {
+		// 2nd parameter is the match, will be normalized
+		assertSuccess("/foo", "");
+		assertSuccess("/foo", "/");
+		assertSuccess("/foo", "//");
+		assertSuccess("/foo", "foo");
+		assertSuccess("/foo", "/foo");
+		assertSuccess("/foo/", "foo");
+		assertSuccess("/foo/", "/foo");
+		assertSuccess("/foo/", "foo/");
+		assertSuccess("/foo/", "/foo/");
+		assertSuccess("/foo/bar", "foo");
+		assertSuccess("/foo/bar", "foo/");
+		assertSuccess("/foo/bar", "foo/bar");
+		assertSuccess("/foo/bar/", "foo/bar");
+		assertSuccess("/foo/bar/", "foo/bar/");
+		assertSuccess("/foo/bar", "/foo/bar");
+		assertSuccess("/foo/bar/", "/foo/bar");
+		assertSuccess("/foo/bar/", "/foo/bar/");
+		assertSuccess("/foo/bar", "/foo/bar/..");
+		assertSuccess("/foo/bar/", "/foo/bar/..");
+		assertSuccess("/foo/bar/", "/foo/bar/../");
+		assertSuccess("/foo/bar", "/foo/./bar");
+		assertSuccess("/foo/bar/", "/foo/./bar/");
+		assertSuccess("/some/repo/.git", "/some/repo");
+		assertSuccess("/some/repo/bare.git", "/some/repo");
+		assertSuccess("/some/repo/.git", "/some/repo/.git");
+		assertSuccess("/some/repo/bare.git", "/some/repo/bare.git");
+	}
+
+	@Test
+	public void testSegmentCompareFailing() {
+		// 2nd parameter is the match, will be normalized
+		assertEquals(-1, HttpConfig.segmentCompare("/foo", "foo/"));
+		assertEquals(-1, HttpConfig.segmentCompare("/foo", "/foo/"));
+		assertEquals(-1, HttpConfig.segmentCompare("/foobar", "foo"));
+		assertEquals(-1, HttpConfig.segmentCompare("/foobar", "/foo"));
+		assertEquals(-1,
+				HttpConfig.segmentCompare("/foo/barbar/baz", "foo/bar"));
+		assertEquals(-1, HttpConfig.segmentCompare("/foo/barbar", "/foo/bar"));
+		assertEquals(-1,
+				HttpConfig.segmentCompare("/some/repo.git", "/some/repo"));
+		assertEquals(-1,
+				HttpConfig.segmentCompare("/some/repo.git", "/some/repo.g"));
+		assertEquals(-1, HttpConfig.segmentCompare("/some/repo/bare.git",
+				"/some/repo/bar"));
+		assertSuccess("/some/repo/bare.git", "/some/repo");
+		// Just to make sure we don't use the PathMatchers...
+		assertEquals(-1, HttpConfig.segmentCompare("/foo/barbar/baz", "**"));
+		assertEquals(-1,
+				HttpConfig.segmentCompare("/foo/barbar/baz", "**/foo"));
+		assertEquals(-1,
+				HttpConfig.segmentCompare("/foo/barbar/baz", "/*/barbar/**"));
+		assertEquals(-1, HttpConfig.segmentCompare("/foo", "/*"));
+		assertEquals(-1, HttpConfig.segmentCompare("/foo", "/???"));
+		assertEquals(-1, HttpConfig.segmentCompare("/foo/bar/baz", "bar"));
+		// Failing to normalize
+		assertEquals(-1,
+				HttpConfig.segmentCompare("/foo/bar/baz", "bar/../.."));
+	}
+
+	private void assertSuccess(String uri, String match) {
+		String normalized = HttpConfig.normalize(match);
+		assertEquals(normalized.length(),
+				HttpConfig.segmentCompare(uri, match));
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/JschConfigSessionFactoryTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/JschConfigSessionFactoryTest.java
new file mode 100644
index 0000000..1e65a20
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/JschConfigSessionFactoryTest.java
@@ -0,0 +1,283 @@
+/*
+ * Copyright (C) 2018, Thomas Wolf <thomas.wolf@paranor.ch>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.transport;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.File;
+import java.nio.file.Files;
+import java.util.Arrays;
+import java.util.concurrent.TimeUnit;
+
+import org.eclipse.jgit.util.FS;
+import org.junit.After;
+import org.junit.Test;
+
+import com.jcraft.jsch.Session;
+
+/**
+ * Tests for correctly interpreting ssh config values when Jsch sessions are
+ * used.
+ */
+public class JschConfigSessionFactoryTest {
+
+	File tmpConfigFile;
+
+	OpenSshConfig tmpConfig;
+
+	DefaultSshSessionFactory factory = new DefaultSshSessionFactory();
+
+	@After
+	public void removeTmpConfig() {
+		if (tmpConfigFile == null) {
+			return;
+		}
+		if (tmpConfigFile.exists() && !tmpConfigFile.delete()) {
+			tmpConfigFile.deleteOnExit();
+		}
+		tmpConfigFile = null;
+	}
+
+	@Test
+	public void testNoConfigEntry() throws Exception {
+		tmpConfigFile = File.createTempFile("jsch", "test");
+		tmpConfig = new OpenSshConfig(tmpConfigFile.getParentFile(),
+				tmpConfigFile);
+		factory.setConfig(tmpConfig);
+		Session session = createSession("ssh://egit/egit/egit");
+		assertEquals("egit", session.getHost());
+		// No user in URI, none in ssh config: default is OS user name
+		assertEquals(System.getProperty("user.name"), session.getUserName());
+		assertEquals(22, session.getPort());
+	}
+
+	@Test
+	public void testAlias() throws Exception {
+		tmpConfigFile = createConfig("Host egit", "Hostname git.eclipse.org",
+				"User foo", "Port 29418");
+		tmpConfig = new OpenSshConfig(tmpConfigFile.getParentFile(),
+				tmpConfigFile);
+		factory.setConfig(tmpConfig);
+		Session session = createSession("ssh://egit/egit/egit");
+		assertEquals("git.eclipse.org", session.getHost());
+		assertEquals("foo", session.getUserName());
+		assertEquals(29418, session.getPort());
+	}
+
+	@Test
+	public void testAliasWithUser() throws Exception {
+		tmpConfigFile = createConfig("Host egit", "Hostname git.eclipse.org",
+				"User foo", "Port 29418");
+		tmpConfig = new OpenSshConfig(tmpConfigFile.getParentFile(),
+				tmpConfigFile);
+		factory.setConfig(tmpConfig);
+		Session session = createSession("ssh://bar@egit/egit/egit");
+		assertEquals("git.eclipse.org", session.getHost());
+		assertEquals("bar", session.getUserName());
+		assertEquals(29418, session.getPort());
+	}
+
+	@Test
+	public void testAliasWithPort() throws Exception {
+		tmpConfigFile = createConfig("Host egit", "Hostname git.eclipse.org",
+				"User foo", "Port 29418");
+		tmpConfig = new OpenSshConfig(tmpConfigFile.getParentFile(),
+				tmpConfigFile);
+		factory.setConfig(tmpConfig);
+		Session session = createSession("ssh://bar@egit:22/egit/egit");
+		assertEquals("git.eclipse.org", session.getHost());
+		assertEquals("bar", session.getUserName());
+		assertEquals(22, session.getPort());
+	}
+
+	@Test
+	public void testAliasIdentical() throws Exception {
+		tmpConfigFile = createConfig("Host git.eclipse.org",
+				"Hostname git.eclipse.org", "User foo", "Port 29418");
+		tmpConfig = new OpenSshConfig(tmpConfigFile.getParentFile(),
+				tmpConfigFile);
+		factory.setConfig(tmpConfig);
+		Session session = createSession("ssh://git.eclipse.org/egit/egit");
+		assertEquals("git.eclipse.org", session.getHost());
+		assertEquals("foo", session.getUserName());
+		assertEquals(29418, session.getPort());
+	}
+
+	@Test
+	public void testAliasIdenticalWithUser() throws Exception {
+		tmpConfigFile = createConfig("Host git.eclipse.org",
+				"Hostname git.eclipse.org", "User foo", "Port 29418");
+		tmpConfig = new OpenSshConfig(tmpConfigFile.getParentFile(),
+				tmpConfigFile);
+		factory.setConfig(tmpConfig);
+		Session session = createSession("ssh://bar@git.eclipse.org/egit/egit");
+		assertEquals("git.eclipse.org", session.getHost());
+		assertEquals("bar", session.getUserName());
+		assertEquals(29418, session.getPort());
+	}
+
+	@Test
+	public void testAliasIdenticalWithPort() throws Exception {
+		tmpConfigFile = createConfig("Host git.eclipse.org",
+				"Hostname git.eclipse.org", "User foo", "Port 29418");
+		tmpConfig = new OpenSshConfig(tmpConfigFile.getParentFile(),
+				tmpConfigFile);
+		factory.setConfig(tmpConfig);
+		Session session = createSession(
+				"ssh://bar@git.eclipse.org:300/egit/egit");
+		assertEquals("git.eclipse.org", session.getHost());
+		assertEquals("bar", session.getUserName());
+		assertEquals(300, session.getPort());
+	}
+
+	@Test
+	public void testConnectTimout() throws Exception {
+		tmpConfigFile = createConfig("Host git.eclipse.org",
+				"Hostname git.eclipse.org", "User foo", "Port 29418",
+				"ConnectTimeout 10");
+		tmpConfig = new OpenSshConfig(tmpConfigFile.getParentFile(),
+				tmpConfigFile);
+		factory.setConfig(tmpConfig);
+		Session session = createSession("ssh://git.eclipse.org/something");
+		assertEquals("git.eclipse.org", session.getHost());
+		assertEquals("foo", session.getUserName());
+		assertEquals(29418, session.getPort());
+		assertEquals(TimeUnit.SECONDS.toMillis(10), session.getTimeout());
+	}
+
+	@Test
+	public void testAliasCaseDifferenceUpcase() throws Exception {
+		tmpConfigFile = createConfig("Host Bitbucket.org",
+				"Hostname bitbucket.org", "User foo", "Port 29418",
+				"ConnectTimeout 10", //
+				"Host bitbucket.org", "Hostname bitbucket.org", "User bar",
+				"Port 22", "ConnectTimeout 5");
+		tmpConfig = new OpenSshConfig(tmpConfigFile.getParentFile(),
+				tmpConfigFile);
+		factory.setConfig(tmpConfig);
+		Session session = createSession("ssh://Bitbucket.org/something");
+		assertEquals("bitbucket.org", session.getHost());
+		assertEquals("foo", session.getUserName());
+		assertEquals(29418, session.getPort());
+		assertEquals(TimeUnit.SECONDS.toMillis(10), session.getTimeout());
+	}
+
+	@Test
+	public void testAliasCaseDifferenceLowcase() throws Exception {
+		tmpConfigFile = createConfig("Host Bitbucket.org",
+				"Hostname bitbucket.org", "User foo", "Port 29418",
+				"ConnectTimeout 10", //
+				"Host bitbucket.org", "Hostname bitbucket.org", "User bar",
+				"Port 22", "ConnectTimeout 5");
+		tmpConfig = new OpenSshConfig(tmpConfigFile.getParentFile(),
+				tmpConfigFile);
+		factory.setConfig(tmpConfig);
+		Session session = createSession("ssh://bitbucket.org/something");
+		assertEquals("bitbucket.org", session.getHost());
+		assertEquals("bar", session.getUserName());
+		assertEquals(22, session.getPort());
+		assertEquals(TimeUnit.SECONDS.toMillis(5), session.getTimeout());
+	}
+
+	@Test
+	public void testAliasCaseDifferenceUpcaseInverted() throws Exception {
+		tmpConfigFile = createConfig("Host bitbucket.org",
+				"Hostname bitbucket.org", "User bar", "Port 22",
+				"ConnectTimeout 5", //
+				"Host Bitbucket.org", "Hostname bitbucket.org", "User foo",
+				"Port 29418", "ConnectTimeout 10");
+		tmpConfig = new OpenSshConfig(tmpConfigFile.getParentFile(),
+				tmpConfigFile);
+		factory.setConfig(tmpConfig);
+		Session session = createSession("ssh://Bitbucket.org/something");
+		assertEquals("bitbucket.org", session.getHost());
+		assertEquals("foo", session.getUserName());
+		assertEquals(29418, session.getPort());
+		assertEquals(TimeUnit.SECONDS.toMillis(10), session.getTimeout());
+	}
+
+	@Test
+	public void testAliasCaseDifferenceLowcaseInverted() throws Exception {
+		tmpConfigFile = createConfig("Host bitbucket.org",
+				"Hostname bitbucket.org", "User bar", "Port 22",
+				"ConnectTimeout 5", //
+				"Host Bitbucket.org", "Hostname bitbucket.org", "User foo",
+				"Port 29418", "ConnectTimeout 10");
+		tmpConfig = new OpenSshConfig(tmpConfigFile.getParentFile(),
+				tmpConfigFile);
+		factory.setConfig(tmpConfig);
+		Session session = createSession("ssh://bitbucket.org/something");
+		assertEquals("bitbucket.org", session.getHost());
+		assertEquals("bar", session.getUserName());
+		assertEquals(22, session.getPort());
+		assertEquals(TimeUnit.SECONDS.toMillis(5), session.getTimeout());
+	}
+
+	private File createConfig(String... lines) throws Exception {
+		File f = File.createTempFile("jsch", "test");
+		Files.write(f.toPath(), Arrays.asList(lines));
+		return f;
+	}
+
+	private Session createSession(String uriText) throws Exception {
+		// For this test to make sense, these few lines must correspond to the
+		// code in JschConfigSessionFactory.getSession(). Because of
+		// side-effects we cannot encapsulate that there properly and so we have
+		// to duplicate this bit here. We also can't test getSession() itself
+		// since it would try to actually connect to a server.
+		URIish uri = new URIish(uriText);
+		String host = uri.getHost();
+		String user = uri.getUser();
+		String password = uri.getPass();
+		int port = uri.getPort();
+		OpenSshConfig.Host hostConfig = tmpConfig.lookup(host);
+		if (port <= 0) {
+			port = hostConfig.getPort();
+		}
+		if (user == null) {
+			user = hostConfig.getUser();
+		}
+		return factory.createSession(null, FS.DETECTED, user, password, host,
+				port, hostConfig);
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/OpenSshConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/OpenSshConfigTest.java
index fc520ab..d604751 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/OpenSshConfigTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/OpenSshConfigTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2008, 2014 Google Inc.
+ * Copyright (C) 2008, 2017 Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -43,10 +43,13 @@
 
 package org.eclipse.jgit.transport;
 
+import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNotSame;
 import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertSame;
 import static org.junit.Assert.assertTrue;
 
 import java.io.File;
@@ -58,9 +61,12 @@
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.transport.OpenSshConfig.Host;
 import org.eclipse.jgit.util.FileUtils;
+import org.eclipse.jgit.util.SystemReader;
 import org.junit.Before;
 import org.junit.Test;
 
+import com.jcraft.jsch.ConfigRepository;
+
 public class OpenSshConfigTest extends RepositoryTestCase {
 	private File home;
 
@@ -79,15 +85,18 @@ public void setUp() throws Exception {
 		configFile = new File(new File(home, ".ssh"), Constants.CONFIG);
 		FileUtils.mkdir(configFile.getParentFile());
 
-		System.setProperty("user.name", "jex_junit");
+		mockSystemReader.setProperty(Constants.OS_USER_NAME_KEY, "jex_junit");
 		osc = new OpenSshConfig(home, configFile);
 	}
 
 	private void config(final String data) throws IOException {
-		final OutputStreamWriter fw = new OutputStreamWriter(
-				new FileOutputStream(configFile), "UTF-8");
-		fw.write(data);
-		fw.close();
+		long lastMtime = configFile.lastModified();
+		do {
+			try (final OutputStreamWriter fw = new OutputStreamWriter(
+					new FileOutputStream(configFile), "UTF-8")) {
+				fw.write(data);
+			}
+		} while (lastMtime == configFile.lastModified());
 	}
 
 	@Test
@@ -155,13 +164,18 @@ public void testQuoteParsing() throws Exception {
 
 	@Test
 	public void testAlias_DoesNotMatch() throws Exception {
-		config("Host orcz\n" + "\tHostName repo.or.cz\n");
+		config("Host orcz\n" + "Port 29418\n" + "\tHostName repo.or.cz\n");
 		final Host h = osc.lookup("repo.or.cz");
 		assertNotNull(h);
 		assertEquals("repo.or.cz", h.getHostName());
 		assertEquals("jex_junit", h.getUser());
 		assertEquals(22, h.getPort());
 		assertNull(h.getIdentityFile());
+		final Host h2 = osc.lookup("orcz");
+		assertEquals("repo.or.cz", h.getHostName());
+		assertEquals("jex_junit", h.getUser());
+		assertEquals(29418, h2.getPort());
+		assertNull(h.getIdentityFile());
 	}
 
 	@Test
@@ -282,4 +296,198 @@ public void testAlias_badConnectionAttempts() throws Exception {
 		assertNotNull(h);
 		assertEquals(1, h.getConnectionAttempts());
 	}
+
+	@Test
+	public void testDefaultBlock() throws Exception {
+		config("ConnectionAttempts 5\n\nHost orcz\nConnectionAttempts 3\n");
+		final Host h = osc.lookup("orcz");
+		assertNotNull(h);
+		assertEquals(5, h.getConnectionAttempts());
+	}
+
+	@Test
+	public void testHostCaseInsensitive() throws Exception {
+		config("hOsT orcz\nConnectionAttempts 3\n");
+		final Host h = osc.lookup("orcz");
+		assertNotNull(h);
+		assertEquals(3, h.getConnectionAttempts());
+	}
+
+	@Test
+	public void testListValueSingle() throws Exception {
+		config("Host orcz\nUserKnownHostsFile /foo/bar\n");
+		final ConfigRepository.Config c = osc.getConfig("orcz");
+		assertNotNull(c);
+		assertEquals("/foo/bar", c.getValue("UserKnownHostsFile"));
+	}
+
+	@Test
+	public void testListValueMultiple() throws Exception {
+		// Tilde expansion occurs within the parser
+		config("Host orcz\nUserKnownHostsFile \"~/foo/ba z\" /foo/bar \n");
+		final ConfigRepository.Config c = osc.getConfig("orcz");
+		assertNotNull(c);
+		assertArrayEquals(new Object[] { new File(home, "foo/ba z").getPath(),
+				"/foo/bar" },
+				c.getValues("UserKnownHostsFile"));
+	}
+
+	@Test
+	public void testRepeatedLookups() throws Exception {
+		config("Host orcz\n" + "\tConnectionAttempts 5\n");
+		final Host h1 = osc.lookup("orcz");
+		final Host h2 = osc.lookup("orcz");
+		assertNotNull(h1);
+		assertSame(h1, h2);
+		assertEquals(5, h1.getConnectionAttempts());
+		assertEquals(h1.getConnectionAttempts(), h2.getConnectionAttempts());
+		final ConfigRepository.Config c = osc.getConfig("orcz");
+		assertNotNull(c);
+		assertSame(c, h1.getConfig());
+		assertSame(c, h2.getConfig());
+	}
+
+	@Test
+	public void testRepeatedLookupsWithModification() throws Exception {
+		config("Host orcz\n" + "\tConnectionAttempts -1\n");
+		final Host h1 = osc.lookup("orcz");
+		assertNotNull(h1);
+		assertEquals(1, h1.getConnectionAttempts());
+		config("Host orcz\n" + "\tConnectionAttempts 5\n");
+		final Host h2 = osc.lookup("orcz");
+		assertNotNull(h2);
+		assertNotSame(h1, h2);
+		assertEquals(5, h2.getConnectionAttempts());
+		assertEquals(1, h1.getConnectionAttempts());
+		assertNotSame(h1.getConfig(), h2.getConfig());
+	}
+
+	@Test
+	public void testIdentityFile() throws Exception {
+		config("Host orcz\nIdentityFile \"~/foo/ba z\"\nIdentityFile /foo/bar");
+		final Host h = osc.lookup("orcz");
+		assertNotNull(h);
+		File f = h.getIdentityFile();
+		assertNotNull(f);
+		// Host does tilde replacement
+		assertEquals(new File(home, "foo/ba z"), f);
+		final ConfigRepository.Config c = h.getConfig();
+		// Config does tilde replacement, too
+		assertArrayEquals(new Object[] { new File(home, "foo/ba z").getPath(),
+				"/foo/bar" },
+				c.getValues("IdentityFile"));
+	}
+
+	@Test
+	public void testMultiIdentityFile() throws Exception {
+		config("IdentityFile \"~/foo/ba z\"\nHost orcz\nIdentityFile /foo/bar\nHOST *\nIdentityFile /foo/baz");
+		final Host h = osc.lookup("orcz");
+		assertNotNull(h);
+		File f = h.getIdentityFile();
+		assertNotNull(f);
+		// Host does tilde replacement
+		assertEquals(new File(home, "foo/ba z"), f);
+		final ConfigRepository.Config c = h.getConfig();
+		// Config does tilde replacement, too
+		assertArrayEquals(new Object[] { new File(home, "foo/ba z").getPath(),
+				"/foo/bar", "/foo/baz" },
+				c.getValues("IdentityFile"));
+	}
+
+	@Test
+	public void testNegatedPattern() throws Exception {
+		config("Host repo.or.cz\nIdentityFile ~/foo/bar\nHOST !*.or.cz\nIdentityFile /foo/baz");
+		final Host h = osc.lookup("repo.or.cz");
+		assertNotNull(h);
+		assertEquals(new File(home, "foo/bar"), h.getIdentityFile());
+		assertArrayEquals(new Object[] { new File(home, "foo/bar").getPath() },
+				h.getConfig().getValues("IdentityFile"));
+	}
+
+	@Test
+	public void testPattern() throws Exception {
+		config("Host repo.or.cz\nIdentityFile ~/foo/bar\nHOST *.or.cz\nIdentityFile /foo/baz");
+		final Host h = osc.lookup("repo.or.cz");
+		assertNotNull(h);
+		assertEquals(new File(home, "foo/bar"), h.getIdentityFile());
+		assertArrayEquals(new Object[] { new File(home, "foo/bar").getPath(),
+				"/foo/baz" },
+				h.getConfig().getValues("IdentityFile"));
+	}
+
+	@Test
+	public void testMultiHost() throws Exception {
+		config("Host orcz *.or.cz\nIdentityFile ~/foo/bar\nHOST *.or.cz\nIdentityFile /foo/baz");
+		final Host h1 = osc.lookup("repo.or.cz");
+		assertNotNull(h1);
+		assertEquals(new File(home, "foo/bar"), h1.getIdentityFile());
+		assertArrayEquals(new Object[] { new File(home, "foo/bar").getPath(),
+				"/foo/baz" },
+				h1.getConfig().getValues("IdentityFile"));
+		final Host h2 = osc.lookup("orcz");
+		assertNotNull(h2);
+		assertEquals(new File(home, "foo/bar"), h2.getIdentityFile());
+		assertArrayEquals(new Object[] { new File(home, "foo/bar").getPath() },
+				h2.getConfig().getValues("IdentityFile"));
+	}
+
+	@Test
+	public void testEqualsSign() throws Exception {
+		config("Host=orcz\n\tConnectionAttempts = 5\n\tUser=\t  foobar\t\n");
+		final Host h = osc.lookup("orcz");
+		assertNotNull(h);
+		assertEquals(5, h.getConnectionAttempts());
+		assertEquals("foobar", h.getUser());
+	}
+
+	@Test
+	public void testMissingArgument() throws Exception {
+		config("Host=orcz\n\tSendEnv\nIdentityFile\t\nForwardX11\n\tUser=\t  foobar\t\n");
+		final Host h = osc.lookup("orcz");
+		assertNotNull(h);
+		assertEquals("foobar", h.getUser());
+		assertArrayEquals(new String[0], h.getConfig().getValues("SendEnv"));
+		assertNull(h.getIdentityFile());
+		assertNull(h.getConfig().getValue("ForwardX11"));
+	}
+
+	@Test
+	public void testHomeDirUserReplacement() throws Exception {
+		config("Host=orcz\n\tIdentityFile %d/.ssh/%u_id_dsa");
+		final Host h = osc.lookup("orcz");
+		assertNotNull(h);
+		assertEquals(new File(new File(home, ".ssh"), "jex_junit_id_dsa"),
+				h.getIdentityFile());
+	}
+
+	@Test
+	public void testHostnameReplacement() throws Exception {
+		config("Host=orcz\nHost *.*\n\tHostname %h\nHost *\n\tHostname %h.example.org");
+		final Host h = osc.lookup("orcz");
+		assertNotNull(h);
+		assertEquals("orcz.example.org", h.getHostName());
+	}
+
+	@Test
+	public void testRemoteUserReplacement() throws Exception {
+		config("Host=orcz\n\tUser foo\n" + "Host *.*\n\tHostname %h\n"
+				+ "Host *\n\tHostname %h.ex%%20ample.org\n\tIdentityFile ~/.ssh/%h_%r_id_dsa");
+		final Host h = osc.lookup("orcz");
+		assertNotNull(h);
+		assertEquals(
+				new File(new File(home, ".ssh"),
+						"orcz.ex%20ample.org_foo_id_dsa"),
+				h.getIdentityFile());
+	}
+
+	@Test
+	public void testLocalhostFQDNReplacement() throws Exception {
+		String localhost = SystemReader.getInstance().getHostname();
+		config("Host=orcz\n\tIdentityFile ~/.ssh/%l_id_dsa");
+		final Host h = osc.lookup("orcz");
+		assertNotNull(h);
+		assertEquals(
+				new File(new File(home, ".ssh"), localhost + "_id_dsa"),
+				h.getIdentityFile());
+	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushConfigTest.java
new file mode 100644
index 0000000..9610fbd
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushConfigTest.java
@@ -0,0 +1,88 @@
+/*
+ * Copyright (C) 2017, David Pursehouse <david.pursehouse@gmail.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.transport;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import org.eclipse.jgit.transport.PushConfig.PushRecurseSubmodulesMode;
+import org.junit.Test;
+
+public class PushConfigTest {
+	@Test
+	public void pushRecurseSubmoduleMatch() throws Exception {
+		assertTrue(PushRecurseSubmodulesMode.CHECK.matchConfigValue("check"));
+		assertTrue(PushRecurseSubmodulesMode.CHECK.matchConfigValue("CHECK"));
+
+		assertTrue(PushRecurseSubmodulesMode.ON_DEMAND
+				.matchConfigValue("on-demand"));
+		assertTrue(PushRecurseSubmodulesMode.ON_DEMAND
+				.matchConfigValue("ON-DEMAND"));
+		assertTrue(PushRecurseSubmodulesMode.ON_DEMAND
+				.matchConfigValue("on_demand"));
+		assertTrue(PushRecurseSubmodulesMode.ON_DEMAND
+				.matchConfigValue("ON_DEMAND"));
+
+		assertTrue(PushRecurseSubmodulesMode.NO.matchConfigValue("no"));
+		assertTrue(PushRecurseSubmodulesMode.NO.matchConfigValue("NO"));
+		assertTrue(PushRecurseSubmodulesMode.NO.matchConfigValue("false"));
+		assertTrue(PushRecurseSubmodulesMode.NO.matchConfigValue("FALSE"));
+	}
+
+	@Test
+	public void pushRecurseSubmoduleNoMatch() throws Exception {
+		assertFalse(PushRecurseSubmodulesMode.NO.matchConfigValue("N"));
+		assertFalse(PushRecurseSubmodulesMode.ON_DEMAND
+				.matchConfigValue("ONDEMAND"));
+	}
+
+	@Test
+	public void pushRecurseSubmoduleToConfigValue() {
+		assertEquals("on-demand",
+				PushRecurseSubmodulesMode.ON_DEMAND.toConfigValue());
+		assertEquals("check", PushRecurseSubmodulesMode.CHECK.toConfigValue());
+		assertEquals("false", PushRecurseSubmodulesMode.NO.toConfigValue());
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/ReceivePackAdvertiseRefsHookTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/ReceivePackAdvertiseRefsHookTest.java
index 3411122..8ef87cb 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/ReceivePackAdvertiseRefsHookTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/ReceivePackAdvertiseRefsHookTest.java
@@ -58,6 +58,8 @@
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.atomic.AtomicReference;
 import java.util.zip.Deflater;
 
 import org.eclipse.jgit.errors.MissingObjectException;
@@ -159,6 +161,45 @@ ReceivePack createReceivePack(final Repository db) {
 	}
 
 	@Test
+	public void resetsHaves() throws Exception {
+		AtomicReference<Set<ObjectId>> haves = new AtomicReference<>();
+		try (TransportLocal t = new TransportLocal(src, uriOf(dst),
+				dst.getDirectory()) {
+			@Override
+			ReceivePack createReceivePack(Repository db) {
+				dst.incrementOpen();
+
+				ReceivePack rp = super.createReceivePack(dst);
+				rp.setAdvertiseRefsHook(new AdvertiseRefsHook() {
+					@Override
+					public void advertiseRefs(BaseReceivePack rp2)
+							throws ServiceMayNotContinueException {
+						rp.setAdvertisedRefs(rp.getRepository().getAllRefs(),
+								null);
+						new HidePrivateHook().advertiseRefs(rp);
+						haves.set(rp.getAdvertisedObjects());
+					}
+
+					@Override
+					public void advertiseRefs(UploadPack uploadPack)
+							throws ServiceMayNotContinueException {
+						throw new UnsupportedOperationException();
+					}
+				});
+				return rp;
+			}
+		}) {
+			try (PushConnection c = t.openPush()) {
+				// Just has to open/close for advertisement.
+			}
+		}
+
+		assertEquals(1, haves.get().size());
+		assertTrue(haves.get().contains(B));
+		assertFalse(haves.get().contains(P));
+	}
+
+	@Test
 	public void testSuccess() throws Exception {
 		// Manually force a delta of an object so we reuse it later.
 		//
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/RemoteConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/RemoteConfigTest.java
index 0cada5c..a0cf0d2 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/RemoteConfigTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/RemoteConfigTest.java
@@ -51,6 +51,7 @@
 import static org.junit.Assert.assertTrue;
 
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 import org.eclipse.jgit.errors.ConfigInvalidException;
@@ -498,24 +499,48 @@ public void noPushInsteadOf() throws Exception {
 	}
 
 	@Test
-	public void singlePushInsteadOf() throws Exception {
+	public void pushInsteadOfNotAppliedToPushUri() throws Exception {
 		config.setString("remote", "origin", "pushurl", "short:project.git");
 		config.setString("url", "https://server/repos/", "pushInsteadOf",
 				"short:");
 		RemoteConfig rc = new RemoteConfig(config, "origin");
 		assertFalse(rc.getPushURIs().isEmpty());
+		assertEquals("short:project.git",
+				rc.getPushURIs().get(0).toASCIIString());
+	}
+
+	@Test
+	public void pushInsteadOfAppliedToUri() throws Exception {
+		config.setString("remote", "origin", "url", "short:project.git");
+		config.setString("url", "https://server/repos/", "pushInsteadOf",
+				"short:");
+		RemoteConfig rc = new RemoteConfig(config, "origin");
+		assertFalse(rc.getPushURIs().isEmpty());
+		assertEquals("https://server/repos/project.git",
+				rc.getPushURIs().get(0).toASCIIString());
+	}
+
+	@Test
+	public void multiplePushInsteadOf() throws Exception {
+		config.setString("remote", "origin", "url", "prefixproject.git");
+		config.setStringList("url", "https://server/repos/", "pushInsteadOf",
+				Arrays.asList("pre", "prefix", "pref", "perf"));
+		RemoteConfig rc = new RemoteConfig(config, "origin");
+		assertFalse(rc.getPushURIs().isEmpty());
 		assertEquals("https://server/repos/project.git", rc.getPushURIs()
 				.get(0).toASCIIString());
 	}
 
 	@Test
-	public void multiplePushInsteadOf() throws Exception {
-		config.setString("remote", "origin", "pushurl", "prefixproject.git");
-		config.setStringList("url", "https://server/repos/", "pushInsteadOf",
-				Arrays.asList("pre", "prefix", "pref", "perf"));
+	public void pushInsteadOfNoPushUrl() throws Exception {
+		config.setString("remote", "origin", "url",
+				"http://git.eclipse.org/gitroot/jgit/jgit");
+		config.setStringList("url", "ssh://someone@git.eclipse.org:29418/",
+				"pushInsteadOf",
+				Collections.singletonList("http://git.eclipse.org/gitroot/"));
 		RemoteConfig rc = new RemoteConfig(config, "origin");
 		assertFalse(rc.getPushURIs().isEmpty());
-		assertEquals("https://server/repos/project.git", rc.getPushURIs()
-				.get(0).toASCIIString());
+		assertEquals("ssh://someone@git.eclipse.org:29418/jgit/jgit",
+				rc.getPushURIs().get(0).toASCIIString());
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/UploadPackTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/UploadPackTest.java
new file mode 100644
index 0000000..27c7674
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/UploadPackTest.java
@@ -0,0 +1,90 @@
+package org.eclipse.jgit.transport;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.util.Collections;
+import org.eclipse.jgit.internal.storage.dfs.DfsRepositoryDescription;
+import org.eclipse.jgit.internal.storage.dfs.InMemoryRepository;
+import org.eclipse.jgit.junit.TestRepository;
+import org.eclipse.jgit.lib.NullProgressMonitor;
+import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.transport.UploadPack.RequestPolicy;
+import org.eclipse.jgit.transport.resolver.ServiceNotAuthorizedException;
+import org.eclipse.jgit.transport.resolver.ServiceNotEnabledException;
+import org.eclipse.jgit.transport.resolver.UploadPackFactory;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Tests for server upload-pack utilities.
+ */
+public class UploadPackTest {
+	private URIish uri;
+
+	private TestProtocol<Object> testProtocol;
+
+	private Object ctx = new Object();
+
+	private InMemoryRepository server;
+
+	private InMemoryRepository client;
+
+	private RevCommit commit0;
+
+	private RevCommit commit1;
+
+	private RevCommit tip;
+
+	@Before
+	public void setUp() throws Exception {
+		server = newRepo("server");
+		client = newRepo("client");
+
+		TestRepository<InMemoryRepository> remote =
+				new TestRepository<>(server);
+		commit0 = remote.commit().message("0").create();
+		commit1 = remote.commit().message("1").parent(commit0).create();
+		tip = remote.commit().message("2").parent(commit1).create();
+		remote.update("master", tip);
+	}
+
+	@After
+	public void tearDown() {
+		Transport.unregister(testProtocol);
+	}
+
+	private static InMemoryRepository newRepo(String name) {
+		return new InMemoryRepository(new DfsRepositoryDescription(name));
+	}
+
+	@Test
+	public void testFetchParentOfShallowCommit() throws Exception {
+		testProtocol = new TestProtocol<>(
+				new UploadPackFactory<Object>() {
+					@Override
+					public UploadPack create(Object req, Repository db)
+							throws ServiceNotEnabledException,
+							ServiceNotAuthorizedException {
+						UploadPack up = new UploadPack(db);
+						up.setRequestPolicy(RequestPolicy.REACHABLE_COMMIT);
+						// assume client has a shallow commit
+						up.getRevWalk().assumeShallow(
+								Collections.singleton(commit1.getId()));
+						return up;
+					}
+				}, null);
+		uri = testProtocol.register(ctx, server);
+
+		assertFalse(client.hasObject(commit0.toObjectId()));
+
+		// Fetch of the parent of the shallow commit
+		try (Transport tn = testProtocol.open(uri, client, "server")) {
+			tn.fetch(NullProgressMonitor.INSTANCE,
+					Collections.singletonList(new RefSpec(commit0.name())));
+			assertTrue(client.hasObject(commit0.toObjectId()));
+		}
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/PathFilterLogicTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/PathFilterLogicTest.java
index 7c819c5..0394f68 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/PathFilterLogicTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/PathFilterLogicTest.java
@@ -42,6 +42,14 @@
  */
 package org.eclipse.jgit.treewalk.filter;
 
+import static org.junit.Assert.assertEquals;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheBuilder;
 import org.eclipse.jgit.dircache.DirCacheEntry;
@@ -53,14 +61,6 @@
 import org.junit.Before;
 import org.junit.Test;
 
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-
-import static org.junit.Assert.assertEquals;
-
 public class PathFilterLogicTest extends RepositoryTestCase {
 
 	private ObjectId treeId;
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/IntListTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/IntListTest.java
index c6eca9d..d6ea8c6 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/IntListTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/IntListTest.java
@@ -44,6 +44,7 @@
 package org.eclipse.jgit.util;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
@@ -186,6 +187,16 @@ public void testSet() {
 	}
 
 	@Test
+	public void testContains() {
+		IntList i = new IntList();
+		i.add(1);
+		i.add(4);
+		assertTrue(i.contains(1));
+		assertTrue(i.contains(4));
+		assertFalse(i.contains(2));
+	}
+
+	@Test
 	public void testToString() {
 		final IntList i = new IntList();
 		i.add(1);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/LongMapTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/LongMapTest.java
similarity index 98%
rename from org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/LongMapTest.java
rename to org.eclipse.jgit.test/tst/org/eclipse/jgit/util/LongMapTest.java
index 1a86aaf..054c61e 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/LongMapTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/LongMapTest.java
@@ -41,7 +41,7 @@
  * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.eclipse.jgit.transport;
+package org.eclipse.jgit.util;
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/NBTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/NBTest.java
index 7e11a61..d2d44ff 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/NBTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/NBTest.java
@@ -90,6 +90,24 @@ public void testDecodeUInt16() {
 	}
 
 	@Test
+	public void testDecodeUInt24() {
+		assertEquals(0, NB.decodeUInt24(b(0, 0, 0), 0));
+		assertEquals(0, NB.decodeUInt24(padb(3, 0, 0, 0), 3));
+
+		assertEquals(3, NB.decodeUInt24(b(0, 0, 3), 0));
+		assertEquals(3, NB.decodeUInt24(padb(3, 0, 0, 3), 3));
+
+		assertEquals(0xcede03, NB.decodeUInt24(b(0xce, 0xde, 3), 0));
+		assertEquals(0xbade03, NB.decodeUInt24(padb(3, 0xba, 0xde, 3), 3));
+
+		assertEquals(0x03bade, NB.decodeUInt24(b(3, 0xba, 0xde), 0));
+		assertEquals(0x03bade, NB.decodeUInt24(padb(3, 3, 0xba, 0xde), 3));
+
+		assertEquals(0xffffff, NB.decodeUInt24(b(0xff, 0xff, 0xff), 0));
+		assertEquals(0xffffff, NB.decodeUInt24(padb(3, 0xff, 0xff, 0xff), 3));
+	}
+
+	@Test
 	public void testDecodeInt32() {
 		assertEquals(0, NB.decodeInt32(b(0, 0, 0, 0), 0));
 		assertEquals(0, NB.decodeInt32(padb(3, 0, 0, 0, 0), 3));
@@ -198,6 +216,39 @@ public void testEncodeInt16() {
 	}
 
 	@Test
+	public void testEncodeInt24() {
+		byte[] out = new byte[16];
+
+		prepareOutput(out);
+		NB.encodeInt24(out, 0, 0);
+		assertOutput(b(0, 0, 0), out, 0);
+
+		prepareOutput(out);
+		NB.encodeInt24(out, 3, 0);
+		assertOutput(b(0, 0, 0), out, 3);
+
+		prepareOutput(out);
+		NB.encodeInt24(out, 0, 3);
+		assertOutput(b(0, 0, 3), out, 0);
+
+		prepareOutput(out);
+		NB.encodeInt24(out, 3, 3);
+		assertOutput(b(0, 0, 3), out, 3);
+
+		prepareOutput(out);
+		NB.encodeInt24(out, 0, 0xc0deac);
+		assertOutput(b(0xc0, 0xde, 0xac), out, 0);
+
+		prepareOutput(out);
+		NB.encodeInt24(out, 3, 0xbadeac);
+		assertOutput(b(0xba, 0xde, 0xac), out, 3);
+
+		prepareOutput(out);
+		NB.encodeInt24(out, 3, -1);
+		assertOutput(b(0xff, 0xff, 0xff), out, 3);
+	}
+
+	@Test
 	public void testEncodeInt32() {
 		final byte[] out = new byte[16];
 
@@ -315,10 +366,24 @@ private static void assertOutput(final byte[] expect, final byte[] buf,
 		return r;
 	}
 
+	private static byte[] b(int a, int b, int c) {
+		return new byte[] { (byte) a, (byte) b, (byte) c };
+	}
+
 	private static byte[] b(final int a, final int b, final int c, final int d) {
 		return new byte[] { (byte) a, (byte) b, (byte) c, (byte) d };
 	}
 
+	private static byte[] padb(int len, int a, int b, int c) {
+		final byte[] r = new byte[len + 4];
+		for (int i = 0; i < len; i++)
+			r[i] = (byte) 0xaf;
+		r[len] = (byte) a;
+		r[len + 1] = (byte) b;
+		r[len + 2] = (byte) c;
+		return r;
+	}
+
 	private static byte[] padb(final int len, final int a, final int b,
 			final int c, final int d) {
 		final byte[] r = new byte[len + 4];
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/RawParseUtils_LineMapTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/RawParseUtils_LineMapTest.java
index 5939714..6efdce6 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/RawParseUtils_LineMapTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/RawParseUtils_LineMapTest.java
@@ -43,7 +43,7 @@
 
 package org.eclipse.jgit.util;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertNotNull;
 
 import java.io.UnsupportedEncodingException;
@@ -55,52 +55,51 @@ public class RawParseUtils_LineMapTest {
 	public void testEmpty() {
 		final IntList map = RawParseUtils.lineMap(new byte[] {}, 0, 0);
 		assertNotNull(map);
-		assertEquals(2, map.size());
-		assertEquals(Integer.MIN_VALUE, map.get(0));
-		assertEquals(0, map.get(1));
+		assertArrayEquals(new int[]{Integer.MIN_VALUE, 0}, asInts(map));
 	}
 
 	@Test
 	public void testOneBlankLine() {
 		final IntList map = RawParseUtils.lineMap(new byte[] { '\n' }, 0, 1);
-		assertEquals(3, map.size());
-		assertEquals(Integer.MIN_VALUE, map.get(0));
-		assertEquals(0, map.get(1));
-		assertEquals(1, map.get(2));
+		assertArrayEquals(new int[]{Integer.MIN_VALUE, 0, 1}, asInts(map));
 	}
 
 	@Test
 	public void testTwoLineFooBar() throws UnsupportedEncodingException {
 		final byte[] buf = "foo\nbar\n".getBytes("ISO-8859-1");
 		final IntList map = RawParseUtils.lineMap(buf, 0, buf.length);
-		assertEquals(4, map.size());
-		assertEquals(Integer.MIN_VALUE, map.get(0));
-		assertEquals(0, map.get(1));
-		assertEquals(4, map.get(2));
-		assertEquals(buf.length, map.get(3));
+		assertArrayEquals(new int[]{Integer.MIN_VALUE, 0, 4, buf.length}, asInts(map));
 	}
 
 	@Test
 	public void testTwoLineNoLF() throws UnsupportedEncodingException {
 		final byte[] buf = "foo\nbar".getBytes("ISO-8859-1");
 		final IntList map = RawParseUtils.lineMap(buf, 0, buf.length);
-		assertEquals(4, map.size());
-		assertEquals(Integer.MIN_VALUE, map.get(0));
-		assertEquals(0, map.get(1));
-		assertEquals(4, map.get(2));
-		assertEquals(buf.length, map.get(3));
+		assertArrayEquals(new int[]{Integer.MIN_VALUE, 0, 4, buf.length}, asInts(map));
+	}
+
+	@Test
+	public void testBinary() throws UnsupportedEncodingException {
+		final byte[] buf = "xxxfoo\nb\0ar".getBytes("ISO-8859-1");
+		final IntList map = RawParseUtils.lineMap(buf, 3, buf.length);
+		assertArrayEquals(new int[]{Integer.MIN_VALUE, 3, buf.length}, asInts(map));
 	}
 
 	@Test
 	public void testFourLineBlanks() throws UnsupportedEncodingException {
 		final byte[] buf = "foo\n\n\nbar\n".getBytes("ISO-8859-1");
 		final IntList map = RawParseUtils.lineMap(buf, 0, buf.length);
-		assertEquals(6, map.size());
-		assertEquals(Integer.MIN_VALUE, map.get(0));
-		assertEquals(0, map.get(1));
-		assertEquals(4, map.get(2));
-		assertEquals(5, map.get(3));
-		assertEquals(6, map.get(4));
-		assertEquals(buf.length, map.get(5));
+
+		assertArrayEquals(new int[]{
+				Integer.MIN_VALUE, 0, 4, 5, 6, buf.length
+		}, asInts(map));
+	}
+
+	private int[] asInts(IntList l) {
+		int[] result = new int[l.size()];
+		for (int i = 0; i < l.size(); i++) {
+			result[i] = l.get(i);
+		}
+		return result;
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/RelativeDateFormatterTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/RelativeDateFormatterTest.java
index 76687d1..fb76ec4 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/RelativeDateFormatterTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/RelativeDateFormatterTest.java
@@ -128,7 +128,14 @@ public void testFormatYearsMonths() {
 		assertFormat(380, DAY_IN_MILLIS, "1 year, 1 month ago");
 		assertFormat(410, DAY_IN_MILLIS, "1 year, 2 months ago");
 		assertFormat(2, YEAR_IN_MILLIS, "2 years ago");
-		assertFormat(1824, DAY_IN_MILLIS, "4 years, 12 months ago");
+	}
+
+	@Test
+	public void testFullYearMissingSomeDays() {
+		// avoid "x year(s), 12 months", as humans would always round this up to
+		// "x+1 years"
+		assertFormat(5 * 365 + 1, DAY_IN_MILLIS, "5 years ago");
+		assertFormat(2 * 365 - 10, DAY_IN_MILLIS, "2 years ago");
 	}
 
 	@Test
diff --git a/org.eclipse.jgit.ui/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit.ui/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit.ui/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit.ui/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit.ui/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit.ui/.settings/org.eclipse.pde.api.tools.prefs
index cd148d9..c0030de 100644
--- a/org.eclipse.jgit.ui/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit.ui/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,4 +1,4 @@
-#Tue Oct 18 00:52:01 CEST 2011
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -8,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -47,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -58,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -75,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -83,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit.ui/META-INF/MANIFEST.MF b/org.eclipse.jgit.ui/META-INF/MANIFEST.MF
index 4312cc3..777ad5a 100644
--- a/org.eclipse.jgit.ui/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.ui/META-INF/MANIFEST.MF
@@ -3,14 +3,14 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit.ui
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Export-Package: org.eclipse.jgit.awtui;version="4.8.1"
-Import-Package: org.eclipse.jgit.errors;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.lib;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.nls;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revplot;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.revwalk;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.transport;version="[4.8.1,4.9.0)",
- org.eclipse.jgit.util;version="[4.8.1,4.9.0)"
+Export-Package: org.eclipse.jgit.awtui;version="4.9.6"
+Import-Package: org.eclipse.jgit.errors;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.lib;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.nls;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revplot;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.revwalk;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.transport;version="[4.9.6,4.10.0)",
+ org.eclipse.jgit.util;version="[4.9.6,4.10.0)"
diff --git a/org.eclipse.jgit.ui/pom.xml b/org.eclipse.jgit.ui/pom.xml
index 06e45ef..e37976f 100644
--- a/org.eclipse.jgit.ui/pom.xml
+++ b/org.eclipse.jgit.ui/pom.xml
@@ -52,7 +52,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.ui</artifactId>
diff --git a/org.eclipse.jgit/.settings/.api_filters b/org.eclipse.jgit/.settings/.api_filters
index 7c175e3..e951189 100644
--- a/org.eclipse.jgit/.settings/.api_filters
+++ b/org.eclipse.jgit/.settings/.api_filters
@@ -3,8 +3,8 @@
     <resource path="META-INF/MANIFEST.MF">
         <filter id="924844039">
             <message_arguments>
-                <message_argument value="4.8.1"/>
-                <message_argument value="4.8.0"/>
+                <message_argument value="4.9.4"/>
+                <message_argument value="4.9.0"/>
             </message_arguments>
         </filter>
     </resource>
@@ -18,39 +18,48 @@
         <filter id="1141899266">
             <message_arguments>
                 <message_argument value="4.5"/>
-                <message_argument value="4.8"/>
+                <message_argument value="4.9"/>
                 <message_argument value="CONFIG_KEY_SUPPORTSATOMICFILECREATION"/>
             </message_arguments>
         </filter>
     </resource>
     <resource path="src/org/eclipse/jgit/lib/Constants.java" type="org.eclipse.jgit.lib.Constants">
-        <filter comment="LOCK_SUFFIX was backported to 4.7.3" id="1141899266">
+        <filter id="1141899266">
             <message_arguments>
                 <message_argument value="4.7"/>
-                <message_argument value="4.8"/>
+                <message_argument value="4.9"/>
                 <message_argument value="LOCK_SUFFIX"/>
             </message_arguments>
         </filter>
     </resource>
+    <resource path="src/org/eclipse/jgit/merge/ResolveMerger.java" type="org.eclipse.jgit.merge.ResolveMerger">
+        <filter id="1141899266">
+            <message_arguments>
+                <message_argument value="3.5"/>
+                <message_argument value="4.9"/>
+                <message_argument value="processEntry(CanonicalTreeParser, CanonicalTreeParser, CanonicalTreeParser, DirCacheBuildIterator, WorkingTreeIterator, boolean)"/>
+            </message_arguments>
+        </filter>
+    </resource>
     <resource path="src/org/eclipse/jgit/util/FS.java" type="org.eclipse.jgit.util.FS">
         <filter id="1141899266">
             <message_arguments>
                 <message_argument value="4.5"/>
-                <message_argument value="4.8"/>
+                <message_argument value="4.9"/>
                 <message_argument value="createNewFile(File)"/>
             </message_arguments>
         </filter>
         <filter id="1141899266">
             <message_arguments>
                 <message_argument value="4.5"/>
-                <message_argument value="4.8"/>
+                <message_argument value="4.9"/>
                 <message_argument value="supportsAtomicCreateNewFile()"/>
             </message_arguments>
         </filter>
         <filter id="1141899266">
             <message_arguments>
                 <message_argument value="4.7"/>
-                <message_argument value="4.8"/>
+                <message_argument value="4.9"/>
                 <message_argument value="createNewFileAtomic(File)"/>
             </message_arguments>
         </filter>
@@ -59,7 +68,7 @@
         <filter id="1141899266">
             <message_arguments>
                 <message_argument value="4.7"/>
-                <message_argument value="4.8"/>
+                <message_argument value="4.9"/>
                 <message_argument value="LockToken"/>
             </message_arguments>
         </filter>
diff --git a/org.eclipse.jgit/.settings/org.eclipse.jdt.ui.prefs b/org.eclipse.jgit/.settings/org.eclipse.jdt.ui.prefs
index c336cce..fef3713 100644
--- a/org.eclipse.jgit/.settings/org.eclipse.jdt.ui.prefs
+++ b/org.eclipse.jgit/.settings/org.eclipse.jdt.ui.prefs
@@ -9,21 +9,23 @@
 org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8"?><templates/>
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
-sp_cleanup.add_missing_annotations=false
+sp_cleanup.add_missing_annotations=true
 sp_cleanup.add_missing_deprecated_annotations=true
 sp_cleanup.add_missing_methods=false
 sp_cleanup.add_missing_nls_tags=false
 sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=false
+sp_cleanup.add_missing_override_annotations_interface_methods=true
 sp_cleanup.add_serial_version_id=false
 sp_cleanup.always_use_blocks=true
 sp_cleanup.always_use_parentheses_in_expressions=false
 sp_cleanup.always_use_this_for_non_static_field_access=false
 sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
 sp_cleanup.format_source_code_changes_only=true
+sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
 sp_cleanup.make_private_fields_final=true
@@ -39,11 +41,12 @@
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_type_arguments=true
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true
 sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=false
-sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=true
 sp_cleanup.remove_unused_imports=false
 sp_cleanup.remove_unused_local_variables=false
 sp_cleanup.remove_unused_private_fields=true
@@ -52,8 +55,10 @@
 sp_cleanup.remove_unused_private_types=true
 sp_cleanup.sort_members=false
 sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
 sp_cleanup.use_blocks=false
 sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=false
 sp_cleanup.use_parentheses_in_expressions=false
 sp_cleanup.use_this_for_non_static_field_access=false
 sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
diff --git a/org.eclipse.jgit/.settings/org.eclipse.pde.api.tools.prefs b/org.eclipse.jgit/.settings/org.eclipse.pde.api.tools.prefs
index cd148d9..c0030de 100644
--- a/org.eclipse.jgit/.settings/org.eclipse.pde.api.tools.prefs
+++ b/org.eclipse.jgit/.settings/org.eclipse.pde.api.tools.prefs
@@ -1,4 +1,4 @@
-#Tue Oct 18 00:52:01 CEST 2011
+ANNOTATION_ELEMENT_TYPE_ADDED_FIELD=Error
 ANNOTATION_ELEMENT_TYPE_ADDED_METHOD_WITHOUT_DEFAULT_VALUE=Error
 ANNOTATION_ELEMENT_TYPE_CHANGED_TYPE_CONVERSION=Error
 ANNOTATION_ELEMENT_TYPE_REMOVED_FIELD=Error
@@ -8,6 +8,10 @@
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_API_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_REEXPORTED_TYPE=Error
 API_COMPONENT_ELEMENT_TYPE_REMOVED_TYPE=Error
+API_USE_SCAN_FIELD_SEVERITY=Error
+API_USE_SCAN_METHOD_SEVERITY=Error
+API_USE_SCAN_TYPE_SEVERITY=Error
+CLASS_ELEMENT_TYPE_ADDED_FIELD=Error
 CLASS_ELEMENT_TYPE_ADDED_METHOD=Error
 CLASS_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
 CLASS_ELEMENT_TYPE_ADDED_TYPE_PARAMETER=Error
@@ -47,6 +51,7 @@
 ILLEGAL_INSTANTIATE=Warning
 ILLEGAL_OVERRIDE=Warning
 ILLEGAL_REFERENCE=Warning
+INTERFACE_ELEMENT_TYPE_ADDED_DEFAULT_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_FIELD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_ADDED_RESTRICTIONS=Error
@@ -58,6 +63,7 @@
 INTERFACE_ELEMENT_TYPE_REMOVED_METHOD=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_MEMBER=Error
 INTERFACE_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+INVALID_ANNOTATION=Ignore
 INVALID_JAVADOC_TAG=Ignore
 INVALID_REFERENCE_IN_SYSTEM_LIBRARIES=Error
 LEAK_EXTEND=Warning
@@ -75,6 +81,7 @@
 METHOD_ELEMENT_TYPE_CHANGED_VARARGS_TO_ARRAY=Error
 METHOD_ELEMENT_TYPE_REMOVED_ANNOTATION_DEFAULT_VALUE=Error
 METHOD_ELEMENT_TYPE_REMOVED_TYPE_PARAMETER=Error
+MISSING_EE_DESCRIPTIONS=Warning
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_CLASS_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_ADDED_INTERFACE_BOUND=Error
 TYPE_PARAMETER_ELEMENT_TYPE_CHANGED_CLASS_BOUND=Error
@@ -83,10 +90,13 @@
 TYPE_PARAMETER_ELEMENT_TYPE_REMOVED_INTERFACE_BOUND=Error
 UNUSED_PROBLEM_FILTERS=Warning
 automatically_removed_unused_problem_filters=false
+changed_execution_env=Error
 eclipse.preferences.version=1
 incompatible_api_component_version=Error
 incompatible_api_component_version_include_major_without_breaking_change=Disabled
 incompatible_api_component_version_include_minor_without_api_change=Disabled
+incompatible_api_component_version_report_major_without_breaking_change=Warning
+incompatible_api_component_version_report_minor_without_api_change=Ignore
 invalid_since_tag_version=Error
 malformed_since_tag=Error
 missing_since_tag=Error
diff --git a/org.eclipse.jgit/META-INF/MANIFEST.MF b/org.eclipse.jgit/META-INF/MANIFEST.MF
index 9b6a9f1..3883ae7 100644
--- a/org.eclipse.jgit/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit/META-INF/MANIFEST.MF
@@ -2,12 +2,12 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit
-Bundle-Version: 4.8.1.qualifier
+Bundle-Version: 4.9.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
-Export-Package: org.eclipse.jgit.annotations;version="4.8.1",
- org.eclipse.jgit.api;version="4.8.1";
+Export-Package: org.eclipse.jgit.annotations;version="4.9.6",
+ org.eclipse.jgit.api;version="4.9.6";
   uses:="org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.diff,
@@ -21,51 +21,52 @@
    org.eclipse.jgit.submodule,
    org.eclipse.jgit.transport,
    org.eclipse.jgit.merge",
- org.eclipse.jgit.api.errors;version="4.8.1";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.errors",
- org.eclipse.jgit.attributes;version="4.8.1",
- org.eclipse.jgit.blame;version="4.8.1";
+ org.eclipse.jgit.api.errors;version="4.9.6";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.errors",
+ org.eclipse.jgit.attributes;version="4.9.6",
+ org.eclipse.jgit.blame;version="4.9.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.diff",
- org.eclipse.jgit.diff;version="4.8.1";
+ org.eclipse.jgit.diff;version="4.9.6";
   uses:="org.eclipse.jgit.patch,
    org.eclipse.jgit.lib,
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.util",
- org.eclipse.jgit.dircache;version="4.8.1";
+ org.eclipse.jgit.dircache;version="4.9.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.util,
    org.eclipse.jgit.events,
    org.eclipse.jgit.attributes",
- org.eclipse.jgit.errors;version="4.8.1";
+ org.eclipse.jgit.errors;version="4.9.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.internal.storage.pack,
    org.eclipse.jgit.transport,
    org.eclipse.jgit.dircache",
- org.eclipse.jgit.events;version="4.8.1";uses:="org.eclipse.jgit.lib",
- org.eclipse.jgit.fnmatch;version="4.8.1",
- org.eclipse.jgit.gitrepo;version="4.8.1";
+ org.eclipse.jgit.events;version="4.9.6";uses:="org.eclipse.jgit.lib",
+ org.eclipse.jgit.fnmatch;version="4.9.6",
+ org.eclipse.jgit.gitrepo;version="4.9.6";
   uses:="org.eclipse.jgit.api,
    org.eclipse.jgit.lib,
    org.eclipse.jgit.revwalk,
    org.xml.sax.helpers,
    org.xml.sax",
- org.eclipse.jgit.gitrepo.internal;version="4.8.1";x-internal:=true,
- org.eclipse.jgit.hooks;version="4.8.1";uses:="org.eclipse.jgit.lib",
- org.eclipse.jgit.ignore;version="4.8.1",
- org.eclipse.jgit.ignore.internal;version="4.8.1";x-friends:="org.eclipse.jgit.test",
- org.eclipse.jgit.internal;version="4.8.1";x-friends:="org.eclipse.jgit.test,org.eclipse.jgit.http.test",
- org.eclipse.jgit.internal.ketch;version="4.8.1";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.internal.storage.dfs;version="4.8.1";
+ org.eclipse.jgit.gitrepo.internal;version="4.9.6";x-internal:=true,
+ org.eclipse.jgit.hooks;version="4.9.6";uses:="org.eclipse.jgit.lib",
+ org.eclipse.jgit.ignore;version="4.9.6",
+ org.eclipse.jgit.ignore.internal;version="4.9.6";x-friends:="org.eclipse.jgit.test",
+ org.eclipse.jgit.internal;version="4.9.6";x-friends:="org.eclipse.jgit.test,org.eclipse.jgit.http.test",
+ org.eclipse.jgit.internal.fsck;version="4.9.6";x-friends:="org.eclipse.jgit.test",
+ org.eclipse.jgit.internal.ketch;version="4.9.6";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.storage.dfs;version="4.9.6";
   x-friends:="org.eclipse.jgit.test,
    org.eclipse.jgit.http.server,
    org.eclipse.jgit.http.test,
    org.eclipse.jgit.lfs.test",
- org.eclipse.jgit.internal.storage.file;version="4.8.1";
+ org.eclipse.jgit.internal.storage.file;version="4.9.6";
   x-friends:="org.eclipse.jgit.test,
    org.eclipse.jgit.junit,
    org.eclipse.jgit.junit.http,
@@ -73,9 +74,11 @@
    org.eclipse.jgit.lfs,
    org.eclipse.jgit.pgm,
    org.eclipse.jgit.pgm.test",
- org.eclipse.jgit.internal.storage.pack;version="4.8.1";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.internal.storage.reftree;version="4.8.1";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.lib;version="4.8.1";
+ org.eclipse.jgit.internal.storage.io;version="4.9.6";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.storage.pack;version="4.9.6";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.storage.reftable;version="4.9.6";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.storage.reftree;version="4.9.6";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.lib;version="4.9.6";
   uses:="org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.util,
@@ -85,33 +88,33 @@
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.transport,
    org.eclipse.jgit.submodule",
- org.eclipse.jgit.lib.internal;version="4.8.1";x-internal:=true,
- org.eclipse.jgit.merge;version="4.8.1";
+ org.eclipse.jgit.lib.internal;version="4.9.6";x-internal:=true,
+ org.eclipse.jgit.merge;version="4.9.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.diff,
    org.eclipse.jgit.dircache,
    org.eclipse.jgit.api",
- org.eclipse.jgit.nls;version="4.8.1",
- org.eclipse.jgit.notes;version="4.8.1";
+ org.eclipse.jgit.nls;version="4.9.6",
+ org.eclipse.jgit.notes;version="4.9.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.merge",
- org.eclipse.jgit.patch;version="4.8.1";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.diff",
- org.eclipse.jgit.revplot;version="4.8.1";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.revwalk",
- org.eclipse.jgit.revwalk;version="4.8.1";
+ org.eclipse.jgit.patch;version="4.9.6";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.diff",
+ org.eclipse.jgit.revplot;version="4.9.6";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.revwalk",
+ org.eclipse.jgit.revwalk;version="4.9.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.diff,
    org.eclipse.jgit.revwalk.filter",
- org.eclipse.jgit.revwalk.filter;version="4.8.1";uses:="org.eclipse.jgit.revwalk,org.eclipse.jgit.lib,org.eclipse.jgit.util",
- org.eclipse.jgit.storage.file;version="4.8.1";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.util",
- org.eclipse.jgit.storage.pack;version="4.8.1";uses:="org.eclipse.jgit.lib",
- org.eclipse.jgit.submodule;version="4.8.1";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.treewalk.filter,org.eclipse.jgit.treewalk",
- org.eclipse.jgit.transport;version="4.8.1";
+ org.eclipse.jgit.revwalk.filter;version="4.9.6";uses:="org.eclipse.jgit.revwalk,org.eclipse.jgit.lib,org.eclipse.jgit.util",
+ org.eclipse.jgit.storage.file;version="4.9.6";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.util",
+ org.eclipse.jgit.storage.pack;version="4.9.6";uses:="org.eclipse.jgit.lib",
+ org.eclipse.jgit.submodule;version="4.9.6";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.treewalk.filter,org.eclipse.jgit.treewalk",
+ org.eclipse.jgit.transport;version="4.9.6";
   uses:="org.eclipse.jgit.transport.resolver,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.internal.storage.pack,
@@ -123,24 +126,24 @@
    org.eclipse.jgit.transport.http,
    org.eclipse.jgit.errors,
    org.eclipse.jgit.storage.pack",
- org.eclipse.jgit.transport.http;version="4.8.1";uses:="javax.net.ssl",
- org.eclipse.jgit.transport.resolver;version="4.8.1";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.transport",
- org.eclipse.jgit.treewalk;version="4.8.1";
+ org.eclipse.jgit.transport.http;version="4.9.6";uses:="javax.net.ssl",
+ org.eclipse.jgit.transport.resolver;version="4.9.6";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.transport",
+ org.eclipse.jgit.treewalk;version="4.9.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.attributes,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.util,
    org.eclipse.jgit.dircache",
- org.eclipse.jgit.treewalk.filter;version="4.8.1";uses:="org.eclipse.jgit.treewalk",
- org.eclipse.jgit.util;version="4.8.1";
+ org.eclipse.jgit.treewalk.filter;version="4.9.6";uses:="org.eclipse.jgit.treewalk",
+ org.eclipse.jgit.util;version="4.9.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.transport.http,
    org.eclipse.jgit.storage.file,
    org.ietf.jgss",
- org.eclipse.jgit.util.io;version="4.8.1",
- org.eclipse.jgit.util.sha1;version="4.8.1",
- org.eclipse.jgit.util.time;version="4.8.1"
+ org.eclipse.jgit.util.io;version="4.9.6",
+ org.eclipse.jgit.util.sha1;version="4.9.6",
+ org.eclipse.jgit.util.time;version="4.9.6"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: com.googlecode.javaewah;version="[1.1.6,2.0.0)",
  com.jcraft.jsch;version="[0.1.37,0.2.0)",
diff --git a/org.eclipse.jgit/META-INF/SOURCE-MANIFEST.MF b/org.eclipse.jgit/META-INF/SOURCE-MANIFEST.MF
index 63e6bbc..1dc1971 100644
--- a/org.eclipse.jgit/META-INF/SOURCE-MANIFEST.MF
+++ b/org.eclipse.jgit/META-INF/SOURCE-MANIFEST.MF
@@ -3,5 +3,5 @@
 Bundle-Name: org.eclipse.jgit - Sources
 Bundle-SymbolicName: org.eclipse.jgit.source
 Bundle-Vendor: Eclipse.org - JGit
-Bundle-Version: 4.8.1.qualifier
-Eclipse-SourceBundle: org.eclipse.jgit;version="4.8.1.qualifier";roots="."
+Bundle-Version: 4.9.6.qualifier
+Eclipse-SourceBundle: org.eclipse.jgit;version="4.9.6.qualifier";roots="."
diff --git a/org.eclipse.jgit/pom.xml b/org.eclipse.jgit/pom.xml
index 673f3ff..31a1629 100644
--- a/org.eclipse.jgit/pom.xml
+++ b/org.eclipse.jgit/pom.xml
@@ -53,7 +53,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.8.1-SNAPSHOT</version>
+    <version>4.9.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit</artifactId>
@@ -206,8 +206,8 @@
     <pluginManagement>
       <plugins>
         <plugin>
-          <groupId>org.codehaus.mojo</groupId>
-          <artifactId>findbugs-maven-plugin</artifactId>
+          <groupId>com.github.hazendaz.spotbugs</groupId>
+          <artifactId>spotbugs-maven-plugin</artifactId>
           <configuration>
             <excludeFilterFile>findBugs/FindBugsExcludeFilter.xml</excludeFilterFile>
           </configuration>
diff --git a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
index c9aaa39..f717cdc 100644
--- a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
+++ b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
@@ -63,7 +63,7 @@
 cannotCreateHEAD=cannot create HEAD
 cannotCreateIndexfile=Cannot create an index file with name {0}
 cannotCreateTempDir=Cannot create a temp dir
-cannotDeleteCheckedOutBranch=Branch {0} is checked out and can not be deleted
+cannotDeleteCheckedOutBranch=Branch {0} is checked out and cannot be deleted
 cannotDeleteFile=Cannot delete file: {0}
 cannotDeleteObjectsPath=Cannot delete {0}/{1}: {2}
 cannotDeleteStaleTrackingRef=Cannot delete stale tracking ref {0}
@@ -81,7 +81,7 @@
 cannotLock=Cannot lock {0}. Ensure that no other process has an open file handle on the lock file {0}.lock, then you may delete the lock file and retry.
 cannotLockPackIn=Cannot lock pack in {0}
 cannotMatchOnEmptyString=Cannot match on empty string.
-cannotMkdirObjectPath=Cannot mkdir {0}/{1}: {2}
+cannotMkdirObjectPath=Cannot create directory {0}/{1}: {2}
 cannotMoveIndexTo=Cannot move index to {0}
 cannotMovePackTo=Cannot move pack to {0}
 cannotOpenService=cannot open {0}
@@ -89,6 +89,7 @@
 cannotParseGitURIish=Cannot parse Git URI-ish
 cannotPullOnARepoWithState=Cannot pull into a repository with state: {0}
 cannotRead=Cannot read {0}
+cannotReadBackDelta=Cannot read delta type {0}
 cannotReadBlob=Cannot read blob {0}
 cannotReadCommit=Cannot read commit {0}
 cannotReadFile=Cannot read file {0}
@@ -121,6 +122,7 @@
 closed=closed
 closeLockTokenFailed=Closing LockToken ''{0}'' failed
 collisionOn=Collision on {0}
+commandClosedStderrButDidntExit=Command {0} closed stderr stream but didn''t exit within timeout {1} seconds
 commandRejectedByHook=Rejected by "{0}" hook.\n{1}
 commandWasCalledInTheWrongState=Command {0} was called in the wrong state
 commitAlreadyExists=exists {0}
@@ -211,12 +213,14 @@
 createBranchFailedUnknownReason=Create branch failed for unknown reason
 createBranchUnexpectedResult=Create branch returned unexpected result {0}
 createNewFileFailed=Could not create new file {0}
+createRequiresZeroOldId=Create requires old ID to be zero
 credentialPassword=Password
 credentialUsername=Username
 daemonAlreadyRunning=Daemon already running
 daysAgo={0} days ago
 deleteBranchUnexpectedResult=Delete branch returned unexpected result {0}
 deleteFileFailed=Could not delete file {0}
+deleteRequiresZeroNewId=Delete requires new ID to be zero
 deleteTagUnexpectedResult=Delete tag returned unexpected result {0}
 deletingNotSupported=Deleting {0} not supported.
 destinationIsNotAWildcard=Destination is not a wildcard.
@@ -245,6 +249,7 @@
 encryptionOnlyPBE=Encryption error: only password-based encryption (PBE) algorithms are supported.
 endOfFileInEscape=End of file in escape
 entryNotFoundByPath=Entry not found by path: {0}
+enumValueNotSupported0=Invalid value: {0}
 enumValueNotSupported2=Invalid value: {0}.{1}={2}
 enumValueNotSupported3=Invalid value: {0}.{1}.{2}={3}
 enumValuesNotAvailable=Enumerated values of type {0} not available
@@ -260,6 +265,7 @@
 exceptionCaughtDuringExecutionOfAddCommand=Exception caught during execution of add command
 exceptionCaughtDuringExecutionOfArchiveCommand=Exception caught during execution of archive command
 exceptionCaughtDuringExecutionOfCherryPickCommand=Exception caught during execution of cherry-pick command. {0}
+exceptionCaughtDuringExecutionOfCommand=Exception caught during execution of command ''{0}'' in ''{1}'', return code ''{2}'', error message ''{3}''
 exceptionCaughtDuringExecutionOfCommitCommand=Exception caught during execution of commit command
 exceptionCaughtDuringExecutionOfFetchCommand=Exception caught during execution of fetch command
 exceptionCaughtDuringExecutionOfLsRemoteCommand=Exception caught during execution of ls-remote command
@@ -270,7 +276,6 @@
 exceptionCaughtDuringExecutionOfRevertCommand=Exception caught during execution of revert command. {0}
 exceptionCaughtDuringExecutionOfRmCommand=Exception caught during execution of rm command
 exceptionCaughtDuringExecutionOfTagCommand=Exception caught during execution of tag command
-exceptionCaughtDuringExcecutionOfCommand=Exception caught during execution of command ''{0}'' in ''{1}'', return code ''{2}'', error message ''{3}''
 exceptionHookExecutionInterrupted=Execution of "{0}" hook interrupted.
 exceptionOccurredDuringAddingOfOptionToALogCommand=Exception occurred during adding of {0} as option to a Log command
 exceptionOccurredDuringReadingOfGIT_DIR=Exception occurred during reading of $GIT_DIR/{0}. {1}
@@ -308,6 +313,8 @@
 gitmodulesNotFound=.gitmodules not found in tree.
 headRequiredToStash=HEAD required to stash local changes
 hoursAgo={0} hours ago
+httpConfigCannotNormalizeURL=Cannot normalize URL path {0}: too many .. segments
+httpConfigInvalidURL=Cannot parse URL from subsection http.{0} in git config; ignored.
 hugeIndexesAreNotSupportedByJgitYet=Huge indexes are not supported by jgit, yet
 hunkBelongsToAnotherFile=Hunk belongs to another file
 hunkDisconnectedFromFile=Hunk disconnected from file
@@ -366,12 +373,17 @@
 invalidPathPeriodAtEndWindows=Invalid path (period at end is ignored by Windows): {0}
 invalidPathSpaceAtEndWindows=Invalid path (space at end is ignored by Windows): {0}
 invalidPathReservedOnWindows=Invalid path (''{0}'' is reserved on Windows): {1}
+invalidRedirectLocation=Invalid redirect location {0} -> {1}
 invalidReflogRevision=Invalid reflog revision: {0}
 invalidRefName=Invalid ref name: {0}
+invalidReftableBlock=Invalid reftable block
+invalidReftableCRC=Invalid reftable CRC-32
+invalidReftableFile=Invalid reftable file
 invalidRemote=Invalid remote: {0}
 invalidRepositoryStateNoHead=Invalid repository --- cannot read HEAD
 invalidShallowObject=invalid shallow object {0}, expected commit
 invalidStageForPath=Invalid stage {0} for path {1}
+invalidSystemProperty=Invalid system property ''{0}'': ''{1}''; using default value {2}
 invalidTagOption=Invalid tag option: {0}
 invalidTimeout=Invalid timeout: {0}
 invalidTimeUnitValue2=Invalid time unit value: {0}.{1}={2}
@@ -410,8 +422,11 @@
 mergeRecursiveTooManyMergeBasesFor = "More than {0} merge bases for:\n a {1}\n b {2} found:\n  count {3}"
 messageAndTaggerNotAllowedInUnannotatedTags = Unannotated tags cannot have a message or tagger
 minutesAgo={0} minutes ago
+mismatchOffset=mismatch offset for object {0}
+mismatchCRC=mismatch CRC for object {0}
 missingAccesskey=Missing accesskey.
 missingConfigurationForKey=No value for key {0} found in configuration
+missingCRC=missing CRC for object {0}
 missingDeltaBase=delta base
 missingForwardImageInGITBinaryPatch=Missing forward-image in GIT binary patch
 missingObject=Missing {0} {1}
@@ -429,6 +444,7 @@
 needPackOut=need packOut
 needsAtLeastOneEntry=Needs at least one entry
 needsWorkdir=Needs workdir
+newIdMustNotBeNull=New ID must not be null
 newlineInQuotesNotAllowed=Newline in quotes not allowed
 noApplyInDelete=No apply in delete
 noClosingBracket=No closing {0} found for {1} at index {2}.
@@ -462,6 +478,7 @@
 objectNotFoundIn=Object {0} not found in {1}.
 obtainingCommitsForCherryPick=Obtaining commits that need to be cherry-picked
 offsetWrittenDeltaBaseForObjectNotFoundInAPack=Offset-written delta base for object not found in a pack
+oldIdMustNotBeNull=Expected old ID must not be null
 onlyAlreadyUpToDateAndFastForwardMergesAreAvailable=only already-up-to-date and fast forward merges are available
 onlyOneFetchSupported=Only one fetch supported
 onlyOneOperationCallPerConnectionIsSupported=Only one operation call per connection is supported.
@@ -469,6 +486,7 @@
 openingConnection=Opening connection
 operationCanceled=Operation {0} was canceled
 outputHasAlreadyBeenStarted=Output has already been started.
+overflowedReftableBlock=Overflowed reftable block
 packChecksumMismatch=Pack checksum mismatch detected for pack file {0}
 packCorruptedWhileWritingToFilesystem=Pack corrupted while writing to filesystem
 packDoesNotMatchIndex=Pack {0} does not match index
@@ -496,6 +514,7 @@
 pathIsNotInWorkingDir=Path is not in working dir
 pathNotConfigured=Submodule path is not configured
 peeledLineBeforeRef=Peeled line before ref.
+peeledRefIsRequired=Peeled ref is required.
 peerDidNotSupplyACompleteObjectGraph=peer did not supply a complete object graph
 personIdentEmailNonNull=E-mail address of PersonIdent must not be null.
 personIdentNameNonNull=Name of PersonIdent must not be null.
@@ -524,10 +543,15 @@
 receivePackInvalidLimit=Illegal limit parameter value {0}
 receivePackTooLarge=Pack exceeds the limit of {0} bytes, rejecting the pack
 receivingObjects=Receiving objects
+redirectBlocked=Redirection blocked: redirect {0} -> {1} not allowed
+redirectHttp=URI ''{0}'': following HTTP redirect #{1}  {2} -> {3}
+redirectLimitExceeded=Redirected more than {0} times; aborted at {1} -> {2}
+redirectLocationMissing=Invalid redirect: no redirect location for {0}
+redirectsOff=Cannot redirect because http.followRedirects is false (HTTP status {0})
 refAlreadyExists=already exists
 refAlreadyExists1=Ref {0} already exists
 reflogEntryNotFound=Entry {0} not found  in reflog for ''{1}''
-refNotResolved=Ref {0} can not be resolved
+refNotResolved=Ref {0} cannot be resolved
 refUpdateReturnCodeWas=RefUpdate return code was: {0}
 remoteConfigHasNoURIAssociated=Remote config "{0}" has no URIs associated
 remoteDoesNotHaveSpec=Remote does not have {0} available for fetch.
@@ -571,7 +595,7 @@
 selectingCommits=Selecting commits
 sequenceTooLargeForDiffAlgorithm=Sequence too large for difference algorithm.
 serviceNotEnabledNoName=Service not enabled
-serviceNotPermitted={0} not permitted
+serviceNotPermitted={1} not permitted on ''{0}''
 sha1CollisionDetected1=SHA-1 collision detected on {0}
 shallowCommitsAlreadyInitialized=Shallow commits have already been initialized
 shallowPacksRequireDepthWalk=Shallow packs require a DepthWalk
@@ -589,6 +613,15 @@
 sourceRefDoesntResolveToAnyObject=Source ref {0} doesn''t resolve to any object.
 sourceRefNotSpecifiedForRefspec=Source ref not specified for refspec: {0}
 squashCommitNotUpdatingHEAD=Squash commit -- not updating HEAD
+sshUserNameError=Jsch error: failed to set SSH user name correctly to ''{0}''; using ''{1}'' picked up from SSH config file.
+sslFailureExceptionMessage=Secure connection to {0} could not be stablished because of SSL problems
+sslFailureInfo=A secure connection to {0}\ncould not be established because the server''s certificate could not be validated.
+sslFailureCause=SSL reported: {0}
+sslFailureTrustExplanation=Do you want to skip SSL verification for this server?
+sslTrustAlways=Always skip SSL verification for this server from now on
+sslTrustForRepo=Skip SSL verification for git operations for repository {0}
+sslTrustNow=Skip SSL verification for this single git operation
+sslVerifyCannotSave=Could not save setting for http.sslVerify
 staleRevFlagsOn=Stale RevFlags on {0}
 startingReadStageWithoutWrittenRequestDataPendingIsNotSupported=Starting read stage without written request data pending is not supported
 stashApplyConflict=Applying stashed changes resulted in a conflict
@@ -600,6 +633,7 @@
 stashDropDeleteRefFailed=Deleting stash reference failed with result: {0}
 stashDropFailed=Dropping stashed commit failed
 stashDropMissingReflog=Stash reflog does not contain entry ''{0}''
+stashDropNotSupported=Dropping stash not supported on this ref backend
 stashFailed=Stashing local changes did not successfully complete
 stashResolveFailed=Reference ''{0}'' does not resolve to stashed commit
 statelessRPCRequiresOptionToBeEnabled=stateless RPC requires {0} to be enabled
@@ -616,6 +650,7 @@
 tagNameInvalid=tag name {0} is invalid
 tagOnRepoWithoutHEADCurrentlyNotSupported=Tag on repository without HEAD currently not supported
 theFactoryMustNotBeNull=The factory must not be null
+threadInterruptedWhileRunning="Current thread interrupted while running {0}"
 timeIsUncertain=Time is uncertain
 timerAlreadyTerminated=Timer already terminated
 tooManyCommands=Too many commands
@@ -653,10 +688,12 @@
 unableToStore=Unable to store {0}.
 unableToWrite=Unable to write {0}
 unauthorized=Unauthorized
+underflowedReftableBlock=Underflowed reftable block
 unencodeableFile=Unencodable file: {0}
 unexpectedCompareResult=Unexpected metadata comparison result: {0}
 unexpectedEndOfConfigFile=Unexpected end of config file
 unexpectedEndOfInput=Unexpected end of input
+unexpectedEofInPack=Unexpected EOF in partially created pack
 unexpectedHunkTrailer=Unexpected hunk trailer
 unexpectedOddResult=odd: {0} + {1} - {2}
 unexpectedRefReport={0}: unexpected ref report: {1}
@@ -667,6 +704,7 @@
 unknownHost=unknown host
 unknownIndexVersionOrCorruptIndex=Unknown index version (or corrupt index): {0}
 unknownObject=unknown object
+unknownObjectInIndex=unknown object {0} found in index but not in pack file
 unknownObjectType=Unknown object type {0}.
 unknownObjectType2=unknown
 unknownRepositoryFormat=Unknown repository format
@@ -689,7 +727,9 @@
 unsupportedOperationNotAddAtEnd=Not add-at-end: {0}
 unsupportedPackIndexVersion=Unsupported pack index version {0}
 unsupportedPackVersion=Unsupported pack version {0}.
+unsupportedReftableVersion=Unsupported reftable version {0}.
 unsupportedRepositoryDescription=Repository description not supported
+updateRequiresOldIdAndNewId=Update requires both old ID and new ID to be nonzero
 updatingHeadFailed=Updating HEAD failed
 updatingReferences=Updating references
 updatingRefFailed=Updating the ref {0} to {1} failed. ReturnCode from RefUpdate.update() was {2}
diff --git a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/storage/dfs/DfsText.properties b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/storage/dfs/DfsText.properties
index 4bbc4cc..2c4bd06 100644
--- a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/storage/dfs/DfsText.properties
+++ b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/storage/dfs/DfsText.properties
@@ -1,6 +1,4 @@
 cannotReadIndex=Cannot read index {0}
-cannotReadBackDelta=Cannot read delta type {0}
 shortReadOfBlock=Short read of block at {0} in pack {1}; expected {2} bytes, received only {3}
 shortReadOfIndex=Short read of index {0}
-unexpectedEofInPack=Unexpected EOF in partially created pack
 willNotStoreEmptyPack=Cannot store empty pack
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
index 21d6283..6b20da3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
@@ -47,8 +47,10 @@
 import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.EnumSet;
+import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Set;
 
 import org.eclipse.jgit.api.CheckoutResult.Status;
 import org.eclipse.jgit.api.errors.CheckoutConflictException;
@@ -66,6 +68,7 @@
 import org.eclipse.jgit.dircache.DirCacheIterator;
 import org.eclipse.jgit.errors.AmbiguousObjectException;
 import org.eclipse.jgit.errors.UnmergedPathException;
+import org.eclipse.jgit.events.WorkingTreeModifiedEvent;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Constants;
@@ -175,6 +178,8 @@ private Stage(int number) {
 
 	private boolean checkoutAllPaths;
 
+	private Set<String> actuallyModifiedPaths;
+
 	/**
 	 * @param repo
 	 */
@@ -410,7 +415,8 @@ public CheckoutCommand setAllPaths(boolean all) {
 	}
 
 	/**
-	 * Checkout paths into index and working directory
+	 * Checkout paths into index and working directory, firing a
+	 * {@link WorkingTreeModifiedEvent} if the working tree was modified.
 	 *
 	 * @return this instance
 	 * @throws IOException
@@ -418,6 +424,7 @@ public CheckoutCommand setAllPaths(boolean all) {
 	 */
 	protected CheckoutCommand checkoutPaths() throws IOException,
 			RefNotFoundException {
+		actuallyModifiedPaths = new HashSet<>();
 		DirCache dc = repo.lockDirCache();
 		try (RevWalk revWalk = new RevWalk(repo);
 				TreeWalk treeWalk = new TreeWalk(repo,
@@ -432,7 +439,16 @@ protected CheckoutCommand checkoutPaths() throws IOException,
 				checkoutPathsFromCommit(treeWalk, dc, commit);
 			}
 		} finally {
-			dc.unlock();
+			try {
+				dc.unlock();
+			} finally {
+				WorkingTreeModifiedEvent event = new WorkingTreeModifiedEvent(
+						actuallyModifiedPaths, null);
+				actuallyModifiedPaths = null;
+				if (!event.isEmpty()) {
+					repo.fireEvent(event);
+				}
+			}
 		}
 		return this;
 	}
@@ -461,9 +477,11 @@ public void apply(DirCacheEntry ent) {
 					int stage = ent.getStage();
 					if (stage > DirCacheEntry.STAGE_0) {
 						if (checkoutStage != null) {
-							if (stage == checkoutStage.number)
+							if (stage == checkoutStage.number) {
 								checkoutPath(ent, r, new CheckoutMetadata(
 										eolStreamType, filterCommand));
+								actuallyModifiedPaths.add(path);
+							}
 						} else {
 							UnmergedPathException e = new UnmergedPathException(
 									ent);
@@ -472,6 +490,7 @@ public void apply(DirCacheEntry ent) {
 					} else {
 						checkoutPath(ent, r, new CheckoutMetadata(eolStreamType,
 								filterCommand));
+						actuallyModifiedPaths.add(path);
 					}
 				}
 			});
@@ -492,13 +511,15 @@ private void checkoutPathsFromCommit(TreeWalk treeWalk, DirCache dc,
 			final EolStreamType eolStreamType = treeWalk.getEolStreamType();
 			final String filterCommand = treeWalk
 					.getFilterCommand(Constants.ATTR_FILTER_TYPE_SMUDGE);
-			editor.add(new PathEdit(treeWalk.getPathString()) {
+			final String path = treeWalk.getPathString();
+			editor.add(new PathEdit(path) {
 				@Override
 				public void apply(DirCacheEntry ent) {
 					ent.setObjectId(blobId);
 					ent.setFileMode(mode);
 					checkoutPath(ent, r,
 							new CheckoutMetadata(eolStreamType, filterCommand));
+					actuallyModifiedPaths.add(path);
 				}
 			});
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CleanCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CleanCommand.java
index c58efb1..e41a03b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CleanCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CleanCommand.java
@@ -54,6 +54,7 @@
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.errors.NoWorkTreeException;
+import org.eclipse.jgit.events.WorkingTreeModifiedEvent;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
@@ -135,6 +136,10 @@ else if (fs.isDirectory(f))
 				}
 		} catch (IOException e) {
 			throw new JGitInternalException(e.getMessage(), e);
+		} finally {
+			if (!files.isEmpty()) {
+				repo.fireEvent(new WorkingTreeModifiedEvent(null, files));
+			}
 		}
 		return files;
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
index d450c64..bde8e63 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
@@ -50,6 +50,7 @@
 import java.util.Collection;
 import java.util.List;
 
+import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRemoteException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
@@ -157,6 +158,16 @@ public CloneCommand() {
 	}
 
 	/**
+	 * Get the git directory. This is primarily used for tests.
+	 *
+	 * @return the git directory
+	 */
+	@Nullable
+	File getDirectory() {
+		return directory;
+	}
+
+	/**
 	 * Executes the {@code Clone} command.
 	 *
 	 * The Git instance returned by this command needs to be closed by the
@@ -232,9 +243,9 @@ private static boolean isNonEmptyDirectory(File dir) {
 		return false;
 	}
 
-	private void verifyDirectories(URIish u) {
+	void verifyDirectories(URIish u) {
 		if (directory == null && gitDir == null) {
-			directory = new File(u.getHumanishName(), Constants.DOT_GIT);
+			directory = new File(u.getHumanishName() + (bare ? Constants.DOT_GIT_EXT : "")); //$NON-NLS-1$
 		}
 		directoryExistsInitially = directory != null && directory.exists();
 		gitDirExistsInitially = gitDir != null && gitDir.exists();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
index 274ece6..e29fc05 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
@@ -482,7 +482,7 @@ private DirCache createTemporaryIndex(ObjectId headId, DirCache index,
 						JGitText.get().entryNotFoundByPath, only.get(i)));
 
 		// there must be at least one change
-		if (emptyCommit)
+		if (emptyCommit && !allowEmpty.booleanValue())
 			// Would like to throw a EmptyCommitException. But this would break the API
 			// TODO(ch): Change this in the next release
 			throw new JGitInternalException(JGitText.get().emptyCommit);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/DescribeCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/DescribeCommand.java
index 389c511..68b1bd9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/DescribeCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/DescribeCommand.java
@@ -47,17 +47,22 @@
 import java.io.IOException;
 import java.text.MessageFormat;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.Comparator;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Optional;
+import java.util.stream.Collectors;
 
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.RefNotFoundException;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
+import org.eclipse.jgit.errors.InvalidPatternException;
 import org.eclipse.jgit.errors.MissingObjectException;
+import org.eclipse.jgit.ignore.internal.IMatcher;
+import org.eclipse.jgit.ignore.internal.PathMatcher;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
@@ -94,6 +99,11 @@ public class DescribeCommand extends GitCommand<String> {
 	private boolean longDesc;
 
 	/**
+	 * Pattern matchers to be applied to tags under consideration
+	 */
+	private List<IMatcher> matchers = new ArrayList<>();
+
+	/**
 	 *
 	 * @param repo
 	 */
@@ -170,6 +180,55 @@ private String longDescription(Ref tag, int depth, ObjectId tip)
 	}
 
 	/**
+	 * Sets one or more {@code glob(7)} patterns that tags must match to be considered.
+	 * If multiple patterns are provided, tags only need match one of them.
+	 *
+	 * @param patterns the {@code glob(7)} pattern or patterns
+	 * @return {@code this}
+	 * @throws InvalidPatternException if the pattern passed in was invalid.
+	 *
+	 * @see <a
+	 *      href="https://www.kernel.org/pub/software/scm/git/docs/git-describe.html"
+	 *      >Git documentation about describe</a>
+	 * @since 4.9
+	 */
+	public DescribeCommand setMatch(String... patterns) throws InvalidPatternException {
+		for (String p : patterns) {
+			matchers.add(PathMatcher.createPathMatcher(p, null, false));
+		}
+		return this;
+	}
+
+	private Optional<Ref> getBestMatch(List<Ref> tags) {
+		if (tags == null || tags.size() == 0) {
+			return Optional.empty();
+		} else if (matchers.size() == 0) {
+			// No matchers, simply return the first tag entry
+			return Optional.of(tags.get(0));
+		} else {
+			// Find the first tag that matches one of the matchers; precedence according to matcher definition order
+			for (IMatcher matcher : matchers) {
+				Optional<Ref> match = tags.stream()
+						.filter(tag -> matcher.matches(tag.getName(), false,
+								false))
+						.findFirst();
+				if (match.isPresent()) {
+					return match;
+				}
+			}
+			return Optional.empty();
+		}
+	}
+
+	private ObjectId getObjectIdFromRef(Ref r) {
+		ObjectId key = repo.peel(r).getPeeledObjectId();
+		if (key == null) {
+			key = r.getObjectId();
+		}
+		return key;
+	}
+
+	/**
 	 * Describes the specified commit. Target defaults to HEAD if no commit was
 	 * set explicitly.
 	 *
@@ -189,14 +248,9 @@ public String call() throws GitAPIException {
 			if (target == null)
 				setTarget(Constants.HEAD);
 
-			Map<ObjectId, Ref> tags = new HashMap<>();
-
-			for (Ref r : repo.getRefDatabase().getRefs(R_TAGS).values()) {
-				ObjectId key = repo.peel(r).getPeeledObjectId();
-				if (key == null)
-					key = r.getObjectId();
-				tags.put(key, r);
-			}
+			Collection<Ref> tagList = repo.getRefDatabase().getRefs(R_TAGS).values();
+			Map<ObjectId, List<Ref>> tags = tagList.stream()
+					.collect(Collectors.groupingBy(this::getObjectIdFromRef));
 
 			// combined flags of all the candidate instances
 			final RevFlagSet allFlags = new RevFlagSet();
@@ -242,11 +296,11 @@ String describe(ObjectId tip) throws IOException {
 			}
 			List<Candidate> candidates = new ArrayList<>();    // all the candidates we find
 
-			// is the target already pointing to a tag? if so, we are done!
-			Ref lucky = tags.get(target);
-			if (lucky != null) {
-				return longDesc ? longDescription(lucky, 0, target) : lucky
-						.getName().substring(R_TAGS.length());
+			// is the target already pointing to a suitable tag? if so, we are done!
+			Optional<Ref> bestMatch = getBestMatch(tags.get(target));
+			if (bestMatch.isPresent()) {
+				return longDesc ? longDescription(bestMatch.get(), 0, target) :
+						bestMatch.get().getName().substring(R_TAGS.length());
 			}
 
 			w.markStart(target);
@@ -258,9 +312,9 @@ String describe(ObjectId tip) throws IOException {
 					// if a tag already dominates this commit,
 					// then there's no point in picking a tag on this commit
 					// since the one that dominates it is always more preferable
-					Ref t = tags.get(c);
-					if (t != null) {
-						Candidate cd = new Candidate(c, t);
+					bestMatch = getBestMatch(tags.get(c));
+					if (bestMatch.isPresent()) {
+						Candidate cd = new Candidate(c, bestMatch.get());
 						candidates.add(cd);
 						cd.depth = seen;
 					}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
index 785c20c..5270283 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
@@ -42,12 +42,16 @@
  */
 package org.eclipse.jgit.api;
 
+import static java.util.stream.Collectors.toList;
+
 import java.io.IOException;
 import java.net.URISyntaxException;
 import java.text.MessageFormat;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
+import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidConfigurationException;
 import org.eclipse.jgit.api.errors.InvalidRemoteException;
@@ -191,6 +195,7 @@ private void fetchSubmodules(FetchResult results)
 							.setThin(thin).setRefSpecs(refSpecs)
 							.setDryRun(dryRun)
 							.setRecurseSubmodules(recurseMode);
+					configure(f);
 					if (callback != null) {
 						callback.fetchingSubmodule(walk.getPath());
 					}
@@ -258,11 +263,19 @@ public FetchResult call() throws GitAPIException, InvalidRemoteException,
 	 * Set the mode to be used for recursing into submodules.
 	 *
 	 * @param recurse
+	 *            corresponds to the
+	 *            --recurse-submodules/--no-recurse-submodules options. If
+	 *            {@code null} use the value of the
+	 *            {@code submodule.name.fetchRecurseSubmodules} option
+	 *            configured per submodule. If not specified there, use the
+	 *            value of the {@code fetch.recurseSubmodules} option configured
+	 *            in git config. If not configured in either, "on-demand" is the
+	 *            built-in default.
 	 * @return {@code this}
 	 * @since 4.7
 	 */
 	public FetchCommand setRecurseSubmodules(
-			FetchRecurseSubmodulesMode recurse) {
+			@Nullable FetchRecurseSubmodulesMode recurse) {
 		checkCallable();
 		submoduleRecurseMode = recurse;
 		return this;
@@ -382,13 +395,21 @@ public List<RefSpec> getRefSpecs() {
 	 *
 	 * @param specs
 	 * @return {@code this}
+	 * @since 4.9
+	 */
+	public FetchCommand setRefSpecs(String... specs) {
+		return setRefSpecs(
+				Arrays.stream(specs).map(RefSpec::new).collect(toList()));
+	}
+
+	/**
+	 * The ref specs to be used in the fetch operation
+	 *
+	 * @param specs
+	 * @return {@code this}
 	 */
 	public FetchCommand setRefSpecs(RefSpec... specs) {
-		checkCallable();
-		this.refSpecs.clear();
-		for (RefSpec spec : specs)
-			refSpecs.add(spec);
-		return this;
+		return setRefSpecs(Arrays.asList(specs));
 	}
 
 	/**
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java
index b5d9e8a..75460fb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java
@@ -53,6 +53,7 @@
 import java.util.Locale;
 import java.util.Map;
 
+import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.api.MergeResult.MergeStatus;
 import org.eclipse.jgit.api.errors.CheckoutConflictException;
 import org.eclipse.jgit.api.errors.ConcurrentRefUpdateException;
@@ -63,6 +64,7 @@
 import org.eclipse.jgit.api.errors.NoMessageException;
 import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
 import org.eclipse.jgit.dircache.DirCacheCheckout;
+import org.eclipse.jgit.events.WorkingTreeModifiedEvent;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Config.ConfigEnum;
@@ -354,6 +356,10 @@ public MergeResult call() throws GitAPIException, NoHeadException,
 							.getMergeResults();
 					failingPaths = resolveMerger.getFailingPaths();
 					unmergedPaths = resolveMerger.getUnmergedPaths();
+					if (!resolveMerger.getModifiedFiles().isEmpty()) {
+						repo.fireEvent(new WorkingTreeModifiedEvent(
+								resolveMerger.getModifiedFiles(), null));
+					}
 				} else
 					noProblems = merger.merge(headCommit, srcCommit);
 				refLogMessage.append(": Merge made by "); //$NON-NLS-1$
@@ -554,12 +560,15 @@ public MergeCommand setSquash(boolean squash) {
 	 * Sets the fast forward mode.
 	 *
 	 * @param fastForwardMode
-	 *            corresponds to the --ff/--no-ff/--ff-only options. --ff is the
-	 *            default option.
+	 *            corresponds to the --ff/--no-ff/--ff-only options. If
+	 *            {@code null} use the value of the {@code merge.ff} option
+	 *            configured in git config. If this option is not configured
+	 *            --ff is the built-in default.
 	 * @return {@code this}
 	 * @since 2.2
 	 */
-	public MergeCommand setFastForward(FastForwardMode fastForwardMode) {
+	public MergeCommand setFastForward(
+			@Nullable FastForwardMode fastForwardMode) {
 		checkCallable();
 		this.fastForwardMode = fastForwardMode;
 		return this;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/PullCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/PullCommand.java
index 9c5ae43..aa97996 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/PullCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/PullCommand.java
@@ -47,6 +47,9 @@
 import java.io.IOException;
 import java.text.MessageFormat;
 
+import org.eclipse.jgit.annotations.Nullable;
+import org.eclipse.jgit.api.MergeCommand.FastForwardMode;
+import org.eclipse.jgit.api.MergeCommand.FastForwardMode.Merge;
 import org.eclipse.jgit.api.RebaseCommand.Operation;
 import org.eclipse.jgit.api.errors.CanceledException;
 import org.eclipse.jgit.api.errors.DetachedHeadException;
@@ -96,6 +99,8 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 
 	private TagOpt tagOption;
 
+	private FastForwardMode fastForwardMode;
+
 	private FetchRecurseSubmodulesMode submoduleRecurseMode = null;
 
 	/**
@@ -347,10 +352,9 @@ public PullResult call() throws GitAPIException,
 			result = new PullResult(fetchRes, remote, rebaseRes);
 		} else {
 			MergeCommand merge = new MergeCommand(repo);
-			merge.include(upstreamName, commitToMerge);
-			merge.setStrategy(strategy);
-			merge.setProgressMonitor(monitor);
-			MergeResult mergeRes = merge.call();
+			MergeResult mergeRes = merge.include(upstreamName, commitToMerge)
+					.setStrategy(strategy).setProgressMonitor(monitor)
+					.setFastForward(getFastForwardMode()).call();
 			monitor.update(1);
 			result = new PullResult(fetchRes, remote, mergeRes);
 		}
@@ -433,14 +437,36 @@ public PullCommand setTagOpt(TagOpt tagOpt) {
 	}
 
 	/**
+	 * Sets the fast forward mode. It is used if pull is configured to do a
+	 * merge as opposed to rebase. If non-{@code null} takes precedence over the
+	 * fast-forward mode configured in git config.
+	 *
+	 * @param fastForwardMode
+	 *            corresponds to the --ff/--no-ff/--ff-only options. If
+	 *            {@code null} use the value of {@code pull.ff} configured in
+	 *            git config. If {@code pull.ff} is not configured fall back to
+	 *            the value of {@code merge.ff}. If {@code merge.ff} is not
+	 *            configured --ff is the built-in default.
+	 * @return {@code this}
+	 * @since 4.9
+	 */
+	public PullCommand setFastForward(
+			@Nullable FastForwardMode fastForwardMode) {
+		checkCallable();
+		this.fastForwardMode = fastForwardMode;
+		return this;
+	}
+
+	/**
 	 * Set the mode to be used for recursing into submodules.
 	 *
 	 * @param recurse
 	 * @return {@code this}
 	 * @since 4.7
+	 * @see FetchCommand#setRecurseSubmodules(FetchRecurseSubmodulesMode)
 	 */
 	public PullCommand setRecurseSubmodules(
-			FetchRecurseSubmodulesMode recurse) {
+			@Nullable FetchRecurseSubmodulesMode recurse) {
 		this.submoduleRecurseMode = recurse;
 		return this;
 	}
@@ -470,4 +496,15 @@ public static BranchRebaseMode getRebaseMode(String branchName,
 		}
 		return mode;
 	}
+
+	private FastForwardMode getFastForwardMode() {
+		if (fastForwardMode != null) {
+			return fastForwardMode;
+		}
+		Config config = repo.getConfig();
+		Merge ffMode = config.getEnum(Merge.values(),
+				ConfigConstants.CONFIG_PULL_SECTION, null,
+				ConfigConstants.CONFIG_KEY_FF, null);
+		return ffMode != null ? FastForwardMode.valueOf(ffMode) : null;
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
index 850ff49..955c50b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
@@ -425,6 +425,7 @@ private void updateStashRef(ObjectId commitId, PersonIdent refLogIdent,
 		refUpdate.setNewObjectId(commitId);
 		refUpdate.setRefLogIdent(refLogIdent);
 		refUpdate.setRefLogMessage(refLogMessage, false);
+		refUpdate.setForceRefLog(true);
 		if (currentRef != null)
 			refUpdate.setExpectedOldObjectId(currentRef.getObjectId());
 		else
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/ReflogCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/ReflogCommand.java
index 04caa0f..394bea5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ReflogCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ReflogCommand.java
@@ -109,4 +109,4 @@ public Collection<ReflogEntry> call() throws GitAPIException,
 		}
 	}
 
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RmCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RmCommand.java
index 9e2cf31..48c23f5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RmCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RmCommand.java
@@ -44,8 +44,10 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.LinkedList;
+import java.util.List;
 
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
@@ -53,6 +55,7 @@
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheBuildIterator;
 import org.eclipse.jgit.dircache.DirCacheBuilder;
+import org.eclipse.jgit.events.WorkingTreeModifiedEvent;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
@@ -145,6 +148,7 @@ public DirCache call() throws GitAPIException,
 		checkCallable();
 		DirCache dc = null;
 
+		List<String> actuallyDeletedFiles = new ArrayList<>();
 		try (final TreeWalk tw = new TreeWalk(repo)) {
 			dc = repo.lockDirCache();
 			DirCacheBuilder builder = dc.builder();
@@ -157,11 +161,14 @@ public DirCache call() throws GitAPIException,
 				if (!cached) {
 					final FileMode mode = tw.getFileMode(0);
 					if (mode.getObjectType() == Constants.OBJ_BLOB) {
+						String relativePath = tw.getPathString();
 						final File path = new File(repo.getWorkTree(),
-								tw.getPathString());
+								relativePath);
 						// Deleting a blob is simply a matter of removing
 						// the file or symlink named by the tree entry.
-						delete(path);
+						if (delete(path)) {
+							actuallyDeletedFiles.add(relativePath);
+						}
 					}
 				}
 			}
@@ -171,16 +178,28 @@ public DirCache call() throws GitAPIException,
 			throw new JGitInternalException(
 					JGitText.get().exceptionCaughtDuringExecutionOfRmCommand, e);
 		} finally {
-			if (dc != null)
-				dc.unlock();
+			try {
+				if (dc != null) {
+					dc.unlock();
+				}
+			} finally {
+				if (!actuallyDeletedFiles.isEmpty()) {
+					repo.fireEvent(new WorkingTreeModifiedEvent(null,
+							actuallyDeletedFiles));
+				}
+			}
 		}
 
 		return dc;
 	}
 
-	private void delete(File p) {
-		while (p != null && !p.equals(repo.getWorkTree()) && p.delete())
+	private boolean delete(File p) {
+		boolean deleted = false;
+		while (p != null && !p.equals(repo.getWorkTree()) && p.delete()) {
+			deleted = true;
 			p = p.getParentFile();
+		}
+		return deleted;
 	}
 
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
index 10ec2a6..b56fb25 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2012, GitHub Inc.
+ * Copyright (C) 2012, 2017 GitHub Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -44,6 +44,9 @@
 
 import java.io.IOException;
 import java.text.MessageFormat;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRefNameException;
@@ -58,6 +61,7 @@
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.dircache.DirCacheIterator;
 import org.eclipse.jgit.errors.CheckoutConflictException;
+import org.eclipse.jgit.events.WorkingTreeModifiedEvent;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.CoreConfig.EolStreamType;
@@ -198,7 +202,13 @@ public ObjectId call() throws GitAPIException,
 					"stash" }); //$NON-NLS-1$
 			merger.setBase(stashHeadCommit);
 			merger.setWorkingTreeIterator(new FileTreeIterator(repo));
-			if (merger.merge(headCommit, stashCommit)) {
+			boolean mergeSucceeded = merger.merge(headCommit, stashCommit);
+			List<String> modifiedByMerge = merger.getModifiedFiles();
+			if (!modifiedByMerge.isEmpty()) {
+				repo.fireEvent(
+						new WorkingTreeModifiedEvent(modifiedByMerge, null));
+			}
+			if (mergeSucceeded) {
 				DirCache dc = repo.lockDirCache();
 				DirCacheCheckout dco = new DirCacheCheckout(repo, headTree,
 						dc, merger.getResultTreeId());
@@ -329,6 +339,7 @@ private void resetIndex(RevTree tree) throws IOException {
 
 	private void resetUntracked(RevTree tree) throws CheckoutConflictException,
 			IOException {
+		Set<String> actuallyModifiedPaths = new HashSet<>();
 		// TODO maybe NameConflictTreeWalk ?
 		try (TreeWalk walk = new TreeWalk(repo)) {
 			walk.addTree(tree);
@@ -361,6 +372,12 @@ private void resetUntracked(RevTree tree) throws CheckoutConflictException,
 
 				checkoutPath(entry, reader,
 						new CheckoutMetadata(eolStreamType, null));
+				actuallyModifiedPaths.add(entry.getPathString());
+			}
+		} finally {
+			if (!actuallyModifiedPaths.isEmpty()) {
+				repo.fireEvent(new WorkingTreeModifiedEvent(
+						actuallyModifiedPaths, null));
 			}
 		}
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java
index 681f8e6..77a7fff 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java
@@ -62,6 +62,7 @@
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.dircache.DirCacheIterator;
 import org.eclipse.jgit.errors.UnmergedPathException;
+import org.eclipse.jgit.events.WorkingTreeModifiedEvent;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.CommitBuilder;
 import org.eclipse.jgit.lib.Constants;
@@ -211,6 +212,7 @@ private void updateStashRef(ObjectId commitId, PersonIdent refLogIdent,
 		refUpdate.setNewObjectId(commitId);
 		refUpdate.setRefLogIdent(refLogIdent);
 		refUpdate.setRefLogMessage(refLogMessage, false);
+		refUpdate.setForceRefLog(true);
 		if (currentRef != null)
 			refUpdate.setExpectedOldObjectId(currentRef.getObjectId());
 		else
@@ -240,6 +242,7 @@ private Ref getHead() throws GitAPIException {
 	public RevCommit call() throws GitAPIException {
 		checkCallable();
 
+		List<String> deletedFiles = new ArrayList<>();
 		Ref head = getHead();
 		try (ObjectReader reader = repo.newObjectReader()) {
 			RevCommit headCommit = parseCommit(reader, head.getObjectId());
@@ -377,9 +380,11 @@ public void apply(DirCacheEntry ent) {
 				// Remove untracked files
 				if (includeUntracked) {
 					for (DirCacheEntry entry : untracked) {
+						String repoRelativePath = entry.getPathString();
 						File file = new File(repo.getWorkTree(),
-								entry.getPathString());
+								repoRelativePath);
 						FileUtils.delete(file);
+						deletedFiles.add(repoRelativePath);
 					}
 				}
 
@@ -394,6 +399,11 @@ public void apply(DirCacheEntry ent) {
 			return parseCommit(reader, commitId);
 		} catch (IOException e) {
 			throw new JGitInternalException(JGitText.get().stashFailed, e);
+		} finally {
+			if (!deletedFiles.isEmpty()) {
+				repo.fireEvent(
+						new WorkingTreeModifiedEvent(null, deletedFiles));
+			}
 		}
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashDropCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashDropCommand.java
index e215bdf..85e7b3d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashDropCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashDropCommand.java
@@ -56,6 +56,7 @@
 import org.eclipse.jgit.api.errors.RefNotFoundException;
 import org.eclipse.jgit.errors.LockFailedException;
 import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.internal.storage.file.RefDirectory;
 import org.eclipse.jgit.internal.storage.file.ReflogWriter;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
@@ -68,6 +69,9 @@
 
 /**
  * Command class to delete a stashed commit reference
+ * <p>
+ * Currently only supported on a traditional file repository using
+ * one-file-per-ref reflogs.
  *
  * @see <a href="http://www.kernel.org/pub/software/scm/git/docs/git-stash.html"
  *      >Git documentation about Stash</a>
@@ -84,6 +88,10 @@ public class StashDropCommand extends GitCommand<ObjectId> {
 	 */
 	public StashDropCommand(Repository repo) {
 		super(repo);
+		if (!(repo.getRefDatabase() instanceof RefDirectory)) {
+			throw new UnsupportedOperationException(
+					JGitText.get().stashDropNotSupported);
+		}
 	}
 
 	/**
@@ -205,10 +213,11 @@ public ObjectId call() throws GitAPIException {
 			return null;
 		}
 
-		ReflogWriter writer = new ReflogWriter(repo, true);
+		RefDirectory refdb = (RefDirectory) repo.getRefDatabase();
+		ReflogWriter writer = new ReflogWriter(refdb, true);
 		String stashLockRef = ReflogWriter.refLockFor(R_STASH);
-		File stashLockFile = writer.logFor(stashLockRef);
-		File stashFile = writer.logFor(R_STASH);
+		File stashLockFile = refdb.logFor(stashLockRef);
+		File stashFile = refdb.logFor(R_STASH);
 		if (stashLockFile.exists())
 			throw new JGitInternalException(JGitText.get().stashDropFailed,
 					new LockFailedException(stashFile));
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleSyncCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleSyncCommand.java
index f97dce9..b5c0b15 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleSyncCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleSyncCommand.java
@@ -162,4 +162,4 @@ public Map<String, String> call() throws GitAPIException {
 			throw new JGitInternalException(e.getMessage(), e);
 		}
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleUpdateCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleUpdateCommand.java
index 4d3dff0..4faaac2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleUpdateCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleUpdateCommand.java
@@ -91,6 +91,10 @@ public class SubmoduleUpdateCommand extends
 
 	private CloneCommand.Callback callback;
 
+	private FetchCommand.Callback fetchCallback;
+
+	private boolean fetch = false;
+
 	/**
 	 * @param repo
 	 */
@@ -114,6 +118,19 @@ public SubmoduleUpdateCommand setProgressMonitor(
 	}
 
 	/**
+	 * Whether to fetch the submodules before we update them. By default, this
+	 * is set to <code>false</code>
+	 *
+	 * @param fetch
+	 * @return this command
+	 * @since 4.9
+	 */
+	public SubmoduleUpdateCommand setFetch(final boolean fetch) {
+		this.fetch = fetch;
+		return this;
+	}
+
+	/**
 	 * Add repository-relative submodule path to initialize
 	 *
 	 * @param path
@@ -161,7 +178,7 @@ public Collection<String> call() throws InvalidConfigurationException,
 					continue;
 
 				Repository submoduleRepo = generator.getRepository();
-				// Clone repository is not present
+				// Clone repository if not present
 				if (submoduleRepo == null) {
 					if (callback != null) {
 						callback.cloningSubmodule(generator.getPath());
@@ -175,6 +192,16 @@ public Collection<String> call() throws InvalidConfigurationException,
 					if (monitor != null)
 						clone.setProgressMonitor(monitor);
 					submoduleRepo = clone.call().getRepository();
+				} else if (this.fetch) {
+					if (fetchCallback != null) {
+						fetchCallback.fetchingSubmodule(generator.getPath());
+					}
+					FetchCommand fetchCommand = Git.wrap(submoduleRepo).fetch();
+					if (monitor != null) {
+						fetchCommand.setProgressMonitor(monitor);
+					}
+					configure(fetchCommand);
+					fetchCommand.call();
 				}
 
 				try (RevWalk walk = new RevWalk(submoduleRepo)) {
@@ -247,4 +274,18 @@ public SubmoduleUpdateCommand setCallback(CloneCommand.Callback callback) {
 		this.callback = callback;
 		return this;
 	}
+
+	/**
+	 * Set status callback for submodule fetch operation.
+	 *
+	 * @param callback
+	 *            the callback
+	 * @return {@code this}
+	 * @since 4.9
+	 */
+	public SubmoduleUpdateCommand setFetchCallback(
+			FetchCommand.Callback callback) {
+		this.fetchCallback = callback;
+		return this;
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/TransportCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/TransportCommand.java
index 3d2e46b..1541df5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/TransportCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/TransportCommand.java
@@ -95,7 +95,7 @@ public C setCredentialsProvider(
 
 	/**
 	 * @param timeout
-	 *            the timeout used for the transport step
+	 *            the timeout (in seconds) used for the transport step
 	 * @return {@code this}
 	 */
 	public C setTimeout(int timeout) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/PatchApplyException.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/PatchApplyException.java
index 389c776..4329860 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/PatchApplyException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/PatchApplyException.java
@@ -44,9 +44,9 @@
 
 /**
  * Exception thrown when applying a patch fails
- * 
+ *
  * @since 2.0
- * 
+ *
  */
 public class PatchApplyException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/PatchFormatException.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/PatchFormatException.java
index caff942..02ab423 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/PatchFormatException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/PatchFormatException.java
@@ -50,9 +50,9 @@
 
 /**
  * Exception thrown when applying a patch fails due to an invalid format
- * 
+ *
  * @since 2.0
- * 
+ *
  */
 public class PatchFormatException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/attributes/Attribute.java b/org.eclipse.jgit/src/org/eclipse/jgit/attributes/Attribute.java
index 905ad76..c256b73 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/attributes/Attribute.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/attributes/Attribute.java
@@ -193,4 +193,4 @@ public String toString() {
 			return key + "=" + value; //$NON-NLS-1$
 		}
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/attributes/Attributes.java b/org.eclipse.jgit/src/org/eclipse/jgit/attributes/Attributes.java
index 0810e31..d3826b3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/attributes/Attributes.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/attributes/Attributes.java
@@ -1,5 +1,6 @@
 /*
- * Copyright (C) 2015, Ivan Motsch <ivan.motsch@bsiag.com>
+ * Copyright (C) 2015, Ivan Motsch <ivan.motsch@bsiag.com>,
+ * Copyright (C) 2017, Obeo (mathieu.cartaud@obeo.fr)
  *
  * This program and the accompanying materials are made available
  * under the terms of the Eclipse Distribution License v1.0 which
@@ -48,6 +49,7 @@
 import java.util.Map;
 
 import org.eclipse.jgit.attributes.Attribute.State;
+import org.eclipse.jgit.lib.Constants;
 
 /**
  * Represents a set of attributes for a path
@@ -170,6 +172,26 @@ public String getValue(String key) {
 		return a != null ? a.getValue() : null;
 	}
 
+	/**
+	 * Test if the given attributes implies to handle the related entry as a
+	 * binary file (i.e. if the entry has an -merge or a merge=binary attribute)
+	 * or if it can be content merged.
+	 *
+	 * @return <code>true</code> if the entry can be content merged,
+	 *         <code>false</code> otherwise
+	 * @since 4.9
+	 */
+	public boolean canBeContentMerged() {
+		if (isUnset(Constants.ATTR_MERGE)) {
+			return false;
+		} else if (isCustom(Constants.ATTR_MERGE)
+				&& getValue(Constants.ATTR_MERGE)
+						.equals(Constants.ATTR_BUILTIN_BINARY_MERGER)) {
+			return false;
+		}
+		return true;
+	}
+
 	@Override
 	public String toString() {
 		StringBuilder buf = new StringBuilder();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/attributes/AttributesHandler.java b/org.eclipse.jgit/src/org/eclipse/jgit/attributes/AttributesHandler.java
index 3bf4179..8d928e3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/attributes/AttributesHandler.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/attributes/AttributesHandler.java
@@ -144,7 +144,8 @@ public Attributes getAttributes() throws IOException {
 		mergeInfoAttributes(entryPath, isDirectory, attributes);
 
 		// Gets the attributes located on the current entry path
-		mergePerDirectoryEntryAttributes(entryPath, isDirectory,
+		mergePerDirectoryEntryAttributes(entryPath, entryPath.lastIndexOf('/'),
+				isDirectory,
 				treeWalk.getTree(WorkingTreeIterator.class),
 				treeWalk.getTree(DirCacheIterator.class),
 				treeWalk.getTree(CanonicalTreeParser.class),
@@ -206,6 +207,8 @@ private void mergeInfoAttributes(String entryPath, boolean isDirectory,
 	 *            the path to test. The path must be relative to this attribute
 	 *            node's own repository path, and in repository path format
 	 *            (uses '/' and not '\').
+	 * @param nameRoot
+	 *            index of the '/' preceeding the current level, or -1 if none
 	 * @param isDirectory
 	 *            true if the target item is a directory.
 	 * @param workingTreeIterator
@@ -217,7 +220,7 @@ private void mergeInfoAttributes(String entryPath, boolean isDirectory,
 	 * @throws IOException
 	 */
 	private void mergePerDirectoryEntryAttributes(String entryPath,
-			boolean isDirectory,
+			int nameRoot, boolean isDirectory,
 			@Nullable WorkingTreeIterator workingTreeIterator,
 			@Nullable DirCacheIterator dirCacheIterator,
 			@Nullable CanonicalTreeParser otherTree, Attributes result)
@@ -228,9 +231,12 @@ private void mergePerDirectoryEntryAttributes(String entryPath,
 			AttributesNode attributesNode = attributesNode(
 					treeWalk, workingTreeIterator, dirCacheIterator, otherTree);
 			if (attributesNode != null) {
-				mergeAttributes(attributesNode, entryPath, isDirectory, result);
+				mergeAttributes(attributesNode,
+						entryPath.substring(nameRoot + 1), isDirectory,
+						result);
 			}
-			mergePerDirectoryEntryAttributes(entryPath, isDirectory,
+			mergePerDirectoryEntryAttributes(entryPath,
+					entryPath.lastIndexOf('/', nameRoot - 1), isDirectory,
 					parentOf(workingTreeIterator), parentOf(dirCacheIterator),
 					parentOf(otherTree), result);
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/attributes/AttributesRule.java b/org.eclipse.jgit/src/org/eclipse/jgit/attributes/AttributesRule.java
index c9c69db..3cf5de8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/attributes/AttributesRule.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/attributes/AttributesRule.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2010, Red Hat Inc.
+ * Copyright (C) 2010, 2017 Red Hat Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -210,7 +210,7 @@ public boolean isMatch(String relativeTarget, boolean isDirectory) {
 			return false;
 		if (relativeTarget.length() == 0)
 			return false;
-		boolean match = matcher.matches(relativeTarget, isDirectory);
+		boolean match = matcher.matches(relativeTarget, isDirectory, true);
 		return match;
 	}
 
@@ -225,4 +225,4 @@ public String toString() {
 		return sb.toString();
 
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffConfig.java
index 324b99e..ee70949 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffConfig.java
@@ -54,12 +54,7 @@
 /** Keeps track of diff related configuration options. */
 public class DiffConfig {
 	/** Key for {@link Config#get(SectionParser)}. */
-	public static final Config.SectionParser<DiffConfig> KEY = new SectionParser<DiffConfig>() {
-		@Override
-		public DiffConfig parse(final Config cfg) {
-			return new DiffConfig(cfg);
-		}
-	};
+	public static final Config.SectionParser<DiffConfig> KEY = DiffConfig::new;
 
 	/** Permissible values for {@code diff.renames}. */
 	public static enum RenameDetectionType {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffEntry.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffEntry.java
index e1dfcff..5eb1942 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffEntry.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffEntry.java
@@ -525,4 +525,4 @@ public String toString() {
 		buf.append("]");
 		return buf.toString();
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/MyersDiff.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/MyersDiff.java
index e1bda11..a3860de 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/MyersDiff.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/MyersDiff.java
@@ -119,7 +119,7 @@ public class MyersDiff<S extends Sequence> {
 		public <S extends Sequence> void diffNonCommon(EditList edits,
 				HashedSequenceComparator<S> cmp, HashedSequence<S> a,
 				HashedSequence<S> b, Edit region) {
-			new MyersDiff<S>(edits, cmp, a, b, region);
+			new MyersDiff<>(edits, cmp, a, b, region);
 		}
 	};
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
index aed76ac..a6ab9c8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
@@ -50,6 +50,7 @@
 import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
@@ -61,6 +62,7 @@
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.IndexWriteException;
 import org.eclipse.jgit.errors.MissingObjectException;
+import org.eclipse.jgit.events.WorkingTreeModifiedEvent;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.CoreConfig.AutoCRLF;
@@ -85,6 +87,7 @@
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FS.ExecutionResult;
 import org.eclipse.jgit.util.FileUtils;
+import org.eclipse.jgit.util.IntList;
 import org.eclipse.jgit.util.RawParseUtils;
 import org.eclipse.jgit.util.SystemReader;
 import org.eclipse.jgit.util.io.EolStreamTypeUtil;
@@ -151,6 +154,8 @@ public CheckoutMetadata(EolStreamType eolStreamType,
 
 	private boolean emptyDirCache;
 
+	private boolean performingCheckout;
+
 	/**
 	 * @return a list of updated paths and smudgeFilterCommands
 	 */
@@ -432,10 +437,11 @@ void processEntry(CanonicalTreeParser m, DirCacheBuildIterator i,
 	}
 
 	/**
-	 * Execute this checkout
+	 * Execute this checkout. A {@link WorkingTreeModifiedEvent} is fired if the
+	 * working tree was modified; even if the checkout fails.
 	 *
 	 * @return <code>false</code> if this method could not delete all the files
-	 *         which should be deleted (e.g. because of of the files was
+	 *         which should be deleted (e.g. because one of the files was
 	 *         locked). In this case {@link #getToBeDeleted()} lists the files
 	 *         which should be tried to be deleted outside of this method.
 	 *         Although <code>false</code> is returned the checkout was
@@ -448,7 +454,17 @@ public boolean checkout() throws IOException {
 		try {
 			return doCheckout();
 		} finally {
-			dc.unlock();
+			try {
+				dc.unlock();
+			} finally {
+				if (performingCheckout) {
+					WorkingTreeModifiedEvent event = new WorkingTreeModifiedEvent(
+							getUpdated().keySet(), getRemoved());
+					if (!event.isEmpty()) {
+						repo.fireEvent(event);
+					}
+				}
+			}
 		}
 	}
 
@@ -472,11 +488,13 @@ private boolean doCheckout() throws CorruptObjectException, IOException,
 			// update our index
 			builder.finish();
 
+			performingCheckout = true;
 			File file = null;
 			String last = null;
 			// when deleting files process them in the opposite order as they have
 			// been reported. This ensures the files are deleted before we delete
 			// their parent folders
+			IntList nonDeleted = new IntList();
 			for (int i = removed.size() - 1; i >= 0; i--) {
 				String r = removed.get(i);
 				file = new File(repo.getWorkTree(), r);
@@ -486,25 +504,47 @@ private boolean doCheckout() throws CorruptObjectException, IOException,
 					// a submodule, in which case we shall not attempt
 					// to delete it. A submodule is not empty, so it
 					// is safe to check this after a failed delete.
-					if (!repo.getFS().isDirectory(file))
+					if (!repo.getFS().isDirectory(file)) {
+						nonDeleted.add(i);
 						toBeDeleted.add(r);
+					}
 				} else {
 					if (last != null && !isSamePrefix(r, last))
 						removeEmptyParents(new File(repo.getWorkTree(), last));
 					last = r;
 				}
 			}
-			if (file != null)
+			if (file != null) {
 				removeEmptyParents(file);
-
-			for (Map.Entry<String, CheckoutMetadata> e : updated.entrySet()) {
-				String path = e.getKey();
-				CheckoutMetadata meta = e.getValue();
-				DirCacheEntry entry = dc.getEntry(path);
-				if (!FileMode.GITLINK.equals(entry.getRawMode()))
-					checkoutEntry(repo, entry, objectReader, false, meta);
 			}
-
+			removed = filterOut(removed, nonDeleted);
+			nonDeleted = null;
+			Iterator<Map.Entry<String, CheckoutMetadata>> toUpdate = updated
+					.entrySet().iterator();
+			Map.Entry<String, CheckoutMetadata> e = null;
+			try {
+				while (toUpdate.hasNext()) {
+					e = toUpdate.next();
+					String path = e.getKey();
+					CheckoutMetadata meta = e.getValue();
+					DirCacheEntry entry = dc.getEntry(path);
+					if (!FileMode.GITLINK.equals(entry.getRawMode())) {
+						checkoutEntry(repo, entry, objectReader, false, meta);
+					}
+					e = null;
+				}
+			} catch (Exception ex) {
+				// We didn't actually modify the current entry nor any that
+				// might follow.
+				if (e != null) {
+					toUpdate.remove();
+				}
+				while (toUpdate.hasNext()) {
+					e = toUpdate.next();
+					toUpdate.remove();
+				}
+				throw ex;
+			}
 			// commit the index builder - a new index is persisted
 			if (!builder.commit())
 				throw new IndexWriteException();
@@ -512,6 +552,36 @@ private boolean doCheckout() throws CorruptObjectException, IOException,
 		return toBeDeleted.size() == 0;
 	}
 
+	private static ArrayList<String> filterOut(ArrayList<String> strings,
+			IntList indicesToRemove) {
+		int n = indicesToRemove.size();
+		if (n == strings.size()) {
+			return new ArrayList<>(0);
+		}
+		switch (n) {
+		case 0:
+			return strings;
+		case 1:
+			strings.remove(indicesToRemove.get(0));
+			return strings;
+		default:
+			int length = strings.size();
+			ArrayList<String> result = new ArrayList<>(length - n);
+			// Process indicesToRemove from the back; we know that it
+			// contains indices in descending order.
+			int j = n - 1;
+			int idx = indicesToRemove.get(j);
+			for (int i = 0; i < length; i++) {
+				if (i == idx) {
+					idx = (--j >= 0) ? indicesToRemove.get(j) : -1;
+				} else {
+					result.add(strings.get(i));
+				}
+			}
+			return result;
+		}
+	}
+
 	private static boolean isSamePrefix(String a, String b) {
 		int as = a.lastIndexOf('/');
 		int bs = b.lastIndexOf('/');
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/errors/CorruptPackIndexException.java b/org.eclipse.jgit/src/org/eclipse/jgit/errors/CorruptPackIndexException.java
new file mode 100644
index 0000000..65d83b3
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/errors/CorruptPackIndexException.java
@@ -0,0 +1,94 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.errors;
+
+import org.eclipse.jgit.annotations.Nullable;
+
+/**
+ * Exception thrown when encounters a corrupt pack index file.
+ *
+ * @since 4.9
+ */
+public class CorruptPackIndexException extends Exception {
+	private static final long serialVersionUID = 1L;
+
+	/** The error type of a corrupt index file. */
+	public enum ErrorType {
+		/** Offset does not match index in pack file. */
+		MISMATCH_OFFSET,
+		/** CRC does not match CRC of the object data in pack file. */
+		MISMATCH_CRC,
+		/** CRC is not present in index file. */
+		MISSING_CRC,
+		/** Object in pack is not present in index file. */
+		MISSING_OBJ,
+		/** Object in index file is not present in pack file. */
+		UNKNOWN_OBJ,
+	}
+
+	private ErrorType errorType;
+
+	/**
+	 * Report a specific error condition discovered in an index file.
+	 *
+	 * @param message
+	 *            the error message.
+	 * @param errorType
+	 *            the error type of corruption.
+	 */
+	public CorruptPackIndexException(String message, ErrorType errorType) {
+		super(message);
+		this.errorType = errorType;
+	}
+
+	/**
+	 * Specific the reason of the corrupt index file.
+	 *
+	 * @return error condition or null.
+	 */
+	@Nullable
+	public ErrorType getErrorType() {
+		return errorType;
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/errors/TooLargeObjectInPackException.java b/org.eclipse.jgit/src/org/eclipse/jgit/errors/TooLargeObjectInPackException.java
index b5b1af5..ece76ed 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/errors/TooLargeObjectInPackException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/errors/TooLargeObjectInPackException.java
@@ -92,4 +92,4 @@ public TooLargeObjectInPackException(long objectSize,
 	public TooLargeObjectInPackException(URIish uri, String s) {
 		super(uri.setPass(null) + ": " + s); //$NON-NLS-1$
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/errors/TranslationBundleLoadingException.java b/org.eclipse.jgit/src/org/eclipse/jgit/errors/TranslationBundleLoadingException.java
index 4f297b9..6cb332d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/errors/TranslationBundleLoadingException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/errors/TranslationBundleLoadingException.java
@@ -69,4 +69,4 @@ public TranslationBundleLoadingException(Class bundleClass, Locale locale, Excep
 				+ bundleClass.getName() + ", " + locale.toString() + "]", //$NON-NLS-1$ //$NON-NLS-2$
 				bundleClass, locale, cause);
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/events/ListenerList.java b/org.eclipse.jgit/src/org/eclipse/jgit/events/ListenerList.java
index 12ef533..cea03db 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/events/ListenerList.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/events/ListenerList.java
@@ -53,6 +53,19 @@ public class ListenerList {
 	private final ConcurrentMap<Class<? extends RepositoryListener>, CopyOnWriteArrayList<ListenerHandle>> lists = new ConcurrentHashMap<>();
 
 	/**
+	 * Register a {@link WorkingTreeModifiedListener}.
+	 *
+	 * @param listener
+	 *            the listener implementation.
+	 * @return handle to later remove the listener.
+	 * @since 4.9
+	 */
+	public ListenerHandle addWorkingTreeModifiedListener(
+			WorkingTreeModifiedListener listener) {
+		return addListener(WorkingTreeModifiedListener.class, listener);
+	}
+
+	/**
 	 * Register an IndexChangedListener.
 	 *
 	 * @param listener
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/events/WorkingTreeModifiedEvent.java b/org.eclipse.jgit/src/org/eclipse/jgit/events/WorkingTreeModifiedEvent.java
new file mode 100644
index 0000000..6517823
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/events/WorkingTreeModifiedEvent.java
@@ -0,0 +1,129 @@
+/*
+ * Copyright (C) 2017, Thomas Wolf <thomas.wolf@paranor.ch>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.events;
+
+import java.util.Collection;
+import java.util.Collections;
+
+import org.eclipse.jgit.annotations.NonNull;
+
+/**
+ * A {@link RepositoryEvent} describing changes to the working tree. It is fired
+ * whenever a {@link org.eclipse.jgit.dircache.DirCacheCheckout} modifies
+ * (adds/deletes/updates) files in the working tree.
+ *
+ * @since 4.9
+ */
+public class WorkingTreeModifiedEvent
+		extends RepositoryEvent<WorkingTreeModifiedListener> {
+
+	private Collection<String> modified;
+
+	private Collection<String> deleted;
+
+	/**
+	 * Creates a new {@link WorkingTreeModifiedEvent} with the given
+	 * collections.
+	 *
+	 * @param modified
+	 *            repository-relative paths that were added or updated
+	 * @param deleted
+	 *            repository-relative paths that were deleted
+	 */
+	public WorkingTreeModifiedEvent(Collection<String> modified,
+			Collection<String> deleted) {
+		this.modified = modified;
+		this.deleted = deleted;
+	}
+
+	/**
+	 * Determines whether there are any changes recorded in this event.
+	 *
+	 * @return {@code true} if no files were modified or deleted, {@code false}
+	 *         otherwise
+	 */
+	public boolean isEmpty() {
+		return (modified == null || modified.isEmpty())
+				&& (deleted == null || deleted.isEmpty());
+	}
+
+	/**
+	 * Retrieves the {@link Collection} of repository-relative paths of files
+	 * that were modified (added or updated).
+	 *
+	 * @return the set
+	 */
+	public @NonNull Collection<String> getModified() {
+		Collection<String> result = modified;
+		if (result == null) {
+			result = Collections.emptyList();
+			modified = result;
+		}
+		return result;
+	}
+
+	/**
+	 * Retrieves the {@link Collection} of repository-relative paths of files
+	 * that were deleted.
+	 *
+	 * @return the set
+	 */
+	public @NonNull Collection<String> getDeleted() {
+		Collection<String> result = deleted;
+		if (result == null) {
+			result = Collections.emptyList();
+			deleted = result;
+		}
+		return result;
+	}
+
+	@Override
+	public Class<WorkingTreeModifiedListener> getListenerType() {
+		return WorkingTreeModifiedListener.class;
+	}
+
+	@Override
+	public void dispatch(WorkingTreeModifiedListener listener) {
+		listener.onWorkingTreeModified(this);
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java b/org.eclipse.jgit/src/org/eclipse/jgit/events/WorkingTreeModifiedListener.java
similarity index 78%
copy from org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
copy to org.eclipse.jgit/src/org/eclipse/jgit/events/WorkingTreeModifiedListener.java
index 98a2a94..402a900 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/events/WorkingTreeModifiedListener.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2011, Google Inc.
+ * Copyright (C) 2017, Thomas Wolf <thomas.wolf@paranor.ch>
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -41,20 +41,21 @@
  * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.eclipse.jgit.internal.storage.dfs;
+package org.eclipse.jgit.events;
 
-import java.util.concurrent.atomic.AtomicLong;
+/**
+ * Receives {@link WorkingTreeModifiedEvent}s, which are fired whenever a
+ * {@link org.eclipse.jgit.dircache.DirCacheCheckout} modifies
+ * (adds/deletes/updates) files in the working tree.
+ *
+ * @since 4.9
+ */
+public interface WorkingTreeModifiedListener extends RepositoryListener {
 
-final class DfsPackKey {
-	final int hash;
-
-	final AtomicLong cachedSize;
-
-	DfsPackKey() {
-		// Multiply by 31 here so we can more directly combine with another
-		// value without doing the multiply there.
-		//
-		hash = System.identityHashCode(this) * 31;
-		cachedSize = new AtomicLong();
-	}
+	/**
+	 * Respond to working tree modifications.
+	 *
+	 * @param event
+	 */
+	void onWorkingTreeModified(WorkingTreeModifiedEvent event);
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java
index 1de8a0b..219babd 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java
@@ -49,7 +49,6 @@
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.lang.UnsupportedOperationException;
 import java.net.URI;
 import java.text.MessageFormat;
 import java.util.ArrayList;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/hooks/GitHook.java b/org.eclipse.jgit/src/org/eclipse/jgit/hooks/GitHook.java
index 62a6749..b684dd6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/hooks/GitHook.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/hooks/GitHook.java
@@ -167,4 +167,4 @@ protected void doRun() throws AbortedByHookException {
 		}
 	}
 
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/ignore/FastIgnoreRule.java b/org.eclipse.jgit/src/org/eclipse/jgit/ignore/FastIgnoreRule.java
index ef67d49..7298a08 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/ignore/FastIgnoreRule.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/ignore/FastIgnoreRule.java
@@ -155,7 +155,7 @@ public boolean isMatch(String path, boolean directory) {
 			return false;
 		if (path.length() == 0)
 			return false;
-		boolean match = matcher.matches(path, directory);
+		boolean match = matcher.matches(path, directory, false);
 		return match;
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/IMatcher.java b/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/IMatcher.java
index 61f7b83..5b184cb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/IMatcher.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/IMatcher.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2014, Andrey Loskutov <loskutov@gmx.de>
+ * Copyright (C) 2014, 2017 Andrey Loskutov <loskutov@gmx.de>
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -52,7 +52,8 @@ public interface IMatcher {
 	 */
 	public static final IMatcher NO_MATCH = new IMatcher() {
 		@Override
-		public boolean matches(String path, boolean assumeDirectory) {
+		public boolean matches(String path, boolean assumeDirectory,
+				boolean pathMatch) {
 			return false;
 		}
 
@@ -71,9 +72,14 @@ public boolean matches(String segment, int startIncl, int endExcl,
 	 * @param assumeDirectory
 	 *            true to assume this path as directory (even if it doesn't end
 	 *            with a slash)
+	 * @param pathMatch
+	 *            {@code true} if the match is for the full path: prefix-only
+	 *            matches are not allowed, and {@link NameMatcher}s must match
+	 *            only the last component (if they can -- they may not, if they
+	 *            are anchored at the beginning)
 	 * @return true if this matcher pattern matches given string
 	 */
-	boolean matches(String path, boolean assumeDirectory);
+	boolean matches(String path, boolean assumeDirectory, boolean pathMatch);
 
 	/**
 	 * Matches only part of given string
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/NameMatcher.java b/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/NameMatcher.java
index 0065123..9667837 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/NameMatcher.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/NameMatcher.java
@@ -64,26 +64,59 @@ public class NameMatcher extends AbstractMatcher {
 			pattern = Strings.deleteBackslash(pattern);
 		}
 		beginning = pattern.length() == 0 ? false : pattern.charAt(0) == slash;
-		if (!beginning)
+		if (!beginning) {
 			this.subPattern = pattern;
-		else
+		} else {
 			this.subPattern = pattern.substring(1);
+		}
 	}
 
 	@Override
-	public boolean matches(String path, boolean assumeDirectory) {
-		int end = 0;
-		int firstChar = 0;
-		do {
-			firstChar = getFirstNotSlash(path, end);
-			end = getFirstSlash(path, firstChar);
-			boolean match = matches(path, firstChar, end, assumeDirectory);
-			if (match)
+	public boolean matches(String path, boolean assumeDirectory,
+			boolean pathMatch) {
+		// A NameMatcher's pattern does not contain a slash.
+		int start = 0;
+		int stop = path.length();
+		if (stop > 0 && path.charAt(0) == slash) {
+			start++;
+		}
+		if (pathMatch) {
+			// Can match only after the last slash
+			int lastSlash = path.lastIndexOf(slash, stop - 1);
+			if (lastSlash == stop - 1) {
+				// Skip trailing slash
+				lastSlash = path.lastIndexOf(slash, lastSlash - 1);
+				stop--;
+			}
+			boolean match;
+			if (lastSlash < start) {
+				match = matches(path, start, stop, assumeDirectory);
+			} else {
+				// Can't match if the path contains a slash if the pattern is
+				// anchored at the beginning
+				match = !beginning
+						&& matches(path, lastSlash + 1, stop, assumeDirectory);
+			}
+			if (match && dirOnly) {
+				match = assumeDirectory;
+			}
+			return match;
+		}
+		while (start < stop) {
+			int end = path.indexOf(slash, start);
+			if (end < 0) {
+				end = stop;
+			}
+			if (end > start && matches(path, start, end, assumeDirectory)) {
 				// make sure the directory matches: either if we are done with
 				// segment and there is next one, or if the directory is assumed
-				return !dirOnly ? true : (end > 0 && end != path.length())
-						|| assumeDirectory;
-		} while (!beginning && end != path.length());
+				return !dirOnly || assumeDirectory || end < stop;
+			}
+			if (beginning) {
+				break;
+			}
+			start = end + 1;
+		}
 		return false;
 	}
 
@@ -92,25 +125,18 @@ public boolean matches(String segment, int startIncl, int endExcl,
 			boolean assumeDirectory) {
 		// faster local access, same as in string.indexOf()
 		String s = subPattern;
-		if (s.length() != (endExcl - startIncl))
+		int length = s.length();
+		if (length != (endExcl - startIncl)) {
 			return false;
-		for (int i = 0; i < s.length(); i++) {
+		}
+		for (int i = 0; i < length; i++) {
 			char c1 = s.charAt(i);
 			char c2 = segment.charAt(i + startIncl);
-			if (c1 != c2)
+			if (c1 != c2) {
 				return false;
+			}
 		}
 		return true;
 	}
 
-	private int getFirstNotSlash(String s, int start) {
-		int slashIdx = s.indexOf(slash, start);
-		return slashIdx == start ? start + 1 : start;
-	}
-
-	private int getFirstSlash(String s, int start) {
-		int slashIdx = s.indexOf(slash, start);
-		return slashIdx == -1 ? s.length() : slashIdx;
-	}
-
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/PathMatcher.java b/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/PathMatcher.java
index 65224ea..9b3a2aa 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/PathMatcher.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/PathMatcher.java
@@ -52,7 +52,6 @@
 import java.util.List;
 
 import org.eclipse.jgit.errors.InvalidPatternException;
-import org.eclipse.jgit.ignore.FastIgnoreRule;
 import org.eclipse.jgit.ignore.internal.Strings.PatternState;
 
 /**
@@ -68,9 +67,10 @@ public class PathMatcher extends AbstractMatcher {
 
 	private final char slash;
 
-	private boolean beginning;
+	private final boolean beginning;
 
-	PathMatcher(String pattern, Character pathSeparator, boolean dirOnly)
+	private PathMatcher(String pattern, Character pathSeparator,
+			boolean dirOnly)
 			throws InvalidPatternException {
 		super(pattern, dirOnly);
 		slash = getPathSeparator(pathSeparator);
@@ -87,7 +87,7 @@ private boolean isSimplePathWithSegments(String path) {
 				&& count(path, slash, true) > 0;
 	}
 
-	static private List<IMatcher> createMatchers(List<String> segments,
+	private static List<IMatcher> createMatchers(List<String> segments,
 			Character pathSeparator, boolean dirOnly)
 			throws InvalidPatternException {
 		List<IMatcher> matchers = new ArrayList<>(segments.size());
@@ -171,10 +171,12 @@ private static IMatcher createNameMatcher0(String segment,
 	}
 
 	@Override
-	public boolean matches(String path, boolean assumeDirectory) {
-		if (matchers == null)
-			return simpleMatch(path, assumeDirectory);
-		return iterate(path, 0, path.length(), assumeDirectory);
+	public boolean matches(String path, boolean assumeDirectory,
+			boolean pathMatch) {
+		if (matchers == null) {
+			return simpleMatch(path, assumeDirectory, pathMatch);
+		}
+		return iterate(path, 0, path.length(), assumeDirectory, pathMatch);
 	}
 
 	/*
@@ -182,31 +184,31 @@ public boolean matches(String path, boolean assumeDirectory) {
 	 * wildcards or single segments (mean: this is multi-segment path which must
 	 * be at the beginning of the another string)
 	 */
-	private boolean simpleMatch(String path, boolean assumeDirectory) {
+	private boolean simpleMatch(String path, boolean assumeDirectory,
+			boolean pathMatch) {
 		boolean hasSlash = path.indexOf(slash) == 0;
-		if (beginning && !hasSlash)
+		if (beginning && !hasSlash) {
 			path = slash + path;
-
-		if (!beginning && hasSlash)
+		}
+		if (!beginning && hasSlash) {
 			path = path.substring(1);
-
-		if (path.equals(pattern))
-			// Exact match
-			if (dirOnly && !assumeDirectory)
-				// Directory expectations not met
-				return false;
-			else
-				// Directory expectations met
-				return true;
-
+		}
+		if (path.equals(pattern)) {
+			// Exact match: must meet directory expectations
+			return !dirOnly || assumeDirectory;
+		}
 		/*
 		 * Add slashes for startsWith check. This avoids matching e.g.
 		 * "/src/new" to /src/newfile" but allows "/src/new" to match
 		 * "/src/new/newfile", as is the git standard
 		 */
-		if (path.startsWith(pattern + FastIgnoreRule.PATH_SEPARATOR))
+		String prefix = pattern + slash;
+		if (pathMatch) {
+			return path.equals(prefix) && (!dirOnly || assumeDirectory);
+		}
+		if (path.startsWith(prefix)) {
 			return true;
-
+		}
 		return false;
 	}
 
@@ -217,61 +219,100 @@ public boolean matches(String segment, int startIncl, int endExcl,
 				"Path matcher works only on entire paths"); //$NON-NLS-1$
 	}
 
-	boolean iterate(final String path, final int startIncl, final int endExcl,
-			boolean assumeDirectory) {
+	private boolean iterate(final String path, final int startIncl,
+			final int endExcl, boolean assumeDirectory, boolean pathMatch) {
 		int matcher = 0;
 		int right = startIncl;
 		boolean match = false;
 		int lastWildmatch = -1;
+		// ** matches may get extended if a later match fails. When that
+		// happens, we must extend the ** by exactly one segment.
+		// wildmatchBacktrackPos records the end of the segment after a **
+		// match, so that we can reset correctly.
+		int wildmatchBacktrackPos = -1;
 		while (true) {
 			int left = right;
 			right = path.indexOf(slash, right);
 			if (right == -1) {
-				if (left < endExcl)
+				if (left < endExcl) {
 					match = matches(matcher, path, left, endExcl,
 							assumeDirectory);
+				} else {
+					// a/** should not match a/ or a
+					match = match && matchers.get(matcher) != WILD;
+				}
 				if (match) {
-					if (matcher == matchers.size() - 2
-							&& matchers.get(matcher + 1) == WILD)
-						// ** can match *nothing*: a/b/** match also a/b
-						return true;
 					if (matcher < matchers.size() - 1
 							&& matchers.get(matcher) == WILD) {
 						// ** can match *nothing*: a/**/b match also a/b
 						matcher++;
 						match = matches(matcher, path, left, endExcl,
 								assumeDirectory);
-					} else if (dirOnly && !assumeDirectory)
+					} else if (dirOnly && !assumeDirectory) {
 						// Directory expectations not met
 						return false;
+					}
 				}
 				return match && matcher + 1 == matchers.size();
 			}
-			if (right - left > 0)
+			if (wildmatchBacktrackPos < 0) {
+				wildmatchBacktrackPos = right;
+			}
+			if (right - left > 0) {
 				match = matches(matcher, path, left, right, assumeDirectory);
-			else {
+			} else {
 				// path starts with slash???
 				right++;
 				continue;
 			}
 			if (match) {
-				if (matchers.get(matcher) == WILD) {
+				boolean wasWild = matchers.get(matcher) == WILD;
+				if (wasWild) {
 					lastWildmatch = matcher;
+					wildmatchBacktrackPos = -1;
 					// ** can match *nothing*: a/**/b match also a/b
 					right = left - 1;
 				}
 				matcher++;
-				if (matcher == matchers.size())
-					return true;
-			} else if (lastWildmatch != -1)
+				if (matcher == matchers.size()) {
+					// We had a prefix match here.
+					if (!pathMatch) {
+						return true;
+					} else {
+						if (right == endExcl - 1) {
+							// Extra slash at the end: actually a full match.
+							// Must meet directory expectations
+							return !dirOnly || assumeDirectory;
+						}
+						// Prefix matches only if pattern ended with /**
+						if (wasWild) {
+							return true;
+						}
+						if (lastWildmatch >= 0) {
+							// Consider pattern **/x and input x/x.
+							// We've matched the prefix x/ so far: we
+							// must try to extend the **!
+							matcher = lastWildmatch + 1;
+							right = wildmatchBacktrackPos;
+							wildmatchBacktrackPos = -1;
+						} else {
+							return false;
+						}
+					}
+				}
+			} else if (lastWildmatch != -1) {
 				matcher = lastWildmatch + 1;
-			else
+				right = wildmatchBacktrackPos;
+				wildmatchBacktrackPos = -1;
+			} else {
 				return false;
+			}
 			right++;
 		}
 	}
 
-	boolean matches(int matcherIdx, String path, int startIncl, int endExcl,
+	private boolean matches(int matcherIdx, String path, int startIncl,
+			int endExcl,
 			boolean assumeDirectory) {
 		IMatcher matcher = matchers.get(matcherIdx);
 		return matcher.matches(path, startIncl, endExcl, assumeDirectory);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/Strings.java b/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/Strings.java
index da482fa..800cdb9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/Strings.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/Strings.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2014, Andrey Loskutov <loskutov@gmx.de>
+ * Copyright (C) 2014, 2017 Andrey Loskutov <loskutov@gmx.de>
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -123,12 +123,15 @@ public static boolean isDirectoryPattern(String pattern) {
 	static int count(String s, char c, boolean ignoreFirstLast) {
 		int start = 0;
 		int count = 0;
-		while (true) {
+		int length = s.length();
+		while (start < length) {
 			start = s.indexOf(c, start);
-			if (start == -1)
+			if (start == -1) {
 				break;
-			if (!ignoreFirstLast || (start != 0 && start != s.length()))
+			}
+			if (!ignoreFirstLast || (start != 0 && start != length - 1)) {
 				count++;
+			}
 			start++;
 		}
 		return count;
@@ -360,7 +363,10 @@ && isLetter(lookAhead(pattern, i)))
 
 			case '[':
 				if (in_brackets > 0) {
-					sb.append('\\').append('[');
+					if (!seenEscape) {
+						sb.append('\\');
+					}
+					sb.append('[');
 					ignoreLastBracket = true;
 				} else {
 					if (!seenEscape) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/WildMatcher.java b/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/WildMatcher.java
index 93ea13c..363b3ce 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/WildMatcher.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/ignore/internal/WildMatcher.java
@@ -62,7 +62,8 @@ private WildMatcher() {
 	}
 
 	@Override
-	public final boolean matches(String path, boolean assumeDirectory) {
+	public final boolean matches(String path, boolean assumeDirectory,
+			boolean pathMatch) {
 		return true;
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
index a8dfc2d..ec19cdc 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
@@ -148,6 +148,7 @@ public static JGitText get() {
 	/***/ public String cannotParseGitURIish;
 	/***/ public String cannotPullOnARepoWithState;
 	/***/ public String cannotRead;
+	/***/ public String cannotReadBackDelta;
 	/***/ public String cannotReadBlob;
 	/***/ public String cannotReadCommit;
 	/***/ public String cannotReadFile;
@@ -180,6 +181,7 @@ public static JGitText get() {
 	/***/ public String closeLockTokenFailed;
 	/***/ public String closed;
 	/***/ public String collisionOn;
+	/***/ public String commandClosedStderrButDidntExit;
 	/***/ public String commandRejectedByHook;
 	/***/ public String commandWasCalledInTheWrongState;
 	/***/ public String commitAlreadyExists;
@@ -270,12 +272,14 @@ public static JGitText get() {
 	/***/ public String createBranchFailedUnknownReason;
 	/***/ public String createBranchUnexpectedResult;
 	/***/ public String createNewFileFailed;
+	/***/ public String createRequiresZeroOldId;
 	/***/ public String credentialPassword;
 	/***/ public String credentialUsername;
 	/***/ public String daemonAlreadyRunning;
 	/***/ public String daysAgo;
 	/***/ public String deleteBranchUnexpectedResult;
 	/***/ public String deleteFileFailed;
+	/***/ public String deleteRequiresZeroNewId;
 	/***/ public String deleteTagUnexpectedResult;
 	/***/ public String deletingNotSupported;
 	/***/ public String destinationIsNotAWildcard;
@@ -304,6 +308,7 @@ public static JGitText get() {
 	/***/ public String encryptionOnlyPBE;
 	/***/ public String endOfFileInEscape;
 	/***/ public String entryNotFoundByPath;
+	/***/ public String enumValueNotSupported0;
 	/***/ public String enumValueNotSupported2;
 	/***/ public String enumValueNotSupported3;
 	/***/ public String enumValuesNotAvailable;
@@ -319,6 +324,7 @@ public static JGitText get() {
 	/***/ public String exceptionCaughtDuringExecutionOfAddCommand;
 	/***/ public String exceptionCaughtDuringExecutionOfArchiveCommand;
 	/***/ public String exceptionCaughtDuringExecutionOfCherryPickCommand;
+	/***/ public String exceptionCaughtDuringExecutionOfCommand;
 	/***/ public String exceptionCaughtDuringExecutionOfCommitCommand;
 	/***/ public String exceptionCaughtDuringExecutionOfFetchCommand;
 	/***/ public String exceptionCaughtDuringExecutionOfLsRemoteCommand;
@@ -329,7 +335,6 @@ public static JGitText get() {
 	/***/ public String exceptionCaughtDuringExecutionOfRevertCommand;
 	/***/ public String exceptionCaughtDuringExecutionOfRmCommand;
 	/***/ public String exceptionCaughtDuringExecutionOfTagCommand;
-	/***/ public String exceptionCaughtDuringExcecutionOfCommand;
 	/***/ public String exceptionHookExecutionInterrupted;
 	/***/ public String exceptionOccurredDuringAddingOfOptionToALogCommand;
 	/***/ public String exceptionOccurredDuringReadingOfGIT_DIR;
@@ -367,6 +372,8 @@ public static JGitText get() {
 	/***/ public String gitmodulesNotFound;
 	/***/ public String headRequiredToStash;
 	/***/ public String hoursAgo;
+	/***/ public String httpConfigCannotNormalizeURL;
+	/***/ public String httpConfigInvalidURL;
 	/***/ public String hugeIndexesAreNotSupportedByJgitYet;
 	/***/ public String hunkBelongsToAnotherFile;
 	/***/ public String hunkDisconnectedFromFile;
@@ -425,11 +432,16 @@ public static JGitText get() {
 	/***/ public String invalidPathPeriodAtEndWindows;
 	/***/ public String invalidPathSpaceAtEndWindows;
 	/***/ public String invalidPathReservedOnWindows;
+	/***/ public String invalidRedirectLocation;
 	/***/ public String invalidReflogRevision;
 	/***/ public String invalidRefName;
+	/***/ public String invalidReftableBlock;
+	/***/ public String invalidReftableCRC;
+	/***/ public String invalidReftableFile;
 	/***/ public String invalidRemote;
 	/***/ public String invalidShallowObject;
 	/***/ public String invalidStageForPath;
+	/***/ public String invalidSystemProperty;
 	/***/ public String invalidTagOption;
 	/***/ public String invalidTimeout;
 	/***/ public String invalidTimeUnitValue2;
@@ -469,8 +481,11 @@ public static JGitText get() {
 	/***/ public String mergeRecursiveTooManyMergeBasesFor;
 	/***/ public String messageAndTaggerNotAllowedInUnannotatedTags;
 	/***/ public String minutesAgo;
+	/***/ public String mismatchOffset;
+	/***/ public String mismatchCRC;
 	/***/ public String missingAccesskey;
 	/***/ public String missingConfigurationForKey;
+	/***/ public String missingCRC;
 	/***/ public String missingDeltaBase;
 	/***/ public String missingForwardImageInGITBinaryPatch;
 	/***/ public String missingObject;
@@ -488,6 +503,7 @@ public static JGitText get() {
 	/***/ public String needPackOut;
 	/***/ public String needsAtLeastOneEntry;
 	/***/ public String needsWorkdir;
+	/***/ public String newIdMustNotBeNull;
 	/***/ public String newlineInQuotesNotAllowed;
 	/***/ public String noApplyInDelete;
 	/***/ public String noClosingBracket;
@@ -521,6 +537,7 @@ public static JGitText get() {
 	/***/ public String objectNotFoundIn;
 	/***/ public String obtainingCommitsForCherryPick;
 	/***/ public String offsetWrittenDeltaBaseForObjectNotFoundInAPack;
+	/***/ public String oldIdMustNotBeNull;
 	/***/ public String onlyAlreadyUpToDateAndFastForwardMergesAreAvailable;
 	/***/ public String onlyOneFetchSupported;
 	/***/ public String onlyOneOperationCallPerConnectionIsSupported;
@@ -528,6 +545,7 @@ public static JGitText get() {
 	/***/ public String openingConnection;
 	/***/ public String operationCanceled;
 	/***/ public String outputHasAlreadyBeenStarted;
+	/***/ public String overflowedReftableBlock;
 	/***/ public String packChecksumMismatch;
 	/***/ public String packCorruptedWhileWritingToFilesystem;
 	/***/ public String packDoesNotMatchIndex;
@@ -555,6 +573,7 @@ public static JGitText get() {
 	/***/ public String pathIsNotInWorkingDir;
 	/***/ public String pathNotConfigured;
 	/***/ public String peeledLineBeforeRef;
+	/***/ public String peeledRefIsRequired;
 	/***/ public String peerDidNotSupplyACompleteObjectGraph;
 	/***/ public String personIdentEmailNonNull;
 	/***/ public String personIdentNameNonNull;
@@ -583,6 +602,11 @@ public static JGitText get() {
 	/***/ public String receivePackInvalidLimit;
 	/***/ public String receivePackTooLarge;
 	/***/ public String receivingObjects;
+	/***/ public String redirectBlocked;
+	/***/ public String redirectHttp;
+	/***/ public String redirectLimitExceeded;
+	/***/ public String redirectLocationMissing;
+	/***/ public String redirectsOff;
 	/***/ public String refAlreadyExists;
 	/***/ public String refAlreadyExists1;
 	/***/ public String reflogEntryNotFound;
@@ -648,6 +672,15 @@ public static JGitText get() {
 	/***/ public String sourceRefDoesntResolveToAnyObject;
 	/***/ public String sourceRefNotSpecifiedForRefspec;
 	/***/ public String squashCommitNotUpdatingHEAD;
+	/***/ public String sshUserNameError;
+	/***/ public String sslFailureExceptionMessage;
+	/***/ public String sslFailureInfo;
+	/***/ public String sslFailureCause;
+	/***/ public String sslFailureTrustExplanation;
+	/***/ public String sslTrustAlways;
+	/***/ public String sslTrustForRepo;
+	/***/ public String sslTrustNow;
+	/***/ public String sslVerifyCannotSave;
 	/***/ public String staleRevFlagsOn;
 	/***/ public String startingReadStageWithoutWrittenRequestDataPendingIsNotSupported;
 	/***/ public String stashApplyConflict;
@@ -659,6 +692,7 @@ public static JGitText get() {
 	/***/ public String stashDropDeleteRefFailed;
 	/***/ public String stashDropFailed;
 	/***/ public String stashDropMissingReflog;
+	/***/ public String stashDropNotSupported;
 	/***/ public String stashFailed;
 	/***/ public String stashResolveFailed;
 	/***/ public String statelessRPCRequiresOptionToBeEnabled;
@@ -676,6 +710,7 @@ public static JGitText get() {
 	/***/ public String tagOnRepoWithoutHEADCurrentlyNotSupported;
 	/***/ public String transactionAborted;
 	/***/ public String theFactoryMustNotBeNull;
+	/***/ public String threadInterruptedWhileRunning;
 	/***/ public String timeIsUncertain;
 	/***/ public String timerAlreadyTerminated;
 	/***/ public String tooManyCommands;
@@ -712,10 +747,12 @@ public static JGitText get() {
 	/***/ public String unableToStore;
 	/***/ public String unableToWrite;
 	/***/ public String unauthorized;
+	/***/ public String underflowedReftableBlock;
 	/***/ public String unencodeableFile;
 	/***/ public String unexpectedCompareResult;
 	/***/ public String unexpectedEndOfConfigFile;
 	/***/ public String unexpectedEndOfInput;
+	/***/ public String unexpectedEofInPack;
 	/***/ public String unexpectedHunkTrailer;
 	/***/ public String unexpectedOddResult;
 	/***/ public String unexpectedRefReport;
@@ -726,6 +763,7 @@ public static JGitText get() {
 	/***/ public String unknownHost;
 	/***/ public String unknownIndexVersionOrCorruptIndex;
 	/***/ public String unknownObject;
+	/***/ public String unknownObjectInIndex;
 	/***/ public String unknownObjectType;
 	/***/ public String unknownObjectType2;
 	/***/ public String unknownRepositoryFormat;
@@ -748,7 +786,9 @@ public static JGitText get() {
 	/***/ public String unsupportedOperationNotAddAtEnd;
 	/***/ public String unsupportedPackIndexVersion;
 	/***/ public String unsupportedPackVersion;
+	/***/ public String unsupportedReftableVersion;
 	/***/ public String unsupportedRepositoryDescription;
+	/***/ public String updateRequiresOldIdAndNewId;
 	/***/ public String updatingHeadFailed;
 	/***/ public String updatingReferences;
 	/***/ public String updatingRefFailed;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckError.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckError.java
new file mode 100644
index 0000000..588ed9b
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckError.java
@@ -0,0 +1,152 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.internal.fsck;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.eclipse.jgit.annotations.Nullable;
+import org.eclipse.jgit.errors.CorruptPackIndexException;
+import org.eclipse.jgit.errors.CorruptPackIndexException.ErrorType;
+import org.eclipse.jgit.lib.ObjectChecker;
+import org.eclipse.jgit.lib.ObjectId;
+
+/** Holds all fsck errors of a git repository. */
+public class FsckError {
+	/** Represents a corrupt object. */
+	public static class CorruptObject {
+		final ObjectId id;
+
+		final int type;
+
+		ObjectChecker.ErrorType errorType;
+
+		/**
+		 * @param id
+		 *            the object identifier.
+		 * @param type
+		 *            type of the object.
+		 */
+		public CorruptObject(ObjectId id, int type) {
+			this.id = id;
+			this.type = type;
+		}
+
+		void setErrorType(ObjectChecker.ErrorType errorType) {
+			this.errorType = errorType;
+		}
+
+		/** @return identifier of the object. */
+		public ObjectId getId() {
+			return id;
+		}
+
+		/** @return type of the object. */
+		public int getType() {
+			return type;
+		}
+
+		/** @return error type of the corruption. */
+		@Nullable
+		public ObjectChecker.ErrorType getErrorType() {
+			return errorType;
+		}
+	}
+
+	/** Represents a corrupt pack index file. */
+	public static class CorruptIndex {
+		String fileName;
+
+		CorruptPackIndexException.ErrorType errorType;
+
+		/**
+		 * @param fileName
+		 *            the file name of the pack index.
+		 * @param errorType
+		 *            the type of error as reported in
+		 *            {@link CorruptPackIndexException}.
+		 */
+		public CorruptIndex(String fileName, ErrorType errorType) {
+			this.fileName = fileName;
+			this.errorType = errorType;
+		}
+
+		/** @return the file name of the index file. */
+		public String getFileName() {
+			return fileName;
+		}
+
+		/** @return the error type of the corruption. */
+		public ErrorType getErrorType() {
+			return errorType;
+		}
+	}
+
+	private final Set<CorruptObject> corruptObjects = new HashSet<>();
+
+	private final Set<ObjectId> missingObjects = new HashSet<>();
+
+	private final Set<CorruptIndex> corruptIndices = new HashSet<>();
+
+	private final Set<String> nonCommitHeads = new HashSet<>();
+
+	/** @return corrupt objects from all pack files. */
+	public Set<CorruptObject> getCorruptObjects() {
+		return corruptObjects;
+	}
+
+	/** @return missing objects that should present in pack files. */
+	public Set<ObjectId> getMissingObjects() {
+		return missingObjects;
+	}
+
+	/** @return corrupt index files associated with the packs. */
+	public Set<CorruptIndex> getCorruptIndices() {
+		return corruptIndices;
+	}
+
+	/** @return refs/heads/* point to non-commit object. */
+	public Set<String> getNonCommitHeads() {
+		return nonCommitHeads;
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckPackParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckPackParser.java
new file mode 100644
index 0000000..3a678a7
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckPackParser.java
@@ -0,0 +1,336 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.fsck;
+
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.channels.Channels;
+import java.text.MessageFormat;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.zip.CRC32;
+
+import org.eclipse.jgit.errors.CorruptObjectException;
+import org.eclipse.jgit.errors.CorruptPackIndexException;
+import org.eclipse.jgit.errors.CorruptPackIndexException.ErrorType;
+import org.eclipse.jgit.errors.MissingObjectException;
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.internal.fsck.FsckError.CorruptObject;
+import org.eclipse.jgit.internal.storage.dfs.ReadableChannel;
+import org.eclipse.jgit.internal.storage.file.PackIndex;
+import org.eclipse.jgit.internal.storage.file.PackIndex.MutableEntry;
+import org.eclipse.jgit.lib.AnyObjectId;
+import org.eclipse.jgit.lib.ObjectChecker;
+import org.eclipse.jgit.lib.ObjectDatabase;
+import org.eclipse.jgit.lib.ObjectIdOwnerMap;
+import org.eclipse.jgit.transport.PackParser;
+import org.eclipse.jgit.transport.PackedObjectInfo;
+
+/** A read-only pack parser for object validity checking. */
+public class FsckPackParser extends PackParser {
+	private final CRC32 crc;
+
+	private final ReadableChannel channel;
+
+	private final Set<CorruptObject> corruptObjects = new HashSet<>();
+
+	private long expectedObjectCount = -1L;
+
+	private long offset;
+
+	private int blockSize;
+
+	/**
+	 * @param db
+	 *            the object database which stores repository's data.
+	 * @param channel
+	 *            readable channel of the pack file.
+	 */
+	public FsckPackParser(ObjectDatabase db, ReadableChannel channel) {
+		super(db, Channels.newInputStream(channel));
+		this.channel = channel;
+		setCheckObjectCollisions(false);
+		this.crc = new CRC32();
+		this.blockSize = channel.blockSize() > 0 ? channel.blockSize() : 65536;
+	}
+
+	@Override
+	protected void onPackHeader(long objCnt) throws IOException {
+		if (expectedObjectCount >= 0) {
+			// Some DFS pack files don't contain the correct object count, e.g.
+			// INSERT/RECEIVE packs don't always contain the correct object
+			// count in their headers. Overwrite the expected object count
+			// after parsing the pack header.
+			setExpectedObjectCount(expectedObjectCount);
+		}
+	}
+
+	@Override
+	protected void onBeginWholeObject(long streamPosition, int type,
+			long inflatedSize) throws IOException {
+		crc.reset();
+	}
+
+	@Override
+	protected void onObjectHeader(Source src, byte[] raw, int pos, int len)
+			throws IOException {
+		crc.update(raw, pos, len);
+	}
+
+	@Override
+	protected void onObjectData(Source src, byte[] raw, int pos, int len)
+			throws IOException {
+		crc.update(raw, pos, len);
+	}
+
+	@Override
+	protected void onEndWholeObject(PackedObjectInfo info) throws IOException {
+		info.setCRC((int) crc.getValue());
+	}
+
+	@Override
+	protected void onBeginOfsDelta(long deltaStreamPosition,
+			long baseStreamPosition, long inflatedSize) throws IOException {
+		crc.reset();
+	}
+
+	@Override
+	protected void onBeginRefDelta(long deltaStreamPosition, AnyObjectId baseId,
+			long inflatedSize) throws IOException {
+		crc.reset();
+	}
+
+	@Override
+	protected UnresolvedDelta onEndDelta() throws IOException {
+		UnresolvedDelta delta = new UnresolvedDelta();
+		delta.setCRC((int) crc.getValue());
+		return delta;
+	}
+
+	@Override
+	protected void onInflatedObjectData(PackedObjectInfo obj, int typeCode,
+			byte[] data) throws IOException {
+		// FsckPackParser ignores this event.
+	}
+
+	@Override
+	protected void verifySafeObject(final AnyObjectId id, final int type,
+			final byte[] data) {
+		try {
+			super.verifySafeObject(id, type, data);
+		} catch (CorruptObjectException e) {
+			// catch the exception and continue parse the pack file
+			CorruptObject o = new CorruptObject(id.toObjectId(), type);
+			if (e.getErrorType() != null) {
+				o.setErrorType(e.getErrorType());
+			}
+			corruptObjects.add(o);
+		}
+	}
+
+	@Override
+	protected void onPackFooter(byte[] hash) throws IOException {
+		// Do nothing.
+	}
+
+	@Override
+	protected boolean onAppendBase(int typeCode, byte[] data,
+			PackedObjectInfo info) throws IOException {
+		// Do nothing.
+		return false;
+	}
+
+	@Override
+	protected void onEndThinPack() throws IOException {
+		// Do nothing.
+	}
+
+	@Override
+	protected ObjectTypeAndSize seekDatabase(PackedObjectInfo obj,
+			ObjectTypeAndSize info) throws IOException {
+		crc.reset();
+		offset = obj.getOffset();
+		return readObjectHeader(info);
+	}
+
+	@Override
+	protected ObjectTypeAndSize seekDatabase(UnresolvedDelta delta,
+			ObjectTypeAndSize info) throws IOException {
+		crc.reset();
+		offset = delta.getOffset();
+		return readObjectHeader(info);
+	}
+
+	@Override
+	protected int readDatabase(byte[] dst, int pos, int cnt)
+			throws IOException {
+		// read from input instead of database.
+		int n = read(offset, dst, pos, cnt);
+		if (n > 0) {
+			offset += n;
+		}
+		return n;
+	}
+
+	int read(long channelPosition, byte[] dst, int pos, int cnt)
+			throws IOException {
+		long block = channelPosition / blockSize;
+		byte[] bytes = readFromChannel(block);
+		if (bytes == null) {
+			return -1;
+		}
+		int offs = (int) (channelPosition - block * blockSize);
+		int bytesToCopy = Math.min(cnt, bytes.length - offs);
+		if (bytesToCopy < 1) {
+			return -1;
+		}
+		System.arraycopy(bytes, offs, dst, pos, bytesToCopy);
+		return bytesToCopy;
+	}
+
+	private byte[] readFromChannel(long block) throws IOException {
+		channel.position(block * blockSize);
+		ByteBuffer buf = ByteBuffer.allocate(blockSize);
+		int totalBytesRead = 0;
+		while (totalBytesRead < blockSize) {
+			int bytesRead = channel.read(buf);
+			if (bytesRead == -1) {
+				if (totalBytesRead == 0) {
+					return null;
+				}
+				return Arrays.copyOf(buf.array(), totalBytesRead);
+			}
+			totalBytesRead += bytesRead;
+		}
+		return buf.array();
+	}
+
+	@Override
+	protected boolean checkCRC(int oldCRC) {
+		return oldCRC == (int) crc.getValue();
+	}
+
+	@Override
+	protected void onStoreStream(byte[] raw, int pos, int len)
+			throws IOException {
+		// Do nothing.
+	}
+
+	/**
+	 * @return corrupt objects that reported by {@link ObjectChecker}.
+	 */
+	public Set<CorruptObject> getCorruptObjects() {
+		return corruptObjects;
+	}
+
+	/**
+	 * Verify the existing index file with all objects from the pack.
+	 *
+	 * @param idx
+	 *            index file associate with the pack
+	 * @throws CorruptPackIndexException
+	 *             when the index file is corrupt.
+	 */
+	public void verifyIndex(PackIndex idx)
+			throws CorruptPackIndexException {
+		ObjectIdOwnerMap<ObjFromPack> inPack = new ObjectIdOwnerMap<>();
+		for (int i = 0; i < getObjectCount(); i++) {
+			PackedObjectInfo entry = getObject(i);
+			inPack.add(new ObjFromPack(entry));
+
+			long offs = idx.findOffset(entry);
+			if (offs == -1) {
+				throw new CorruptPackIndexException(
+						MessageFormat.format(JGitText.get().missingObject,
+								Integer.valueOf(entry.getType()),
+								entry.getName()),
+						ErrorType.MISSING_OBJ);
+			} else if (offs != entry.getOffset()) {
+				throw new CorruptPackIndexException(MessageFormat
+						.format(JGitText.get().mismatchOffset, entry.getName()),
+						ErrorType.MISMATCH_OFFSET);
+			}
+
+			try {
+				if (idx.hasCRC32Support()
+						&& (int) idx.findCRC32(entry) != entry.getCRC()) {
+					throw new CorruptPackIndexException(
+							MessageFormat.format(JGitText.get().mismatchCRC,
+									entry.getName()),
+							ErrorType.MISMATCH_CRC);
+				}
+			} catch (MissingObjectException e) {
+				throw new CorruptPackIndexException(MessageFormat
+						.format(JGitText.get().missingCRC, entry.getName()),
+						ErrorType.MISSING_CRC);
+			}
+		}
+
+		for (MutableEntry entry : idx) {
+			if (!inPack.contains(entry.toObjectId())) {
+				throw new CorruptPackIndexException(MessageFormat.format(
+						JGitText.get().unknownObjectInIndex, entry.name()),
+						ErrorType.UNKNOWN_OBJ);
+			}
+		}
+	}
+
+	/**
+	 * Set the object count for overwriting the expected object count from pack
+	 * header.
+	 *
+	 * @param objectCount
+	 *            the actual expected object count.
+	 */
+	public void overwriteObjectCount(long objectCount) {
+		this.expectedObjectCount = objectCount;
+	}
+
+	static class ObjFromPack extends ObjectIdOwnerMap.Entry {
+		ObjFromPack(AnyObjectId id) {
+			super(id);
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/package-info.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/package-info.java
new file mode 100644
index 0000000..361b61f
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/package-info.java
@@ -0,0 +1,4 @@
+/**
+ * Git fsck support.
+ */
+package org.eclipse.jgit.internal.fsck;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/BlockBasedFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/BlockBasedFile.java
new file mode 100644
index 0000000..b9758bd
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/BlockBasedFile.java
@@ -0,0 +1,210 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.dfs;
+
+import java.io.EOFException;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.text.MessageFormat;
+
+import org.eclipse.jgit.annotations.Nullable;
+import org.eclipse.jgit.errors.PackInvalidException;
+import org.eclipse.jgit.internal.storage.pack.PackExt;
+
+/** Block based file stored in {@link DfsBlockCache}. */
+abstract class BlockBasedFile {
+	/** Cache that owns this file and its data. */
+	final DfsBlockCache cache;
+
+	/** Unique identity of this file while in-memory. */
+	final DfsStreamKey key;
+
+	/** Description of the associated pack file's storage. */
+	final DfsPackDescription desc;
+	final PackExt ext;
+
+	/**
+	 * Preferred alignment for loading blocks from the backing file.
+	 * <p>
+	 * It is initialized to 0 and filled in on the first read made from the
+	 * file. Block sizes may be odd, e.g. 4091, caused by the underling DFS
+	 * storing 4091 user bytes and 5 bytes block metadata into a lower level
+	 * 4096 byte block on disk.
+	 */
+	volatile int blockSize;
+
+	/**
+	 * Total number of bytes in this pack file.
+	 * <p>
+	 * This field initializes to -1 and gets populated when a block is loaded.
+	 */
+	volatile long length;
+
+	/** True once corruption has been detected that cannot be worked around. */
+	volatile boolean invalid;
+
+	BlockBasedFile(DfsBlockCache cache, DfsPackDescription desc, PackExt ext) {
+		this.cache = cache;
+		this.key = desc.getStreamKey(ext);
+		this.desc = desc;
+		this.ext = ext;
+	}
+
+	String getFileName() {
+		return desc.getFileName(ext);
+	}
+
+	boolean invalid() {
+		return invalid;
+	}
+
+	void setInvalid() {
+		invalid = true;
+	}
+
+	void setBlockSize(int newSize) {
+		blockSize = newSize;
+	}
+
+	long alignToBlock(long pos) {
+		int size = blockSize;
+		if (size == 0)
+			size = cache.getBlockSize();
+		return (pos / size) * size;
+	}
+
+	int blockSize(ReadableChannel rc) {
+		// If the block alignment is not yet known, discover it. Prefer the
+		// larger size from either the cache or the file itself.
+		int size = blockSize;
+		if (size == 0) {
+			size = rc.blockSize();
+			if (size <= 0)
+				size = cache.getBlockSize();
+			else if (size < cache.getBlockSize())
+				size = (cache.getBlockSize() / size) * size;
+			blockSize = size;
+		}
+		return size;
+	}
+
+	DfsBlock getOrLoadBlock(long pos, DfsReader ctx) throws IOException {
+		return cache.getOrLoad(this, pos, ctx, null);
+	}
+
+	DfsBlock readOneBlock(long pos, DfsReader ctx,
+			@Nullable ReadableChannel fileChannel) throws IOException {
+		if (invalid)
+			throw new PackInvalidException(getFileName());
+
+		ctx.stats.readBlock++;
+		long start = System.nanoTime();
+		ReadableChannel rc = fileChannel != null ? fileChannel
+				: ctx.db.openFile(desc, ext);
+		try {
+			int size = blockSize(rc);
+			pos = (pos / size) * size;
+
+			// If the size of the file is not yet known, try to discover it.
+			// Channels may choose to return -1 to indicate they don't
+			// know the length yet, in this case read up to the size unit
+			// given by the caller, then recheck the length.
+			long len = length;
+			if (len < 0) {
+				len = rc.size();
+				if (0 <= len)
+					length = len;
+			}
+
+			if (0 <= len && len < pos + size)
+				size = (int) (len - pos);
+			if (size <= 0)
+				throw new EOFException(MessageFormat.format(
+						DfsText.get().shortReadOfBlock, Long.valueOf(pos),
+						getFileName(), Long.valueOf(0), Long.valueOf(0)));
+
+			byte[] buf = new byte[size];
+			rc.position(pos);
+			int cnt = read(rc, ByteBuffer.wrap(buf, 0, size));
+			ctx.stats.readBlockBytes += cnt;
+			if (cnt != size) {
+				if (0 <= len) {
+					throw new EOFException(MessageFormat.format(
+							DfsText.get().shortReadOfBlock, Long.valueOf(pos),
+							getFileName(), Integer.valueOf(size),
+							Integer.valueOf(cnt)));
+				}
+
+				// Assume the entire thing was read in a single shot, compact
+				// the buffer to only the space required.
+				byte[] n = new byte[cnt];
+				System.arraycopy(buf, 0, n, 0, n.length);
+				buf = n;
+			} else if (len < 0) {
+				// With no length at the start of the read, the channel should
+				// have the length available at the end.
+				length = len = rc.size();
+			}
+
+			return new DfsBlock(key, pos, buf);
+		} finally {
+			if (rc != fileChannel) {
+				rc.close();
+			}
+			ctx.stats.readBlockMicros += elapsedMicros(start);
+		}
+	}
+
+	static int read(ReadableChannel rc, ByteBuffer buf) throws IOException {
+		int n;
+		do {
+			n = rc.read(buf);
+		} while (0 < n && buf.hasRemaining());
+		return buf.position();
+	}
+
+	static long elapsedMicros(long start) {
+		return (System.nanoTime() - start) / 1000L;
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DeltaBaseCache.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DeltaBaseCache.java
index 64a63d7..bd4b4d2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DeltaBaseCache.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DeltaBaseCache.java
@@ -75,7 +75,7 @@ private static int hash(long position) {
 		table = new Entry[1 << TABLE_BITS];
 	}
 
-	Entry get(DfsPackKey key, long position) {
+	Entry get(DfsStreamKey key, long position) {
 		Entry e = table[hash(position)];
 		for (; e != null; e = e.tableNext) {
 			if (e.offset == position && key.equals(e.pack)) {
@@ -86,7 +86,7 @@ Entry get(DfsPackKey key, long position) {
 		return null;
 	}
 
-	void put(DfsPackKey key, long offset, int objectType, byte[] data) {
+	void put(DfsStreamKey key, long offset, int objectType, byte[] data) {
 		if (data.length > maxByteCount)
 			return; // Too large to cache.
 
@@ -189,7 +189,7 @@ int getMemoryUsedByTableForTest() {
 	}
 
 	static class Entry {
-		final DfsPackKey pack;
+		final DfsStreamKey pack;
 		final long offset;
 		final int type;
 		final byte[] data;
@@ -198,7 +198,7 @@ static class Entry {
 		Entry lruPrev;
 		Entry lruNext;
 
-		Entry(DfsPackKey key, long offset, int type, byte[] data) {
+		Entry(DfsStreamKey key, long offset, int type, byte[] data) {
 			this.pack = key;
 			this.offset = offset;
 			this.type = type;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlock.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlock.java
index 4a33fb8..62a9be3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlock.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlock.java
@@ -46,24 +46,22 @@
 package org.eclipse.jgit.internal.storage.dfs;
 
 import java.io.IOException;
+import java.nio.ByteBuffer;
 import java.util.zip.CRC32;
 import java.util.zip.DataFormatException;
 import java.util.zip.Inflater;
 
 import org.eclipse.jgit.internal.storage.pack.PackOutputStream;
 
-/** A cached slice of a {@link DfsPackFile}. */
+/** A cached slice of a {@link BlockBasedFile}. */
 final class DfsBlock {
-	final DfsPackKey pack;
-
+	final DfsStreamKey stream;
 	final long start;
-
 	final long end;
-
 	private final byte[] block;
 
-	DfsBlock(DfsPackKey p, long pos, byte[] buf) {
-		pack = p;
+	DfsBlock(DfsStreamKey p, long pos, byte[] buf) {
+		stream = p;
 		start = pos;
 		end = pos + buf.length;
 		block = buf;
@@ -73,8 +71,14 @@ int size() {
 		return block.length;
 	}
 
-	boolean contains(DfsPackKey want, long pos) {
-		return pack == want && start <= pos && pos < end;
+	ByteBuffer zeroCopyByteBuffer(int n) {
+		ByteBuffer b = ByteBuffer.wrap(block);
+		b.position(n);
+		return b;
+	}
+
+	boolean contains(DfsStreamKey want, long pos) {
+		return stream.equals(want) && start <= pos && pos < end;
 	}
 
 	int copy(long pos, byte[] dstbuf, int dstoff, int cnt) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlockCache.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlockCache.java
index 6fff656..45202b5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlockCache.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlockCache.java
@@ -45,23 +45,20 @@
 package org.eclipse.jgit.internal.storage.dfs;
 
 import java.io.IOException;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Map;
-import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.atomic.AtomicLong;
 import java.util.concurrent.atomic.AtomicReferenceArray;
 import java.util.concurrent.locks.ReentrantLock;
 
+import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.internal.JGitText;
 
 /**
- * Caches slices of a {@link DfsPackFile} in memory for faster read access.
+ * Caches slices of a {@link BlockBasedFile} in memory for faster read access.
  * <p>
  * The DfsBlockCache serves as a Java based "buffer cache", loading segments of
- * a DfsPackFile into the JVM heap prior to use. As JGit often wants to do reads
- * of only tiny slices of a file, the DfsBlockCache tries to smooth out these
- * tiny reads into larger block-sized IO operations.
+ * a BlockBasedFile into the JVM heap prior to use. As JGit often wants to do
+ * reads of only tiny slices of a file, the DfsBlockCache tries to smooth out
+ * these tiny reads into larger block-sized IO operations.
  * <p>
  * Whenever a cache miss occurs, loading is invoked by exactly one thread for
  * the given <code>(DfsPackKey,position)</code> key tuple. This is ensured by an
@@ -108,14 +105,7 @@ public final class DfsBlockCache {
 	 *             settings, usually too low of a limit.
 	 */
 	public static void reconfigure(DfsBlockCacheConfig cfg) {
-		DfsBlockCache nc = new DfsBlockCache(cfg);
-		DfsBlockCache oc = cache;
-		cache = nc;
-
-		if (oc != null) {
-			for (DfsPackFile pack : oc.getPackFiles())
-				pack.key.cachedSize.set(0);
-		}
+		cache = new DfsBlockCache(cfg);
 	}
 
 	/** @return the currently active DfsBlockCache. */
@@ -153,12 +143,6 @@ public static DfsBlockCache getInstance() {
 	/** As {@link #blockSize} is a power of 2, bits to shift for a / blockSize. */
 	private final int blockSizeShift;
 
-	/** Cache of pack files, indexed by description. */
-	private final Map<DfsPackDescription, DfsPackFile> packCache;
-
-	/** View of pack files in the pack cache. */
-	private final Collection<DfsPackFile> packFiles;
-
 	/** Number of times a block was found in the cache. */
 	private final AtomicLong statHit;
 
@@ -194,13 +178,12 @@ private DfsBlockCache(final DfsBlockCacheConfig cfg) {
 		blockSizeShift = Integer.numberOfTrailingZeros(blockSize);
 
 		clockLock = new ReentrantLock(true /* fair */);
-		clockHand = new Ref<>(new DfsPackKey(), -1, 0, null);
+		String none = ""; //$NON-NLS-1$
+		clockHand = new Ref<>(
+				DfsStreamKey.of(new DfsRepositoryDescription(none), none),
+				-1, 0, null);
 		clockHand.next = clockHand;
 
-		packCache = new ConcurrentHashMap<>(
-				16, 0.75f, 1);
-		packFiles = Collections.unmodifiableCollection(packCache.values());
-
 		statHit = new AtomicLong();
 		statMiss = new AtomicLong();
 	}
@@ -249,38 +232,6 @@ public long getEvictions() {
 		return statEvict;
 	}
 
-	/**
-	 * Get the pack files stored in this cache.
-	 *
-	 * @return a collection of pack files, some of which may not actually be
-	 *             present; the caller should check the pack's cached size.
-	 */
-	public Collection<DfsPackFile> getPackFiles() {
-		return packFiles;
-	}
-
-	DfsPackFile getOrCreate(DfsPackDescription dsc, DfsPackKey key) {
-		// TODO This table grows without bound. It needs to clean up
-		// entries that aren't in cache anymore, and aren't being used
-		// by a live DfsObjDatabase reference.
-
-		DfsPackFile pack = packCache.get(dsc);
-		if (pack != null && !pack.invalid()) {
-			return pack;
-		}
-
-		// 'pack' either didn't exist or was invalid. Compute a new
-		// entry atomically (guaranteed by ConcurrentHashMap).
-		return packCache.compute(dsc, (k, v) -> {
-			if (v != null && !v.invalid()) { // valid value added by
-				return v;                    // another thread
-			} else {
-				return new DfsPackFile(
-						this, dsc, key != null ? key : new DfsPackKey());
-			}
-		});
-	}
-
 	private int hash(int packHash, long off) {
 		return packHash + (int) (off >>> blockSizeShift);
 	}
@@ -302,26 +253,28 @@ private static int tableSize(final DfsBlockCacheConfig cfg) {
 	/**
 	 * Lookup a cached object, creating and loading it if it doesn't exist.
 	 *
-	 * @param pack
+	 * @param file
 	 *            the pack that "contains" the cached object.
 	 * @param position
 	 *            offset within <code>pack</code> of the object.
 	 * @param ctx
 	 *            current thread's reader.
+	 * @param fileChannel
+	 *            optional channel to read {@code pack}.
 	 * @return the object reference.
 	 * @throws IOException
 	 *             the reference was not in the cache and could not be loaded.
 	 */
-	DfsBlock getOrLoad(DfsPackFile pack, long position, DfsReader ctx)
-			throws IOException {
+	DfsBlock getOrLoad(BlockBasedFile file, long position, DfsReader ctx,
+			@Nullable ReadableChannel fileChannel) throws IOException {
 		final long requestedPosition = position;
-		position = pack.alignToBlock(position);
+		position = file.alignToBlock(position);
 
-		DfsPackKey key = pack.key;
+		DfsStreamKey key = file.key;
 		int slot = slot(key, position);
 		HashEntry e1 = table.get(slot);
 		DfsBlock v = scan(e1, key, position);
-		if (v != null) {
+		if (v != null && v.contains(key, requestedPosition)) {
 			ctx.stats.blockCacheHit++;
 			statHit.incrementAndGet();
 			return v;
@@ -345,7 +298,7 @@ DfsBlock getOrLoad(DfsPackFile pack, long position, DfsReader ctx)
 			statMiss.incrementAndGet();
 			boolean credit = true;
 			try {
-				v = pack.readOneBlock(position, ctx);
+				v = file.readOneBlock(requestedPosition, ctx, fileChannel);
 				credit = false;
 			} finally {
 				if (credit)
@@ -358,7 +311,6 @@ DfsBlock getOrLoad(DfsPackFile pack, long position, DfsReader ctx)
 				e2 = table.get(slot);
 			}
 
-			key.cachedSize.addAndGet(v.size());
 			Ref<DfsBlock> ref = new Ref<>(key, position, v.size(), v);
 			ref.hot = true;
 			for (;;) {
@@ -374,9 +326,9 @@ DfsBlock getOrLoad(DfsPackFile pack, long position, DfsReader ctx)
 
 		// If the block size changed from the default, it is possible the block
 		// that was loaded is the wrong block for the requested position.
-		if (v.contains(pack.key, requestedPosition))
+		if (v.contains(file.key, requestedPosition))
 			return v;
-		return getOrLoad(pack, requestedPosition, ctx);
+		return getOrLoad(file, requestedPosition, ctx, fileChannel);
 	}
 
 	@SuppressWarnings("unchecked")
@@ -406,7 +358,6 @@ private void reserveSpace(int reserve) {
 					dead.next = null;
 					dead.value = null;
 					live -= dead.size;
-					dead.pack.cachedSize.addAndGet(-dead.size);
 					statEvict++;
 				} while (maxBytes < live);
 				clockHand = prev;
@@ -439,10 +390,14 @@ private void addToClock(Ref ref, int credit) {
 	}
 
 	void put(DfsBlock v) {
-		put(v.pack, v.start, v.size(), v);
+		put(v.stream, v.start, v.size(), v);
 	}
 
-	<T> Ref<T> put(DfsPackKey key, long pos, int size, T v) {
+	<T> Ref<T> putRef(DfsStreamKey key, long size, T v) {
+		return put(key, 0, (int) Math.min(size, Integer.MAX_VALUE), v);
+	}
+
+	<T> Ref<T> put(DfsStreamKey key, long pos, int size, T v) {
 		int slot = slot(key, pos);
 		HashEntry e1 = table.get(slot);
 		Ref<T> ref = scanRef(e1, key, pos);
@@ -462,7 +417,6 @@ <T> Ref<T> put(DfsPackKey key, long pos, int size, T v) {
 				}
 			}
 
-			key.cachedSize.addAndGet(size);
 			ref = new Ref<>(key, pos, size, v);
 			ref.hot = true;
 			for (;;) {
@@ -478,12 +432,12 @@ <T> Ref<T> put(DfsPackKey key, long pos, int size, T v) {
 		return ref;
 	}
 
-	boolean contains(DfsPackKey key, long position) {
+	boolean contains(DfsStreamKey key, long position) {
 		return scan(table.get(slot(key, position)), key, position) != null;
 	}
 
 	@SuppressWarnings("unchecked")
-	<T> T get(DfsPackKey key, long position) {
+	<T> T get(DfsStreamKey key, long position) {
 		T val = (T) scan(table.get(slot(key, position)), key, position);
 		if (val == null)
 			statMiss.incrementAndGet();
@@ -492,31 +446,36 @@ <T> T get(DfsPackKey key, long position) {
 		return val;
 	}
 
-	private <T> T scan(HashEntry n, DfsPackKey pack, long position) {
-		Ref<T> r = scanRef(n, pack, position);
+	private <T> T scan(HashEntry n, DfsStreamKey key, long position) {
+		Ref<T> r = scanRef(n, key, position);
 		return r != null ? r.get() : null;
 	}
 
+	<T> Ref<T> getRef(DfsStreamKey key) {
+		Ref<T> r = scanRef(table.get(slot(key, 0)), key, 0);
+		if (r != null)
+			statHit.incrementAndGet();
+		else
+			statMiss.incrementAndGet();
+		return r;
+	}
+
 	@SuppressWarnings("unchecked")
-	private <T> Ref<T> scanRef(HashEntry n, DfsPackKey pack, long position) {
+	private <T> Ref<T> scanRef(HashEntry n, DfsStreamKey key, long position) {
 		for (; n != null; n = n.next) {
 			Ref<T> r = n.ref;
-			if (r.pack == pack && r.position == position)
+			if (r.position == position && r.key.equals(key))
 				return r.get() != null ? r : null;
 		}
 		return null;
 	}
 
-	void remove(DfsPackFile pack) {
-		packCache.remove(pack.getPackDescription());
+	private int slot(DfsStreamKey key, long position) {
+		return (hash(key.hash, position) >>> 1) % tableSize;
 	}
 
-	private int slot(DfsPackKey pack, long position) {
-		return (hash(pack.hash, position) >>> 1) % tableSize;
-	}
-
-	private ReentrantLock lockFor(DfsPackKey pack, long position) {
-		return loadLocks[(hash(pack.hash, position) >>> 1) % loadLocks.length];
+	private ReentrantLock lockFor(DfsStreamKey key, long position) {
+		return loadLocks[(hash(key.hash, position) >>> 1) % loadLocks.length];
 	}
 
 	private static HashEntry clean(HashEntry top) {
@@ -542,15 +501,15 @@ private static final class HashEntry {
 	}
 
 	static final class Ref<T> {
-		final DfsPackKey pack;
+		final DfsStreamKey key;
 		final long position;
 		final int size;
 		volatile T value;
 		Ref next;
 		volatile boolean hot;
 
-		Ref(DfsPackKey pack, long position, int size, T v) {
-			this.pack = pack;
+		Ref(DfsStreamKey key, long position, int size, T v) {
+			this.key = key;
 			this.position = position;
 			this.size = size;
 			this.value = v;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsFsck.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsFsck.java
new file mode 100644
index 0000000..75eade2
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsFsck.java
@@ -0,0 +1,172 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.dfs;
+
+import static org.eclipse.jgit.internal.storage.pack.PackExt.INDEX;
+import static org.eclipse.jgit.internal.storage.pack.PackExt.PACK;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+
+import org.eclipse.jgit.errors.CorruptPackIndexException;
+import org.eclipse.jgit.errors.MissingObjectException;
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.internal.fsck.FsckError;
+import org.eclipse.jgit.internal.fsck.FsckError.CorruptIndex;
+import org.eclipse.jgit.internal.fsck.FsckPackParser;
+import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.NullProgressMonitor;
+import org.eclipse.jgit.lib.ObjectChecker;
+import org.eclipse.jgit.lib.ProgressMonitor;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.revwalk.ObjectWalk;
+import org.eclipse.jgit.revwalk.RevObject;
+
+/** Verify the validity and connectivity of a DFS repository. */
+public class DfsFsck {
+	private final DfsRepository repo;
+	private final DfsObjDatabase objdb;
+	private ObjectChecker objChecker = new ObjectChecker();
+
+	/**
+	 * Initialize DFS fsck.
+	 *
+	 * @param repository
+	 *            the dfs repository to check.
+	 */
+	public DfsFsck(DfsRepository repository) {
+		repo = repository;
+		objdb = repo.getObjectDatabase();
+	}
+
+	/**
+	 * Verify the integrity and connectivity of all objects in the object
+	 * database.
+	 *
+	 * @param pm
+	 *            callback to provide progress feedback during the check.
+	 * @return all errors about the repository.
+	 * @throws IOException
+	 *             if encounters IO errors during the process.
+	 */
+	public FsckError check(ProgressMonitor pm) throws IOException {
+		if (pm == null) {
+			pm = NullProgressMonitor.INSTANCE;
+		}
+
+		FsckError errors = new FsckError();
+		checkPacks(pm, errors);
+		checkConnectivity(pm, errors);
+		return errors;
+	}
+
+	private void checkPacks(ProgressMonitor pm, FsckError errors)
+			throws IOException, FileNotFoundException {
+		try (DfsReader ctx = objdb.newReader()) {
+			for (DfsPackFile pack : objdb.getPacks()) {
+				DfsPackDescription packDesc = pack.getPackDescription();
+				try (ReadableChannel rc = objdb.openFile(packDesc, PACK)) {
+					verifyPack(pm, errors, ctx, pack, rc);
+				} catch (MissingObjectException e) {
+					errors.getMissingObjects().add(e.getObjectId());
+				} catch (CorruptPackIndexException e) {
+					errors.getCorruptIndices().add(new CorruptIndex(
+							pack.getPackDescription().getFileName(INDEX),
+							e.getErrorType()));
+				}
+			}
+		}
+	}
+
+	private void verifyPack(ProgressMonitor pm, FsckError errors, DfsReader ctx,
+			DfsPackFile pack, ReadableChannel ch)
+					throws IOException, CorruptPackIndexException {
+		FsckPackParser fpp = new FsckPackParser(objdb, ch);
+		fpp.setObjectChecker(objChecker);
+		fpp.overwriteObjectCount(pack.getPackDescription().getObjectCount());
+		fpp.parse(pm);
+		errors.getCorruptObjects().addAll(fpp.getCorruptObjects());
+
+		fpp.verifyIndex(pack.getPackIndex(ctx));
+	}
+
+	private void checkConnectivity(ProgressMonitor pm, FsckError errors)
+			throws IOException {
+		pm.beginTask(JGitText.get().countingObjects, ProgressMonitor.UNKNOWN);
+		try (ObjectWalk ow = new ObjectWalk(repo)) {
+			for (Ref r : repo.getAllRefs().values()) {
+				RevObject tip;
+				try {
+					tip = ow.parseAny(r.getObjectId());
+					if (r.getLeaf().getName().startsWith(Constants.R_HEADS)
+							&& tip.getType() != Constants.OBJ_COMMIT) {
+						// heads should only point to a commit object
+						errors.getNonCommitHeads().add(r.getLeaf().getName());
+					}
+				} catch (MissingObjectException e) {
+					errors.getMissingObjects().add(e.getObjectId());
+					continue;
+				}
+				ow.markStart(tip);
+			}
+			try {
+				ow.checkConnectivity();
+			} catch (MissingObjectException e) {
+				errors.getMissingObjects().add(e.getObjectId());
+			}
+		}
+		pm.endTask();
+	}
+
+	/**
+	 * Use a customized object checker instead of the default one. Caller can
+	 * specify a skip list to ignore some errors.
+	 *
+	 * @param objChecker
+	 *            A customized object checker.
+	 */
+	public void setObjectChecker(ObjectChecker objChecker) {
+		this.objChecker = objChecker;
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java
index 55f9cc2..304a931 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java
@@ -50,13 +50,16 @@
 import static org.eclipse.jgit.internal.storage.dfs.DfsObjDatabase.PackSource.INSERT;
 import static org.eclipse.jgit.internal.storage.dfs.DfsObjDatabase.PackSource.RECEIVE;
 import static org.eclipse.jgit.internal.storage.dfs.DfsObjDatabase.PackSource.UNREACHABLE_GARBAGE;
+import static org.eclipse.jgit.internal.storage.dfs.DfsPackCompactor.configureReftable;
 import static org.eclipse.jgit.internal.storage.pack.PackExt.BITMAP_INDEX;
 import static org.eclipse.jgit.internal.storage.pack.PackExt.INDEX;
 import static org.eclipse.jgit.internal.storage.pack.PackExt.PACK;
+import static org.eclipse.jgit.internal.storage.pack.PackExt.REFTABLE;
 import static org.eclipse.jgit.internal.storage.pack.PackWriter.NONE;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Calendar;
 import java.util.Collection;
 import java.util.EnumSet;
@@ -72,6 +75,9 @@
 import org.eclipse.jgit.internal.storage.file.PackReverseIndex;
 import org.eclipse.jgit.internal.storage.pack.PackExt;
 import org.eclipse.jgit.internal.storage.pack.PackWriter;
+import org.eclipse.jgit.internal.storage.reftable.ReftableCompactor;
+import org.eclipse.jgit.internal.storage.reftable.ReftableConfig;
+import org.eclipse.jgit.internal.storage.reftable.ReftableWriter;
 import org.eclipse.jgit.internal.storage.reftree.RefTreeNames;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Constants;
@@ -94,14 +100,16 @@ public class DfsGarbageCollector {
 	private final DfsObjDatabase objdb;
 
 	private final List<DfsPackDescription> newPackDesc;
-
 	private final List<PackStatistics> newPackStats;
-
 	private final List<ObjectIdSet> newPackObj;
 
 	private DfsReader ctx;
 
 	private PackConfig packConfig;
+	private ReftableConfig reftableConfig;
+	private boolean convertToReftable = true;
+	private long reftableInitialMinUpdateIndex = 1;
+	private long reftableInitialMaxUpdateIndex = 1;
 
 	// See packIsCoalesceableGarbage(), below, for how these two variables
 	// interact.
@@ -110,8 +118,10 @@ public class DfsGarbageCollector {
 
 	private long startTimeMillis;
 	private List<DfsPackFile> packsBefore;
+	private List<DfsReftable> reftablesBefore;
 	private List<DfsPackFile> expiredGarbagePacks;
 
+	private Collection<Ref> refsBefore;
 	private Set<ObjectId> allHeadsAndTags;
 	private Set<ObjectId> allTags;
 	private Set<ObjectId> nonHeads;
@@ -151,6 +161,60 @@ public DfsGarbageCollector setPackConfig(PackConfig newConfig) {
 		return this;
 	}
 
+	/**
+	 * @param cfg
+	 *            configuration to write a reftable. Reftable writing is
+	 *            disabled (default) when {@code cfg} is {@code null}.
+	 * @return {@code this}
+	 */
+	public DfsGarbageCollector setReftableConfig(ReftableConfig cfg) {
+		reftableConfig = cfg;
+		return this;
+	}
+
+	/**
+	 * @param convert
+	 *            if true, {@link #setReftableConfig(ReftableConfig)} has been
+	 *            set non-null, and a GC reftable doesn't yet exist, the garbage
+	 *            collector will make one by scanning the existing references,
+	 *            and writing a new reftable. Default is {@code true}.
+	 * @return {@code this}
+	 */
+	public DfsGarbageCollector setConvertToReftable(boolean convert) {
+		convertToReftable = convert;
+		return this;
+	}
+
+	/**
+	 * Set minUpdateIndex for the initial reftable created during conversion.
+	 *
+	 * @param u
+	 *            minUpdateIndex for the initial reftable created by scanning
+	 *            {@link DfsRefDatabase#getRefs(String)}. Ignored unless caller
+	 *            has also set {@link #setReftableConfig(ReftableConfig)}.
+	 *            Defaults to {@code 1}. Must be {@code u >= 0}.
+	 * @return {@code this}
+	 */
+	public DfsGarbageCollector setReftableInitialMinUpdateIndex(long u) {
+		reftableInitialMinUpdateIndex = Math.max(u, 0);
+		return this;
+	}
+
+	/**
+	 * Set maxUpdateIndex for the initial reftable created during conversion.
+	 *
+	 * @param u
+	 *            maxUpdateIndex for the initial reftable created by scanning
+	 *            {@link DfsRefDatabase#getRefs(String)}. Ignored unless caller
+	 *            has also set {@link #setReftableConfig(ReftableConfig)}.
+	 *            Defaults to {@code 1}. Must be {@code u >= 0}.
+	 * @return {@code this}
+	 */
+	public DfsGarbageCollector setReftableInitialMaxUpdateIndex(long u) {
+		reftableInitialMaxUpdateIndex = Math.max(0, u);
+		return this;
+	}
+
 	/** @return garbage packs smaller than this size will be repacked. */
 	public long getCoalesceGarbageLimit() {
 		return coalesceGarbageLimit;
@@ -240,8 +304,9 @@ public boolean pack(ProgressMonitor pm) throws IOException {
 			refdb.refresh();
 			objdb.clearCache();
 
-			Collection<Ref> refsBefore = getAllRefs();
+			refsBefore = getAllRefs();
 			readPacksBefore();
+			readReftablesBefore();
 
 			Set<ObjectId> allHeads = new HashSet<>();
 			allHeadsAndTags = new HashSet<>();
@@ -274,6 +339,12 @@ public boolean pack(ProgressMonitor pm) throws IOException {
 			// Hoist all branch tips and tags earlier in the pack file
 			tagTargets.addAll(allHeadsAndTags);
 
+			// Combine the GC_REST objects into the GC pack if requested
+			if (packConfig.getSinglePack()) {
+				allHeadsAndTags.addAll(nonHeads);
+				nonHeads.clear();
+			}
+
 			boolean rollback = true;
 			try {
 				packHeads(pm);
@@ -327,6 +398,11 @@ private void readPacksBefore() throws IOException {
 		}
 	}
 
+	private void readReftablesBefore() throws IOException {
+		DfsReftable[] tables = objdb.getReftables();
+		reftablesBefore = new ArrayList<>(Arrays.asList(tables));
+	}
+
 	private boolean packIsExpiredGarbage(DfsPackDescription d, long now) {
 		// Consider the garbage pack as expired when it's older than
 		// garbagePackTtl. This check gives concurrent inserter threads
@@ -401,7 +477,7 @@ private static long dayStartInMillis(long timeInMillis) {
 	}
 
 	/** @return all of the source packs that fed into this compaction. */
-	public List<DfsPackDescription> getSourcePacks() {
+	public Set<DfsPackDescription> getSourcePacks() {
 		return toPrune();
 	}
 
@@ -415,28 +491,37 @@ public List<PackStatistics> getNewPackStatistics() {
 		return newPackStats;
 	}
 
-	private List<DfsPackDescription> toPrune() {
-		int cnt = packsBefore.size();
-		List<DfsPackDescription> all = new ArrayList<>(cnt);
+	private Set<DfsPackDescription> toPrune() {
+		Set<DfsPackDescription> toPrune = new HashSet<>();
 		for (DfsPackFile pack : packsBefore) {
-			all.add(pack.getPackDescription());
+			toPrune.add(pack.getPackDescription());
+		}
+		if (reftableConfig != null) {
+			for (DfsReftable table : reftablesBefore) {
+				toPrune.add(table.getPackDescription());
+			}
 		}
 		for (DfsPackFile pack : expiredGarbagePacks) {
-			all.add(pack.getPackDescription());
+			toPrune.add(pack.getPackDescription());
 		}
-		return all;
+		return toPrune;
 	}
 
 	private void packHeads(ProgressMonitor pm) throws IOException {
-		if (allHeadsAndTags.isEmpty())
+		if (allHeadsAndTags.isEmpty()) {
+			writeReftable();
 			return;
+		}
 
 		try (PackWriter pw = newPackWriter()) {
 			pw.setTagTargets(tagTargets);
 			pw.preparePack(pm, allHeadsAndTags, NONE, NONE, allTags);
-			if (0 < pw.getObjectCount())
-				writePack(GC, pw, pm,
-						estimateGcPackSize(INSERT, RECEIVE, COMPACT, GC));
+			if (0 < pw.getObjectCount()) {
+				long estSize = estimateGcPackSize(INSERT, RECEIVE, COMPACT, GC);
+				writePack(GC, pw, pm, estSize);
+			} else {
+				writeReftable();
+			}
 		}
 	}
 
@@ -554,25 +639,32 @@ private DfsPackDescription writePack(PackSource source, PackWriter pw,
 				estimatedPackSize);
 		newPackDesc.add(pack);
 
+		if (source == GC && reftableConfig != null) {
+			writeReftable(pack);
+		}
+
 		try (DfsOutputStream out = objdb.writeFile(pack, PACK)) {
 			pw.writePack(pm, pm, out);
 			pack.addFileExt(PACK);
+			pack.setBlockSize(PACK, out.blockSize());
 		}
 
-		try (CountingOutputStream cnt =
-				new CountingOutputStream(objdb.writeFile(pack, INDEX))) {
+		try (DfsOutputStream out = objdb.writeFile(pack, INDEX)) {
+			CountingOutputStream cnt = new CountingOutputStream(out);
 			pw.writeIndex(cnt);
 			pack.addFileExt(INDEX);
 			pack.setFileSize(INDEX, cnt.getCount());
+			pack.setBlockSize(INDEX, out.blockSize());
 			pack.setIndexVersion(pw.getIndexVersion());
 		}
 
 		if (pw.prepareBitmapIndex(pm)) {
-			try (CountingOutputStream cnt = new CountingOutputStream(
-					objdb.writeFile(pack, BITMAP_INDEX))) {
+			try (DfsOutputStream out = objdb.writeFile(pack, BITMAP_INDEX)) {
+				CountingOutputStream cnt = new CountingOutputStream(out);
 				pw.writeBitmapIndex(cnt);
 				pack.addFileExt(BITMAP_INDEX);
 				pack.setFileSize(BITMAP_INDEX, cnt.getCount());
+				pack.setBlockSize(BITMAP_INDEX, out.blockSize());
 			}
 		}
 
@@ -581,8 +673,62 @@ private DfsPackDescription writePack(PackSource source, PackWriter pw,
 		pack.setLastModified(startTimeMillis);
 		newPackStats.add(stats);
 		newPackObj.add(pw.getObjectSet());
-
-		DfsBlockCache.getInstance().getOrCreate(pack, null);
 		return pack;
 	}
+
+	private void writeReftable() throws IOException {
+		if (reftableConfig != null) {
+			DfsPackDescription pack = objdb.newPack(GC);
+			newPackDesc.add(pack);
+			writeReftable(pack);
+		}
+	}
+
+	private void writeReftable(DfsPackDescription pack) throws IOException {
+		if (convertToReftable && !hasGcReftable()) {
+			writeReftable(pack, refsBefore);
+			return;
+		}
+
+		try (ReftableStack stack = ReftableStack.open(ctx, reftablesBefore)) {
+			ReftableCompactor compact = new ReftableCompactor();
+			compact.addAll(stack.readers());
+			compact.setIncludeDeletes(false);
+			compactReftable(pack, compact);
+		}
+	}
+
+	private boolean hasGcReftable() {
+		for (DfsReftable table : reftablesBefore) {
+			if (table.getPackDescription().getPackSource() == GC) {
+				return true;
+			}
+		}
+		return false;
+	}
+
+	private void writeReftable(DfsPackDescription pack, Collection<Ref> refs)
+			throws IOException {
+		try (DfsOutputStream out = objdb.writeFile(pack, REFTABLE)) {
+			ReftableConfig cfg = configureReftable(reftableConfig, out);
+			ReftableWriter writer = new ReftableWriter(cfg)
+					.setMinUpdateIndex(reftableInitialMinUpdateIndex)
+					.setMaxUpdateIndex(reftableInitialMaxUpdateIndex)
+					.begin(out)
+					.sortAndWriteRefs(refs)
+					.finish();
+			pack.addFileExt(REFTABLE);
+			pack.setReftableStats(writer.getStats());
+		}
+	}
+
+	private void compactReftable(DfsPackDescription pack,
+			ReftableCompactor compact) throws IOException {
+		try (DfsOutputStream out = objdb.writeFile(pack, REFTABLE)) {
+			compact.setConfig(configureReftable(reftableConfig, out));
+			compact.compact(out);
+			pack.addFileExt(REFTABLE);
+			pack.setReftableStats(compact.getStats());
+		}
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsInserter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsInserter.java
index e65c9fd..19e8652 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsInserter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsInserter.java
@@ -104,7 +104,7 @@ public class DfsInserter extends ObjectInserter {
 	ObjectIdOwnerMap<PackedObjectInfo> objectMap;
 
 	DfsBlockCache cache;
-	DfsPackKey packKey;
+	DfsStreamKey packKey;
 	DfsPackDescription packDsc;
 	PackStream packOut;
 	private boolean rollback;
@@ -221,7 +221,7 @@ public void flush() throws IOException {
 		db.commitPack(Collections.singletonList(packDsc), null);
 		rollback = false;
 
-		DfsPackFile p = cache.getOrCreate(packDsc, packKey);
+		DfsPackFile p = new DfsPackFile(cache, packDsc);
 		if (index != null)
 			p.setPackIndex(index);
 		db.addPack(p);
@@ -281,8 +281,10 @@ private void beginPack() throws IOException {
 
 		rollback = true;
 		packDsc = db.newPack(DfsObjDatabase.PackSource.INSERT);
-		packOut = new PackStream(db.writeFile(packDsc, PACK));
-		packKey = new DfsPackKey();
+		DfsOutputStream dfsOut = db.writeFile(packDsc, PACK);
+		packDsc.setBlockSize(PACK, dfsOut.blockSize());
+		packOut = new PackStream(dfsOut);
+		packKey = packDsc.getStreamKey(PACK);
 
 		// Write the header as though it were a single object pack.
 		byte[] buf = packOut.hdrBuf;
@@ -312,13 +314,14 @@ PackIndex writePackIndex(DfsPackDescription pack, byte[] packHash,
 			packIndex = PackIndex.read(buf.openInputStream());
 		}
 
-		DfsOutputStream os = db.writeFile(pack, INDEX);
-		try (CountingOutputStream cnt = new CountingOutputStream(os)) {
+		try (DfsOutputStream os = db.writeFile(pack, INDEX)) {
+			CountingOutputStream cnt = new CountingOutputStream(os);
 			if (buf != null)
 				buf.writeTo(cnt, null);
 			else
 				index(cnt, packHash, list);
 			pack.addFileExt(INDEX);
+			pack.setBlockSize(INDEX, os.blockSize());
 			pack.setFileSize(INDEX, cnt.getCount());
 		} finally {
 			if (buf != null) {
@@ -497,7 +500,7 @@ private int setInput(long pos, Inflater inf)
 				inf.setInput(currBuf, s, n);
 				return n;
 			}
-			throw new EOFException(DfsText.get().unexpectedEofInPack);
+			throw new EOFException(JGitText.get().unexpectedEofInPack);
 		}
 
 		private DfsBlock getOrLoadBlock(long pos) throws IOException {
@@ -510,7 +513,7 @@ private DfsBlock getOrLoadBlock(long pos) throws IOException {
 			for (int p = 0; p < blockSize;) {
 				int n = out.read(s + p, ByteBuffer.wrap(d, p, blockSize - p));
 				if (n <= 0)
-					throw new EOFException(DfsText.get().unexpectedEofInPack);
+					throw new EOFException(JGitText.get().unexpectedEofInPack);
 				p += n;
 			}
 			b = new DfsBlock(packKey, s, d);
@@ -566,13 +569,13 @@ public ObjectLoader open(AnyObjectId objectId, int typeHint)
 			byte[] buf = buffer();
 			int cnt = packOut.read(obj.getOffset(), buf, 0, 20);
 			if (cnt <= 0)
-					throw new EOFException(DfsText.get().unexpectedEofInPack);
+					throw new EOFException(JGitText.get().unexpectedEofInPack);
 
 			int c = buf[0] & 0xff;
 			int type = (c >> 4) & 7;
 			if (type == OBJ_OFS_DELTA || type == OBJ_REF_DELTA)
 				throw new IOException(MessageFormat.format(
-						DfsText.get().cannotReadBackDelta, Integer.toString(type)));
+						JGitText.get().cannotReadBackDelta, Integer.toString(type)));
 			if (typeHint != OBJ_ANY && type != typeHint) {
 				throw new IncorrectObjectTypeException(objectId.copy(), typeHint);
 			}
@@ -582,7 +585,7 @@ public ObjectLoader open(AnyObjectId objectId, int typeHint)
 			int shift = 4;
 			while ((c & 0x80) != 0) {
 				if (ptr >= cnt)
-					throw new EOFException(DfsText.get().unexpectedEofInPack);
+					throw new EOFException(JGitText.get().unexpectedEofInPack);
 				c = buf[ptr++] & 0xff;
 				sz += ((long) (c & 0x7f)) << shift;
 				shift += 7;
@@ -633,11 +636,11 @@ private class StreamLoader extends ObjectLoader {
 		private final int type;
 		private final long size;
 
-		private final DfsPackKey srcPack;
+		private final DfsStreamKey srcPack;
 		private final long pos;
 
 		StreamLoader(ObjectId id, int type, long sz,
-				DfsPackKey key, long pos) {
+				DfsStreamKey key, long pos) {
 			this.id = id;
 			this.type = type;
 			this.size = sz;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsObjDatabase.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsObjDatabase.java
index 32ee6c2..9439822 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsObjDatabase.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsObjDatabase.java
@@ -48,6 +48,7 @@
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -61,7 +62,9 @@
 
 /** Manages objects stored in {@link DfsPackFile} on a storage system. */
 public abstract class DfsObjDatabase extends ObjectDatabase {
-	private static final PackList NO_PACKS = new PackList(new DfsPackFile[0]) {
+	private static final PackList NO_PACKS = new PackList(
+			new DfsPackFile[0],
+			new DfsReftable[0]) {
 		@Override
 		boolean dirty() {
 			return true;
@@ -192,6 +195,18 @@ public ObjectInserter newInserter() {
 	}
 
 	/**
+	 * Scan and list all available reftable files in the repository.
+	 *
+	 * @return list of available reftables. The returned array is shared with
+	 *         the implementation and must not be modified by the caller.
+	 * @throws IOException
+	 *             the pack list cannot be initialized.
+	 */
+	public DfsReftable[] getReftables() throws IOException {
+		return getPackList().reftables;
+	}
+
+	/**
 	 * Scan and list all available pack files in the repository.
 	 *
 	 * @return list of available packs, with some additional metadata. The
@@ -220,6 +235,16 @@ protected DfsRepository getRepository() {
 	}
 
 	/**
+	 * List currently known reftable files in the repository, without scanning.
+	 *
+	 * @return list of available reftables. The returned array is shared with
+	 *         the implementation and must not be modified by the caller.
+	 */
+	public DfsReftable[] getCurrentReftables() {
+		return getCurrentPackList().reftables;
+	}
+
+	/**
 	 * List currently known pack files in the repository, without scanning.
 	 *
 	 * @return list of available packs, with some additional metadata. The
@@ -428,7 +453,7 @@ void addPack(DfsPackFile newPack) throws IOException {
 			DfsPackFile[] packs = new DfsPackFile[1 + o.packs.length];
 			packs[0] = newPack;
 			System.arraycopy(o.packs, 0, packs, 1, o.packs.length);
-			n = new PackListImpl(packs);
+			n = new PackListImpl(packs, o.reftables);
 		} while (!packList.compareAndSet(o, n));
 	}
 
@@ -454,60 +479,93 @@ PackList scanPacks(final PackList original) throws IOException {
 
 	private PackList scanPacksImpl(PackList old) throws IOException {
 		DfsBlockCache cache = DfsBlockCache.getInstance();
-		Map<DfsPackDescription, DfsPackFile> forReuse = reuseMap(old);
+		Map<DfsPackDescription, DfsPackFile> packs = packMap(old);
+		Map<DfsPackDescription, DfsReftable> reftables = reftableMap(old);
+
 		List<DfsPackDescription> scanned = listPacks();
 		Collections.sort(scanned);
 
-		List<DfsPackFile> list = new ArrayList<>(scanned.size());
+		List<DfsPackFile> newPacks = new ArrayList<>(scanned.size());
+		List<DfsReftable> newReftables = new ArrayList<>(scanned.size());
 		boolean foundNew = false;
 		for (DfsPackDescription dsc : scanned) {
-			DfsPackFile oldPack = forReuse.remove(dsc);
+			DfsPackFile oldPack = packs.remove(dsc);
 			if (oldPack != null) {
-				list.add(oldPack);
-			} else {
-				list.add(cache.getOrCreate(dsc, null));
+				newPacks.add(oldPack);
+			} else if (dsc.hasFileExt(PackExt.PACK)) {
+				newPacks.add(new DfsPackFile(cache, dsc));
+				foundNew = true;
+			}
+
+			DfsReftable oldReftable = reftables.remove(dsc);
+			if (oldReftable != null) {
+				newReftables.add(oldReftable);
+			} else if (dsc.hasFileExt(PackExt.REFTABLE)) {
+				newReftables.add(new DfsReftable(cache, dsc));
 				foundNew = true;
 			}
 		}
 
-		for (DfsPackFile p : forReuse.values())
-			p.close();
-		if (list.isEmpty())
-			return new PackListImpl(NO_PACKS.packs);
+		if (newPacks.isEmpty())
+			return new PackListImpl(NO_PACKS.packs, NO_PACKS.reftables);
 		if (!foundNew) {
 			old.clearDirty();
 			return old;
 		}
-		return new PackListImpl(list.toArray(new DfsPackFile[list.size()]));
+		Collections.sort(newReftables, reftableComparator());
+		return new PackListImpl(
+				newPacks.toArray(new DfsPackFile[0]),
+				newReftables.toArray(new DfsReftable[0]));
 	}
 
-	private static Map<DfsPackDescription, DfsPackFile> reuseMap(PackList old) {
-		Map<DfsPackDescription, DfsPackFile> forReuse
-			= new HashMap<>();
+	private static Map<DfsPackDescription, DfsPackFile> packMap(PackList old) {
+		Map<DfsPackDescription, DfsPackFile> forReuse = new HashMap<>();
 		for (DfsPackFile p : old.packs) {
-			if (p.invalid()) {
-				// The pack instance is corrupted, and cannot be safely used
-				// again. Do not include it in our reuse map.
-				//
-				p.close();
-				continue;
-			}
-
-			DfsPackFile prior = forReuse.put(p.getPackDescription(), p);
-			if (prior != null) {
-				// This should never occur. It should be impossible for us
-				// to have two pack files with the same name, as all of them
-				// came out of the same directory. If it does, we promised to
-				// close any PackFiles we did not reuse, so close the second,
-				// readers are likely to be actively using the first.
-				//
-				forReuse.put(prior.getPackDescription(), prior);
-				p.close();
+			if (!p.invalid()) {
+				forReuse.put(p.desc, p);
 			}
 		}
 		return forReuse;
 	}
 
+	private static Map<DfsPackDescription, DfsReftable> reftableMap(PackList old) {
+		Map<DfsPackDescription, DfsReftable> forReuse = new HashMap<>();
+		for (DfsReftable p : old.reftables) {
+			if (!p.invalid()) {
+				forReuse.put(p.desc, p);
+			}
+		}
+		return forReuse;
+	}
+
+	/** @return comparator to sort {@link DfsReftable} by priority. */
+	protected Comparator<DfsReftable> reftableComparator() {
+		return (fa, fb) -> {
+			DfsPackDescription a = fa.getPackDescription();
+			DfsPackDescription b = fb.getPackDescription();
+
+			// GC, COMPACT reftables first by higher category.
+			int c = category(b) - category(a);
+			if (c != 0) {
+				return c;
+			}
+
+			// Lower maxUpdateIndex first.
+			c = Long.signum(a.getMaxUpdateIndex() - b.getMaxUpdateIndex());
+			if (c != 0) {
+				return c;
+			}
+
+			// Older reftable first.
+			return Long.signum(a.getLastModified() - b.getLastModified());
+		};
+	}
+
+	static int category(DfsPackDescription d) {
+		PackSource s = d.getPackSource();
+		return s != null ? s.category : 0;
+	}
+
 	/** Clears the cached list of packs, forcing them to be scanned again. */
 	protected void clearCache() {
 		packList.set(NO_PACKS);
@@ -515,12 +573,7 @@ protected void clearCache() {
 
 	@Override
 	public void close() {
-		// PackList packs = packList.get();
 		packList.set(NO_PACKS);
-
-		// TODO Close packs if they aren't cached.
-		// for (DfsPackFile p : packs.packs)
-		// p.close();
 	}
 
 	/** Snapshot of packs scanned in a single pass. */
@@ -528,10 +581,14 @@ public static abstract class PackList {
 		/** All known packs, sorted. */
 		public final DfsPackFile[] packs;
 
+		/** All known reftables, sorted. */
+		public final DfsReftable[] reftables;
+
 		private long lastModified = -1;
 
-		PackList(DfsPackFile[] packs) {
+		PackList(DfsPackFile[] packs, DfsReftable[] reftables) {
 			this.packs = packs;
+			this.reftables = reftables;
 		}
 
 		/** @return last modified time of all packs, in milliseconds. */
@@ -562,8 +619,8 @@ public long getLastModified() {
 	private static final class PackListImpl extends PackList {
 		private volatile boolean dirty;
 
-		PackListImpl(DfsPackFile[] packs) {
-			super(packs);
+		PackListImpl(DfsPackFile[] packs, DfsReftable[] reftables) {
+			super(packs, reftables);
 		}
 
 		@Override
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackCompactor.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackCompactor.java
index f7c87a4..99663eb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackCompactor.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackCompactor.java
@@ -44,21 +44,29 @@
 package org.eclipse.jgit.internal.storage.dfs;
 
 import static org.eclipse.jgit.internal.storage.dfs.DfsObjDatabase.PackSource.COMPACT;
+import static org.eclipse.jgit.internal.storage.dfs.DfsObjDatabase.PackSource.GC;
 import static org.eclipse.jgit.internal.storage.pack.PackExt.INDEX;
 import static org.eclipse.jgit.internal.storage.pack.PackExt.PACK;
+import static org.eclipse.jgit.internal.storage.pack.PackExt.REFTABLE;
 import static org.eclipse.jgit.internal.storage.pack.StoredObjectRepresentation.PACK_DELTA;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.Comparator;
+import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
+import java.util.Set;
 
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.internal.storage.file.PackIndex;
 import org.eclipse.jgit.internal.storage.file.PackReverseIndex;
 import org.eclipse.jgit.internal.storage.pack.PackWriter;
+import org.eclipse.jgit.internal.storage.reftable.ReftableCompactor;
+import org.eclipse.jgit.internal.storage.reftable.ReftableConfig;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.NullProgressMonitor;
 import org.eclipse.jgit.lib.ObjectId;
@@ -89,16 +97,15 @@
  */
 public class DfsPackCompactor {
 	private final DfsRepository repo;
-
 	private final List<DfsPackFile> srcPacks;
-
+	private final List<DfsReftable> srcReftables;
 	private final List<ObjectIdSet> exclude;
 
-	private final List<DfsPackDescription> newPacks;
-
-	private final List<PackStatistics> newStats;
+	private PackStatistics newStats;
+	private DfsPackDescription outDesc;
 
 	private int autoAddSize;
+	private ReftableConfig reftableConfig;
 
 	private RevWalk rw;
 	private RevFlag added;
@@ -114,9 +121,19 @@ public DfsPackCompactor(DfsRepository repository) {
 		repo = repository;
 		autoAddSize = 5 * 1024 * 1024; // 5 MiB
 		srcPacks = new ArrayList<>();
+		srcReftables = new ArrayList<>();
 		exclude = new ArrayList<>(4);
-		newPacks = new ArrayList<>(1);
-		newStats = new ArrayList<>(1);
+	}
+
+	/**
+	 * @param cfg
+	 *            configuration to write a reftable. Reftable compacting is
+	 *            disabled (default) when {@code cfg} is {@code null}.
+	 * @return {@code this}
+	 */
+	public DfsPackCompactor setReftableConfig(ReftableConfig cfg) {
+		reftableConfig = cfg;
+		return this;
 	}
 
 	/**
@@ -137,7 +154,19 @@ public DfsPackCompactor add(DfsPackFile pack) {
 	}
 
 	/**
-	 * Automatically select packs to be included, and add them.
+	 * Add a reftable to be compacted.
+	 *
+	 * @param table
+	 *            a reftable to combine.
+	 * @return {@code this}
+	 */
+	public DfsPackCompactor add(DfsReftable table) {
+		srcReftables.add(table);
+		return this;
+	}
+
+	/**
+	 * Automatically select pack and reftables to be included, and add them.
 	 * <p>
 	 * Packs are selected based on size, smaller packs get included while bigger
 	 * ones are omitted.
@@ -155,6 +184,16 @@ public DfsPackCompactor autoAdd() throws IOException {
 			else
 				exclude(pack);
 		}
+
+		if (reftableConfig != null) {
+			for (DfsReftable table : objdb.getReftables()) {
+				DfsPackDescription d = table.getPackDescription();
+				if (d.getPackSource() != GC
+						&& d.getFileSize(REFTABLE) < autoAddSize) {
+					add(table);
+				}
+			}
+		}
 		return this;
 	}
 
@@ -197,61 +236,71 @@ public DfsPackCompactor exclude(DfsPackFile pack) throws IOException {
 	 *             the packs cannot be compacted.
 	 */
 	public void compact(ProgressMonitor pm) throws IOException {
-		if (pm == null)
+		if (pm == null) {
 			pm = NullProgressMonitor.INSTANCE;
+		}
 
 		DfsObjDatabase objdb = repo.getObjectDatabase();
 		try (DfsReader ctx = objdb.newReader()) {
-			PackConfig pc = new PackConfig(repo);
-			pc.setIndexVersion(2);
-			pc.setDeltaCompress(false);
-			pc.setReuseDeltas(true);
-			pc.setReuseObjects(true);
+			if (reftableConfig != null && !srcReftables.isEmpty()) {
+				compactReftables(ctx);
+			}
+			compactPacks(ctx, pm);
 
-			PackWriter pw = new PackWriter(pc, ctx);
-			try {
-				pw.setDeltaBaseAsOffset(true);
-				pw.setReuseDeltaCommits(false);
-
-				addObjectsToPack(pw, ctx, pm);
-				if (pw.getObjectCount() == 0) {
-					List<DfsPackDescription> remove = toPrune();
-					if (remove.size() > 0)
-						objdb.commitPack(
-								Collections.<DfsPackDescription>emptyList(),
-								remove);
-					return;
-				}
-
-				boolean rollback = true;
-				DfsPackDescription pack = objdb.newPack(COMPACT,
-						estimatePackSize());
-				try {
-					writePack(objdb, pack, pw, pm);
-					writeIndex(objdb, pack, pw);
-
-					PackStatistics stats = pw.getStatistics();
-					pw.close();
-					pw = null;
-
-					pack.setPackStats(stats);
-					objdb.commitPack(Collections.singletonList(pack), toPrune());
-					newPacks.add(pack);
-					newStats.add(stats);
-					rollback = false;
-				} finally {
-					if (rollback)
-						objdb.rollbackPack(Collections.singletonList(pack));
-				}
-			} finally {
-				if (pw != null)
-					pw.close();
+			List<DfsPackDescription> commit = getNewPacks();
+			Collection<DfsPackDescription> remove = toPrune();
+			if (!commit.isEmpty() || !remove.isEmpty()) {
+				objdb.commitPack(commit, remove);
 			}
 		} finally {
 			rw = null;
 		}
 	}
 
+	private void compactPacks(DfsReader ctx, ProgressMonitor pm)
+			throws IOException, IncorrectObjectTypeException {
+		DfsObjDatabase objdb = repo.getObjectDatabase();
+		PackConfig pc = new PackConfig(repo);
+		pc.setIndexVersion(2);
+		pc.setDeltaCompress(false);
+		pc.setReuseDeltas(true);
+		pc.setReuseObjects(true);
+
+		PackWriter pw = new PackWriter(pc, ctx);
+		try {
+			pw.setDeltaBaseAsOffset(true);
+			pw.setReuseDeltaCommits(false);
+
+			addObjectsToPack(pw, ctx, pm);
+			if (pw.getObjectCount() == 0) {
+				return;
+			}
+
+			boolean rollback = true;
+			initOutDesc(objdb);
+			try {
+				writePack(objdb, outDesc, pw, pm);
+				writeIndex(objdb, outDesc, pw);
+
+				PackStatistics stats = pw.getStatistics();
+				pw.close();
+				pw = null;
+
+				outDesc.setPackStats(stats);
+				newStats = stats;
+				rollback = false;
+			} finally {
+				if (rollback) {
+					objdb.rollbackPack(Collections.singletonList(outDesc));
+				}
+			}
+		} finally {
+			if (pw != null) {
+				pw.close();
+			}
+		}
+	}
+
 	private long estimatePackSize() {
 		// Every pack file contains 12 bytes of header and 20 bytes of trailer.
 		// Include the final pack file header and trailer size here and ignore
@@ -263,27 +312,81 @@ private long estimatePackSize() {
 		return size;
 	}
 
+	private void compactReftables(DfsReader ctx) throws IOException {
+		DfsObjDatabase objdb = repo.getObjectDatabase();
+		Collections.sort(srcReftables, objdb.reftableComparator());
+
+		try (ReftableStack stack = ReftableStack.open(ctx, srcReftables)) {
+			initOutDesc(objdb);
+			ReftableCompactor compact = new ReftableCompactor();
+			compact.addAll(stack.readers());
+			compact.setIncludeDeletes(true);
+			writeReftable(objdb, outDesc, compact);
+		}
+	}
+
+	private void initOutDesc(DfsObjDatabase objdb) throws IOException {
+		if (outDesc == null) {
+			outDesc = objdb.newPack(COMPACT, estimatePackSize());
+		}
+	}
+
 	/** @return all of the source packs that fed into this compaction. */
-	public List<DfsPackDescription> getSourcePacks() {
-		return toPrune();
+	public Collection<DfsPackDescription> getSourcePacks() {
+		Set<DfsPackDescription> src = new HashSet<>();
+		for (DfsPackFile pack : srcPacks) {
+			src.add(pack.getPackDescription());
+		}
+		for (DfsReftable table : srcReftables) {
+			src.add(table.getPackDescription());
+		}
+		return src;
 	}
 
 	/** @return new packs created by this compaction. */
 	public List<DfsPackDescription> getNewPacks() {
-		return newPacks;
+		return outDesc != null
+				? Collections.singletonList(outDesc)
+				: Collections.emptyList();
 	}
 
 	/** @return statistics corresponding to the {@link #getNewPacks()}. */
 	public List<PackStatistics> getNewPackStatistics() {
-		return newStats;
+		return newStats != null
+				? Collections.singletonList(newStats)
+				: Collections.emptyList();
 	}
 
-	private List<DfsPackDescription> toPrune() {
-		int cnt = srcPacks.size();
-		List<DfsPackDescription> all = new ArrayList<>(cnt);
-		for (DfsPackFile pack : srcPacks)
-			all.add(pack.getPackDescription());
-		return all;
+	private Collection<DfsPackDescription> toPrune() {
+		Set<DfsPackDescription> packs = new HashSet<>();
+		for (DfsPackFile pack : srcPacks) {
+			packs.add(pack.getPackDescription());
+		}
+
+		Set<DfsPackDescription> reftables = new HashSet<>();
+		for (DfsReftable table : srcReftables) {
+			reftables.add(table.getPackDescription());
+		}
+
+		for (Iterator<DfsPackDescription> i = packs.iterator(); i.hasNext();) {
+			DfsPackDescription d = i.next();
+			if (d.hasFileExt(REFTABLE) && !reftables.contains(d)) {
+				i.remove();
+			}
+		}
+
+		for (Iterator<DfsPackDescription> i = reftables.iterator();
+				i.hasNext();) {
+			DfsPackDescription d = i.next();
+			if (d.hasFileExt(PACK) && !packs.contains(d)) {
+				i.remove();
+			}
+		}
+
+		Set<DfsPackDescription> toPrune = new HashSet<>();
+		toPrune.addAll(packs);
+		toPrune.addAll(reftables);
+		return toPrune;
 	}
 
 	private void addObjectsToPack(PackWriter pw, DfsReader ctx,
@@ -370,30 +473,47 @@ public int compare(ObjectIdWithOffset a, ObjectIdWithOffset b) {
 	private static void writePack(DfsObjDatabase objdb,
 			DfsPackDescription pack,
 			PackWriter pw, ProgressMonitor pm) throws IOException {
-		DfsOutputStream out = objdb.writeFile(pack, PACK);
-		try {
+		try (DfsOutputStream out = objdb.writeFile(pack, PACK)) {
 			pw.writePack(pm, pm, out);
 			pack.addFileExt(PACK);
-		} finally {
-			out.close();
+			pack.setBlockSize(PACK, out.blockSize());
 		}
 	}
 
 	private static void writeIndex(DfsObjDatabase objdb,
 			DfsPackDescription pack,
 			PackWriter pw) throws IOException {
-		DfsOutputStream out = objdb.writeFile(pack, INDEX);
-		try {
+		try (DfsOutputStream out = objdb.writeFile(pack, INDEX)) {
 			CountingOutputStream cnt = new CountingOutputStream(out);
 			pw.writeIndex(cnt);
 			pack.addFileExt(INDEX);
 			pack.setFileSize(INDEX, cnt.getCount());
+			pack.setBlockSize(INDEX, out.blockSize());
 			pack.setIndexVersion(pw.getIndexVersion());
-		} finally {
-			out.close();
 		}
 	}
 
+	private void writeReftable(DfsObjDatabase objdb, DfsPackDescription pack,
+			ReftableCompactor compact) throws IOException {
+		try (DfsOutputStream out = objdb.writeFile(pack, REFTABLE)) {
+			compact.setConfig(configureReftable(reftableConfig, out));
+			compact.compact(out);
+			pack.addFileExt(REFTABLE);
+			pack.setReftableStats(compact.getStats());
+		}
+	}
+
+	static ReftableConfig configureReftable(ReftableConfig cfg,
+			DfsOutputStream out) {
+		int bs = out.blockSize();
+		if (bs > 0) {
+			cfg = new ReftableConfig(cfg);
+			cfg.setRefBlockSize(bs);
+			cfg.setAlignBlocks(true);
+		}
+		return cfg;
+	}
+
 	private static class ObjectIdWithOffset extends ObjectId {
 		final long offset;
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackDescription.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackDescription.java
index e825f1a..e865e6b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackDescription.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackDescription.java
@@ -44,12 +44,13 @@
 package org.eclipse.jgit.internal.storage.dfs;
 
 import static org.eclipse.jgit.internal.storage.pack.PackExt.PACK;
+import static org.eclipse.jgit.internal.storage.pack.PackExt.REFTABLE;
 
-import java.util.HashMap;
-import java.util.Map;
+import java.util.Arrays;
 
 import org.eclipse.jgit.internal.storage.dfs.DfsObjDatabase.PackSource;
 import org.eclipse.jgit.internal.storage.pack.PackExt;
+import org.eclipse.jgit.internal.storage.reftable.ReftableWriter;
 import org.eclipse.jgit.storage.pack.PackStatistics;
 
 /**
@@ -62,25 +63,20 @@
  */
 public class DfsPackDescription implements Comparable<DfsPackDescription> {
 	private final DfsRepositoryDescription repoDesc;
-
 	private final String packName;
-
 	private PackSource packSource;
-
 	private long lastModified;
-
-	private final Map<PackExt, Long> sizeMap;
-
+	private long[] sizeMap;
+	private int[] blockSizeMap;
 	private long objectCount;
-
 	private long deltaCount;
+	private long minUpdateIndex;
+	private long maxUpdateIndex;
 
-	private PackStatistics stats;
-
+	private PackStatistics packStats;
+	private ReftableWriter.Stats refStats;
 	private int extensions;
-
 	private int indexVersion;
-
 	private long estimatedPackSize;
 
 	/**
@@ -102,7 +98,10 @@ public DfsPackDescription(DfsRepositoryDescription repoDesc, String name) {
 		this.repoDesc = repoDesc;
 		int dot = name.lastIndexOf('.');
 		this.packName = (dot < 0) ? name : name.substring(0, dot);
-		this.sizeMap = new HashMap<>(PackExt.values().length * 2);
+
+		int extCnt = PackExt.values().length;
+		sizeMap = new long[extCnt];
+		blockSizeMap = new int[extCnt];
 	}
 
 	/** @return description of the repository. */
@@ -138,6 +137,15 @@ public String getFileName(PackExt ext) {
 		return packName + '.' + ext.getExtension();
 	}
 
+	/**
+	 * @param ext
+	 *            the file extension.
+	 * @return cache key for use by the block cache.
+	 */
+	public DfsStreamKey getStreamKey(PackExt ext) {
+		return DfsStreamKey.of(getRepositoryDescription(), getFileName(ext));
+	}
+
 	/** @return the source of the pack. */
 	public PackSource getPackSource() {
 		return packSource;
@@ -168,6 +176,36 @@ public DfsPackDescription setLastModified(long timeMillis) {
 		return this;
 	}
 
+	/** @return minUpdateIndex for the reftable, if present. */
+	public long getMinUpdateIndex() {
+		return minUpdateIndex;
+	}
+
+	/**
+	 * @param min
+	 *            minUpdateIndex for the reftable, or 0.
+	 * @return {@code this}
+	 */
+	public DfsPackDescription setMinUpdateIndex(long min) {
+		minUpdateIndex = min;
+		return this;
+	}
+
+	/** @return maxUpdateIndex for the reftable, if present. */
+	public long getMaxUpdateIndex() {
+		return maxUpdateIndex;
+	}
+
+	/**
+	 * @param max
+	 *            maxUpdateIndex for the reftable, or 0.
+	 * @return {@code this}
+	 */
+	public DfsPackDescription setMaxUpdateIndex(long max) {
+		maxUpdateIndex = max;
+		return this;
+	}
+
 	/**
 	 * @param ext
 	 *            the file extension.
@@ -177,7 +215,11 @@ public DfsPackDescription setLastModified(long timeMillis) {
 	 * @return {@code this}
 	 */
 	public DfsPackDescription setFileSize(PackExt ext, long bytes) {
-		sizeMap.put(ext, Long.valueOf(Math.max(0, bytes)));
+		int i = ext.getPosition();
+		if (i >= sizeMap.length) {
+			sizeMap = Arrays.copyOf(sizeMap, i + 1);
+		}
+		sizeMap[i] = Math.max(0, bytes);
 		return this;
 	}
 
@@ -187,8 +229,36 @@ public DfsPackDescription setFileSize(PackExt ext, long bytes) {
 	 * @return size of the file, in bytes. If 0 the file size is not yet known.
 	 */
 	public long getFileSize(PackExt ext) {
-		Long size = sizeMap.get(ext);
-		return size == null ? 0 : size.longValue();
+		int i = ext.getPosition();
+		return i < sizeMap.length ? sizeMap[i] : 0;
+	}
+
+	/**
+	 * @param ext
+	 *            the file extension.
+	 * @return blockSize of the file, in bytes. If 0 the blockSize size is not
+	 *         yet known and may be discovered when opening the file.
+	 */
+	public int getBlockSize(PackExt ext) {
+		int i = ext.getPosition();
+		return i < blockSizeMap.length ? blockSizeMap[i] : 0;
+	}
+
+	/**
+	 * @param ext
+	 *            the file extension.
+	 * @param blockSize
+	 *            blockSize of the file, in bytes. If 0 the blockSize is not
+	 *            known and will be determined on first read.
+	 * @return {@code this}
+	 */
+	public DfsPackDescription setBlockSize(PackExt ext, int blockSize) {
+		int i = ext.getPosition();
+		if (i >= blockSizeMap.length) {
+			blockSizeMap = Arrays.copyOf(blockSizeMap, i + 1);
+		}
+		blockSizeMap[i] = Math.max(0, blockSize);
+		return this;
 	}
 
 	/**
@@ -247,24 +317,38 @@ public DfsPackDescription setDeltaCount(long cnt) {
 	 *         is being committed to the repository.
 	 */
 	public PackStatistics getPackStats() {
-		return stats;
+		return packStats;
 	}
 
 	DfsPackDescription setPackStats(PackStatistics stats) {
-		this.stats = stats;
+		this.packStats = stats;
 		setFileSize(PACK, stats.getTotalBytes());
 		setObjectCount(stats.getTotalObjects());
 		setDeltaCount(stats.getTotalDeltas());
 		return this;
 	}
 
+	/** @return stats from the sibling reftable, if created. */
+	public ReftableWriter.Stats getReftableStats() {
+		return refStats;
+	}
+
+	void setReftableStats(ReftableWriter.Stats stats) {
+		this.refStats = stats;
+		setMinUpdateIndex(stats.minUpdateIndex());
+		setMaxUpdateIndex(stats.maxUpdateIndex());
+		setFileSize(REFTABLE, stats.totalBytes());
+		setBlockSize(REFTABLE, stats.refBlockSize());
+	}
+
 	/**
 	 * Discard the pack statistics, if it was populated.
 	 *
 	 * @return {@code this}
 	 */
 	public DfsPackDescription clearPackStats() {
-		stats = null;
+		packStats = null;
+		refStats = null;
 		return this;
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackFile.java
index ae2e7e4..dfb41e2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackFile.java
@@ -72,7 +72,6 @@
 import org.eclipse.jgit.internal.storage.file.PackIndex;
 import org.eclipse.jgit.internal.storage.file.PackReverseIndex;
 import org.eclipse.jgit.internal.storage.pack.BinaryDelta;
-import org.eclipse.jgit.internal.storage.pack.PackExt;
 import org.eclipse.jgit.internal.storage.pack.PackOutputStream;
 import org.eclipse.jgit.internal.storage.pack.StoredObjectRepresentation;
 import org.eclipse.jgit.lib.AbbreviatedObjectId;
@@ -88,53 +87,7 @@
  * delta packed format yielding high compression of lots of object where some
  * objects are similar.
  */
-public final class DfsPackFile {
-	/**
-	 * File offset used to cache {@link #index} in {@link DfsBlockCache}.
-	 * <p>
-	 * To better manage memory, the forward index is stored as a single block in
-	 * the block cache under this file position. A negative value is used
-	 * because it cannot occur in a normal pack file, and it is less likely to
-	 * collide with a valid data block from the file as the high bits will all
-	 * be set when treated as an unsigned long by the cache code.
-	 */
-	private static final long POS_INDEX = -1;
-
-	/** Offset used to cache {@link #reverseIndex}. See {@link #POS_INDEX}. */
-	private static final long POS_REVERSE_INDEX = -2;
-
-	/** Offset used to cache {@link #bitmapIndex}. See {@link #POS_INDEX}. */
-	private static final long POS_BITMAP_INDEX = -3;
-
-	/** Cache that owns this pack file and its data. */
-	private final DfsBlockCache cache;
-
-	/** Description of the pack file's storage. */
-	private final DfsPackDescription packDesc;
-
-	/** Unique identity of this pack while in-memory. */
-	final DfsPackKey key;
-
-	/**
-	 * Total number of bytes in this pack file.
-	 * <p>
-	 * This field initializes to -1 and gets populated when a block is loaded.
-	 */
-	volatile long length;
-
-	/**
-	 * Preferred alignment for loading blocks from the backing file.
-	 * <p>
-	 * It is initialized to 0 and filled in on the first read made from the
-	 * file. Block sizes may be odd, e.g. 4091, caused by the underling DFS
-	 * storing 4091 user bytes and 5 bytes block metadata into a lower level
-	 * 4096 byte block on disk.
-	 */
-	private volatile int blockSize;
-
-	/** True once corruption has been detected that cannot be worked around. */
-	private volatile boolean invalid;
-
+public final class DfsPackFile extends BlockBasedFile {
 	/**
 	 * Lock for initialization of {@link #index} and {@link #corruptObjects}.
 	 * <p>
@@ -167,22 +120,22 @@ public final class DfsPackFile {
 	 *            cache that owns the pack data.
 	 * @param desc
 	 *            description of the pack within the DFS.
-	 * @param key
-	 *            interned key used to identify blocks in the block cache.
 	 */
-	DfsPackFile(DfsBlockCache cache, DfsPackDescription desc, DfsPackKey key) {
-		this.cache = cache;
-		this.packDesc = desc;
-		this.key = key;
+	DfsPackFile(DfsBlockCache cache, DfsPackDescription desc) {
+		super(cache, desc, PACK);
 
-		length = desc.getFileSize(PACK);
-		if (length <= 0)
-			length = -1;
+		int bs = desc.getBlockSize(PACK);
+		if (bs > 0) {
+			setBlockSize(bs);
+		}
+
+		long sz = desc.getFileSize(PACK);
+		length = sz > 0 ? sz : -1;
 	}
 
 	/** @return description that was originally used to configure this pack file. */
 	public DfsPackDescription getPackDescription() {
-		return packDesc;
+		return desc;
 	}
 
 	/**
@@ -193,24 +146,11 @@ public boolean isIndexLoaded() {
 		return idxref != null && idxref.has();
 	}
 
-	/** @return bytes cached in memory for this pack, excluding the index. */
-	public long getCachedSize() {
-		return key.cachedSize.get();
-	}
-
-	String getPackName() {
-		return packDesc.getFileName(PACK);
-	}
-
-	void setBlockSize(int newSize) {
-		blockSize = newSize;
-	}
-
 	void setPackIndex(PackIndex idx) {
 		long objCnt = idx.getObjectCount();
 		int recSize = Constants.OBJECT_ID_LENGTH + 8;
-		int sz = (int) Math.min(objCnt * recSize, Integer.MAX_VALUE);
-		index = cache.put(key, POS_INDEX, sz, idx);
+		long sz = objCnt * recSize;
+		index = cache.putRef(desc.getStreamKey(INDEX), sz, idx);
 	}
 
 	/**
@@ -236,7 +176,7 @@ private PackIndex idx(DfsReader ctx) throws IOException {
 		}
 
 		if (invalid)
-			throw new PackInvalidException(getPackName());
+			throw new PackInvalidException(getFileName());
 
 		Repository.getGlobalListenerList()
 				.dispatch(new BeforeDfsPackIndexLoadedEvent(this));
@@ -249,11 +189,21 @@ private PackIndex idx(DfsReader ctx) throws IOException {
 					return idx;
 			}
 
+			DfsStreamKey idxKey = desc.getStreamKey(INDEX);
+			idxref = cache.getRef(idxKey);
+			if (idxref != null) {
+				PackIndex idx = idxref.get();
+				if (idx != null) {
+					index = idxref;
+					return idx;
+				}
+			}
+
 			PackIndex idx;
 			try {
 				ctx.stats.readIdx++;
 				long start = System.nanoTime();
-				ReadableChannel rc = ctx.db.openFile(packDesc, INDEX);
+				ReadableChannel rc = ctx.db.openFile(desc, INDEX);
 				try {
 					InputStream in = Channels.newInputStream(rc);
 					int wantSize = 8192;
@@ -270,18 +220,14 @@ else if (bs <= 0)
 				}
 			} catch (EOFException e) {
 				invalid = true;
-				IOException e2 = new IOException(MessageFormat.format(
+				throw new IOException(MessageFormat.format(
 						DfsText.get().shortReadOfIndex,
-						packDesc.getFileName(INDEX)));
-				e2.initCause(e);
-				throw e2;
+						desc.getFileName(INDEX)), e);
 			} catch (IOException e) {
 				invalid = true;
-				IOException e2 = new IOException(MessageFormat.format(
+				throw new IOException(MessageFormat.format(
 						DfsText.get().cannotReadIndex,
-						packDesc.getFileName(INDEX)));
-				e2.initCause(e);
-				throw e2;
+						desc.getFileName(INDEX)), e);
 			}
 
 			setPackIndex(idx);
@@ -289,17 +235,14 @@ else if (bs <= 0)
 		}
 	}
 
-	private static long elapsedMicros(long start) {
-		return (System.nanoTime() - start) / 1000L;
-	}
-
 	final boolean isGarbage() {
-		return packDesc.getPackSource() == UNREACHABLE_GARBAGE;
+		return desc.getPackSource() == UNREACHABLE_GARBAGE;
 	}
 
 	PackBitmapIndex getBitmapIndex(DfsReader ctx) throws IOException {
-		if (invalid || isGarbage())
+		if (invalid || isGarbage() || !desc.hasFileExt(BITMAP_INDEX))
 			return null;
+
 		DfsBlockCache.Ref<PackBitmapIndex> idxref = bitmapIndex;
 		if (idxref != null) {
 			PackBitmapIndex idx = idxref.get();
@@ -307,9 +250,6 @@ PackBitmapIndex getBitmapIndex(DfsReader ctx) throws IOException {
 				return idx;
 		}
 
-		if (!packDesc.hasFileExt(PackExt.BITMAP_INDEX))
-			return null;
-
 		synchronized (initLock) {
 			idxref = bitmapIndex;
 			if (idxref != null) {
@@ -318,12 +258,22 @@ PackBitmapIndex getBitmapIndex(DfsReader ctx) throws IOException {
 					return idx;
 			}
 
+			DfsStreamKey bitmapKey = desc.getStreamKey(BITMAP_INDEX);
+			idxref = cache.getRef(bitmapKey);
+			if (idxref != null) {
+				PackBitmapIndex idx = idxref.get();
+				if (idx != null) {
+					bitmapIndex = idxref;
+					return idx;
+				}
+			}
+
 			long size;
 			PackBitmapIndex idx;
 			try {
 				ctx.stats.readBitmap++;
 				long start = System.nanoTime();
-				ReadableChannel rc = ctx.db.openFile(packDesc, BITMAP_INDEX);
+				ReadableChannel rc = ctx.db.openFile(desc, BITMAP_INDEX);
 				try {
 					InputStream in = Channels.newInputStream(rc);
 					int wantSize = 8192;
@@ -342,21 +292,16 @@ else if (bs <= 0)
 					ctx.stats.readIdxMicros += elapsedMicros(start);
 				}
 			} catch (EOFException e) {
-				IOException e2 = new IOException(MessageFormat.format(
+				throw new IOException(MessageFormat.format(
 						DfsText.get().shortReadOfIndex,
-						packDesc.getFileName(BITMAP_INDEX)));
-				e2.initCause(e);
-				throw e2;
+						desc.getFileName(BITMAP_INDEX)), e);
 			} catch (IOException e) {
-				IOException e2 = new IOException(MessageFormat.format(
+				throw new IOException(MessageFormat.format(
 						DfsText.get().cannotReadIndex,
-						packDesc.getFileName(BITMAP_INDEX)));
-				e2.initCause(e);
-				throw e2;
+						desc.getFileName(BITMAP_INDEX)), e);
 			}
 
-			bitmapIndex = cache.put(key, POS_BITMAP_INDEX,
-					(int) Math.min(size, Integer.MAX_VALUE), idx);
+			bitmapIndex = cache.putRef(bitmapKey, size, idx);
 			return idx;
 		}
 	}
@@ -377,11 +322,21 @@ PackReverseIndex getReverseIdx(DfsReader ctx) throws IOException {
 					return revidx;
 			}
 
+			DfsStreamKey revKey =
+					new DfsStreamKey.ForReverseIndex(desc.getStreamKey(INDEX));
+			revref = cache.getRef(revKey);
+			if (revref != null) {
+				PackReverseIndex idx = revref.get();
+				if (idx != null) {
+					reverseIndex = revref;
+					return idx;
+				}
+			}
+
 			PackIndex idx = idx(ctx);
 			PackReverseIndex revidx = new PackReverseIndex(idx);
-			int sz = (int) Math.min(
-					idx.getObjectCount() * 8, Integer.MAX_VALUE);
-			reverseIndex = cache.put(key, POS_REVERSE_INDEX, sz, revidx);
+			long cnt = idx.getObjectCount();
+			reverseIndex = cache.putRef(revKey, cnt * 8, revidx);
 			return revidx;
 		}
 	}
@@ -430,13 +385,6 @@ void resolve(DfsReader ctx, Set<ObjectId> matches, AbbreviatedObjectId id,
 		idx(ctx).resolve(matches, id, matchLimit);
 	}
 
-	/** Release all memory used by this DfsPackFile instance. */
-	public void close() {
-		cache.remove(this);
-		index = null;
-		reverseIndex = null;
-	}
-
 	/**
 	 * Obtain the total number of objects available in this pack. This method
 	 * relies on pack index, giving number of effectively available objects.
@@ -489,21 +437,42 @@ void copyPackAsIs(PackOutputStream out, DfsReader ctx)
 
 	private void copyPackThroughCache(PackOutputStream out, DfsReader ctx)
 			throws IOException {
-		long position = 12;
-		long remaining = length - (12 + 20);
-		while (0 < remaining) {
-			DfsBlock b = cache.getOrLoad(this, position, ctx);
-			int ptr = (int) (position - b.start);
-			int n = (int) Math.min(b.size() - ptr, remaining);
-			b.write(out, position, n);
-			position += n;
-			remaining -= n;
+		ReadableChannel rc = null;
+		try {
+			long position = 12;
+			long remaining = length - (12 + 20);
+			while (0 < remaining) {
+				DfsBlock b;
+				if (rc != null) {
+					b = cache.getOrLoad(this, position, ctx, rc);
+				} else {
+					b = cache.get(key, alignToBlock(position));
+					if (b == null) {
+						rc = ctx.db.openFile(desc, PACK);
+						int sz = ctx.getOptions().getStreamPackBufferSize();
+						if (sz > 0) {
+							rc.setReadAheadBytes(sz);
+						}
+						b = cache.getOrLoad(this, position, ctx, rc);
+					}
+				}
+
+				int ptr = (int) (position - b.start);
+				int n = (int) Math.min(b.size() - ptr, remaining);
+				b.write(out, position, n);
+				position += n;
+				remaining -= n;
+			}
+		} finally {
+			if (rc != null) {
+				rc.close();
+			}
 		}
 	}
 
 	private long copyPackBypassCache(PackOutputStream out, DfsReader ctx)
 			throws IOException {
-		try (ReadableChannel rc = ctx.db.openFile(packDesc, PACK)) {
+		try (ReadableChannel rc = ctx.db.openFile(desc, PACK)) {
 			ByteBuffer buf = newCopyBuffer(out, rc);
 			if (ctx.getOptions().getStreamPackBufferSize() > 0)
 				rc.setReadAheadBytes(ctx.getOptions().getStreamPackBufferSize());
@@ -642,7 +611,7 @@ void copyAsIs(PackOutputStream out, DfsObjectToPack src,
 					setCorrupt(src.offset);
 					throw new CorruptObjectException(MessageFormat.format(
 							JGitText.get().objectAtHasBadZlibStream,
-							Long.valueOf(src.offset), getPackName()));
+							Long.valueOf(src.offset), getFileName()));
 				}
 			} else if (validate) {
 				assert(crc1 != null);
@@ -684,7 +653,7 @@ void copyAsIs(PackOutputStream out, DfsObjectToPack src,
 			CorruptObjectException corruptObject = new CorruptObjectException(
 					MessageFormat.format(
 							JGitText.get().objectAtHasBadZlibStream,
-							Long.valueOf(src.offset), getPackName()));
+							Long.valueOf(src.offset), getFileName()));
 			corruptObject.initCause(dataFormat);
 
 			StoredObjectRepresentationNotAvailableException gone;
@@ -746,24 +715,16 @@ void copyAsIs(PackOutputStream out, DfsObjectToPack src,
 				if (crc2.getValue() != expectedCRC) {
 					throw new CorruptObjectException(MessageFormat.format(
 							JGitText.get().objectAtHasBadZlibStream,
-							Long.valueOf(src.offset), getPackName()));
+							Long.valueOf(src.offset), getFileName()));
 				}
 			}
 		}
 	}
 
-	boolean invalid() {
-		return invalid;
-	}
-
-	void setInvalid() {
-		invalid = true;
-	}
-
 	private IOException packfileIsTruncated() {
 		invalid = true;
 		return new IOException(MessageFormat.format(
-				JGitText.get().packfileIsTruncated, getPackName()));
+				JGitText.get().packfileIsTruncated, getFileName()));
 	}
 
 	private void readFully(long position, byte[] dstbuf, int dstoff, int cnt,
@@ -772,103 +733,6 @@ private void readFully(long position, byte[] dstbuf, int dstoff, int cnt,
 			throw new EOFException();
 	}
 
-	long alignToBlock(long pos) {
-		int size = blockSize;
-		if (size == 0)
-			size = cache.getBlockSize();
-		return (pos / size) * size;
-	}
-
-	DfsBlock getOrLoadBlock(long pos, DfsReader ctx) throws IOException {
-		return cache.getOrLoad(this, pos, ctx);
-	}
-
-	DfsBlock readOneBlock(long pos, DfsReader ctx)
-			throws IOException {
-		if (invalid)
-			throw new PackInvalidException(getPackName());
-
-		ctx.stats.readBlock++;
-		long start = System.nanoTime();
-		ReadableChannel rc = ctx.db.openFile(packDesc, PACK);
-		try {
-			int size = blockSize(rc);
-			pos = (pos / size) * size;
-
-			// If the size of the file is not yet known, try to discover it.
-			// Channels may choose to return -1 to indicate they don't
-			// know the length yet, in this case read up to the size unit
-			// given by the caller, then recheck the length.
-			long len = length;
-			if (len < 0) {
-				len = rc.size();
-				if (0 <= len)
-					length = len;
-			}
-
-			if (0 <= len && len < pos + size)
-				size = (int) (len - pos);
-			if (size <= 0)
-				throw new EOFException(MessageFormat.format(
-						DfsText.get().shortReadOfBlock, Long.valueOf(pos),
-						getPackName(), Long.valueOf(0), Long.valueOf(0)));
-
-			byte[] buf = new byte[size];
-			rc.position(pos);
-			int cnt = read(rc, ByteBuffer.wrap(buf, 0, size));
-			ctx.stats.readBlockBytes += cnt;
-			if (cnt != size) {
-				if (0 <= len) {
-					throw new EOFException(MessageFormat.format(
-						    DfsText.get().shortReadOfBlock,
-						    Long.valueOf(pos),
-						    getPackName(),
-						    Integer.valueOf(size),
-						    Integer.valueOf(cnt)));
-				}
-
-				// Assume the entire thing was read in a single shot, compact
-				// the buffer to only the space required.
-				byte[] n = new byte[cnt];
-				System.arraycopy(buf, 0, n, 0, n.length);
-				buf = n;
-			} else if (len < 0) {
-				// With no length at the start of the read, the channel should
-				// have the length available at the end.
-				length = len = rc.size();
-			}
-
-			return new DfsBlock(key, pos, buf);
-		} finally {
-			rc.close();
-			ctx.stats.readBlockMicros += elapsedMicros(start);
-		}
-	}
-
-	private int blockSize(ReadableChannel rc) {
-		// If the block alignment is not yet known, discover it. Prefer the
-		// larger size from either the cache or the file itself.
-		int size = blockSize;
-		if (size == 0) {
-			size = rc.blockSize();
-			if (size <= 0)
-				size = cache.getBlockSize();
-			else if (size < cache.getBlockSize())
-				size = (cache.getBlockSize() / size) * size;
-			blockSize = size;
-		}
-		return size;
-	}
-
-	private static int read(ReadableChannel rc, ByteBuffer buf)
-			throws IOException {
-		int n;
-		do {
-			n = rc.read(buf);
-		} while (0 < n && buf.hasRemaining());
-		return buf.position();
-	}
-
 	ObjectLoader load(DfsReader ctx, long pos)
 			throws IOException {
 		try {
@@ -1005,7 +869,7 @@ else if (delta.next == null)
 			CorruptObjectException coe = new CorruptObjectException(
 					MessageFormat.format(
 							JGitText.get().objectAtHasBadZlibStream, Long.valueOf(pos),
-							getPackName()));
+							getFileName()));
 			coe.initCause(dfe);
 			throw coe;
 		}
@@ -1153,7 +1017,7 @@ long getObjectSize(DfsReader ctx, long pos)
 			CorruptObjectException coe = new CorruptObjectException(
 					MessageFormat.format(
 							JGitText.get().objectAtHasBadZlibStream, Long.valueOf(pos),
-							getPackName()));
+							getFileName()));
 			coe.initCause(dfe);
 			throw coe;
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackParser.java
index 6430ea9..fd99db1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackParser.java
@@ -94,7 +94,7 @@ public class DfsPackParser extends PackParser {
 	private DfsPackDescription packDsc;
 
 	/** Key used during delta resolution reading delta chains. */
-	private DfsPackKey packKey;
+	private DfsStreamKey packKey;
 
 	/** If the index was small enough, the entire index after writing. */
 	private PackIndex packIndex;
@@ -150,12 +150,13 @@ public PackLock parse(ProgressMonitor receiving, ProgressMonitor resolving)
 			readBlock = null;
 			packDsc.addFileExt(PACK);
 			packDsc.setFileSize(PACK, packEnd);
+			packDsc.setBlockSize(PACK, blockSize);
 
 			writePackIndex();
 			objdb.commitPack(Collections.singletonList(packDsc), null);
 			rollback = false;
 
-			DfsPackFile p = blockCache.getOrCreate(packDsc, packKey);
+			DfsPackFile p = new DfsPackFile(blockCache, packDsc);
 			p.setBlockSize(blockSize);
 			if (packIndex != null)
 				p.setPackIndex(packIndex);
@@ -206,9 +207,9 @@ protected void onPackHeader(long objectCount) throws IOException {
 		}
 
 		packDsc = objdb.newPack(DfsObjDatabase.PackSource.RECEIVE);
-		packKey = new DfsPackKey();
-
 		out = objdb.writeFile(packDsc, PACK);
+		packKey = packDsc.getStreamKey(PACK);
+
 		int size = out.blockSize();
 		if (size <= 0)
 			size = blockCache.getBlockSize();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsReader.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsReader.java
index d611469..3c84220 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsReader.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsReader.java
@@ -655,7 +655,7 @@ public void copyPackAsIs(PackOutputStream out, CachedPack pack)
 	/**
 	 * Copy bytes from the window to a caller supplied buffer.
 	 *
-	 * @param pack
+	 * @param file
 	 *            the file the desired window is stored within.
 	 * @param position
 	 *            position within the file to read from.
@@ -674,24 +674,24 @@ public void copyPackAsIs(PackOutputStream out, CachedPack pack)
 	 *             this cursor does not match the provider or id and the proper
 	 *             window could not be acquired through the provider's cache.
 	 */
-	int copy(DfsPackFile pack, long position, byte[] dstbuf, int dstoff, int cnt)
-			throws IOException {
+	int copy(BlockBasedFile file, long position, byte[] dstbuf, int dstoff,
+			int cnt) throws IOException {
 		if (cnt == 0)
 			return 0;
 
-		long length = pack.length;
+		long length = file.length;
 		if (0 <= length && length <= position)
 			return 0;
 
 		int need = cnt;
 		do {
-			pin(pack, position);
+			pin(file, position);
 			int r = block.copy(position, dstbuf, dstoff, need);
 			position += r;
 			dstoff += r;
 			need -= r;
 			if (length < 0)
-				length = pack.length;
+				length = file.length;
 		} while (0 < need && position < length);
 		return cnt - need;
 	}
@@ -756,15 +756,14 @@ private void prepareInflater() {
 			inf.reset();
 	}
 
-	void pin(DfsPackFile pack, long position) throws IOException {
-		DfsBlock b = block;
-		if (b == null || !b.contains(pack.key, position)) {
+	void pin(BlockBasedFile file, long position) throws IOException {
+		if (block == null || !block.contains(file.key, position)) {
 			// If memory is low, we may need what is in our window field to
 			// be cleaned up by the GC during the get for the next window.
 			// So we always clear it, even though we are just going to set
 			// it again.
 			block = null;
-			block = pack.getOrLoadBlock(position, this);
+			block = file.getOrLoadBlock(position, this);
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsReftable.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsReftable.java
new file mode 100644
index 0000000..5a8ea92
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsReftable.java
@@ -0,0 +1,178 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.dfs;
+
+import static org.eclipse.jgit.internal.storage.pack.PackExt.REFTABLE;
+
+import java.io.IOException;
+import java.nio.ByteBuffer;
+
+import org.eclipse.jgit.internal.storage.io.BlockSource;
+import org.eclipse.jgit.internal.storage.reftable.ReftableReader;
+
+/** A reftable stored in {@link DfsBlockCache}. */
+public class DfsReftable extends BlockBasedFile {
+	/**
+	 * Construct a reader for an existing reftable.
+	 *
+	 * @param desc
+	 *            description of the reftable within the DFS.
+	 */
+	public DfsReftable(DfsPackDescription desc) {
+		this(DfsBlockCache.getInstance(), desc);
+	}
+
+	/**
+	 * Construct a reader for an existing reftable.
+	 *
+	 * @param cache
+	 *            cache that will store the reftable data.
+	 * @param desc
+	 *            description of the reftable within the DFS.
+	 */
+	public DfsReftable(DfsBlockCache cache, DfsPackDescription desc) {
+		super(cache, desc, REFTABLE);
+
+		int bs = desc.getBlockSize(REFTABLE);
+		if (bs > 0) {
+			setBlockSize(bs);
+		}
+
+		long sz = desc.getFileSize(REFTABLE);
+		length = sz > 0 ? sz : -1;
+	}
+
+	/** @return description that was originally used to configure this file. */
+	public DfsPackDescription getPackDescription() {
+		return desc;
+	}
+
+	/**
+	 * Open reader on the reftable.
+	 * <p>
+	 * The returned reader is not thread safe.
+	 *
+	 * @param ctx
+	 *            reader to access the DFS storage.
+	 * @return cursor to read the table; caller must close.
+	 * @throws IOException
+	 *             table cannot be opened.
+	 */
+	public ReftableReader open(DfsReader ctx) throws IOException {
+		return new ReftableReader(new CacheSource(this, cache, ctx));
+	}
+
+	private static final class CacheSource extends BlockSource {
+		private final DfsReftable file;
+		private final DfsBlockCache cache;
+		private final DfsReader ctx;
+		private ReadableChannel ch;
+		private int readAhead;
+
+		CacheSource(DfsReftable file, DfsBlockCache cache, DfsReader ctx) {
+			this.file = file;
+			this.cache = cache;
+			this.ctx = ctx;
+		}
+
+		@Override
+		public ByteBuffer read(long pos, int cnt) throws IOException {
+			if (ch == null && readAhead > 0 && notInCache(pos)) {
+				open().setReadAheadBytes(readAhead);
+			}
+
+			DfsBlock block = cache.getOrLoad(file, pos, ctx, ch);
+			if (block.start == pos && block.size() >= cnt) {
+				return block.zeroCopyByteBuffer(cnt);
+			}
+
+			byte[] dst = new byte[cnt];
+			ByteBuffer buf = ByteBuffer.wrap(dst);
+			buf.position(ctx.copy(file, pos, dst, 0, cnt));
+			return buf;
+		}
+
+		private boolean notInCache(long pos) {
+			return cache.get(file.key, file.alignToBlock(pos)) == null;
+		}
+
+		@Override
+		public long size() throws IOException {
+			long n = file.length;
+			if (n < 0) {
+				n = open().size();
+				file.length = n;
+			}
+			return n;
+		}
+
+		@Override
+		public void adviseSequentialRead(long start, long end) {
+			int sz = ctx.getOptions().getStreamPackBufferSize();
+			if (sz > 0) {
+				readAhead = (int) Math.min(sz, end - start);
+			}
+		}
+
+		private ReadableChannel open() throws IOException {
+			if (ch == null) {
+				ch = ctx.db.openFile(file.desc, file.ext);
+			}
+			return ch;
+		}
+
+		@Override
+		public void close() {
+			if (ch != null) {
+				try {
+					ch.close();
+				} catch (IOException e) {
+					// Ignore read close failures.
+				} finally {
+					ch = null;
+				}
+			}
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsStreamKey.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsStreamKey.java
new file mode 100644
index 0000000..54a7489
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsStreamKey.java
@@ -0,0 +1,125 @@
+/*
+ * Copyright (C) 2011, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.dfs;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+
+import java.util.Arrays;
+
+/** Key used by {@link DfsBlockCache} to disambiguate streams. */
+public abstract class DfsStreamKey {
+	/**
+	 * @param repo
+	 *            description of the containing repository.
+	 * @param name
+	 *            compute the key from a string name.
+	 * @return key for {@code name}
+	 */
+	public static DfsStreamKey of(DfsRepositoryDescription repo, String name) {
+		return new ByteArrayDfsStreamKey(repo, name.getBytes(UTF_8));
+	}
+
+	final int hash;
+
+	/**
+	 * @param hash
+	 *            hash of the other identifying components of the key.
+	 */
+	protected DfsStreamKey(int hash) {
+		// Multiply by 31 here so we can more directly combine with another
+		// value without doing the multiply there.
+		this.hash = hash * 31;
+	}
+
+	@Override
+	public int hashCode() {
+		return hash;
+	}
+
+	@Override
+	public abstract boolean equals(Object o);
+
+	@SuppressWarnings("boxing")
+	@Override
+	public String toString() {
+		return String.format("DfsStreamKey[hash=%08x]", hash); //$NON-NLS-1$
+	}
+
+	private static final class ByteArrayDfsStreamKey extends DfsStreamKey {
+		private final DfsRepositoryDescription repo;
+		private final byte[] name;
+
+		ByteArrayDfsStreamKey(DfsRepositoryDescription repo, byte[] name) {
+			super(repo.hashCode() * 31 + Arrays.hashCode(name));
+			this.repo = repo;
+			this.name = name;
+		}
+
+		@Override
+		public boolean equals(Object o) {
+			if (o instanceof ByteArrayDfsStreamKey) {
+				ByteArrayDfsStreamKey k = (ByteArrayDfsStreamKey) o;
+				return hash == k.hash
+						&& repo.equals(k.repo)
+						&& Arrays.equals(name, k.name);
+			}
+			return false;
+		}
+	}
+
+	static final class ForReverseIndex extends DfsStreamKey {
+		private final DfsStreamKey idxKey;
+
+		ForReverseIndex(DfsStreamKey idxKey) {
+			super(idxKey.hash + 1);
+			this.idxKey = idxKey;
+		}
+
+		@Override
+		public boolean equals(Object o) {
+			return o instanceof ForReverseIndex
+					&& idxKey.equals(((ForReverseIndex) o).idxKey);
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsText.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsText.java
index 8624547..dedcab0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsText.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsText.java
@@ -55,9 +55,7 @@ public static DfsText get() {
 
 	// @formatter:off
 	/***/ public String cannotReadIndex;
-	/***/ public String cannotReadBackDelta;
 	/***/ public String shortReadOfBlock;
 	/***/ public String shortReadOfIndex;
-	/***/ public String unexpectedEofInPack;
 	/***/ public String willNotStoreEmptyPack;
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/InMemoryRepository.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/InMemoryRepository.java
index 527e46b..1e31878 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/InMemoryRepository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/InMemoryRepository.java
@@ -53,7 +53,7 @@ public InMemoryRepository build() throws IOException {
 
 	static final AtomicInteger packId = new AtomicInteger();
 
-	private final DfsObjDatabase objdb;
+	private final MemObjDatabase objdb;
 	private final RefDatabase refdb;
 	private String gitwebDescription;
 	private boolean performsAtomicTransactions = true;
@@ -75,7 +75,7 @@ public InMemoryRepository(DfsRepositoryDescription repoDesc) {
 	}
 
 	@Override
-	public DfsObjDatabase getObjectDatabase() {
+	public MemObjDatabase getObjectDatabase() {
 		return objdb;
 	}
 
@@ -106,13 +106,23 @@ public void setGitwebDescription(@Nullable String d) {
 		gitwebDescription = d;
 	}
 
-	private class MemObjDatabase extends DfsObjDatabase {
+	/** DfsObjDatabase used by InMemoryRepository. */
+	public static class MemObjDatabase extends DfsObjDatabase {
 		private List<DfsPackDescription> packs = new ArrayList<>();
+		private int blockSize;
 
 		MemObjDatabase(DfsRepository repo) {
 			super(repo, new DfsReaderOptions());
 		}
 
+		/**
+		 * @param blockSize
+		 *            force a different block size for testing.
+		 */
+		public void setReadableChannelBlockSizeForTest(int blockSize) {
+			this.blockSize = blockSize;
+		}
+
 		@Override
 		protected synchronized List<DfsPackDescription> listPacks() {
 			return packs;
@@ -152,7 +162,7 @@ protected ReadableChannel openFile(DfsPackDescription desc, PackExt ext)
 			byte[] file = memPack.fileMap.get(ext);
 			if (file == null)
 				throw new FileNotFoundException(desc.getFileName(ext));
-			return new ByteArrayReadableChannel(file);
+			return new ByteArrayReadableChannel(file, blockSize);
 		}
 
 		@Override
@@ -216,13 +226,13 @@ public void close() {
 
 	private static class ByteArrayReadableChannel implements ReadableChannel {
 		private final byte[] data;
-
+		private final int blockSize;
 		private int position;
-
 		private boolean open = true;
 
-		ByteArrayReadableChannel(byte[] buf) {
+		ByteArrayReadableChannel(byte[] buf, int blockSize) {
 			data = buf;
+			this.blockSize = blockSize;
 		}
 
 		@Override
@@ -262,7 +272,7 @@ public long size() {
 
 		@Override
 		public int blockSize() {
-			return 0;
+			return blockSize;
 		}
 
 		@Override
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/ReftableStack.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/ReftableStack.java
new file mode 100644
index 0000000..8d1cc98
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/ReftableStack.java
@@ -0,0 +1,108 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.dfs;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.eclipse.jgit.internal.storage.reftable.Reftable;
+
+/** Tracks multiple open {@link Reftable} instances. */
+public class ReftableStack implements AutoCloseable {
+	/**
+	 * Opens a stack of tables for reading.
+	 *
+	 * @param ctx
+	 *            context to read the tables with. This {@code ctx} will be
+	 *            retained by the stack and each of the table readers.
+	 * @param tables
+	 *            the tables to open.
+	 * @return stack reference to close the tables.
+	 * @throws IOException
+	 *             a table could not be opened
+	 */
+	public static ReftableStack open(DfsReader ctx, List<DfsReftable> tables)
+			throws IOException {
+		ReftableStack stack = new ReftableStack(tables.size());
+		boolean close = true;
+		try {
+			for (DfsReftable t : tables) {
+				stack.tables.add(t.open(ctx));
+			}
+			close = false;
+			return stack;
+		} finally {
+			if (close) {
+				stack.close();
+			}
+		}
+	}
+
+	private final List<Reftable> tables;
+
+	private ReftableStack(int tableCnt) {
+		this.tables = new ArrayList<>(tableCnt);
+	}
+
+	/**
+	 * @return unmodifiable list of tables, in the same order the files were
+	 *         passed to {@link #open(DfsReader, List)}.
+	 */
+	public List<Reftable> readers() {
+		return Collections.unmodifiableList(tables);
+	}
+
+	@Override
+	public void close() {
+		for (Reftable t : tables) {
+			try {
+				t.close();
+			} catch (IOException e) {
+				// Ignore close failures.
+			}
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/CheckoutEntryImpl.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/CheckoutEntryImpl.java
index 4b4337d..2eacb7a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/CheckoutEntryImpl.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/CheckoutEntryImpl.java
@@ -74,4 +74,4 @@ public String getFromBranch() {
 	public String getToBranch() {
 		return to;
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
index 6a674aa..646feac 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
@@ -216,7 +216,7 @@ public void onConfigChanged(ConfigChangedEvent event) {
 				ConfigConstants.CONFIG_KEY_REPO_FORMAT_VERSION, 0);
 
 		String reftype = repoConfig.getString(
-				"extensions", null, "refsStorage"); //$NON-NLS-1$ //$NON-NLS-2$
+				"extensions", null, "refStorage"); //$NON-NLS-1$ //$NON-NLS-2$
 		if (repositoryFormatVersion >= 1 && reftype != null) {
 			if (StringUtils.equalsIgnoreCase(reftype, "reftree")) { //$NON-NLS-1$
 				refs = new RefTreeDatabase(this, new RefDirectory(this));
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
index 7ff209f..9300f02 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
@@ -106,10 +106,10 @@
 import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Ref.Storage;
-import org.eclipse.jgit.lib.internal.WorkQueue;
 import org.eclipse.jgit.lib.RefDatabase;
 import org.eclipse.jgit.lib.ReflogEntry;
 import org.eclipse.jgit.lib.ReflogReader;
+import org.eclipse.jgit.lib.internal.WorkQueue;
 import org.eclipse.jgit.revwalk.ObjectWalk;
 import org.eclipse.jgit.revwalk.RevObject;
 import org.eclipse.jgit.revwalk.RevWalk;
@@ -851,6 +851,12 @@ public Collection<PackFile> repack() throws IOException {
 		tagTargets.addAll(allHeadsAndTags);
 		nonHeads.addAll(indexObjects);
 
+		// Combine the GC_REST objects into the GC pack if requested
+		if (pconfig != null && pconfig.getSinglePack()) {
+			allHeadsAndTags.addAll(nonHeads);
+			nonHeads.clear();
+		}
+
 		List<PackFile> ret = new ArrayList<>(2);
 		PackFile heads = null;
 		if (!allHeadsAndTags.isEmpty()) {
@@ -884,6 +890,7 @@ public Collection<PackFile> repack() throws IOException {
 		prunePacked();
 		deleteEmptyRefsFolders();
 		deleteOrphans();
+		deleteTempPacksIdx();
 
 		lastPackedRefs = refsBefore;
 		lastRepackTime = time;
@@ -991,6 +998,28 @@ private void deleteOrphans() {
 		}
 	}
 
+	private void deleteTempPacksIdx() {
+		Path packDir = Paths.get(repo.getObjectsDirectory().getAbsolutePath(),
+				"pack"); //$NON-NLS-1$
+		Instant threshold = Instant.now().minus(1, ChronoUnit.DAYS);
+		try (DirectoryStream<Path> stream =
+				Files.newDirectoryStream(packDir, "gc_*_tmp")) { //$NON-NLS-1$
+			stream.forEach(t -> {
+				try {
+					Instant lastModified = Files.getLastModifiedTime(t)
+							.toInstant();
+					if (lastModified.isBefore(threshold)) {
+						Files.deleteIfExists(t);
+					}
+				} catch (IOException e) {
+					LOG.error(e.getMessage(), e);
+				}
+			});
+		} catch (IOException e) {
+			LOG.error(e.getMessage(), e);
+		}
+	}
+
 	/**
 	 * @param ref
 	 *            the ref which log should be inspected
@@ -1205,16 +1234,7 @@ public int compare(PackExt o1, PackExt o2) {
 			// rename the temporary files to real files
 			File realPack = nameFor(id, ".pack"); //$NON-NLS-1$
 
-			// if the packfile already exists (because we are rewriting a
-			// packfile for the same set of objects maybe with different
-			// PackConfig) then make sure we get rid of all handles on the file.
-			// Windows will not allow for rename otherwise.
-			if (realPack.exists())
-				for (PackFile p : repo.getObjectDatabase().getPacks())
-					if (realPack.getPath().equals(p.getPackFile().getPath())) {
-						p.close();
-						break;
-					}
+			repo.getObjectDatabase().closeAllPackHandles(realPack);
 			tmpPack.setReadOnly();
 
 			FileUtils.rename(tmpPack, realPack, StandardCopyOption.ATOMIC_MOVE);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GcLog.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GcLog.java
index 35049d4..e5fc0c5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GcLog.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GcLog.java
@@ -43,11 +43,6 @@
 
 package org.eclipse.jgit.internal.storage.file;
 
-import org.eclipse.jgit.api.errors.JGitInternalException;
-import org.eclipse.jgit.lib.ConfigConstants;
-import org.eclipse.jgit.util.GitDateParser;
-import org.eclipse.jgit.util.SystemReader;
-
 import static java.nio.charset.StandardCharsets.UTF_8;
 
 import java.io.File;
@@ -58,6 +53,11 @@
 import java.text.ParseException;
 import java.time.Instant;
 
+import org.eclipse.jgit.api.errors.JGitInternalException;
+import org.eclipse.jgit.lib.ConfigConstants;
+import org.eclipse.jgit.util.GitDateParser;
+import org.eclipse.jgit.util.SystemReader;
+
 /**
  * This class manages the gc.log file for a {@link FileRepository}.
  */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/InfoAttributesNode.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/InfoAttributesNode.java
index bda5cbe..3f82e2a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/InfoAttributesNode.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/InfoAttributesNode.java
@@ -78,4 +78,4 @@ public AttributesNode load() throws IOException {
 		return r.getRules().isEmpty() ? null : r;
 	}
 
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LockFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LockFile.java
index 15c5280..56f42b3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LockFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LockFile.java
@@ -385,7 +385,7 @@ public void close() throws IOException {
 		};
 	}
 
-	private void requireLock() {
+	void requireLock() {
 		if (os == null) {
 			unlock();
 			throw new IllegalStateException(MessageFormat.format(JGitText.get().lockOnNotHeld, ref));
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java
index d953b87..153c7dd 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java
@@ -220,6 +220,16 @@ public ObjectDirectoryInserter newInserter() {
 		return new ObjectDirectoryInserter(this, config);
 	}
 
+	/**
+	 * Create a new inserter that inserts all objects as pack files, not loose
+	 * objects.
+	 *
+	 * @return new inserter.
+	 */
+	public PackInserter newPackInserter() {
+		return new PackInserter(this);
+	}
+
 	@Override
 	public void close() {
 		unpackedObjectCache.clear();
@@ -814,8 +824,6 @@ private void insertPack(final PackFile pf) {
 			final PackFile[] oldList = o.packs;
 			final String name = pf.getPackFile().getName();
 			for (PackFile p : oldList) {
-				if (PackFile.SORT.compare(pf, p) < 0)
-					break;
 				if (name.equals(p.getPackFile().getName()))
 					return;
 			}
@@ -971,6 +979,21 @@ private Set<String> listPackDirectory() {
 		return nameSet;
 	}
 
+	void closeAllPackHandles(File packFile) {
+		// if the packfile already exists (because we are rewriting a
+		// packfile for the same set of objects maybe with different
+		// PackConfig) then make sure we get rid of all handles on the file.
+		// Windows will not allow for rename otherwise.
+		if (packFile.exists()) {
+			for (PackFile p : getPacks()) {
+				if (packFile.getPath().equals(p.getPackFile().getPath())) {
+					p.close();
+					break;
+				}
+			}
+		}
+	}
+
 	AlternateHandle[] myAlternates() {
 		AlternateHandle[] alt = alternates.get();
 		if (alt == null) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInputStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInputStream.java
index 154809b..962f765 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInputStream.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInputStream.java
@@ -82,4 +82,4 @@ public int read() throws IOException {
 	public void close() {
 		wc.close();
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInserter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInserter.java
new file mode 100644
index 0000000..ff959e8
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackInserter.java
@@ -0,0 +1,708 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *	 notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *	 copyright notice, this list of conditions and the following
+ *	 disclaimer in the documentation and/or other materials provided
+ *	 with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *	 names of its contributors may be used to endorse or promote
+ *	 products derived from this software without specific prior
+ *	 written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.file;
+
+import static java.nio.file.StandardCopyOption.ATOMIC_MOVE;
+import static org.eclipse.jgit.lib.Constants.OBJECT_ID_LENGTH;
+import static org.eclipse.jgit.lib.Constants.OBJ_OFS_DELTA;
+import static org.eclipse.jgit.lib.Constants.OBJ_REF_DELTA;
+
+import java.io.BufferedInputStream;
+import java.io.EOFException;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FilterInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.io.RandomAccessFile;
+import java.nio.channels.Channels;
+import java.text.MessageFormat;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.zip.CRC32;
+import java.util.zip.DataFormatException;
+import java.util.zip.Deflater;
+import java.util.zip.DeflaterOutputStream;
+import java.util.zip.Inflater;
+import java.util.zip.InflaterInputStream;
+
+import org.eclipse.jgit.errors.CorruptObjectException;
+import org.eclipse.jgit.errors.IncorrectObjectTypeException;
+import org.eclipse.jgit.errors.LargeObjectException;
+import org.eclipse.jgit.errors.MissingObjectException;
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.lib.AbbreviatedObjectId;
+import org.eclipse.jgit.lib.AnyObjectId;
+import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.InflaterCache;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectIdOwnerMap;
+import org.eclipse.jgit.lib.ObjectInserter;
+import org.eclipse.jgit.lib.ObjectLoader;
+import org.eclipse.jgit.lib.ObjectReader;
+import org.eclipse.jgit.lib.ObjectStream;
+import org.eclipse.jgit.transport.PackParser;
+import org.eclipse.jgit.transport.PackedObjectInfo;
+import org.eclipse.jgit.util.BlockList;
+import org.eclipse.jgit.util.FileUtils;
+import org.eclipse.jgit.util.IO;
+import org.eclipse.jgit.util.NB;
+import org.eclipse.jgit.util.io.CountingOutputStream;
+import org.eclipse.jgit.util.sha1.SHA1;
+
+/**
+ * Object inserter that inserts one pack per call to {@link #flush()}, and never
+ * inserts loose objects.
+ */
+public class PackInserter extends ObjectInserter {
+	/** Always produce version 2 indexes, to get CRC data. */
+	private static final int INDEX_VERSION = 2;
+
+	private final ObjectDirectory db;
+
+	private List<PackedObjectInfo> objectList;
+	private ObjectIdOwnerMap<PackedObjectInfo> objectMap;
+	private boolean rollback;
+	private boolean checkExisting = true;
+
+	private int compression = Deflater.BEST_COMPRESSION;
+	private File tmpPack;
+	private PackStream packOut;
+	private Inflater cachedInflater;
+
+	PackInserter(ObjectDirectory db) {
+		this.db = db;
+	}
+
+	/**
+	 * @param check
+	 *            if false, will write out possibly-duplicate objects without
+	 *            first checking whether they exist in the repo; default is true.
+	 */
+	public void checkExisting(boolean check) {
+		checkExisting = check;
+	}
+
+	/**
+	 * @param compression
+	 *            compression level for zlib deflater.
+	 */
+	public void setCompressionLevel(int compression) {
+		this.compression = compression;
+	}
+
+	int getBufferSize() {
+		return buffer().length;
+	}
+
+	@Override
+	public ObjectId insert(int type, byte[] data, int off, int len)
+			throws IOException {
+		ObjectId id = idFor(type, data, off, len);
+		if (objectMap != null && objectMap.contains(id)) {
+			return id;
+		}
+		// Ignore loose objects, which are potentially unreachable.
+		if (checkExisting && db.hasPackedObject(id)) {
+			return id;
+		}
+
+		long offset = beginObject(type, len);
+		packOut.compress.write(data, off, len);
+		packOut.compress.finish();
+		return endObject(id, offset);
+	}
+
+	@Override
+	public ObjectId insert(int type, long len, InputStream in)
+			throws IOException {
+		byte[] buf = buffer();
+		if (len <= buf.length) {
+			IO.readFully(in, buf, 0, (int) len);
+			return insert(type, buf, 0, (int) len);
+		}
+
+		long offset = beginObject(type, len);
+		SHA1 md = digest();
+		md.update(Constants.encodedTypeString(type));
+		md.update((byte) ' ');
+		md.update(Constants.encodeASCII(len));
+		md.update((byte) 0);
+
+		while (0 < len) {
+			int n = in.read(buf, 0, (int) Math.min(buf.length, len));
+			if (n <= 0) {
+				throw new EOFException();
+			}
+			md.update(buf, 0, n);
+			packOut.compress.write(buf, 0, n);
+			len -= n;
+		}
+		packOut.compress.finish();
+		return endObject(md.toObjectId(), offset);
+	}
+
+	private long beginObject(int type, long len) throws IOException {
+		if (packOut == null) {
+			beginPack();
+		}
+		long offset = packOut.getOffset();
+		packOut.beginObject(type, len);
+		return offset;
+	}
+
+	private ObjectId endObject(ObjectId id, long offset) {
+		PackedObjectInfo obj = new PackedObjectInfo(id);
+		obj.setOffset(offset);
+		obj.setCRC((int) packOut.crc32.getValue());
+		objectList.add(obj);
+		objectMap.addIfAbsent(obj);
+		return id;
+	}
+
+	private static File idxFor(File packFile) {
+		String p = packFile.getName();
+		return new File(
+				packFile.getParentFile(),
+				p.substring(0, p.lastIndexOf('.')) + ".idx"); //$NON-NLS-1$
+	}
+
+	private void beginPack() throws IOException {
+		objectList = new BlockList<>();
+		objectMap = new ObjectIdOwnerMap<>();
+
+		rollback = true;
+		tmpPack = File.createTempFile("insert_", ".pack", db.getDirectory()); //$NON-NLS-1$ //$NON-NLS-2$
+		packOut = new PackStream(tmpPack);
+
+		// Write the header as though it were a single object pack.
+		packOut.write(packOut.hdrBuf, 0, writePackHeader(packOut.hdrBuf, 1));
+	}
+
+	private static int writePackHeader(byte[] buf, int objectCount) {
+		System.arraycopy(Constants.PACK_SIGNATURE, 0, buf, 0, 4);
+		NB.encodeInt32(buf, 4, 2); // Always use pack version 2.
+		NB.encodeInt32(buf, 8, objectCount);
+		return 12;
+	}
+
+	@Override
+	public PackParser newPackParser(InputStream in) {
+		throw new UnsupportedOperationException();
+	}
+
+	@Override
+	public ObjectReader newReader() {
+		return new Reader();
+	}
+
+	@Override
+	public void flush() throws IOException {
+		if (tmpPack == null) {
+			return;
+		}
+
+		if (packOut == null) {
+			throw new IOException();
+		}
+
+		byte[] packHash;
+		try {
+			packHash = packOut.finishPack();
+		} finally {
+			packOut = null;
+		}
+
+		Collections.sort(objectList);
+		File tmpIdx = idxFor(tmpPack);
+		writePackIndex(tmpIdx, packHash, objectList);
+
+		File realPack = new File(
+				new File(db.getDirectory(), "pack"), //$NON-NLS-1$
+				"pack-" + computeName(objectList).name() + ".pack"); //$NON-NLS-1$ //$NON-NLS-2$
+		db.closeAllPackHandles(realPack);
+		tmpPack.setReadOnly();
+		FileUtils.rename(tmpPack, realPack, ATOMIC_MOVE);
+
+		File realIdx = idxFor(realPack);
+		tmpIdx.setReadOnly();
+		try {
+			FileUtils.rename(tmpIdx, realIdx, ATOMIC_MOVE);
+		} catch (IOException e) {
+			File newIdx = new File(
+					realIdx.getParentFile(), realIdx.getName() + ".new"); //$NON-NLS-1$
+			try {
+				FileUtils.rename(tmpIdx, newIdx, ATOMIC_MOVE);
+			} catch (IOException e2) {
+				newIdx = tmpIdx;
+				e = e2;
+			}
+			throw new IOException(MessageFormat.format(
+					JGitText.get().panicCantRenameIndexFile, newIdx,
+					realIdx), e);
+		}
+
+		db.openPack(realPack);
+		rollback = false;
+		clear();
+	}
+
+	private static void writePackIndex(File idx, byte[] packHash,
+			List<PackedObjectInfo> list) throws IOException {
+		try (OutputStream os = new FileOutputStream(idx)) {
+			PackIndexWriter w = PackIndexWriter.createVersion(os, INDEX_VERSION);
+			w.write(list, packHash);
+		}
+	}
+
+	private ObjectId computeName(List<PackedObjectInfo> list) {
+		SHA1 md = digest().reset();
+		byte[] buf = buffer();
+		for (PackedObjectInfo otp : list) {
+			otp.copyRawTo(buf, 0);
+			md.update(buf, 0, OBJECT_ID_LENGTH);
+		}
+		return ObjectId.fromRaw(md.digest());
+	}
+
+	@Override
+	public void close() {
+		try {
+			if (packOut != null) {
+				try {
+					packOut.close();
+				} catch (IOException err) {
+					// Ignore a close failure, the pack should be removed.
+				}
+			}
+			if (rollback && tmpPack != null) {
+				try {
+					FileUtils.delete(tmpPack);
+				} catch (IOException e) {
+					// Still delete idx.
+				}
+				try {
+					FileUtils.delete(idxFor(tmpPack));
+				} catch (IOException e) {
+					// Ignore error deleting temp idx.
+				}
+				rollback = false;
+			}
+		} finally {
+			clear();
+			try {
+				InflaterCache.release(cachedInflater);
+			} finally {
+				cachedInflater = null;
+			}
+		}
+	}
+
+	private void clear() {
+		objectList = null;
+		objectMap = null;
+		tmpPack = null;
+		packOut = null;
+	}
+
+	private Inflater inflater() {
+		if (cachedInflater == null) {
+			cachedInflater = InflaterCache.get();
+		} else {
+			cachedInflater.reset();
+		}
+		return cachedInflater;
+	}
+
+	/**
+	 * Stream that writes to a pack file.
+	 * <p>
+	 * Backed by two views of the same open file descriptor: a random-access file,
+	 * and an output stream. Seeking in the file causes subsequent writes to the
+	 * output stream to occur wherever the file pointer is pointing, so we need to
+	 * take care to always seek to the end of the file before writing a new
+	 * object.
+	 * <p>
+	 * Callers should always use {@link #seek(long)} to seek, rather than reaching
+	 * into the file member. As long as this contract is followed, calls to {@link
+	 * #write(byte[], int, int)} are guaranteed to write at the end of the file,
+	 * even if there have been intermediate seeks.
+	 */
+	private class PackStream extends OutputStream {
+		final byte[] hdrBuf;
+		final CRC32 crc32;
+		final DeflaterOutputStream compress;
+
+		private final RandomAccessFile file;
+		private final CountingOutputStream out;
+		private final Deflater deflater;
+
+		private boolean atEnd;
+
+		PackStream(File pack) throws IOException {
+			file = new RandomAccessFile(pack, "rw"); //$NON-NLS-1$
+			out = new CountingOutputStream(new FileOutputStream(file.getFD()));
+			deflater = new Deflater(compression);
+			compress = new DeflaterOutputStream(this, deflater, 8192);
+			hdrBuf = new byte[32];
+			crc32 = new CRC32();
+			atEnd = true;
+		}
+
+		long getOffset() {
+			// This value is accurate as long as we only ever write to the end of the
+			// file, and don't seek back to overwrite any previous segments. Although
+			// this is subtle, storing the stream counter this way is still preferable
+			// to returning file.length() here, as it avoids a syscall and possible
+			// IOException.
+			return out.getCount();
+		}
+
+		void seek(long offset) throws IOException {
+			file.seek(offset);
+			atEnd = false;
+		}
+
+		void beginObject(int objectType, long length) throws IOException {
+			crc32.reset();
+			deflater.reset();
+			write(hdrBuf, 0, encodeTypeSize(objectType, length));
+		}
+
+		private int encodeTypeSize(int type, long rawLength) {
+			long nextLength = rawLength >>> 4;
+			hdrBuf[0] = (byte) ((nextLength > 0 ? 0x80 : 0x00) | (type << 4) | (rawLength & 0x0F));
+			rawLength = nextLength;
+			int n = 1;
+			while (rawLength > 0) {
+				nextLength >>>= 7;
+				hdrBuf[n++] = (byte) ((nextLength > 0 ? 0x80 : 0x00) | (rawLength & 0x7F));
+				rawLength = nextLength;
+			}
+			return n;
+		}
+
+		@Override
+		public void write(final int b) throws IOException {
+			hdrBuf[0] = (byte) b;
+			write(hdrBuf, 0, 1);
+		}
+
+		@Override
+		public void write(byte[] data, int off, int len) throws IOException {
+			crc32.update(data, off, len);
+			if (!atEnd) {
+				file.seek(file.length());
+				atEnd = true;
+			}
+			out.write(data, off, len);
+		}
+
+		byte[] finishPack() throws IOException {
+			// Overwrite placeholder header with actual object count, then hash. This
+			// method intentionally uses direct seek/write calls rather than the
+			// wrappers which keep track of atEnd. This leaves atEnd, the file
+			// pointer, and out's counter in an inconsistent state; that's ok, since
+			// this method closes the file anyway.
+			try {
+				file.seek(0);
+				out.write(hdrBuf, 0, writePackHeader(hdrBuf, objectList.size()));
+
+				byte[] buf = buffer();
+				SHA1 md = digest().reset();
+				file.seek(0);
+				while (true) {
+					int r = file.read(buf);
+					if (r < 0) {
+						break;
+					}
+					md.update(buf, 0, r);
+				}
+				byte[] packHash = md.digest();
+				out.write(packHash, 0, packHash.length);
+				return packHash;
+			} finally {
+				close();
+			}
+		}
+
+		@Override
+		public void close() throws IOException {
+			deflater.end();
+			try {
+				out.close();
+			} finally {
+				file.close();
+			}
+		}
+
+		byte[] inflate(long filePos, int len) throws IOException, DataFormatException {
+			byte[] dstbuf;
+			try {
+				dstbuf = new byte[len];
+			} catch (OutOfMemoryError noMemory) {
+				return null; // Caller will switch to large object streaming.
+			}
+
+			byte[] srcbuf = buffer();
+			Inflater inf = inflater();
+			filePos += setInput(filePos, inf, srcbuf);
+			for (int dstoff = 0;;) {
+				int n = inf.inflate(dstbuf, dstoff, dstbuf.length - dstoff);
+				dstoff += n;
+				if (inf.finished()) {
+					return dstbuf;
+				}
+				if (inf.needsInput()) {
+					filePos += setInput(filePos, inf, srcbuf);
+				} else if (n == 0) {
+					throw new DataFormatException();
+				}
+			}
+		}
+
+		private int setInput(long filePos, Inflater inf, byte[] buf)
+				throws IOException {
+			if (file.getFilePointer() != filePos) {
+				seek(filePos);
+			}
+			int n = file.read(buf);
+			if (n < 0) {
+				throw new EOFException(JGitText.get().unexpectedEofInPack);
+			}
+			inf.setInput(buf, 0, n);
+			return n;
+		}
+	}
+
+	private class Reader extends ObjectReader {
+		private final ObjectReader ctx;
+
+		private Reader() {
+			ctx = db.newReader();
+			setStreamFileThreshold(ctx.getStreamFileThreshold());
+		}
+
+		@Override
+		public ObjectReader newReader() {
+			return db.newReader();
+		}
+
+		@Override
+		public ObjectInserter getCreatedFromInserter() {
+			return PackInserter.this;
+		}
+
+		@Override
+		public Collection<ObjectId> resolve(AbbreviatedObjectId id)
+				throws IOException {
+			Collection<ObjectId> stored = ctx.resolve(id);
+			if (objectList == null) {
+				return stored;
+			}
+
+			Set<ObjectId> r = new HashSet<>(stored.size() + 2);
+			r.addAll(stored);
+			for (PackedObjectInfo obj : objectList) {
+				if (id.prefixCompare(obj) == 0) {
+					r.add(obj.copy());
+				}
+			}
+			return r;
+		}
+
+		@Override
+		public ObjectLoader open(AnyObjectId objectId, int typeHint)
+				throws MissingObjectException, IncorrectObjectTypeException,
+				IOException {
+			if (objectMap == null) {
+				return ctx.open(objectId, typeHint);
+			}
+
+			PackedObjectInfo obj = objectMap.get(objectId);
+			if (obj == null) {
+				return ctx.open(objectId, typeHint);
+			}
+
+			byte[] buf = buffer();
+			packOut.seek(obj.getOffset());
+			int cnt = packOut.file.read(buf, 0, 20);
+			if (cnt <= 0) {
+				throw new EOFException(JGitText.get().unexpectedEofInPack);
+			}
+
+			int c = buf[0] & 0xff;
+			int type = (c >> 4) & 7;
+			if (type == OBJ_OFS_DELTA || type == OBJ_REF_DELTA) {
+				throw new IOException(MessageFormat.format(
+						JGitText.get().cannotReadBackDelta, Integer.toString(type)));
+			}
+			if (typeHint != OBJ_ANY && type != typeHint) {
+				throw new IncorrectObjectTypeException(objectId.copy(), typeHint);
+			}
+
+			long sz = c & 0x0f;
+			int ptr = 1;
+			int shift = 4;
+			while ((c & 0x80) != 0) {
+				if (ptr >= cnt) {
+					throw new EOFException(JGitText.get().unexpectedEofInPack);
+				}
+				c = buf[ptr++] & 0xff;
+				sz += ((long) (c & 0x7f)) << shift;
+				shift += 7;
+			}
+
+			long zpos = obj.getOffset() + ptr;
+			if (sz < getStreamFileThreshold()) {
+				byte[] data = inflate(obj, zpos, (int) sz);
+				if (data != null) {
+					return new ObjectLoader.SmallObject(type, data);
+				}
+			}
+			return new StreamLoader(type, sz, zpos);
+		}
+
+		private byte[] inflate(PackedObjectInfo obj, long zpos, int sz)
+				throws IOException, CorruptObjectException {
+			try {
+				return packOut.inflate(zpos, sz);
+			} catch (DataFormatException dfe) {
+				CorruptObjectException coe = new CorruptObjectException(
+						MessageFormat.format(
+								JGitText.get().objectAtHasBadZlibStream,
+								Long.valueOf(obj.getOffset()),
+								tmpPack.getAbsolutePath()));
+				coe.initCause(dfe);
+				throw coe;
+			}
+		}
+
+		@Override
+		public Set<ObjectId> getShallowCommits() throws IOException {
+			return ctx.getShallowCommits();
+		}
+
+		@Override
+		public void close() {
+			ctx.close();
+		}
+
+		private class StreamLoader extends ObjectLoader {
+			private final int type;
+			private final long size;
+			private final long pos;
+
+			StreamLoader(int type, long size, long pos) {
+				this.type = type;
+				this.size = size;
+				this.pos = pos;
+			}
+
+			@Override
+			public ObjectStream openStream()
+					throws MissingObjectException, IOException {
+				int bufsz = buffer().length;
+				packOut.seek(pos);
+
+				InputStream fileStream = new FilterInputStream(
+						Channels.newInputStream(packOut.file.getChannel())) {
+							// atEnd was already set to false by the previous seek, but it's
+							// technically possible for a caller to call insert on the
+							// inserter in the middle of reading from this stream. Behavior is
+							// undefined in this case, so it would arguably be ok to ignore,
+							// but it's not hard to at least make an attempt to not corrupt
+							// the data.
+							@Override
+							public int read() throws IOException {
+								packOut.atEnd = false;
+								return super.read();
+							}
+
+							@Override
+							public int read(byte[] b) throws IOException {
+								packOut.atEnd = false;
+								return super.read(b);
+							}
+
+							@Override
+							public int read(byte[] b, int off, int len) throws IOException {
+								packOut.atEnd = false;
+								return super.read(b,off,len);
+							}
+
+							@Override
+							public void close() {
+								// Never close underlying RandomAccessFile, which lasts the
+								// lifetime of the enclosing PackStream.
+							}
+						};
+				return new ObjectStream.Filter(
+						type, size,
+						new BufferedInputStream(
+								new InflaterInputStream(fileStream, inflater(), bufsz), bufsz));
+			}
+
+			@Override
+			public int getType() {
+				return type;
+			}
+
+			@Override
+			public long getSize() {
+				return size;
+			}
+
+			@Override
+			public byte[] getCachedBytes() throws LargeObjectException {
+				throw new LargeObjectException.ExceedsLimit(
+						getStreamFileThreshold(), size);
+			}
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackedBatchRefUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackedBatchRefUpdate.java
new file mode 100644
index 0000000..c1f5476
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackedBatchRefUpdate.java
@@ -0,0 +1,531 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.file;
+
+import static java.util.stream.Collectors.toList;
+import static org.eclipse.jgit.transport.ReceiveCommand.Result.LOCK_FAILURE;
+import static org.eclipse.jgit.transport.ReceiveCommand.Result.NOT_ATTEMPTED;
+import static org.eclipse.jgit.transport.ReceiveCommand.Result.REJECTED_NONFASTFORWARD;
+
+import java.io.IOException;
+import java.text.MessageFormat;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.eclipse.jgit.annotations.Nullable;
+import org.eclipse.jgit.errors.LockFailedException;
+import org.eclipse.jgit.errors.MissingObjectException;
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.internal.storage.file.RefDirectory.PackedRefList;
+import org.eclipse.jgit.lib.BatchRefUpdate;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectIdRef;
+import org.eclipse.jgit.lib.PersonIdent;
+import org.eclipse.jgit.lib.ProgressMonitor;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.RefDatabase;
+import org.eclipse.jgit.lib.ReflogEntry;
+import org.eclipse.jgit.revwalk.RevObject;
+import org.eclipse.jgit.revwalk.RevTag;
+import org.eclipse.jgit.revwalk.RevWalk;
+import org.eclipse.jgit.transport.ReceiveCommand;
+import org.eclipse.jgit.util.RefList;
+
+/**
+ * Implementation of {@link BatchRefUpdate} that uses the {@code packed-refs}
+ * file to support atomically updating multiple refs.
+ * <p>
+ * The algorithm is designed to be compatible with traditional single ref
+ * updates operating on single refs only. Regardless of success or failure, the
+ * results are atomic: from the perspective of any reader, either all updates in
+ * the batch will be visible, or none will. In the case of process failure
+ * during any of the following steps, removal of stale lock files is always
+ * safe, and will never result in an inconsistent state, although the update may
+ * or may not have been applied.
+ * <p>
+ * The algorithm is:
+ * <ol>
+ * <li>Pack loose refs involved in the transaction using the normal pack-refs
+ * operation. This ensures that creating lock files in the following step
+ * succeeds even if a batch contains both a delete of {@code refs/x} (loose) and
+ * a create of {@code refs/x/y}.</li>
+ * <li>Create locks for all loose refs involved in the transaction, even if they
+ * are not currently loose.</li>
+ * <li>Pack loose refs again, this time while holding all lock files (see {@link
+ * RefDirectory#pack(Map)}), without deleting them afterwards. This covers a
+ * potential race where new loose refs were created after the initial packing
+ * step. If no new loose refs were created during this race, this step does not
+ * modify any files on disk. Keep the merged state in memory.</li>
+ * <li>Update the in-memory packed refs with the commands in the batch, possibly
+ * failing the whole batch if any old ref values do not match.</li>
+ * <li>If the update succeeds, lock {@code packed-refs} and commit by atomically
+ * renaming the lock file.</li>
+ * <li>Delete loose ref lock files.</li>
+ * </ol>
+ *
+ * Because the packed-refs file format is a sorted list, this algorithm is
+ * linear in the total number of refs, regardless of the batch size. This can be
+ * a significant slowdown on repositories with large numbers of refs; callers
+ * that prefer speed over atomicity should use {@code setAtomic(false)}. As an
+ * optimization, an update containing a single ref update does not use the
+ * packed-refs protocol.
+ */
+class PackedBatchRefUpdate extends BatchRefUpdate {
+	private RefDirectory refdb;
+
+	PackedBatchRefUpdate(RefDirectory refdb) {
+		super(refdb);
+		this.refdb = refdb;
+	}
+
+	@Override
+	public void execute(RevWalk walk, ProgressMonitor monitor,
+			List<String> options) throws IOException {
+		if (!isAtomic()) {
+			// Use default one-by-one implementation.
+			super.execute(walk, monitor, options);
+			return;
+		}
+		List<ReceiveCommand> pending =
+				ReceiveCommand.filter(getCommands(), NOT_ATTEMPTED);
+		if (pending.isEmpty()) {
+			return;
+		}
+		if (pending.size() == 1) {
+			// Single-ref updates are always atomic, no need for packed-refs.
+			super.execute(walk, monitor, options);
+			return;
+		}
+
+		// Required implementation details copied from super.execute.
+		if (!blockUntilTimestamps(MAX_WAIT)) {
+			return;
+		}
+		if (options != null) {
+			setPushOptions(options);
+		}
+		// End required implementation details.
+
+		// Check for conflicting names before attempting to acquire locks, since
+		// lockfile creation may fail on file/directory conflicts.
+		if (!checkConflictingNames(pending)) {
+			return;
+		}
+
+		if (!checkObjectExistence(walk, pending)) {
+			return;
+		}
+
+		if (!checkNonFastForwards(walk, pending)) {
+			return;
+		}
+
+		// Pack refs normally, so we can create lock files even in the case where
+		// refs/x is deleted and refs/x/y is created in this batch.
+		try {
+			refdb.pack(
+					pending.stream().map(ReceiveCommand::getRefName).collect(toList()));
+		} catch (LockFailedException e) {
+			lockFailure(pending.get(0), pending);
+			return;
+		}
+
+		Map<String, LockFile> locks = null;
+		refdb.inProcessPackedRefsLock.lock();
+		try {
+			PackedRefList oldPackedList;
+			if (!refdb.isInClone()) {
+				locks = lockLooseRefs(pending);
+				if (locks == null) {
+					return;
+				}
+				oldPackedList = refdb.pack(locks);
+			} else {
+				// During clone locking isn't needed since no refs exist yet.
+				// This also helps to avoid problems with refs only differing in
+				// case on a case insensitive filesystem (bug 528497)
+				oldPackedList = refdb.getPackedRefs();
+			}
+			RefList<Ref> newRefs = applyUpdates(walk, oldPackedList, pending);
+			if (newRefs == null) {
+				return;
+			}
+			LockFile packedRefsLock = refdb.lockPackedRefs();
+			if (packedRefsLock == null) {
+				lockFailure(pending.get(0), pending);
+				return;
+			}
+			// commitPackedRefs removes lock file (by renaming over real file).
+			refdb.commitPackedRefs(packedRefsLock, newRefs, oldPackedList,
+					true);
+		} finally {
+			try {
+				unlockAll(locks);
+			} finally {
+				refdb.inProcessPackedRefsLock.unlock();
+			}
+		}
+
+		refdb.fireRefsChanged();
+		pending.forEach(c -> c.setResult(ReceiveCommand.Result.OK));
+		writeReflog(pending);
+	}
+
+	private boolean checkConflictingNames(List<ReceiveCommand> commands)
+			throws IOException {
+		Set<String> takenNames = new HashSet<>();
+		Set<String> takenPrefixes = new HashSet<>();
+		Set<String> deletes = new HashSet<>();
+		for (ReceiveCommand cmd : commands) {
+			if (cmd.getType() != ReceiveCommand.Type.DELETE) {
+				takenNames.add(cmd.getRefName());
+				addPrefixesTo(cmd.getRefName(), takenPrefixes);
+			} else {
+				deletes.add(cmd.getRefName());
+			}
+		}
+		Set<String> initialRefs = refdb.getRefs(RefDatabase.ALL).keySet();
+		for (String name : initialRefs) {
+			if (!deletes.contains(name)) {
+				takenNames.add(name);
+				addPrefixesTo(name, takenPrefixes);
+			}
+		}
+
+		for (ReceiveCommand cmd : commands) {
+			if (cmd.getType() != ReceiveCommand.Type.DELETE &&
+					takenPrefixes.contains(cmd.getRefName())) {
+				// This ref is a prefix of some other ref. This check doesn't apply when
+				// this command is a delete, because if the ref is deleted nobody will
+				// ever be creating a loose ref with that name.
+				lockFailure(cmd, commands);
+				return false;
+			}
+			for (String prefix : getPrefixes(cmd.getRefName())) {
+				if (takenNames.contains(prefix)) {
+					// A prefix of this ref is already a refname. This check does apply
+					// when this command is a delete, because we would need to create the
+					// refname as a directory in order to create a lockfile for the
+					// to-be-deleted ref.
+					lockFailure(cmd, commands);
+					return false;
+				}
+			}
+		}
+		return true;
+	}
+
+	private boolean checkObjectExistence(RevWalk walk,
+			List<ReceiveCommand> commands) throws IOException {
+		for (ReceiveCommand cmd : commands) {
+			try {
+				if (!cmd.getNewId().equals(ObjectId.zeroId())) {
+					walk.parseAny(cmd.getNewId());
+				}
+			} catch (MissingObjectException e) {
+				// ReceiveCommand#setResult(Result) converts REJECTED to
+				// REJECTED_NONFASTFORWARD, even though that result is also used for a
+				// missing object. Eagerly handle this case so we can set the right
+				// result.
+				reject(cmd, ReceiveCommand.Result.REJECTED_MISSING_OBJECT, commands);
+				return false;
+			}
+		}
+		return true;
+	}
+
+	private boolean checkNonFastForwards(RevWalk walk,
+			List<ReceiveCommand> commands) throws IOException {
+		if (isAllowNonFastForwards()) {
+			return true;
+		}
+		for (ReceiveCommand cmd : commands) {
+			cmd.updateType(walk);
+			if (cmd.getType() == ReceiveCommand.Type.UPDATE_NONFASTFORWARD) {
+				reject(cmd, REJECTED_NONFASTFORWARD, commands);
+				return false;
+			}
+		}
+		return true;
+	}
+
+	/**
+	 * Lock loose refs corresponding to a list of commands.
+	 *
+	 * @param commands
+	 *            commands that we intend to execute.
+	 * @return map of ref name in the input commands to lock file. Always contains
+	 *         one entry for each ref in the input list. All locks are acquired
+	 *         before returning. If any lock was not able to be acquired: the
+	 *         return value is null; no locks are held; and all commands that were
+	 *         pending are set to fail with {@code LOCK_FAILURE}.
+	 * @throws IOException
+	 *             an error occurred other than a failure to acquire; no locks are
+	 *             held if this exception is thrown.
+	 */
+	@Nullable
+	private Map<String, LockFile> lockLooseRefs(List<ReceiveCommand> commands)
+			throws IOException {
+		ReceiveCommand failed = null;
+		Map<String, LockFile> locks = new HashMap<>();
+		try {
+			RETRY: for (int ms : refdb.getRetrySleepMs()) {
+				failed = null;
+				// Release all locks before trying again, to prevent deadlock.
+				unlockAll(locks);
+				locks.clear();
+				RefDirectory.sleep(ms);
+
+				for (ReceiveCommand c : commands) {
+					String name = c.getRefName();
+					LockFile lock = new LockFile(refdb.fileFor(name));
+					if (locks.put(name, lock) != null) {
+						throw new IOException(
+								MessageFormat.format(JGitText.get().duplicateRef, name));
+					}
+					if (!lock.lock()) {
+						failed = c;
+						continue RETRY;
+					}
+				}
+				Map<String, LockFile> result = locks;
+				locks = null;
+				return result;
+			}
+		} finally {
+			unlockAll(locks);
+		}
+		lockFailure(failed != null ? failed : commands.get(0), commands);
+		return null;
+	}
+
+	private static RefList<Ref> applyUpdates(RevWalk walk, RefList<Ref> refs,
+			List<ReceiveCommand> commands) throws IOException {
+		int nDeletes = 0;
+		List<ReceiveCommand> adds = new ArrayList<>(commands.size());
+		for (ReceiveCommand c : commands) {
+			if (c.getType() == ReceiveCommand.Type.CREATE) {
+				adds.add(c);
+			} else if (c.getType() == ReceiveCommand.Type.DELETE) {
+				nDeletes++;
+			}
+		}
+		int addIdx = 0;
+
+		// Construct a new RefList by linearly scanning the old list, and merging in
+		// any updates.
+		Map<String, ReceiveCommand> byName = byName(commands);
+		RefList.Builder<Ref> b =
+				new RefList.Builder<>(refs.size() - nDeletes + adds.size());
+		for (Ref ref : refs) {
+			String name = ref.getName();
+			ReceiveCommand cmd = byName.remove(name);
+			if (cmd == null) {
+				b.add(ref);
+				continue;
+			}
+			if (!cmd.getOldId().equals(ref.getObjectId())) {
+				lockFailure(cmd, commands);
+				return null;
+			}
+
+			// Consume any adds between the last and current ref.
+			while (addIdx < adds.size()) {
+				ReceiveCommand currAdd = adds.get(addIdx);
+				if (currAdd.getRefName().compareTo(name) < 0) {
+					b.add(peeledRef(walk, currAdd));
+					byName.remove(currAdd.getRefName());
+				} else {
+					break;
+				}
+				addIdx++;
+			}
+
+			if (cmd.getType() != ReceiveCommand.Type.DELETE) {
+				b.add(peeledRef(walk, cmd));
+			}
+		}
+
+		// All remaining adds are valid, since the refs didn't exist.
+		while (addIdx < adds.size()) {
+			ReceiveCommand cmd = adds.get(addIdx++);
+			byName.remove(cmd.getRefName());
+			b.add(peeledRef(walk, cmd));
+		}
+
+		// Any remaining updates/deletes do not correspond to any existing refs, so
+		// they are lock failures.
+		if (!byName.isEmpty()) {
+			lockFailure(byName.values().iterator().next(), commands);
+			return null;
+		}
+
+		return b.toRefList();
+	}
+
+	private void writeReflog(List<ReceiveCommand> commands) {
+		PersonIdent ident = getRefLogIdent();
+		if (ident == null) {
+			ident = new PersonIdent(refdb.getRepository());
+		}
+		for (ReceiveCommand cmd : commands) {
+			// Assume any pending commands have already been executed atomically.
+			if (cmd.getResult() != ReceiveCommand.Result.OK) {
+				continue;
+			}
+			String name = cmd.getRefName();
+
+			if (cmd.getType() == ReceiveCommand.Type.DELETE) {
+				try {
+					RefDirectory.delete(refdb.logFor(name), RefDirectory.levelsIn(name));
+				} catch (IOException e) {
+					// Ignore failures, see below.
+				}
+				continue;
+			}
+
+			if (isRefLogDisabled(cmd)) {
+				continue;
+			}
+
+			String msg = getRefLogMessage(cmd);
+			if (isRefLogIncludingResult(cmd)) {
+				String strResult = toResultString(cmd);
+				if (strResult != null) {
+					msg = msg.isEmpty()
+							? strResult : msg + ": " + strResult; //$NON-NLS-1$
+				}
+			}
+			try {
+				new ReflogWriter(refdb, isForceRefLog(cmd))
+						.log(name, cmd.getOldId(), cmd.getNewId(), ident, msg);
+			} catch (IOException e) {
+				// Ignore failures, but continue attempting to write more reflogs.
+				//
+				// In this storage format, it is impossible to atomically write the
+				// reflog with the ref updates, so we have to choose between:
+				// a. Propagating this exception and claiming failure, even though the
+				//    actual ref updates succeeded.
+				// b. Ignoring failures writing the reflog, so we claim success if and
+				//    only if the ref updates succeeded.
+				// We choose (b) in order to surprise callers the least.
+				//
+				// Possible future improvements:
+				// * Log a warning to a logger.
+				// * Retry a fixed number of times in case the error was transient.
+			}
+		}
+	}
+
+	private String toResultString(ReceiveCommand cmd) {
+		switch (cmd.getType()) {
+		case CREATE:
+			return ReflogEntry.PREFIX_CREATED;
+		case UPDATE:
+			// Match the behavior of a single RefUpdate. In that case, setting the
+			// force bit completely bypasses the potentially expensive isMergedInto
+			// check, by design, so the reflog message may be inaccurate.
+			//
+			// Similarly, this class bypasses the isMergedInto checks when the force
+			// bit is set, meaning we can't actually distinguish between UPDATE and
+			// UPDATE_NONFASTFORWARD when isAllowNonFastForwards() returns true.
+			return isAllowNonFastForwards()
+					? ReflogEntry.PREFIX_FORCED_UPDATE : ReflogEntry.PREFIX_FAST_FORWARD;
+		case UPDATE_NONFASTFORWARD:
+			return ReflogEntry.PREFIX_FORCED_UPDATE;
+		default:
+			return null;
+		}
+	}
+
+	private static Map<String, ReceiveCommand> byName(
+			List<ReceiveCommand> commands) {
+		Map<String, ReceiveCommand> ret = new LinkedHashMap<>();
+		for (ReceiveCommand cmd : commands) {
+			ret.put(cmd.getRefName(), cmd);
+		}
+		return ret;
+	}
+
+	private static Ref peeledRef(RevWalk walk, ReceiveCommand cmd)
+			throws IOException {
+		ObjectId newId = cmd.getNewId().copy();
+		RevObject obj = walk.parseAny(newId);
+		if (obj instanceof RevTag) {
+			return new ObjectIdRef.PeeledTag(
+					Ref.Storage.PACKED, cmd.getRefName(), newId, walk.peel(obj).copy());
+		}
+		return new ObjectIdRef.PeeledNonTag(
+				Ref.Storage.PACKED, cmd.getRefName(), newId);
+	}
+
+	private static void unlockAll(@Nullable Map<?, LockFile> locks) {
+		if (locks != null) {
+			locks.values().forEach(LockFile::unlock);
+		}
+	}
+
+	private static void lockFailure(ReceiveCommand cmd,
+			List<ReceiveCommand> commands) {
+		reject(cmd, LOCK_FAILURE, commands);
+	}
+
+	private static void reject(ReceiveCommand cmd, ReceiveCommand.Result result,
+			List<ReceiveCommand> commands) {
+		cmd.setResult(result);
+		for (ReceiveCommand c2 : commands) {
+			if (c2.getResult() == ReceiveCommand.Result.OK) {
+				// Undo OK status so ReceiveCommand#abort aborts it. Assumes this method
+				// is always called before committing any updates to disk.
+				c2.setResult(ReceiveCommand.Result.NOT_ATTEMPTED);
+			}
+		}
+		ReceiveCommand.abort(commands);
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
index 8338b2c..4003b27 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
@@ -48,6 +48,7 @@
 
 import static org.eclipse.jgit.lib.Constants.CHARSET;
 import static org.eclipse.jgit.lib.Constants.HEAD;
+import static org.eclipse.jgit.lib.Constants.LOGS;
 import static org.eclipse.jgit.lib.Constants.OBJECT_ID_STRING_LENGTH;
 import static org.eclipse.jgit.lib.Constants.PACKED_REFS;
 import static org.eclipse.jgit.lib.Constants.R_HEADS;
@@ -63,19 +64,24 @@
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.io.InterruptedIOException;
 import java.nio.file.DirectoryNotEmptyException;
 import java.nio.file.Files;
 import java.security.DigestInputStream;
 import java.security.MessageDigest;
 import java.text.MessageFormat;
 import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.concurrent.atomic.AtomicReference;
+import java.util.concurrent.locks.ReentrantLock;
 
 import org.eclipse.jgit.annotations.NonNull;
+import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.errors.InvalidObjectIdException;
 import org.eclipse.jgit.errors.LockFailedException;
 import org.eclipse.jgit.errors.MissingObjectException;
@@ -138,15 +144,21 @@ public class RefDirectory extends RefDatabase {
 			Constants.MERGE_HEAD, Constants.FETCH_HEAD, Constants.ORIG_HEAD,
 			Constants.CHERRY_PICK_HEAD };
 
+	@SuppressWarnings("boxing")
+	private static final List<Integer> RETRY_SLEEP_MS =
+			Collections.unmodifiableList(Arrays.asList(0, 100, 200, 400, 800, 1600));
+
 	private final FileRepository parent;
 
 	private final File gitDir;
 
 	final File refsDir;
 
-	private final ReflogWriter logWriter;
+	final File packedRefsFile;
 
-	private final File packedRefsFile;
+	final File logsDir;
+
+	final File logsRefsDir;
 
 	/**
 	 * Immutable sorted list of loose references.
@@ -162,6 +174,22 @@ public class RefDirectory extends RefDatabase {
 	final AtomicReference<PackedRefList> packedRefs = new AtomicReference<>();
 
 	/**
+	 * Lock for coordinating operations within a single process that may contend
+	 * on the {@code packed-refs} file.
+	 * <p>
+	 * All operations that write {@code packed-refs} must still acquire a
+	 * {@link LockFile} on {@link #packedRefsFile}, even after they have acquired
+	 * this lock, since there may be multiple {@link RefDirectory} instances or
+	 * other processes operating on the same repo on disk.
+	 * <p>
+	 * This lock exists so multiple threads in the same process can wait in a fair
+	 * queue without trying, failing, and retrying to acquire the on-disk lock. If
+	 * {@code RepositoryCache} is used, this lock instance will be used by all
+	 * threads.
+	 */
+	final ReentrantLock inProcessPackedRefsLock = new ReentrantLock(true);
+
+	/**
 	 * Number of modifications made to this database.
 	 * <p>
 	 * This counter is incremented when a change is made, or detected from the
@@ -177,24 +205,43 @@ public class RefDirectory extends RefDatabase {
 	 */
 	private final AtomicInteger lastNotifiedModCnt = new AtomicInteger();
 
+	private List<Integer> retrySleepMs = RETRY_SLEEP_MS;
+
 	RefDirectory(final FileRepository db) {
 		final FS fs = db.getFS();
 		parent = db;
 		gitDir = db.getDirectory();
-		logWriter = new ReflogWriter(db);
 		refsDir = fs.resolve(gitDir, R_REFS);
+		logsDir = fs.resolve(gitDir, LOGS);
+		logsRefsDir = fs.resolve(gitDir, LOGS + '/' + R_REFS);
 		packedRefsFile = fs.resolve(gitDir, PACKED_REFS);
 
 		looseRefs.set(RefList.<LooseRef> emptyList());
-		packedRefs.set(PackedRefList.NO_PACKED_REFS);
+		packedRefs.set(NO_PACKED_REFS);
 	}
 
 	Repository getRepository() {
 		return parent;
 	}
 
-	ReflogWriter getLogWriter() {
-		return logWriter;
+	ReflogWriter newLogWriter(boolean force) {
+		return new ReflogWriter(this, force);
+	}
+
+	/**
+	 * Locate the log file on disk for a single reference name.
+	 *
+	 * @param name
+	 *            name of the ref, relative to the Git repository top level
+	 *            directory (so typically starts with refs/).
+	 * @return the log file location.
+	 */
+	public File logFor(String name) {
+		if (name.startsWith(R_REFS)) {
+			name = name.substring(R_REFS.length());
+			return new File(logsRefsDir, name);
+		}
+		return new File(logsDir, name);
 	}
 
 	@Override
@@ -202,7 +249,7 @@ public void create() throws IOException {
 		FileUtils.mkdir(refsDir);
 		FileUtils.mkdir(new File(refsDir, R_HEADS.substring(R_REFS.length())));
 		FileUtils.mkdir(new File(refsDir, R_TAGS.substring(R_REFS.length())));
-		logWriter.create();
+		newLogWriter(false).create();
 	}
 
 	@Override
@@ -212,7 +259,7 @@ public void close() {
 
 	private void clearReferences() {
 		looseRefs.set(RefList.<LooseRef> emptyList());
-		packedRefs.set(PackedRefList.NO_PACKED_REFS);
+		packedRefs.set(NO_PACKED_REFS);
 	}
 
 	@Override
@@ -565,6 +612,16 @@ public RefDirectoryRename newRename(String fromName, String toName)
 		return new RefDirectoryRename(from, to);
 	}
 
+	@Override
+	public PackedBatchRefUpdate newBatchUpdate() {
+		return new PackedBatchRefUpdate(this);
+	}
+
+	@Override
+	public boolean performsAtomicTransactions() {
+		return true;
+	}
+
 	void stored(RefDirectoryUpdate update, FileSnapshot snapshot) {
 		final ObjectId target = update.getNewObjectId().copy();
 		final Ref leaf = update.getRef().getLeaf();
@@ -583,6 +640,9 @@ private void putLooseRef(LooseRef ref) {
 
 	void delete(RefDirectoryUpdate update) throws IOException {
 		Ref dst = update.getRef();
+		if (!update.isDetachingSymbolicRef()) {
+			dst = dst.getLeaf();
+		}
 		String name = dst.getName();
 
 		// Write the packed-refs file using an atomic update. We might
@@ -590,16 +650,20 @@ void delete(RefDirectoryUpdate update) throws IOException {
 		// we don't miss an edit made externally.
 		final PackedRefList packed = getPackedRefs();
 		if (packed.contains(name)) {
-			LockFile lck = new LockFile(packedRefsFile);
-			if (!lck.lock())
-				throw new LockFailedException(packedRefsFile);
+			inProcessPackedRefsLock.lock();
 			try {
-				PackedRefList cur = readPackedRefs();
-				int idx = cur.find(name);
-				if (0 <= idx)
-					commitPackedRefs(lck, cur.remove(idx), packed);
+				LockFile lck = lockPackedRefsOrThrow();
+				try {
+					PackedRefList cur = readPackedRefs();
+					int idx = cur.find(name);
+					if (0 <= idx) {
+						commitPackedRefs(lck, cur.remove(idx), packed, true);
+					}
+				} finally {
+					lck.unlock();
+				}
 			} finally {
-				lck.unlock();
+				inProcessPackedRefsLock.unlock();
 			}
 		}
 
@@ -613,7 +677,7 @@ void delete(RefDirectoryUpdate update) throws IOException {
 		} while (!looseRefs.compareAndSet(curLoose, newLoose));
 
 		int levels = levelsIn(name) - 2;
-		delete(logWriter.logFor(name), levels);
+		delete(logFor(name), levels);
 		if (dst.getStorage().isLoose()) {
 			update.unlock();
 			delete(fileFor(name), levels);
@@ -635,75 +699,145 @@ void delete(RefDirectoryUpdate update) throws IOException {
 	 * @throws IOException
 	 */
 	public void pack(List<String> refs) throws IOException {
-		if (refs.size() == 0)
-			return;
+		pack(refs, Collections.emptyMap());
+	}
+
+	PackedRefList pack(Map<String, LockFile> heldLocks) throws IOException {
+		return pack(heldLocks.keySet(), heldLocks);
+	}
+
+	private PackedRefList pack(Collection<String> refs,
+			Map<String, LockFile> heldLocks) throws IOException {
+		for (LockFile ol : heldLocks.values()) {
+			ol.requireLock();
+		}
+		if (refs.size() == 0) {
+			return null;
+		}
 		FS fs = parent.getFS();
 
 		// Lock the packed refs file and read the content
-		LockFile lck = new LockFile(packedRefsFile);
-		if (!lck.lock())
-			throw new IOException(MessageFormat.format(
-					JGitText.get().cannotLock, packedRefsFile));
-
+		inProcessPackedRefsLock.lock();
 		try {
-			final PackedRefList packed = getPackedRefs();
-			RefList<Ref> cur = readPackedRefs();
+			LockFile lck = lockPackedRefsOrThrow();
+			try {
+				final PackedRefList packed = getPackedRefs();
+				RefList<Ref> cur = readPackedRefs();
 
-			// Iterate over all refs to be packed
-			for (String refName : refs) {
-				Ref ref = readRef(refName, cur);
-				if (ref.isSymbolic())
-					continue; // can't pack symbolic refs
-				// Add/Update it to packed-refs
-				int idx = cur.find(refName);
-				if (idx >= 0)
-					cur = cur.set(idx, peeledPackedRef(ref));
-				else
-					cur = cur.add(idx, peeledPackedRef(ref));
-			}
-
-			// The new content for packed-refs is collected. Persist it.
-			commitPackedRefs(lck, cur, packed);
-
-			// Now delete the loose refs which are now packed
-			for (String refName : refs) {
-				// Lock the loose ref
-				File refFile = fileFor(refName);
-				if (!fs.exists(refFile))
-					continue;
-				LockFile rLck = new LockFile(refFile);
-				if (!rLck.lock())
-					continue;
-				try {
-					LooseRef currentLooseRef = scanRef(null, refName);
-					if (currentLooseRef == null || currentLooseRef.isSymbolic())
-						continue;
-					Ref packedRef = cur.get(refName);
-					ObjectId clr_oid = currentLooseRef.getObjectId();
-					if (clr_oid != null
-							&& clr_oid.equals(packedRef.getObjectId())) {
-						RefList<LooseRef> curLoose, newLoose;
-						do {
-							curLoose = looseRefs.get();
-							int idx = curLoose.find(refName);
-							if (idx < 0)
-								break;
-							newLoose = curLoose.remove(idx);
-						} while (!looseRefs.compareAndSet(curLoose, newLoose));
-						int levels = levelsIn(refName) - 2;
-						delete(refFile, levels, rLck);
+				// Iterate over all refs to be packed
+				boolean dirty = false;
+				for (String refName : refs) {
+					Ref oldRef = readRef(refName, cur);
+					if (oldRef == null) {
+						continue; // A non-existent ref is already correctly packed.
 					}
-				} finally {
-					rLck.unlock();
+					if (oldRef.isSymbolic()) {
+						continue; // can't pack symbolic refs
+					}
+					// Add/Update it to packed-refs
+					Ref newRef = peeledPackedRef(oldRef);
+					if (newRef == oldRef) {
+						// No-op; peeledPackedRef returns the input ref only if it's already
+						// packed, and readRef returns a packed ref only if there is no
+						// loose ref.
+						continue;
+					}
+
+					dirty = true;
+					int idx = cur.find(refName);
+					if (idx >= 0) {
+						cur = cur.set(idx, newRef);
+					} else {
+						cur = cur.add(idx, newRef);
+					}
 				}
+				if (!dirty) {
+					// All requested refs were already packed accurately
+					return packed;
+				}
+
+				// The new content for packed-refs is collected. Persist it.
+				PackedRefList result = commitPackedRefs(lck, cur, packed,
+						false);
+
+				// Now delete the loose refs which are now packed
+				for (String refName : refs) {
+					// Lock the loose ref
+					File refFile = fileFor(refName);
+					if (!fs.exists(refFile)) {
+						continue;
+					}
+
+					LockFile rLck = heldLocks.get(refName);
+					boolean shouldUnlock;
+					if (rLck == null) {
+						rLck = new LockFile(refFile);
+						if (!rLck.lock()) {
+							continue;
+						}
+						shouldUnlock = true;
+					} else {
+						shouldUnlock = false;
+					}
+
+					try {
+						LooseRef currentLooseRef = scanRef(null, refName);
+						if (currentLooseRef == null || currentLooseRef.isSymbolic()) {
+							continue;
+						}
+						Ref packedRef = cur.get(refName);
+						ObjectId clr_oid = currentLooseRef.getObjectId();
+						if (clr_oid != null
+								&& clr_oid.equals(packedRef.getObjectId())) {
+							RefList<LooseRef> curLoose, newLoose;
+							do {
+								curLoose = looseRefs.get();
+								int idx = curLoose.find(refName);
+								if (idx < 0) {
+									break;
+								}
+								newLoose = curLoose.remove(idx);
+							} while (!looseRefs.compareAndSet(curLoose, newLoose));
+							int levels = levelsIn(refName) - 2;
+							delete(refFile, levels, rLck);
+						}
+					} finally {
+						if (shouldUnlock) {
+							rLck.unlock();
+						}
+					}
+				}
+				// Don't fire refsChanged. The refs have not change, only their
+				// storage.
+				return result;
+			} finally {
+				lck.unlock();
 			}
-			// Don't fire refsChanged. The refs have not change, only their
-			// storage.
 		} finally {
-			lck.unlock();
+			inProcessPackedRefsLock.unlock();
 		}
 	}
 
+	@Nullable
+	LockFile lockPackedRefs() throws IOException {
+		LockFile lck = new LockFile(packedRefsFile);
+		for (int ms : getRetrySleepMs()) {
+			sleep(ms);
+			if (lck.lock()) {
+				return lck;
+			}
+		}
+		return null;
+	}
+
+	private LockFile lockPackedRefsOrThrow() throws IOException {
+		LockFile lck = lockPackedRefs();
+		if (lck == null) {
+			throw new LockFailedException(packedRefsFile);
+		}
+		return lck;
+	}
+
 	/**
 	 * Make sure a ref is peeled and has the Storage PACKED. If the given ref
 	 * has this attributes simply return it. Otherwise create a new peeled
@@ -732,9 +866,9 @@ private Ref peeledPackedRef(Ref f)
 		}
 	}
 
-	void log(final RefUpdate update, final String msg, final boolean deref)
+	void log(boolean force, RefUpdate update, String msg, boolean deref)
 			throws IOException {
-		logWriter.log(update, msg, deref);
+		newLogWriter(force).log(update, msg, deref);
 	}
 
 	private Ref resolve(final Ref ref, int depth, String prefix,
@@ -769,7 +903,7 @@ else if (0 <= (idx = packed.find(dst.getName())))
 		return ref;
 	}
 
-	private PackedRefList getPackedRefs() throws IOException {
+	PackedRefList getPackedRefs() throws IOException {
 		boolean trustFolderStat = getRepository().getConfig().getBoolean(
 				ConfigConstants.CONFIG_CORE_SECTION,
 				ConfigConstants.CONFIG_KEY_TRUSTFOLDERSTAT, true);
@@ -803,7 +937,7 @@ private PackedRefList readPackedRefs() throws IOException {
 					throw noPackedRefs;
 				}
 				// Ignore it and leave the new list empty.
-				return PackedRefList.NO_PACKED_REFS;
+				return NO_PACKED_REFS;
 			}
 			try {
 				return new PackedRefList(parsePackedRefs(br), snapshot,
@@ -884,8 +1018,12 @@ private static String copy(final String src, final int off, final int end) {
 		return new StringBuilder(end - off).append(src, off, end).toString();
 	}
 
-	private void commitPackedRefs(final LockFile lck, final RefList<Ref> refs,
-			final PackedRefList oldPackedList) throws IOException {
+	PackedRefList commitPackedRefs(final LockFile lck, final RefList<Ref> refs,
+			final PackedRefList oldPackedList, boolean changed)
+			throws IOException {
+		// Can't just return packedRefs.get() from this method; it might have been
+		// updated again after writePackedRefs() returns.
+		AtomicReference<PackedRefList> result = new AtomicReference<>();
 		new RefWriter(refs) {
 			@Override
 			protected void writeFile(String name, byte[] content)
@@ -907,10 +1045,31 @@ protected void writeFile(String name, byte[] content)
 					throw new ObjectWritingException(MessageFormat.format(JGitText.get().unableToWrite, name));
 
 				byte[] digest = Constants.newMessageDigest().digest(content);
-				packedRefs.compareAndSet(oldPackedList, new PackedRefList(refs,
-						lck.getCommitSnapshot(), ObjectId.fromRaw(digest)));
+				PackedRefList newPackedList = new PackedRefList(
+						refs, lck.getCommitSnapshot(), ObjectId.fromRaw(digest));
+
+				// This thread holds the file lock, so no other thread or process should
+				// be able to modify the packed-refs file on disk. If the list changed,
+				// it means something is very wrong, so throw an exception.
+				//
+				// However, we can't use a naive compareAndSet to check whether the
+				// update was successful, because another thread might _read_ the
+				// packed refs file that was written out by this thread while holding
+				// the lock, and update the packedRefs reference to point to that. So
+				// compare the actual contents instead.
+				PackedRefList afterUpdate = packedRefs.updateAndGet(
+						p -> p.id.equals(oldPackedList.id) ? newPackedList : p);
+				if (!afterUpdate.id.equals(newPackedList.id)) {
+					throw new ObjectWritingException(
+							MessageFormat.format(JGitText.get().unableToWrite, name));
+				}
+				if (changed) {
+					modCnt.incrementAndGet();
+				}
+				result.set(newPackedList);
 			}
 		}.writePackedRefs();
+		return result.get();
 	}
 
 	private Ref readRef(String name, RefList<Ref> packed) throws IOException {
@@ -1031,8 +1190,31 @@ private static boolean isSymRef(final byte[] buf, int n) {
 				&& buf[4] == ' ';
 	}
 
+	/**
+	 * Detect if we are in a clone command execution
+	 *
+	 * @return {@code true} if we are currently cloning a repository
+	 * @throws IOException
+	 */
+	boolean isInClone() throws IOException {
+		return hasDanglingHead() && !packedRefsFile.exists() && !hasLooseRef();
+	}
+
+	private boolean hasDanglingHead() throws IOException {
+		Ref head = exactRef(Constants.HEAD);
+		if (head != null) {
+			ObjectId id = head.getObjectId();
+			return id == null || id.equals(ObjectId.zeroId());
+		}
+		return false;
+	}
+
+	private boolean hasLooseRef() throws IOException {
+		return Files.walk(refsDir.toPath()).anyMatch(Files::isRegularFile);
+	}
+
 	/** If the parent should fire listeners, fires them. */
-	private void fireRefsChanged() {
+	void fireRefsChanged() {
 		final int last = lastNotifiedModCnt.get();
 		final int curr = modCnt.get();
 		if (last != curr && lastNotifiedModCnt.compareAndSet(last, curr) && last != 0)
@@ -1107,22 +1289,80 @@ private static void delete(final File file, final int depth, LockFile rLck)
 		}
 	}
 
-	private static class PackedRefList extends RefList<Ref> {
-		static final PackedRefList NO_PACKED_REFS = new PackedRefList(
-				RefList.emptyList(), FileSnapshot.MISSING_FILE,
-				ObjectId.zeroId());
+	/**
+	 * Get times to sleep while retrying a possibly contentious operation.
+	 * <p>
+	 * For retrying an operation that might have high contention, such as locking
+	 * the {@code packed-refs} file, the caller may implement a retry loop using
+	 * the returned values:
+	 *
+	 * <pre>
+	 * for (int toSleepMs : getRetrySleepMs()) {
+	 *   sleep(toSleepMs);
+	 *   if (isSuccessful(doSomething())) {
+	 *     return success;
+	 *   }
+	 * }
+	 * return failure;
+	 * </pre>
+	 *
+	 * The first value in the returned iterable is 0, and the caller should treat
+	 * a fully-consumed iterator as a timeout.
+	 *
+	 * @return iterable of times, in milliseconds, that the caller should sleep
+	 *         before attempting an operation.
+	 */
+	Iterable<Integer> getRetrySleepMs() {
+		return retrySleepMs;
+	}
 
-		final FileSnapshot snapshot;
+	void setRetrySleepMs(List<Integer> retrySleepMs) {
+		if (retrySleepMs == null || retrySleepMs.isEmpty()
+				|| retrySleepMs.get(0).intValue() != 0) {
+			throw new IllegalArgumentException();
+		}
+		this.retrySleepMs = retrySleepMs;
+	}
 
-		final ObjectId id;
+	/**
+	 * Sleep with {@link Thread#sleep(long)}, converting {@link
+	 * InterruptedException} to {@link InterruptedIOException}.
+	 *
+	 * @param ms
+	 *            time to sleep, in milliseconds; zero or negative is a no-op.
+	 * @throws InterruptedIOException
+	 *             if sleeping was interrupted.
+	 */
+	static void sleep(long ms) throws InterruptedIOException {
+		if (ms <= 0) {
+			return;
+		}
+		try {
+			Thread.sleep(ms);
+		} catch (InterruptedException e) {
+			InterruptedIOException ie = new InterruptedIOException();
+			ie.initCause(e);
+			throw ie;
+		}
+	}
 
-		PackedRefList(RefList<Ref> src, FileSnapshot s, ObjectId i) {
+	static class PackedRefList extends RefList<Ref> {
+
+		private final FileSnapshot snapshot;
+
+		private final ObjectId id;
+
+		private PackedRefList(RefList<Ref> src, FileSnapshot s, ObjectId i) {
 			super(src);
 			snapshot = s;
 			id = i;
 		}
 	}
 
+	private static final PackedRefList NO_PACKED_REFS = new PackedRefList(
+			RefList.emptyList(), FileSnapshot.MISSING_FILE,
+			ObjectId.zeroId());
+
 	private static LooseSymbolicRef newSymbolicRef(FileSnapshot snapshot,
 			String name, String target) {
 		Ref dst = new ObjectIdRef.Unpeeled(NEW, target, null);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryRename.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryRename.java
index 4b803a5..09456c8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryRename.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryRename.java
@@ -188,8 +188,8 @@ protected Result doRename() throws IOException {
 	}
 
 	private boolean renameLog(RefUpdate src, RefUpdate dst) {
-		File srcLog = refdb.getLogWriter().logFor(src.getName());
-		File dstLog = refdb.getLogWriter().logFor(dst.getName());
+		File srcLog = refdb.logFor(src.getName());
+		File dstLog = refdb.logFor(dst.getName());
 
 		if (!srcLog.exists())
 			return true;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryUpdate.java
index 3c1916b..7ab30fa 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectoryUpdate.java
@@ -50,6 +50,7 @@
 
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.RefUpdate;
+import org.eclipse.jgit.lib.ReflogEntry;
 import org.eclipse.jgit.lib.Repository;
 
 /** Updates any reference stored by {@link RefDirectory}. */
@@ -119,7 +120,7 @@ protected Result doUpdate(final Result status) throws IOException {
 						msg = strResult;
 				}
 			}
-			database.log(this, msg, shouldDeref);
+			database.log(isForceRefLog(), this, msg, shouldDeref);
 		}
 		if (!lock.commit())
 			return Result.LOCK_FAILURE;
@@ -127,14 +128,14 @@ protected Result doUpdate(final Result status) throws IOException {
 		return status;
 	}
 
-	private String toResultString(final Result status) {
+	private String toResultString(Result status) {
 		switch (status) {
 		case FORCED:
-			return "forced-update"; //$NON-NLS-1$
+			return ReflogEntry.PREFIX_FORCED_UPDATE;
 		case FAST_FORWARD:
-			return "fast forward"; //$NON-NLS-1$
+			return ReflogEntry.PREFIX_FAST_FORWARD;
 		case NEW:
-			return "created"; //$NON-NLS-1$
+			return ReflogEntry.PREFIX_CREATED;
 		default:
 			return null;
 		}
@@ -158,7 +159,7 @@ protected Result doLink(final String target) throws IOException {
 
 		String msg = getRefLogMessage();
 		if (msg != null)
-			database.log(this, msg, false);
+			database.log(isForceRefLog(), this, msg, false);
 		if (!lock.commit())
 			return Result.LOCK_FAILURE;
 		database.storedSymbolicRef(this, lock.getCommitSnapshot(), target);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogEntryImpl.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogEntryImpl.java
index 16b2a46..8723a8b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogEntryImpl.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogEntryImpl.java
@@ -139,4 +139,4 @@ public CheckoutEntry parseCheckout() {
 		else
 			return null;
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogWriter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogWriter.java
index 892c1c8..f0bb9c5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogWriter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ReflogWriter.java
@@ -46,12 +46,11 @@
 package org.eclipse.jgit.internal.storage.file;
 
 import static org.eclipse.jgit.lib.Constants.HEAD;
-import static org.eclipse.jgit.lib.Constants.LOGS;
 import static org.eclipse.jgit.lib.Constants.LOCK_SUFFIX;
 import static org.eclipse.jgit.lib.Constants.R_HEADS;
+import static org.eclipse.jgit.lib.Constants.R_NOTES;
 import static org.eclipse.jgit.lib.Constants.R_REFS;
 import static org.eclipse.jgit.lib.Constants.R_REMOTES;
-import static org.eclipse.jgit.lib.Constants.R_STASH;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -69,110 +68,75 @@
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.RefUpdate;
 import org.eclipse.jgit.lib.ReflogEntry;
-import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
 
 /**
- * Utility for writing reflog entries
+ * Utility for writing reflog entries using the traditional one-file-per-log
+ * format.
  */
 public class ReflogWriter {
 
 	/**
-	 * Get the ref name to be used for when locking a ref's log for rewriting
+	 * Get the ref name to be used for when locking a ref's log for rewriting.
 	 *
 	 * @param name
 	 *            name of the ref, relative to the Git repository top level
 	 *            directory (so typically starts with refs/).
-	 * @return the name of the ref's lock ref
+	 * @return the name of the ref's lock ref.
 	 */
-	public static String refLockFor(final String name) {
+	public static String refLockFor(String name) {
 		return name + LOCK_SUFFIX;
 	}
 
-	private final Repository parent;
-
-	private final File logsDir;
-
-	private final File logsRefsDir;
+	private final RefDirectory refdb;
 
 	private final boolean forceWrite;
 
 	/**
-	 * Create write for repository
+	 * Create writer for ref directory.
 	 *
-	 * @param repository
+	 * @param refdb
 	 */
-	public ReflogWriter(final Repository repository) {
-		this(repository, false);
+	public ReflogWriter(RefDirectory refdb) {
+		this(refdb, false);
 	}
 
 	/**
-	 * Create write for repository
+	 * Create writer for ref directory.
 	 *
-	 * @param repository
+	 * @param refdb
 	 * @param forceWrite
 	 *            true to write to disk all entries logged, false to respect the
-	 *            repository's config and current log file status
+	 *            repository's config and current log file status.
 	 */
-	public ReflogWriter(final Repository repository, final boolean forceWrite) {
-		final FS fs = repository.getFS();
-		parent = repository;
-		File gitDir = repository.getDirectory();
-		logsDir = fs.resolve(gitDir, LOGS);
-		logsRefsDir = fs.resolve(gitDir, LOGS + '/' + R_REFS);
+	public ReflogWriter(RefDirectory refdb, boolean forceWrite) {
+		this.refdb = refdb;
 		this.forceWrite = forceWrite;
 	}
 
 	/**
-	 * Get repository that reflog is being written for
-	 *
-	 * @return file repository
-	 */
-	public Repository getRepository() {
-		return parent;
-	}
-
-	/**
-	 * Create the log directories
+	 * Create the log directories.
 	 *
 	 * @throws IOException
-	 * @return this writer
+	 * @return this writer.
 	 */
 	public ReflogWriter create() throws IOException {
-		FileUtils.mkdir(logsDir);
-		FileUtils.mkdir(logsRefsDir);
-		FileUtils.mkdir(new File(logsRefsDir,
-				R_HEADS.substring(R_REFS.length())));
+		FileUtils.mkdir(refdb.logsDir);
+		FileUtils.mkdir(refdb.logsRefsDir);
+		FileUtils.mkdir(
+				new File(refdb.logsRefsDir, R_HEADS.substring(R_REFS.length())));
 		return this;
 	}
 
 	/**
-	 * Locate the log file on disk for a single reference name.
-	 *
-	 * @param name
-	 *            name of the ref, relative to the Git repository top level
-	 *            directory (so typically starts with refs/).
-	 * @return the log file location.
-	 */
-	public File logFor(String name) {
-		if (name.startsWith(R_REFS)) {
-			name = name.substring(R_REFS.length());
-			return new File(logsRefsDir, name);
-		}
-		return new File(logsDir, name);
-	}
-
-	/**
-	 * Write the given {@link ReflogEntry} entry to the ref's log
+	 * Write the given entry to the ref's log.
 	 *
 	 * @param refName
-	 *
 	 * @param entry
 	 * @return this writer
 	 * @throws IOException
 	 */
-	public ReflogWriter log(final String refName, final ReflogEntry entry)
+	public ReflogWriter log(String refName, ReflogEntry entry)
 			throws IOException {
 		return log(refName, entry.getOldId(), entry.getNewId(), entry.getWho(),
 				entry.getComment());
@@ -189,15 +153,14 @@ public ReflogWriter log(final String refName, final ReflogEntry entry)
 	 * @return this writer
 	 * @throws IOException
 	 */
-	public ReflogWriter log(final String refName, final ObjectId oldId,
-			final ObjectId newId, final PersonIdent ident, final String message)
-			throws IOException {
+	public ReflogWriter log(String refName, ObjectId oldId,
+			ObjectId newId, PersonIdent ident, String message) throws IOException {
 		byte[] encoded = encode(oldId, newId, ident, message);
 		return log(refName, encoded);
 	}
 
 	/**
-	 * Write the given ref update to the ref's log
+	 * Write the given ref update to the ref's log.
 	 *
 	 * @param update
 	 * @param msg
@@ -205,19 +168,19 @@ public ReflogWriter log(final String refName, final ObjectId oldId,
 	 * @return this writer
 	 * @throws IOException
 	 */
-	public ReflogWriter log(final RefUpdate update, final String msg,
-			final boolean deref) throws IOException {
-		final ObjectId oldId = update.getOldObjectId();
-		final ObjectId newId = update.getNewObjectId();
-		final Ref ref = update.getRef();
+	public ReflogWriter log(RefUpdate update, String msg,
+			boolean deref) throws IOException {
+		ObjectId oldId = update.getOldObjectId();
+		ObjectId newId = update.getNewObjectId();
+		Ref ref = update.getRef();
 
 		PersonIdent ident = update.getRefLogIdent();
 		if (ident == null)
-			ident = new PersonIdent(parent);
+			ident = new PersonIdent(refdb.getRepository());
 		else
 			ident = new PersonIdent(ident);
 
-		final byte[] rec = encode(oldId, newId, ident, msg);
+		byte[] rec = encode(oldId, newId, ident, msg);
 		if (deref && ref.isSymbolic()) {
 			log(ref.getName(), rec);
 			log(ref.getLeaf().getName(), rec);
@@ -229,33 +192,34 @@ public ReflogWriter log(final RefUpdate update, final String msg,
 
 	private byte[] encode(ObjectId oldId, ObjectId newId, PersonIdent ident,
 			String message) {
-		final StringBuilder r = new StringBuilder();
+		StringBuilder r = new StringBuilder();
 		r.append(ObjectId.toString(oldId));
 		r.append(' ');
 		r.append(ObjectId.toString(newId));
 		r.append(' ');
 		r.append(ident.toExternalString());
 		r.append('\t');
-		r.append(message.replace("\r\n", " ").replace("\n", " ")); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
+		r.append(
+				message.replace("\r\n", " ") //$NON-NLS-1$ //$NON-NLS-2$
+						.replace("\n", " ")); //$NON-NLS-1$ //$NON-NLS-2$
 		r.append('\n');
 		return Constants.encode(r.toString());
 	}
 
-	private ReflogWriter log(final String refName, final byte[] rec)
-			throws IOException {
-		final File log = logFor(refName);
-		final boolean write = forceWrite
+	private ReflogWriter log(String refName, byte[] rec) throws IOException {
+		File log = refdb.logFor(refName);
+		boolean write = forceWrite
 				|| (isLogAllRefUpdates() && shouldAutoCreateLog(refName))
 				|| log.isFile();
 		if (!write)
 			return this;
 
-		WriteConfig wc = getRepository().getConfig().get(WriteConfig.KEY);
+		WriteConfig wc = refdb.getRepository().getConfig().get(WriteConfig.KEY);
 		FileOutputStream out;
 		try {
 			out = new FileOutputStream(log, true);
 		} catch (FileNotFoundException err) {
-			final File dir = log.getParentFile();
+			File dir = log.getParentFile();
 			if (dir.exists())
 				throw err;
 			if (!dir.mkdirs() && !dir.isDirectory())
@@ -279,13 +243,14 @@ private ReflogWriter log(final String refName, final byte[] rec)
 	}
 
 	private boolean isLogAllRefUpdates() {
-		return parent.getConfig().get(CoreConfig.KEY).isLogAllRefUpdates();
+		return refdb.getRepository().getConfig().get(CoreConfig.KEY)
+				.isLogAllRefUpdates();
 	}
 
-	private boolean shouldAutoCreateLog(final String refName) {
-		return refName.equals(HEAD) //
-				|| refName.startsWith(R_HEADS) //
-				|| refName.startsWith(R_REMOTES) //
-				|| refName.equals(R_STASH);
+	private boolean shouldAutoCreateLog(String refName) {
+		return refName.equals(HEAD)
+				|| refName.startsWith(R_HEADS)
+				|| refName.startsWith(R_REMOTES)
+				|| refName.startsWith(R_NOTES);
 	}
-}
+}
\ No newline at end of file
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/SimpleDataOutput.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/SimpleDataOutput.java
index 373a494..5fe0429 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/SimpleDataOutput.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/SimpleDataOutput.java
@@ -136,4 +136,4 @@ public void writeChars(String s) throws IOException {
 	public void writeUTF(String s) throws IOException {
 		throw new UnsupportedOperationException();
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCache.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCache.java
index a525c85..6196006 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCache.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCache.java
@@ -496,31 +496,16 @@ private void removeAll(final PackFile pack) {
 	private void gc() {
 		Ref r;
 		while ((r = (Ref) queue.poll()) != null) {
-			// Sun's Java 5 and 6 implementation have a bug where a Reference
-			// can be enqueued and dequeued twice on the same reference queue
-			// due to a race condition within ReferenceQueue.enqueue(Reference).
-			//
-			// http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6837858
-			//
-			// We CANNOT permit a Reference to come through us twice, as it will
-			// skew the resource counters we maintain. Our canClear() check here
-			// provides a way to skip the redundant dequeues, if any.
-			//
-			if (r.canClear()) {
-				clear(r);
+			clear(r);
 
-				boolean found = false;
-				final int s = slot(r.pack, r.position);
-				final Entry e1 = table.get(s);
-				for (Entry n = e1; n != null; n = n.next) {
-					if (n.ref == r) {
-						n.dead = true;
-						found = true;
-						break;
-					}
-				}
-				if (found)
+			final int s = slot(r.pack, r.position);
+			final Entry e1 = table.get(s);
+			for (Entry n = e1; n != null; n = n.next) {
+				if (n.ref == r) {
+					n.dead = true;
 					table.compareAndSet(s, e1, clean(e1));
+					break;
+				}
 			}
 		}
 	}
@@ -581,8 +566,6 @@ private static class Ref extends SoftReference<ByteWindow> {
 
 		long lastAccess;
 
-		private boolean cleared;
-
 		protected Ref(final PackFile pack, final long position,
 				final ByteWindow v, final ReferenceQueue<ByteWindow> queue) {
 			super(v, queue);
@@ -590,13 +573,6 @@ protected Ref(final PackFile pack, final long position,
 			this.position = position;
 			this.size = v.size();
 		}
-
-		final synchronized boolean canClear() {
-			if (cleared)
-				return false;
-			cleared = true;
-			return true;
-		}
 	}
 
 	private static final class Lock {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WriteConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WriteConfig.java
index 1e2b239..d9cbbd8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WriteConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WriteConfig.java
@@ -49,12 +49,7 @@
 
 class WriteConfig {
 	/** Key for {@link Config#get(SectionParser)}. */
-	static final Config.SectionParser<WriteConfig> KEY = new SectionParser<WriteConfig>() {
-		@Override
-		public WriteConfig parse(final Config cfg) {
-			return new WriteConfig(cfg);
-		}
-	};
+	static final Config.SectionParser<WriteConfig> KEY = WriteConfig::new;
 
 	private final int compression;
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/io/BlockSource.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/io/BlockSource.java
new file mode 100644
index 0000000..0a5f9c1
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/io/BlockSource.java
@@ -0,0 +1,185 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.io;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.channels.FileChannel;
+
+/**
+ * Provides content blocks of file.
+ * <p>
+ * {@code BlockSource} implementations must decide if they will be thread-safe,
+ * or not.
+ */
+public abstract class BlockSource implements AutoCloseable {
+	/**
+	 * Wrap a byte array as a {@code BlockSource}.
+	 *
+	 * @param content
+	 *            input file.
+	 * @return block source to read from {@code content}.
+	 */
+	public static BlockSource from(byte[] content) {
+		return new BlockSource() {
+			@Override
+			public ByteBuffer read(long pos, int cnt) {
+				ByteBuffer buf = ByteBuffer.allocate(cnt);
+				if (pos < content.length) {
+					int p = (int) pos;
+					int n = Math.min(cnt, content.length - p);
+					buf.put(content, p, n);
+				}
+				return buf;
+			}
+
+			@Override
+			public long size() {
+				return content.length;
+			}
+
+			@Override
+			public void close() {
+				// Do nothing.
+			}
+		};
+	}
+
+	/**
+	 * Read from a {@code FileInputStream}.
+	 * <p>
+	 * The returned {@code BlockSource} is not thread-safe, as it must seek the
+	 * file channel to read a block.
+	 *
+	 * @param in
+	 *            the file. The {@code BlockSource} will close {@code in}.
+	 * @return wrapper for {@code in}.
+	 */
+	public static BlockSource from(FileInputStream in) {
+		return from(in.getChannel());
+	}
+
+	/**
+	 * Read from a {@code FileChannel}.
+	 * <p>
+	 * The returned {@code BlockSource} is not thread-safe, as it must seek the
+	 * file channel to read a block.
+	 *
+	 * @param ch
+	 *            the file. The {@code BlockSource} will close {@code ch}.
+	 * @return wrapper for {@code ch}.
+	 */
+	public static BlockSource from(FileChannel ch) {
+		return new BlockSource() {
+			@Override
+			public ByteBuffer read(long pos, int blockSize) throws IOException {
+				ByteBuffer b = ByteBuffer.allocate(blockSize);
+				ch.position(pos);
+				int n;
+				do {
+					n = ch.read(b);
+				} while (n > 0 && b.position() < blockSize);
+				return b;
+			}
+
+			@Override
+			public long size() throws IOException {
+				return ch.size();
+			}
+
+			@Override
+			public void close() {
+				try {
+					ch.close();
+				} catch (IOException e) {
+					// Ignore close failures of read-only files.
+				}
+			}
+		};
+	}
+
+	/**
+	 * Read a block from the file.
+	 * <p>
+	 * To reduce copying, the returned ByteBuffer should have an accessible
+	 * array and {@code arrayOffset() == 0}. The caller will discard the
+	 * ByteBuffer and directly use the backing array.
+	 *
+	 * @param position
+	 *            position of the block in the file, specified in bytes from the
+	 *            beginning of the file.
+	 * @param blockSize
+	 *            size to read.
+	 * @return buffer containing the block content.
+	 * @throws IOException
+	 *             if block cannot be read.
+	 */
+	public abstract ByteBuffer read(long position, int blockSize)
+			throws IOException;
+
+	/**
+	 * Determine the size of the file.
+	 *
+	 * @return total number of bytes in the file.
+	 * @throws IOException
+	 *             if size cannot be obtained.
+	 */
+	public abstract long size() throws IOException;
+
+	/**
+	 * Advise the {@code BlockSource} a sequential scan is starting.
+	 *
+	 * @param startPos
+	 *            starting position.
+	 * @param endPos
+	 *            ending position.
+	 */
+	public void adviseSequentialRead(long startPos, long endPos) {
+		// Do nothing by default.
+	}
+
+	@Override
+	public abstract void close();
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/DeltaIndexScanner.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/DeltaIndexScanner.java
index 7e10878..969d02b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/DeltaIndexScanner.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/DeltaIndexScanner.java
@@ -127,4 +127,4 @@ private static int tableSize(final int worstCaseBlockCnt) {
 			sz <<= 1;
 		return sz;
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/ObjectToPack.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/ObjectToPack.java
index a089657..bc7a603 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/ObjectToPack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/ObjectToPack.java
@@ -182,6 +182,7 @@ public final boolean isWritten() {
 	}
 
 	/** @return the type of this object. */
+	@Override
 	public final int getType() {
 		return (flags >> TYPE_SHIFT) & 0x7;
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackExt.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackExt.java
index 248692f..e8bbf78 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackExt.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackExt.java
@@ -59,6 +59,9 @@ public class PackExt {
 	/** A pack bitmap index file extension. */
 	public static final PackExt BITMAP_INDEX = newPackExt("bitmap"); //$NON-NLS-1$
 
+	/** A reftable file. */
+	public static final PackExt REFTABLE = newPackExt("ref"); //$NON-NLS-1$
+
 	/** @return all of the PackExt values. */
 	public static PackExt[] values() {
 		return VALUES;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/BlockReader.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/BlockReader.java
new file mode 100644
index 0000000..ce2ba4a
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/BlockReader.java
@@ -0,0 +1,589 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.reftable;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.eclipse.jgit.internal.storage.reftable.BlockWriter.compare;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.FILE_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.FILE_HEADER_LEN;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.INDEX_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.LOG_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.LOG_DATA;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.LOG_NONE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.OBJ_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.REF_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.VALUE_1ID;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.VALUE_2ID;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.VALUE_NONE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.VALUE_SYMREF;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.VALUE_TYPE_MASK;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.reverseUpdateIndex;
+import static org.eclipse.jgit.lib.Constants.OBJECT_ID_LENGTH;
+import static org.eclipse.jgit.lib.Ref.Storage.NEW;
+import static org.eclipse.jgit.lib.Ref.Storage.PACKED;
+
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.util.Arrays;
+import java.util.zip.DataFormatException;
+import java.util.zip.Inflater;
+
+import org.eclipse.jgit.annotations.Nullable;
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.internal.storage.io.BlockSource;
+import org.eclipse.jgit.lib.CheckoutEntry;
+import org.eclipse.jgit.lib.InflaterCache;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectIdRef;
+import org.eclipse.jgit.lib.PersonIdent;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.ReflogEntry;
+import org.eclipse.jgit.lib.SymbolicRef;
+import org.eclipse.jgit.util.LongList;
+import org.eclipse.jgit.util.NB;
+import org.eclipse.jgit.util.RawParseUtils;
+
+/** Reads a single block for {@link ReftableReader}. */
+class BlockReader {
+	private byte blockType;
+	private long endPosition;
+	private boolean truncated;
+
+	private byte[] buf;
+	private int bufLen;
+	private int ptr;
+
+	private int keysStart;
+	private int keysEnd;
+
+	private int restartCnt;
+	private int restartTbl;
+
+	private byte[] nameBuf = new byte[256];
+	private int nameLen;
+	private int valueType;
+
+	byte type() {
+		return blockType;
+	}
+
+	boolean truncated() {
+		return truncated;
+	}
+
+	long endPosition() {
+		return endPosition;
+	}
+
+	boolean next() {
+		return ptr < keysEnd;
+	}
+
+	void parseKey() {
+		int pfx = readVarint32();
+		valueType = readVarint32();
+		int sfx = valueType >>> 3;
+		if (pfx + sfx > nameBuf.length) {
+			int n = Math.max(pfx + sfx, nameBuf.length * 2);
+			nameBuf = Arrays.copyOf(nameBuf, n);
+		}
+		System.arraycopy(buf, ptr, nameBuf, pfx, sfx);
+		ptr += sfx;
+		nameLen = pfx + sfx;
+	}
+
+	String name() {
+		int len = nameLen;
+		if (blockType == LOG_BLOCK_TYPE) {
+			len -= 9;
+		}
+		return RawParseUtils.decode(UTF_8, nameBuf, 0, len);
+	}
+
+	boolean match(byte[] match, boolean matchIsPrefix) {
+		int len = nameLen;
+		if (blockType == LOG_BLOCK_TYPE) {
+			len -= 9;
+		}
+		if (matchIsPrefix) {
+			return len >= match.length
+					&& compare(
+							match, 0, match.length,
+							nameBuf, 0, match.length) == 0;
+		}
+		return compare(match, 0, match.length, nameBuf, 0, len) == 0;
+	}
+
+	long readPositionFromIndex() throws IOException {
+		if (blockType != INDEX_BLOCK_TYPE) {
+			throw invalidBlock();
+		}
+
+		readVarint32(); // skip prefix length
+		int n = readVarint32() >>> 3;
+		ptr += n; // skip name
+		return readVarint64();
+	}
+
+	long readUpdateIndexDelta() {
+		return readVarint64();
+	}
+
+	Ref readRef() throws IOException {
+		String name = RawParseUtils.decode(UTF_8, nameBuf, 0, nameLen);
+		switch (valueType & VALUE_TYPE_MASK) {
+		case VALUE_NONE: // delete
+			return newRef(name);
+
+		case VALUE_1ID:
+			return new ObjectIdRef.PeeledNonTag(PACKED, name, readValueId());
+
+		case VALUE_2ID: { // annotated tag
+			ObjectId id1 = readValueId();
+			ObjectId id2 = readValueId();
+			return new ObjectIdRef.PeeledTag(PACKED, name, id1, id2);
+		}
+
+		case VALUE_SYMREF: {
+			String val = readValueString();
+			return new SymbolicRef(name, newRef(val));
+		}
+
+		default:
+			throw invalidBlock();
+		}
+	}
+
+	@Nullable
+	LongList readBlockPositionList() {
+		int n = valueType & VALUE_TYPE_MASK;
+		if (n == 0) {
+			n = readVarint32();
+			if (n == 0) {
+				return null;
+			}
+		}
+
+		LongList b = new LongList(n);
+		b.add(readVarint64());
+		for (int j = 1; j < n; j++) {
+			long prior = b.get(j - 1);
+			b.add(prior + readVarint64());
+		}
+		return b;
+	}
+
+	long readLogUpdateIndex() {
+		return reverseUpdateIndex(NB.decodeUInt64(nameBuf, nameLen - 8));
+	}
+
+	@Nullable
+	ReflogEntry readLogEntry() {
+		if ((valueType & VALUE_TYPE_MASK) == LOG_NONE) {
+			return null;
+		}
+
+		ObjectId oldId = readValueId();
+		ObjectId newId = readValueId();
+		PersonIdent who = readPersonIdent();
+		String msg = readValueString();
+
+		return new ReflogEntry() {
+			@Override
+			public ObjectId getOldId() {
+				return oldId;
+			}
+
+			@Override
+			public ObjectId getNewId() {
+				return newId;
+			}
+
+			@Override
+			public PersonIdent getWho() {
+				return who;
+			}
+
+			@Override
+			public String getComment() {
+				return msg;
+			}
+
+			@Override
+			public CheckoutEntry parseCheckout() {
+				return null;
+			}
+		};
+	}
+
+	private ObjectId readValueId() {
+		ObjectId id = ObjectId.fromRaw(buf, ptr);
+		ptr += OBJECT_ID_LENGTH;
+		return id;
+	}
+
+	private String readValueString() {
+		int len = readVarint32();
+		int end = ptr + len;
+		String s = RawParseUtils.decode(UTF_8, buf, ptr, end);
+		ptr = end;
+		return s;
+	}
+
+	private PersonIdent readPersonIdent() {
+		String name = readValueString();
+		String email = readValueString();
+		long ms = readVarint64() * 1000;
+		int tz = readInt16();
+		return new PersonIdent(name, email, ms, tz);
+	}
+
+	void readBlock(BlockSource src, long pos, int fileBlockSize)
+			throws IOException {
+		readBlockIntoBuf(src, pos, fileBlockSize);
+		parseBlockStart(src, pos, fileBlockSize);
+	}
+
+	private void readBlockIntoBuf(BlockSource src, long pos, int size)
+			throws IOException {
+		ByteBuffer b = src.read(pos, size);
+		bufLen = b.position();
+		if (bufLen <= 0) {
+			throw invalidBlock();
+		}
+		if (b.hasArray() && b.arrayOffset() == 0) {
+			buf = b.array();
+		} else {
+			buf = new byte[bufLen];
+			b.flip();
+			b.get(buf);
+		}
+		endPosition = pos + bufLen;
+	}
+
+	private void parseBlockStart(BlockSource src, long pos, int fileBlockSize)
+			throws IOException {
+		ptr = 0;
+		if (pos == 0) {
+			if (bufLen == FILE_HEADER_LEN) {
+				setupEmptyFileBlock();
+				return;
+			}
+			ptr += FILE_HEADER_LEN; // first block begins with file header
+		}
+
+		int typeAndSize = NB.decodeInt32(buf, ptr);
+		ptr += 4;
+
+		blockType = (byte) (typeAndSize >>> 24);
+		int blockLen = decodeBlockLen(typeAndSize);
+		if (blockType == LOG_BLOCK_TYPE) {
+			// Log blocks must be inflated after the header.
+			long deflatedSize = inflateBuf(src, pos, blockLen, fileBlockSize);
+			endPosition = pos + 4 + deflatedSize;
+		}
+		if (bufLen < blockLen) {
+			if (blockType != INDEX_BLOCK_TYPE) {
+				throw invalidBlock();
+			}
+			// Its OK during sequential scan for an index block to have been
+			// partially read and be truncated in-memory. This happens when
+			// the index block is larger than the file's blockSize. Caller
+			// will break out of its scan loop once it sees the blockType.
+			truncated = true;
+		} else if (bufLen > blockLen) {
+			bufLen = blockLen;
+		}
+
+		if (blockType != FILE_BLOCK_TYPE) {
+			restartCnt = NB.decodeUInt16(buf, bufLen - 2);
+			restartTbl = bufLen - (restartCnt * 3 + 2);
+			keysStart = ptr;
+			keysEnd = restartTbl;
+		} else {
+			keysStart = ptr;
+			keysEnd = ptr;
+		}
+	}
+
+	static int decodeBlockLen(int typeAndSize) {
+		return typeAndSize & 0xffffff;
+	}
+
+	private long inflateBuf(BlockSource src, long pos, int blockLen,
+			int fileBlockSize) throws IOException {
+		byte[] dst = new byte[blockLen];
+		System.arraycopy(buf, 0, dst, 0, 4);
+
+		long deflatedSize = 0;
+		Inflater inf = InflaterCache.get();
+		try {
+			inf.setInput(buf, ptr, bufLen - ptr);
+			for (int o = 4;;) {
+				int n = inf.inflate(dst, o, dst.length - o);
+				o += n;
+				if (inf.finished()) {
+					deflatedSize = inf.getBytesRead();
+					break;
+				} else if (n <= 0 && inf.needsInput()) {
+					long p = pos + 4 + inf.getBytesRead();
+					readBlockIntoBuf(src, p, fileBlockSize);
+					inf.setInput(buf, 0, bufLen);
+				} else if (n <= 0) {
+					throw invalidBlock();
+				}
+			}
+		} catch (DataFormatException e) {
+			throw invalidBlock(e);
+		} finally {
+			InflaterCache.release(inf);
+		}
+
+		buf = dst;
+		bufLen = dst.length;
+		return deflatedSize;
+	}
+
+	private void setupEmptyFileBlock() {
+		// An empty reftable has only the file header in first block.
+		blockType = FILE_BLOCK_TYPE;
+		ptr = FILE_HEADER_LEN;
+		restartCnt = 0;
+		restartTbl = bufLen;
+		keysStart = bufLen;
+		keysEnd = bufLen;
+	}
+
+	void verifyIndex() throws IOException {
+		if (blockType != INDEX_BLOCK_TYPE || truncated) {
+			throw invalidBlock();
+		}
+	}
+
+	/**
+	 * Finds a key in the block and positions the current pointer on its record.
+	 * <p>
+	 * As a side-effect this method arranges for the current pointer to be near
+	 * or exactly on {@code key}, allowing other methods to access data from
+	 * that current record:
+	 * <ul>
+	 * <li>{@link #name()}
+	 * <li>{@link #match(byte[], boolean)}
+	 * <li>{@link #readRef()}
+	 * <li>{@link #readLogUpdateIndex()}
+	 * <li>{@link #readLogEntry()}
+	 * <li>{@link #readBlockPositionList()}
+	 * </ul>
+	 *
+	 * @param key
+	 *            key to find.
+	 * @return {@code <0} if the key occurs before the start of this block;
+	 *         {@code 0} if the block is positioned on the key; {@code >0} if
+	 *         the key occurs after the last key of this block.
+	 */
+	int seekKey(byte[] key) {
+		int low = 0;
+		int end = restartCnt;
+		for (;;) {
+			int mid = (low + end) >>> 1;
+			int p = NB.decodeUInt24(buf, restartTbl + mid * 3);
+			ptr = p + 1; // skip 0 prefix length
+			int n = readVarint32() >>> 3;
+			int cmp = compare(key, 0, key.length, buf, ptr, n);
+			if (cmp < 0) {
+				end = mid;
+			} else if (cmp == 0) {
+				ptr = p;
+				return 0;
+			} else /* if (cmp > 0) */ {
+				low = mid + 1;
+			}
+			if (low >= end) {
+				return scanToKey(key, p, low, cmp);
+			}
+		}
+	}
+
+	/**
+	 * Performs the linear search step within a restart interval.
+	 * <p>
+	 * Starts at a restart position whose key sorts before (or equal to)
+	 * {@code key} and walks sequentially through the following prefix
+	 * compressed records to find {@code key}.
+	 *
+	 * @param key
+	 *            key the caller wants to find.
+	 * @param rPtr
+	 *            current record pointer from restart table binary search.
+	 * @param rIdx
+	 *            current restart table index.
+	 * @param rCmp
+	 *            result of compare from restart table binary search.
+	 * @return {@code <0} if the key occurs before the start of this block;
+	 *         {@code 0} if the block is positioned on the key; {@code >0} if
+	 *         the key occurs after the last key of this block.
+	 */
+	private int scanToKey(byte[] key, int rPtr, int rIdx, int rCmp) {
+		if (rCmp < 0) {
+			if (rIdx == 0) {
+				ptr = keysStart;
+				return -1;
+			}
+			ptr = NB.decodeUInt24(buf, restartTbl + (rIdx - 1) * 3);
+		} else {
+			ptr = rPtr;
+		}
+
+		int cmp;
+		do {
+			int savePtr = ptr;
+			parseKey();
+			cmp = compare(key, 0, key.length, nameBuf, 0, nameLen);
+			if (cmp <= 0) {
+				// cmp < 0, name should be in this block, but is not.
+				// cmp = 0, block is positioned at name.
+				ptr = savePtr;
+				return cmp < 0 && savePtr == keysStart ? -1 : 0;
+			}
+			skipValue();
+		} while (ptr < keysEnd);
+		return cmp;
+	}
+
+	void skipValue() {
+		switch (blockType) {
+		case REF_BLOCK_TYPE:
+			readVarint64(); // update_index_delta
+			switch (valueType & VALUE_TYPE_MASK) {
+			case VALUE_NONE:
+				return;
+			case VALUE_1ID:
+				ptr += OBJECT_ID_LENGTH;
+				return;
+			case VALUE_2ID:
+				ptr += 2 * OBJECT_ID_LENGTH;
+				return;
+			case VALUE_SYMREF:
+				skipString();
+				return;
+			}
+			break;
+
+		case OBJ_BLOCK_TYPE: {
+			int n = valueType & VALUE_TYPE_MASK;
+			if (n == 0) {
+				n = readVarint32();
+			}
+			while (n-- > 0) {
+				readVarint32();
+			}
+			return;
+		}
+
+		case INDEX_BLOCK_TYPE:
+			readVarint32();
+			return;
+
+		case LOG_BLOCK_TYPE:
+			if ((valueType & VALUE_TYPE_MASK) == LOG_NONE) {
+				return;
+			} else if ((valueType & VALUE_TYPE_MASK) == LOG_DATA) {
+				ptr += 2 * OBJECT_ID_LENGTH; // oldId, newId
+				skipString(); // name
+				skipString(); // email
+				readVarint64(); // time
+				ptr += 2; // tz
+				skipString(); // msg
+				return;
+			}
+		}
+
+		throw new IllegalStateException();
+	}
+
+	private void skipString() {
+		int n = readVarint32(); // string length
+		ptr += n;
+	}
+
+	private short readInt16() {
+		return (short) NB.decodeUInt16(buf, ptr += 2);
+	}
+
+	private int readVarint32() {
+		byte c = buf[ptr++];
+		int val = c & 0x7f;
+		while ((c & 0x80) != 0) {
+			c = buf[ptr++];
+			val++;
+			val <<= 7;
+			val |= (c & 0x7f);
+		}
+		return val;
+	}
+
+	private long readVarint64() {
+		byte c = buf[ptr++];
+		long val = c & 0x7f;
+		while ((c & 0x80) != 0) {
+			c = buf[ptr++];
+			val++;
+			val <<= 7;
+			val |= (c & 0x7f);
+		}
+		return val;
+	}
+
+	private static Ref newRef(String name) {
+		return new ObjectIdRef.Unpeeled(NEW, name, null);
+	}
+
+	private static IOException invalidBlock() {
+		return invalidBlock(null);
+	}
+
+	private static IOException invalidBlock(Throwable cause) {
+		return new IOException(JGitText.get().invalidReftableBlock, cause);
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/BlockSizeTooSmallException.java
similarity index 78%
rename from org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
rename to org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/BlockSizeTooSmallException.java
index 98a2a94..cb0f988 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/BlockSizeTooSmallException.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2011, Google Inc.
+ * Copyright (C) 2017, Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -41,20 +41,22 @@
  * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.eclipse.jgit.internal.storage.dfs;
+package org.eclipse.jgit.internal.storage.reftable;
 
-import java.util.concurrent.atomic.AtomicLong;
+import java.io.IOException;
 
-final class DfsPackKey {
-	final int hash;
+/** Thrown if {@link ReftableWriter} cannot fit a reference. */
+public class BlockSizeTooSmallException extends IOException {
+	private static final long serialVersionUID = 1L;
 
-	final AtomicLong cachedSize;
+	private final int minBlockSize;
 
-	DfsPackKey() {
-		// Multiply by 31 here so we can more directly combine with another
-		// value without doing the multiply there.
-		//
-		hash = System.identityHashCode(this) * 31;
-		cachedSize = new AtomicLong();
+	BlockSizeTooSmallException(int b) {
+		minBlockSize = b;
+	}
+
+	/** @return minimum block size in bytes reftable requires to write a ref. */
+	public int getMinimumBlockSize() {
+		return minBlockSize;
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/BlockWriter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/BlockWriter.java
new file mode 100644
index 0000000..b3173e8
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/BlockWriter.java
@@ -0,0 +1,605 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.reftable;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.FILE_HEADER_LEN;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.INDEX_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.LOG_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.LOG_DATA;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.LOG_NONE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.MAX_RESTARTS;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.OBJ_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.REF_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.VALUE_1ID;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.VALUE_2ID;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.VALUE_NONE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.VALUE_SYMREF;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.VALUE_TYPE_MASK;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.reverseUpdateIndex;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableOutputStream.computeVarintSize;
+import static org.eclipse.jgit.lib.Constants.OBJECT_ID_LENGTH;
+import static org.eclipse.jgit.lib.Ref.Storage.NEW;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.PersonIdent;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.util.IntList;
+import org.eclipse.jgit.util.LongList;
+import org.eclipse.jgit.util.NB;
+
+/** Formats and writes blocks for {@link ReftableWriter}. */
+class BlockWriter {
+	private final byte blockType;
+	private final byte keyType;
+	private final List<Entry> entries;
+	private final int blockLimitBytes;
+	private final int restartInterval;
+
+	private int entriesSumBytes;
+	private int restartCnt;
+
+	BlockWriter(byte type, byte kt, int bs, int ri) {
+		blockType = type;
+		keyType = kt;
+		blockLimitBytes = bs;
+		restartInterval = ri;
+		entries = new ArrayList<>(estimateEntryCount(type, kt, bs));
+	}
+
+	private static int estimateEntryCount(byte blockType, byte keyType,
+			int blockLimitBytes) {
+		double avgBytesPerEntry;
+		switch (blockType) {
+		case REF_BLOCK_TYPE:
+		default:
+			avgBytesPerEntry = 35.31;
+			break;
+
+		case OBJ_BLOCK_TYPE:
+			avgBytesPerEntry = 4.19;
+			break;
+
+		case LOG_BLOCK_TYPE:
+			avgBytesPerEntry = 101.14;
+			break;
+
+		case INDEX_BLOCK_TYPE:
+			switch (keyType) {
+			case REF_BLOCK_TYPE:
+			case LOG_BLOCK_TYPE:
+			default:
+				avgBytesPerEntry = 27.44;
+				break;
+
+			case OBJ_BLOCK_TYPE:
+				avgBytesPerEntry = 11.57;
+				break;
+			}
+		}
+
+		int cnt = (int) (Math.ceil(blockLimitBytes / avgBytesPerEntry));
+		return Math.min(cnt, 4096);
+	}
+
+	byte blockType() {
+		return blockType;
+	}
+
+	boolean padBetweenBlocks() {
+		return padBetweenBlocks(blockType)
+				|| (blockType == INDEX_BLOCK_TYPE && padBetweenBlocks(keyType));
+	}
+
+	static boolean padBetweenBlocks(byte type) {
+		return type == REF_BLOCK_TYPE || type == OBJ_BLOCK_TYPE;
+	}
+
+	byte[] lastKey() {
+		return entries.get(entries.size() - 1).key;
+	}
+
+	int currentSize() {
+		return computeBlockBytes(0, false);
+	}
+
+	void mustAdd(Entry entry) throws BlockSizeTooSmallException {
+		if (!tryAdd(entry, true)) {
+			// Insanely long names need a larger block size.
+			throw blockSizeTooSmall(entry);
+		}
+	}
+
+	boolean tryAdd(Entry entry) {
+		if (entry instanceof ObjEntry
+				&& computeBlockBytes(entry.sizeBytes(), 1) > blockLimitBytes) {
+			// If the ObjEntry has so many ref block pointers that its
+			// encoding overflows any block, reconfigure it to tell readers to
+			// instead scan all refs for this ObjectId. That significantly
+			// shrinks the entry to a very small size, which may now fit into
+			// this block.
+			((ObjEntry) entry).markScanRequired();
+		}
+
+		if (tryAdd(entry, true)) {
+			return true;
+		} else if (nextShouldBeRestart()) {
+			// It was time for another restart, but the entry doesn't fit
+			// with its complete key, as the block is nearly full. Try to
+			// force it to fit with prefix compression rather than waste
+			// the tail of the block with padding.
+			return tryAdd(entry, false);
+		}
+		return false;
+	}
+
+	private boolean tryAdd(Entry entry, boolean tryRestart) {
+		byte[] key = entry.key;
+		int prefixLen = 0;
+		boolean restart = tryRestart && nextShouldBeRestart();
+		if (!restart) {
+			Entry priorEntry = entries.get(entries.size() - 1);
+			byte[] prior = priorEntry.key;
+			prefixLen = commonPrefix(prior, prior.length, key);
+			if (prefixLen <= 5 /* "refs/" */ && keyType == REF_BLOCK_TYPE) {
+				// Force restart points at transitions between namespaces
+				// such as "refs/heads/" to "refs/tags/".
+				restart = true;
+				prefixLen = 0;
+			} else if (prefixLen == 0) {
+				restart = true;
+			}
+		}
+
+		entry.restart = restart;
+		entry.prefixLen = prefixLen;
+		int entryBytes = entry.sizeBytes();
+		if (computeBlockBytes(entryBytes, restart) > blockLimitBytes) {
+			return false;
+		}
+
+		entriesSumBytes += entryBytes;
+		entries.add(entry);
+		if (restart) {
+			restartCnt++;
+		}
+		return true;
+	}
+
+	private boolean nextShouldBeRestart() {
+		int cnt = entries.size();
+		return (cnt == 0 || ((cnt + 1) % restartInterval) == 0)
+				&& restartCnt < MAX_RESTARTS;
+	}
+
+	private int computeBlockBytes(int entryBytes, boolean restart) {
+		return computeBlockBytes(
+				entriesSumBytes + entryBytes,
+				restartCnt + (restart ? 1 : 0));
+	}
+
+	private static int computeBlockBytes(int entryBytes, int restartCnt) {
+		return 4 // 4-byte block header
+				+ entryBytes
+				+ restartCnt * 3 // restart_offset
+				+ 2; // 2-byte restart_count
+	}
+
+	void writeTo(ReftableOutputStream os) throws IOException {
+		os.beginBlock(blockType);
+		IntList restarts = new IntList(restartCnt);
+		for (Entry entry : entries) {
+			if (entry.restart) {
+				restarts.add(os.bytesWrittenInBlock());
+			}
+			entry.writeKey(os);
+			entry.writeValue(os);
+		}
+		if (restarts.size() == 0 || restarts.size() > MAX_RESTARTS) {
+			throw new IllegalStateException();
+		}
+		for (int i = 0; i < restarts.size(); i++) {
+			os.writeInt24(restarts.get(i));
+		}
+		os.writeInt16(restarts.size());
+		os.flushBlock();
+	}
+
+	private BlockSizeTooSmallException blockSizeTooSmall(Entry entry) {
+		// Compute size required to fit this entry by itself.
+		int min = FILE_HEADER_LEN + computeBlockBytes(entry.sizeBytes(), 1);
+		return new BlockSizeTooSmallException(min);
+	}
+
+	static int commonPrefix(byte[] a, int n, byte[] b) {
+		int len = Math.min(n, Math.min(a.length, b.length));
+		for (int i = 0; i < len; i++) {
+			if (a[i] != b[i]) {
+				return i;
+			}
+		}
+		return len;
+	}
+
+	static int encodeSuffixAndType(int sfx, int valueType) {
+		return (sfx << 3) | valueType;
+	}
+
+	static int compare(
+			byte[] a, int ai, int aLen,
+			byte[] b, int bi, int bLen) {
+		int aEnd = ai + aLen;
+		int bEnd = bi + bLen;
+		while (ai < aEnd && bi < bEnd) {
+			int c = (a[ai++] & 0xff) - (b[bi++] & 0xff);
+			if (c != 0) {
+				return c;
+			}
+		}
+		return aLen - bLen;
+	}
+
+	static abstract class Entry {
+		static int compare(Entry ea, Entry eb) {
+			byte[] a = ea.key;
+			byte[] b = eb.key;
+			return BlockWriter.compare(a, 0, a.length, b, 0, b.length);
+		}
+
+		final byte[] key;
+		int prefixLen;
+		boolean restart;
+
+		Entry(byte[] key) {
+			this.key = key;
+		}
+
+		void writeKey(ReftableOutputStream os) {
+			int sfxLen = key.length - prefixLen;
+			os.writeVarint(prefixLen);
+			os.writeVarint(encodeSuffixAndType(sfxLen, valueType()));
+			os.write(key, prefixLen, sfxLen);
+		}
+
+		int sizeBytes() {
+			int sfxLen = key.length - prefixLen;
+			int sfx = encodeSuffixAndType(sfxLen, valueType());
+			return computeVarintSize(prefixLen)
+					+ computeVarintSize(sfx)
+					+ sfxLen
+					+ valueSize();
+		}
+
+		abstract byte blockType();
+		abstract int valueType();
+		abstract int valueSize();
+		abstract void writeValue(ReftableOutputStream os) throws IOException;
+	}
+
+	static class IndexEntry extends Entry {
+		private final long blockPosition;
+
+		IndexEntry(byte[] key, long blockPosition) {
+			super(key);
+			this.blockPosition = blockPosition;
+		}
+
+		@Override
+		byte blockType() {
+			return INDEX_BLOCK_TYPE;
+		}
+
+		@Override
+		int valueType() {
+			return 0;
+		}
+
+		@Override
+		int valueSize() {
+			return computeVarintSize(blockPosition);
+		}
+
+		@Override
+		void writeValue(ReftableOutputStream os) {
+			os.writeVarint(blockPosition);
+		}
+	}
+
+	static class RefEntry extends Entry {
+		final Ref ref;
+		final long updateIndexDelta;
+
+		RefEntry(Ref ref, long updateIndexDelta) {
+			super(nameUtf8(ref));
+			this.ref = ref;
+			this.updateIndexDelta = updateIndexDelta;
+		}
+
+		@Override
+		byte blockType() {
+			return REF_BLOCK_TYPE;
+		}
+
+		@Override
+		int valueType() {
+			if (ref.isSymbolic()) {
+				return VALUE_SYMREF;
+			} else if (ref.getStorage() == NEW && ref.getObjectId() == null) {
+				return VALUE_NONE;
+			} else if (ref.getPeeledObjectId() != null) {
+				return VALUE_2ID;
+			} else {
+				return VALUE_1ID;
+			}
+		}
+
+		@Override
+		int valueSize() {
+			int n = computeVarintSize(updateIndexDelta);
+			switch (valueType()) {
+			case VALUE_NONE:
+				return n;
+			case VALUE_1ID:
+				return n + OBJECT_ID_LENGTH;
+			case VALUE_2ID:
+				return n + 2 * OBJECT_ID_LENGTH;
+			case VALUE_SYMREF:
+				if (ref.isSymbolic()) {
+					int nameLen = nameUtf8(ref.getTarget()).length;
+					return n + computeVarintSize(nameLen) + nameLen;
+				}
+			}
+			throw new IllegalStateException();
+		}
+
+		@Override
+		void writeValue(ReftableOutputStream os) throws IOException {
+			os.writeVarint(updateIndexDelta);
+			switch (valueType()) {
+			case VALUE_NONE:
+				return;
+
+			case VALUE_1ID: {
+				ObjectId id1 = ref.getObjectId();
+				if (!ref.isPeeled()) {
+					throw new IOException(JGitText.get().peeledRefIsRequired);
+				} else if (id1 == null) {
+					throw new IOException(JGitText.get().invalidId0);
+				}
+				os.writeId(id1);
+				return;
+			}
+
+			case VALUE_2ID: {
+				ObjectId id1 = ref.getObjectId();
+				ObjectId id2 = ref.getPeeledObjectId();
+				if (!ref.isPeeled()) {
+					throw new IOException(JGitText.get().peeledRefIsRequired);
+				} else if (id1 == null || id2 == null) {
+					throw new IOException(JGitText.get().invalidId0);
+				}
+				os.writeId(id1);
+				os.writeId(id2);
+				return;
+			}
+
+			case VALUE_SYMREF:
+				if (ref.isSymbolic()) {
+					os.writeVarintString(ref.getTarget().getName());
+					return;
+				}
+			}
+			throw new IllegalStateException();
+		}
+
+		private static byte[] nameUtf8(Ref ref) {
+			return ref.getName().getBytes(UTF_8);
+		}
+	}
+
+	static class ObjEntry extends Entry {
+		final LongList blockPos;
+
+		ObjEntry(int idLen, ObjectId id, LongList blockPos) {
+			super(key(idLen, id));
+			this.blockPos = blockPos;
+		}
+
+		private static byte[] key(int idLen, ObjectId id) {
+			byte[] key = new byte[OBJECT_ID_LENGTH];
+			id.copyRawTo(key, 0);
+			if (idLen < OBJECT_ID_LENGTH) {
+				return Arrays.copyOf(key, idLen);
+			}
+			return key;
+		}
+
+		void markScanRequired() {
+			blockPos.clear();
+		}
+
+		@Override
+		byte blockType() {
+			return OBJ_BLOCK_TYPE;
+		}
+
+		@Override
+		int valueType() {
+			int cnt = blockPos.size();
+			return cnt != 0 && cnt <= VALUE_TYPE_MASK ? cnt : 0;
+		}
+
+		@Override
+		int valueSize() {
+			int cnt = blockPos.size();
+			if (cnt == 0) {
+				return computeVarintSize(0);
+			}
+
+			int n = 0;
+			if (cnt > VALUE_TYPE_MASK) {
+				n += computeVarintSize(cnt);
+			}
+			n += computeVarintSize(blockPos.get(0));
+			for (int j = 1; j < cnt; j++) {
+				long prior = blockPos.get(j - 1);
+				long b = blockPos.get(j);
+				n += computeVarintSize(b - prior);
+			}
+			return n;
+		}
+
+		@Override
+		void writeValue(ReftableOutputStream os) throws IOException {
+			int cnt = blockPos.size();
+			if (cnt == 0) {
+				os.writeVarint(0);
+				return;
+			}
+
+			if (cnt > VALUE_TYPE_MASK) {
+				os.writeVarint(cnt);
+			}
+			os.writeVarint(blockPos.get(0));
+			for (int j = 1; j < cnt; j++) {
+				long prior = blockPos.get(j - 1);
+				long b = blockPos.get(j);
+				os.writeVarint(b - prior);
+			}
+		}
+	}
+
+	static class DeleteLogEntry extends Entry {
+		DeleteLogEntry(String refName, long updateIndex) {
+			super(LogEntry.key(refName, updateIndex));
+		}
+
+		@Override
+		byte blockType() {
+			return LOG_BLOCK_TYPE;
+		}
+
+		@Override
+		int valueType() {
+			return LOG_NONE;
+		}
+
+		@Override
+		int valueSize() {
+			return 0;
+		}
+
+		@Override
+		void writeValue(ReftableOutputStream os) {
+			// Nothing in a delete log record.
+		}
+	}
+
+	static class LogEntry extends Entry {
+		final ObjectId oldId;
+		final ObjectId newId;
+		final long timeSecs;
+		final short tz;
+		final byte[] name;
+		final byte[] email;
+		final byte[] msg;
+
+		LogEntry(String refName, long updateIndex, PersonIdent who,
+				ObjectId oldId, ObjectId newId, String message) {
+			super(key(refName, updateIndex));
+
+			this.oldId = oldId;
+			this.newId = newId;
+			this.timeSecs = who.getWhen().getTime() / 1000L;
+			this.tz = (short) who.getTimeZoneOffset();
+			this.name = who.getName().getBytes(UTF_8);
+			this.email = who.getEmailAddress().getBytes(UTF_8);
+			this.msg = message.getBytes(UTF_8);
+		}
+
+		static byte[] key(String ref, long index) {
+			byte[] name = ref.getBytes(UTF_8);
+			byte[] key = Arrays.copyOf(name, name.length + 1 + 8);
+			NB.encodeInt64(key, key.length - 8, reverseUpdateIndex(index));
+			return key;
+		}
+
+		@Override
+		byte blockType() {
+			return LOG_BLOCK_TYPE;
+		}
+
+		@Override
+		int valueType() {
+			return LOG_DATA;
+		}
+
+		@Override
+		int valueSize() {
+			return 2 * OBJECT_ID_LENGTH
+					+ computeVarintSize(name.length) + name.length
+					+ computeVarintSize(email.length) + email.length
+					+ computeVarintSize(timeSecs)
+					+ 2 // tz
+					+ computeVarintSize(msg.length) + msg.length;
+		}
+
+		@Override
+		void writeValue(ReftableOutputStream os) {
+			os.writeId(oldId);
+			os.writeId(newId);
+			os.writeVarintString(name);
+			os.writeVarintString(email);
+			os.writeVarint(timeSecs);
+			os.writeInt16(tz);
+			os.writeVarintString(msg);
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/EmptyLogCursor.java
similarity index 76%
copy from org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
copy to org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/EmptyLogCursor.java
index 98a2a94..d774589 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/EmptyLogCursor.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2011, Google Inc.
+ * Copyright (C) 2017, Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -41,20 +41,36 @@
  * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.eclipse.jgit.internal.storage.dfs;
+package org.eclipse.jgit.internal.storage.reftable;
 
-import java.util.concurrent.atomic.AtomicLong;
+import java.io.IOException;
 
-final class DfsPackKey {
-	final int hash;
+import org.eclipse.jgit.lib.ReflogEntry;
 
-	final AtomicLong cachedSize;
+/** Empty {@link LogCursor} with no results. */
+class EmptyLogCursor extends LogCursor {
+	@Override
+	public boolean next() throws IOException {
+		return false;
+	}
 
-	DfsPackKey() {
-		// Multiply by 31 here so we can more directly combine with another
-		// value without doing the multiply there.
-		//
-		hash = System.identityHashCode(this) * 31;
-		cachedSize = new AtomicLong();
+	@Override
+	public String getRefName() {
+		return null;
+	}
+
+	@Override
+	public long getUpdateIndex() {
+		return 0;
+	}
+
+	@Override
+	public ReflogEntry getReflogEntry() {
+		return null;
+	}
+
+	@Override
+	public void close() {
+		// Do nothing.
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/LogCursor.java
similarity index 69%
copy from org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
copy to org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/LogCursor.java
index 98a2a94..c19968c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/LogCursor.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2011, Google Inc.
+ * Copyright (C) 2017, Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -41,20 +41,32 @@
  * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.eclipse.jgit.internal.storage.dfs;
+package org.eclipse.jgit.internal.storage.reftable;
 
-import java.util.concurrent.atomic.AtomicLong;
+import java.io.IOException;
 
-final class DfsPackKey {
-	final int hash;
+import org.eclipse.jgit.lib.ReflogEntry;
 
-	final AtomicLong cachedSize;
+/** Iterator over logs inside a {@link Reftable}. */
+public abstract class LogCursor implements AutoCloseable {
+	/**
+	 * Check if another log record is available.
+	 *
+	 * @return {@code true} if there is another result.
+	 * @throws IOException
+	 *             logs cannot be read.
+	 */
+	public abstract boolean next() throws IOException;
 
-	DfsPackKey() {
-		// Multiply by 31 here so we can more directly combine with another
-		// value without doing the multiply there.
-		//
-		hash = System.identityHashCode(this) * 31;
-		cachedSize = new AtomicLong();
-	}
+	/** @return name of the current reference. */
+	public abstract String getRefName();
+
+	/** @return identifier of the transaction that created the log record. */
+	public abstract long getUpdateIndex();
+
+	/** @return current log entry. */
+	public abstract ReflogEntry getReflogEntry();
+
+	@Override
+	public abstract void close();
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/MergedReftable.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/MergedReftable.java
new file mode 100644
index 0000000..9fc6ae2
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/MergedReftable.java
@@ -0,0 +1,376 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.reftable;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.PriorityQueue;
+
+import org.eclipse.jgit.lib.AnyObjectId;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.ReflogEntry;
+
+/**
+ * Merges multiple reference tables together.
+ * <p>
+ * A {@link MergedReftable} merge-joins multiple {@link ReftableReader} on the
+ * fly. Tables higher/later in the stack shadow lower/earlier tables, hiding
+ * references that been updated/replaced.
+ * <p>
+ * By default deleted references are skipped and not returned to the caller.
+ * {@link #setIncludeDeletes(boolean)} can be used to modify this behavior if
+ * the caller needs to preserve deletions during partial compaction.
+ * <p>
+ * A {@code MergedReftable} is not thread-safe.
+ */
+public class MergedReftable extends Reftable {
+	private final Reftable[] tables;
+
+	/**
+	 * Initialize a merged table reader.
+	 * <p>
+	 * The tables in {@code tableStack} will be closed when this
+	 * {@code MergedReftable} is closed.
+	 *
+	 * @param tableStack
+	 *            stack of tables to read from. The base of the stack is at
+	 *            index 0, the most recent should be at the top of the stack at
+	 *            {@code tableStack.size() - 1}. The top of the stack (higher
+	 *            index) shadows the base of the stack (lower index).
+	 */
+	public MergedReftable(List<Reftable> tableStack) {
+		tables = tableStack.toArray(new Reftable[0]);
+
+		// Tables must expose deletes to this instance to correctly
+		// shadow references from lower tables.
+		for (Reftable t : tables) {
+			t.setIncludeDeletes(true);
+		}
+	}
+
+	@Override
+	public RefCursor allRefs() throws IOException {
+		MergedRefCursor m = new MergedRefCursor();
+		for (int i = 0; i < tables.length; i++) {
+			m.add(new RefQueueEntry(tables[i].allRefs(), i));
+		}
+		return m;
+	}
+
+	@Override
+	public RefCursor seekRef(String name) throws IOException {
+		MergedRefCursor m = new MergedRefCursor();
+		for (int i = 0; i < tables.length; i++) {
+			m.add(new RefQueueEntry(tables[i].seekRef(name), i));
+		}
+		return m;
+	}
+
+	@Override
+	public RefCursor byObjectId(AnyObjectId name) throws IOException {
+		MergedRefCursor m = new MergedRefCursor();
+		for (int i = 0; i < tables.length; i++) {
+			m.add(new RefQueueEntry(tables[i].byObjectId(name), i));
+		}
+		return m;
+	}
+
+	@Override
+	public LogCursor allLogs() throws IOException {
+		MergedLogCursor m = new MergedLogCursor();
+		for (int i = 0; i < tables.length; i++) {
+			m.add(new LogQueueEntry(tables[i].allLogs(), i));
+		}
+		return m;
+	}
+
+	@Override
+	public LogCursor seekLog(String refName, long updateIdx)
+			throws IOException {
+		MergedLogCursor m = new MergedLogCursor();
+		for (int i = 0; i < tables.length; i++) {
+			m.add(new LogQueueEntry(tables[i].seekLog(refName, updateIdx), i));
+		}
+		return m;
+	}
+
+	@Override
+	public void close() throws IOException {
+		for (Reftable t : tables) {
+			t.close();
+		}
+	}
+
+	int queueSize() {
+		return Math.max(1, tables.length);
+	}
+
+	private class MergedRefCursor extends RefCursor {
+		private final PriorityQueue<RefQueueEntry> queue;
+		private RefQueueEntry head;
+		private Ref ref;
+		private long updateIndex;
+
+		MergedRefCursor() {
+			queue = new PriorityQueue<>(queueSize(), RefQueueEntry::compare);
+		}
+
+		void add(RefQueueEntry t) throws IOException {
+			// Common case is many iterations over the same RefQueueEntry
+			// for the bottom of the stack (scanning all refs). Its almost
+			// always less than the top of the queue. Avoid the queue's
+			// O(log N) insertion and removal costs for this common case.
+			if (!t.rc.next()) {
+				t.rc.close();
+			} else if (head == null) {
+				RefQueueEntry p = queue.peek();
+				if (p == null || RefQueueEntry.compare(t, p) < 0) {
+					head = t;
+				} else {
+					head = queue.poll();
+					queue.add(t);
+				}
+			} else if (RefQueueEntry.compare(t, head) > 0) {
+				queue.add(t);
+			} else {
+				queue.add(head);
+				head = t;
+			}
+		}
+
+		@Override
+		public boolean next() throws IOException {
+			for (;;) {
+				RefQueueEntry t = poll();
+				if (t == null) {
+					return false;
+				}
+
+				ref = t.rc.getRef();
+				updateIndex = t.rc.getUpdateIndex();
+				boolean include = includeDeletes || !t.rc.wasDeleted();
+				skipShadowedRefs(ref.getName());
+				add(t);
+				if (include) {
+					return true;
+				}
+			}
+		}
+
+		private RefQueueEntry poll() {
+			RefQueueEntry e = head;
+			if (e != null) {
+				head = null;
+				return e;
+			}
+			return queue.poll();
+		}
+
+		private void skipShadowedRefs(String name) throws IOException {
+			for (;;) {
+				RefQueueEntry t = head != null ? head : queue.peek();
+				if (t != null && name.equals(t.name())) {
+					add(poll());
+				} else {
+					break;
+				}
+			}
+		}
+
+		@Override
+		public Ref getRef() {
+			return ref;
+		}
+
+		@Override
+		public long getUpdateIndex() {
+			return updateIndex;
+		}
+
+		@Override
+		public void close() {
+			if (head != null) {
+				head.rc.close();
+				head = null;
+			}
+			while (!queue.isEmpty()) {
+				queue.remove().rc.close();
+			}
+		}
+	}
+
+	private static class RefQueueEntry {
+		static int compare(RefQueueEntry a, RefQueueEntry b) {
+			int cmp = a.name().compareTo(b.name());
+			if (cmp == 0) {
+				// higher updateIndex shadows lower updateIndex.
+				cmp = Long.signum(b.updateIndex() - a.updateIndex());
+			}
+			if (cmp == 0) {
+				// higher index shadows lower index, so higher index first.
+				cmp = b.stackIdx - a.stackIdx;
+			}
+			return cmp;
+		}
+
+		final RefCursor rc;
+		final int stackIdx;
+
+		RefQueueEntry(RefCursor rc, int stackIdx) {
+			this.rc = rc;
+			this.stackIdx = stackIdx;
+		}
+
+		String name() {
+			return rc.getRef().getName();
+		}
+
+		long updateIndex() {
+			return rc.getUpdateIndex();
+		}
+	}
+
+	private class MergedLogCursor extends LogCursor {
+		private final PriorityQueue<LogQueueEntry> queue;
+		private String refName;
+		private long updateIndex;
+		private ReflogEntry entry;
+
+		MergedLogCursor() {
+			queue = new PriorityQueue<>(queueSize(), LogQueueEntry::compare);
+		}
+
+		void add(LogQueueEntry t) throws IOException {
+			if (t.lc.next()) {
+				queue.add(t);
+			} else {
+				t.lc.close();
+			}
+		}
+
+		@Override
+		public boolean next() throws IOException {
+			for (;;) {
+				LogQueueEntry t = queue.poll();
+				if (t == null) {
+					return false;
+				}
+
+				refName = t.lc.getRefName();
+				updateIndex = t.lc.getUpdateIndex();
+				entry = t.lc.getReflogEntry();
+				boolean include = includeDeletes || entry != null;
+				skipShadowed(refName, updateIndex);
+				add(t);
+				if (include) {
+					return true;
+				}
+			}
+		}
+
+		private void skipShadowed(String name, long index) throws IOException {
+			for (;;) {
+				LogQueueEntry t = queue.peek();
+				if (t != null && name.equals(t.name()) && index == t.index()) {
+					add(queue.remove());
+				} else {
+					break;
+				}
+			}
+		}
+
+		@Override
+		public String getRefName() {
+			return refName;
+		}
+
+		@Override
+		public long getUpdateIndex() {
+			return updateIndex;
+		}
+
+		@Override
+		public ReflogEntry getReflogEntry() {
+			return entry;
+		}
+
+		@Override
+		public void close() {
+			while (!queue.isEmpty()) {
+				queue.remove().lc.close();
+			}
+		}
+	}
+
+	private static class LogQueueEntry {
+		static int compare(LogQueueEntry a, LogQueueEntry b) {
+			int cmp = a.name().compareTo(b.name());
+			if (cmp == 0) {
+				// higher update index sorts first.
+				cmp = Long.signum(b.index() - a.index());
+			}
+			if (cmp == 0) {
+				// higher index comes first.
+				cmp = b.stackIdx - a.stackIdx;
+			}
+			return cmp;
+		}
+
+		final LogCursor lc;
+		final int stackIdx;
+
+		LogQueueEntry(LogCursor lc, int stackIdx) {
+			this.lc = lc;
+			this.stackIdx = stackIdx;
+		}
+
+		String name() {
+			return lc.getRefName();
+		}
+
+		long index() {
+			return lc.getUpdateIndex();
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/RefCursor.java
similarity index 67%
copy from org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
copy to org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/RefCursor.java
index 98a2a94..d8e9c60 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/RefCursor.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2011, Google Inc.
+ * Copyright (C) 2017, Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -41,20 +41,35 @@
  * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.eclipse.jgit.internal.storage.dfs;
+package org.eclipse.jgit.internal.storage.reftable;
 
-import java.util.concurrent.atomic.AtomicLong;
+import java.io.IOException;
 
-final class DfsPackKey {
-	final int hash;
+import org.eclipse.jgit.lib.Ref;
 
-	final AtomicLong cachedSize;
+/** Iterator over references inside a {@link Reftable}. */
+public abstract class RefCursor implements AutoCloseable {
+	/**
+	 * Check if another reference is available.
+	 *
+	 * @return {@code true} if there is another result.
+	 * @throws IOException
+	 *             references cannot be read.
+	 */
+	public abstract boolean next() throws IOException;
 
-	DfsPackKey() {
-		// Multiply by 31 here so we can more directly combine with another
-		// value without doing the multiply there.
-		//
-		hash = System.identityHashCode(this) * 31;
-		cachedSize = new AtomicLong();
+	/** @return reference at the current position. */
+	public abstract Ref getRef();
+
+	/** @return updateIndex that last modified the current reference, */
+	public abstract long getUpdateIndex();
+
+	/** @return {@code true} if the current reference was deleted. */
+	public boolean wasDeleted() {
+		Ref r = getRef();
+		return r.getStorage() == Ref.Storage.NEW && r.getObjectId() == null;
 	}
+
+	@Override
+	public abstract void close();
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/Reftable.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/Reftable.java
new file mode 100644
index 0000000..1189ed3
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/Reftable.java
@@ -0,0 +1,262 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.reftable;
+
+import static org.eclipse.jgit.lib.RefDatabase.MAX_SYMBOLIC_REF_DEPTH;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.util.Collection;
+
+import org.eclipse.jgit.annotations.Nullable;
+import org.eclipse.jgit.internal.storage.io.BlockSource;
+import org.eclipse.jgit.lib.AnyObjectId;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.SymbolicRef;
+
+/** Abstract table of references. */
+public abstract class Reftable implements AutoCloseable {
+	/**
+	 * @param refs
+	 *            references to convert into a reftable; may be empty.
+	 * @return a reader for the supplied references.
+	 */
+	public static Reftable from(Collection<Ref> refs) {
+		try {
+			ReftableConfig cfg = new ReftableConfig();
+			cfg.setIndexObjects(false);
+			cfg.setAlignBlocks(false);
+			ByteArrayOutputStream buf = new ByteArrayOutputStream();
+			new ReftableWriter()
+				.setConfig(cfg)
+				.begin(buf)
+				.sortAndWriteRefs(refs)
+				.finish();
+			return new ReftableReader(BlockSource.from(buf.toByteArray()));
+		} catch (IOException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	/** {@code true} if deletions should be included in results. */
+	protected boolean includeDeletes;
+
+	/**
+	 * @param deletes
+	 *            if {@code true} deleted references will be returned. If
+	 *            {@code false} (default behavior), deleted references will be
+	 *            skipped, and not returned.
+	 */
+	public void setIncludeDeletes(boolean deletes) {
+		includeDeletes = deletes;
+	}
+
+	/**
+	 * Seek to the first reference, to iterate in order.
+	 *
+	 * @return cursor to iterate.
+	 * @throws IOException
+	 *             if references cannot be read.
+	 */
+	public abstract RefCursor allRefs() throws IOException;
+
+	/**
+	 * Seek either to a reference, or a reference subtree.
+	 * <p>
+	 * If {@code refName} ends with {@code "/"} the method will seek to the
+	 * subtree of all references starting with {@code refName} as a prefix. If
+	 * no references start with this prefix, an empty cursor is returned.
+	 * <p>
+	 * Otherwise exactly {@code refName} will be looked for. If present, the
+	 * returned cursor will iterate exactly one entry. If not found, an empty
+	 * cursor is returned.
+	 *
+	 * @param refName
+	 *            reference name or subtree to find.
+	 * @return cursor to iterate; empty cursor if no references match.
+	 * @throws IOException
+	 *             if references cannot be read.
+	 */
+	public abstract RefCursor seekRef(String refName) throws IOException;
+
+	/**
+	 * Match references pointing to a specific object.
+	 *
+	 * @param id
+	 *            object to find.
+	 * @return cursor to iterate; empty cursor if no references match.
+	 * @throws IOException
+	 *             if references cannot be read.
+	 */
+	public abstract RefCursor byObjectId(AnyObjectId id) throws IOException;
+
+	/**
+	 * Seek reader to read log records.
+	 *
+	 * @return cursor to iterate; empty cursor if no logs are present.
+	 * @throws IOException
+	 *             if logs cannot be read.
+	 */
+	public abstract LogCursor allLogs() throws IOException;
+
+	/**
+	 * Read a single reference's log.
+	 *
+	 * @param refName
+	 *            exact name of the reference whose log to read.
+	 * @return cursor to iterate; empty cursor if no logs match.
+	 * @throws IOException
+	 *             if logs cannot be read.
+	 */
+	public LogCursor seekLog(String refName) throws IOException {
+		return seekLog(refName, Long.MAX_VALUE);
+	}
+
+	/**
+	 * Seek to an update index in a reference's log.
+	 *
+	 * @param refName
+	 *            exact name of the reference whose log to read.
+	 * @param updateIndex
+	 *            most recent index to return first in the log cursor. Log
+	 *            records at or before {@code updateIndex} will be returned.
+	 * @return cursor to iterate; empty cursor if no logs match.
+	 * @throws IOException
+	 *             if logs cannot be read.
+	 */
+	public abstract LogCursor seekLog(String refName, long updateIndex)
+			throws IOException;
+
+	/**
+	 * Lookup a reference, or null if not found.
+	 *
+	 * @param refName
+	 *            reference name to find.
+	 * @return the reference, or {@code null} if not found.
+	 * @throws IOException
+	 *             if references cannot be read.
+	 */
+	@Nullable
+	public Ref exactRef(String refName) throws IOException {
+		try (RefCursor rc = seekRef(refName)) {
+			return rc.next() ? rc.getRef() : null;
+		}
+	}
+
+	/**
+	 * Test if a reference or reference subtree exists.
+	 * <p>
+	 * If {@code refName} ends with {@code "/"}, the method tests if any
+	 * reference starts with {@code refName} as a prefix.
+	 * <p>
+	 * Otherwise, the method checks if {@code refName} exists.
+	 *
+	 * @param refName
+	 *            reference name or subtree to find.
+	 * @return {@code true} if the reference exists, or at least one reference
+	 *         exists in the subtree.
+	 * @throws IOException
+	 *             if references cannot be read.
+	 */
+	public boolean hasRef(String refName) throws IOException {
+		try (RefCursor rc = seekRef(refName)) {
+			return rc.next();
+		}
+	}
+
+	/**
+	 * Test if any reference directly refers to the object.
+	 *
+	 * @param id
+	 *            ObjectId to find.
+	 * @return {@code true} if any reference exists directly referencing
+	 *         {@code id}, or a annotated tag that peels to {@code id}.
+	 * @throws IOException
+	 *             if references cannot be read.
+	 */
+	public boolean hasId(AnyObjectId id) throws IOException {
+		try (RefCursor rc = byObjectId(id)) {
+			return rc.next();
+		}
+	}
+
+	/**
+	 * Resolve a symbolic reference to populate its value.
+	 *
+	 * @param symref
+	 *            reference to resolve.
+	 * @return resolved {@code symref}, or {@code null}.
+	 * @throws IOException
+	 *             if references cannot be read.
+	 */
+	@Nullable
+	public Ref resolve(Ref symref) throws IOException {
+		return resolve(symref, 0);
+	}
+
+	private Ref resolve(Ref ref, int depth) throws IOException {
+		if (!ref.isSymbolic()) {
+			return ref;
+		}
+
+		Ref dst = ref.getTarget();
+		if (MAX_SYMBOLIC_REF_DEPTH <= depth) {
+			return null; // claim it doesn't exist
+		}
+
+		dst = exactRef(dst.getName());
+		if (dst == null) {
+			return ref;
+		}
+
+		dst = resolve(dst, depth + 1);
+		if (dst == null) {
+			return null; // claim it doesn't exist
+		}
+		return new SymbolicRef(ref.getName(), dst);
+	}
+
+	@Override
+	public abstract void close() throws IOException;
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableCompactor.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableCompactor.java
new file mode 100644
index 0000000..c221577
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableCompactor.java
@@ -0,0 +1,281 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.reftable;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.eclipse.jgit.internal.storage.reftable.ReftableWriter.Stats;
+import org.eclipse.jgit.lib.PersonIdent;
+import org.eclipse.jgit.lib.ReflogEntry;
+
+/**
+ * Merges reftables and compacts them into a single output.
+ * <p>
+ * For a partial compaction callers should {@link #setIncludeDeletes(boolean)}
+ * to {@code true} to ensure the new reftable continues to use a delete marker
+ * to shadow any lower reftable that may have the reference present.
+ * <p>
+ * By default all log entries within the range defined by
+ * {@link #setMinUpdateIndex(long)} and {@link #setMaxUpdateIndex(long)} are
+ * copied, even if no references in the output file match the log records.
+ * Callers may truncate the log to a more recent time horizon with
+ * {@link #setOldestReflogTimeMillis(long)}, or disable the log altogether with
+ * {@code setOldestReflogTimeMillis(Long.MAX_VALUE)}.
+ */
+public class ReftableCompactor {
+	private final ReftableWriter writer = new ReftableWriter();
+	private final ArrayDeque<Reftable> tables = new ArrayDeque<>();
+
+	private long compactBytesLimit;
+	private long bytesToCompact;
+	private boolean includeDeletes;
+	private long minUpdateIndex;
+	private long maxUpdateIndex;
+	private long oldestReflogTimeMillis;
+	private Stats stats;
+
+	/**
+	 * @param cfg
+	 *            configuration for the reftable.
+	 * @return {@code this}
+	 */
+	public ReftableCompactor setConfig(ReftableConfig cfg) {
+		writer.setConfig(cfg);
+		return this;
+	}
+
+	/**
+	 * @param bytes
+	 *            limit on number of bytes from source tables to compact.
+	 * @return {@code this}
+	 */
+	public ReftableCompactor setCompactBytesLimit(long bytes) {
+		compactBytesLimit = bytes;
+		return this;
+	}
+
+	/**
+	 * @param deletes
+	 *            {@code true} to include deletions in the output, which may be
+	 *            necessary for partial compaction.
+	 * @return {@code this}
+	 */
+	public ReftableCompactor setIncludeDeletes(boolean deletes) {
+		includeDeletes = deletes;
+		return this;
+	}
+
+	/**
+	 * @param min
+	 *            the minimum update index for log entries that appear in the
+	 *            compacted reftable. This should be 1 higher than the prior
+	 *            reftable's {@code maxUpdateIndex} if this table will be used
+	 *            in a stack.
+	 * @return {@code this}
+	 */
+	public ReftableCompactor setMinUpdateIndex(long min) {
+		minUpdateIndex = min;
+		return this;
+	}
+
+	/**
+	 * @param max
+	 *            the maximum update index for log entries that appear in the
+	 *            compacted reftable. This should be at least 1 higher than the
+	 *            prior reftable's {@code maxUpdateIndex} if this table will be
+	 *            used in a stack.
+	 * @return {@code this}
+	 */
+	public ReftableCompactor setMaxUpdateIndex(long max) {
+		maxUpdateIndex = max;
+		return this;
+	}
+
+	/**
+	 * @param timeMillis
+	 *            oldest log time to preserve. Entries whose timestamps are
+	 *            {@code >= timeMillis} will be copied into the output file. Log
+	 *            entries that predate {@code timeMillis} will be discarded.
+	 *            Specified in Java standard milliseconds since the epoch.
+	 * @return {@code this}
+	 */
+	public ReftableCompactor setOldestReflogTimeMillis(long timeMillis) {
+		oldestReflogTimeMillis = timeMillis;
+		return this;
+	}
+
+	/**
+	 * Add all of the tables, in the specified order.
+	 * <p>
+	 * Unconditionally adds all tables, ignoring the
+	 * {@link #setCompactBytesLimit(long)}.
+	 *
+	 * @param readers
+	 *            tables to compact. Tables should be ordered oldest first/most
+	 *            recent last so that the more recent tables can shadow the
+	 *            older results. Caller is responsible for closing the readers.
+	 * @throws IOException
+	 *             update indexes of a reader cannot be accessed.
+	 */
+	public void addAll(List<? extends Reftable> readers) throws IOException {
+		tables.addAll(readers);
+		for (Reftable r : readers) {
+			if (r instanceof ReftableReader) {
+				adjustUpdateIndexes((ReftableReader) r);
+			}
+		}
+	}
+
+	/**
+	 * Try to add this reader at the bottom of the stack.
+	 * <p>
+	 * A reader may be rejected by returning {@code false} if the compactor is
+	 * already rewriting its {@link #setCompactBytesLimit(long)}. When this
+	 * happens the caller should stop trying to add tables, and execute the
+	 * compaction.
+	 *
+	 * @param reader
+	 *            the reader to insert at the bottom of the stack. Caller is
+	 *            responsible for closing the reader.
+	 * @return {@code true} if the compactor accepted this table; {@code false}
+	 *         if the compactor has reached its limit.
+	 * @throws IOException
+	 *             if size of {@code reader}, or its update indexes cannot be read.
+	 */
+	public boolean tryAddFirst(ReftableReader reader) throws IOException {
+		long sz = reader.size();
+		if (compactBytesLimit > 0 && bytesToCompact + sz > compactBytesLimit) {
+			return false;
+		}
+		bytesToCompact += sz;
+		adjustUpdateIndexes(reader);
+		tables.addFirst(reader);
+		return true;
+	}
+
+	private void adjustUpdateIndexes(ReftableReader reader) throws IOException {
+		if (minUpdateIndex == 0) {
+			minUpdateIndex = reader.minUpdateIndex();
+		} else {
+			minUpdateIndex = Math.min(minUpdateIndex, reader.minUpdateIndex());
+		}
+		maxUpdateIndex = Math.max(maxUpdateIndex, reader.maxUpdateIndex());
+	}
+
+	/**
+	 * Write a compaction to {@code out}.
+	 *
+	 * @param out
+	 *            stream to write the compacted tables to. Caller is responsible
+	 *            for closing {@code out}.
+	 * @throws IOException
+	 *             if tables cannot be read, or cannot be written.
+	 */
+	public void compact(OutputStream out) throws IOException {
+		MergedReftable mr = new MergedReftable(new ArrayList<>(tables));
+		mr.setIncludeDeletes(includeDeletes);
+
+		writer.setMinUpdateIndex(minUpdateIndex);
+		writer.setMaxUpdateIndex(maxUpdateIndex);
+		writer.begin(out);
+		mergeRefs(mr);
+		mergeLogs(mr);
+		writer.finish();
+		stats = writer.getStats();
+	}
+
+	/** @return statistics of the last written reftable. */
+	public Stats getStats() {
+		return stats;
+	}
+
+	private void mergeRefs(MergedReftable mr) throws IOException {
+		try (RefCursor rc = mr.allRefs()) {
+			while (rc.next()) {
+				writer.writeRef(rc.getRef(), rc.getUpdateIndex());
+			}
+		}
+	}
+
+	private void mergeLogs(MergedReftable mr) throws IOException {
+		if (oldestReflogTimeMillis == Long.MAX_VALUE) {
+			return;
+		}
+
+		try (LogCursor lc = mr.allLogs()) {
+			while (lc.next()) {
+				long updateIndex = lc.getUpdateIndex();
+				if (updateIndex < minUpdateIndex
+						|| updateIndex > maxUpdateIndex) {
+					// Cannot merge log records outside the header's range.
+					continue;
+				}
+
+				String refName = lc.getRefName();
+				ReflogEntry log = lc.getReflogEntry();
+				if (log == null) {
+					if (includeDeletes) {
+						writer.deleteLog(refName, updateIndex);
+					}
+					continue;
+				}
+
+				PersonIdent who = log.getWho();
+				if (who.getWhen().getTime() >= oldestReflogTimeMillis) {
+					writer.writeLog(
+							refName,
+							updateIndex,
+							who,
+							log.getOldId(),
+							log.getNewId(),
+							log.getComment());
+				}
+			}
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableConfig.java
new file mode 100644
index 0000000..f7a1fbe
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableConfig.java
@@ -0,0 +1,216 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.reftable;
+
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.MAX_BLOCK_SIZE;
+
+import org.eclipse.jgit.lib.Config;
+import org.eclipse.jgit.lib.Repository;
+
+/** Configuration used by a reftable writer when constructing the stream. */
+public class ReftableConfig {
+	private int refBlockSize = 4 << 10;
+	private int logBlockSize;
+	private int restartInterval;
+	private int maxIndexLevels;
+	private boolean alignBlocks = true;
+	private boolean indexObjects = true;
+
+	/** Create a default configuration. */
+	public ReftableConfig() {
+	}
+
+	/**
+	 * Create a configuration honoring the repository's settings.
+	 *
+	 * @param db
+	 *            the repository to read settings from. The repository is not
+	 *            retained by the new configuration, instead its settings are
+	 *            copied during the constructor.
+	 */
+	public ReftableConfig(Repository db) {
+		fromConfig(db.getConfig());
+	}
+
+	/**
+	 * Create a configuration honoring settings in a {@link Config}.
+	 *
+	 * @param cfg
+	 *            the source to read settings from. The source is not retained
+	 *            by the new configuration, instead its settings are copied
+	 *            during the constructor.
+	 */
+	public ReftableConfig(Config cfg) {
+		fromConfig(cfg);
+	}
+
+	/**
+	 * Copy an existing configuration to a new instance.
+	 *
+	 * @param cfg
+	 *            the source configuration to copy from.
+	 */
+	public ReftableConfig(ReftableConfig cfg) {
+		this.refBlockSize = cfg.refBlockSize;
+		this.logBlockSize = cfg.logBlockSize;
+		this.restartInterval = cfg.restartInterval;
+		this.maxIndexLevels = cfg.maxIndexLevels;
+		this.alignBlocks = cfg.alignBlocks;
+		this.indexObjects = cfg.indexObjects;
+	}
+
+	/** @return desired output block size for references, in bytes */
+	public int getRefBlockSize() {
+		return refBlockSize;
+	}
+
+	/**
+	 * @param szBytes
+	 *            desired output block size for references, in bytes.
+	 */
+	public void setRefBlockSize(int szBytes) {
+		if (szBytes > MAX_BLOCK_SIZE) {
+			throw new IllegalArgumentException();
+		}
+		refBlockSize = Math.max(0, szBytes);
+	}
+
+	/**
+	 * @return desired output block size for log entries, in bytes. If 0 the
+	 *         writer will default to {@code 2 * getRefBlockSize()}.
+	 */
+	public int getLogBlockSize() {
+		return logBlockSize;
+	}
+
+	/**
+	 * @param szBytes
+	 *            desired output block size for log entries, in bytes. If 0 will
+	 *            default to {@code 2 * getRefBlockSize()}.
+	 */
+	public void setLogBlockSize(int szBytes) {
+		if (szBytes > MAX_BLOCK_SIZE) {
+			throw new IllegalArgumentException();
+		}
+		logBlockSize = Math.max(0, szBytes);
+	}
+
+	/** @return number of references between binary search markers. */
+	public int getRestartInterval() {
+		return restartInterval;
+	}
+
+	/**
+	 * @param interval
+	 *            number of references between binary search markers. If
+	 *            {@code interval} is 0 (default), the writer will select a
+	 *            default value based on the block size.
+	 */
+	public void setRestartInterval(int interval) {
+		restartInterval = Math.max(0, interval);
+	}
+
+	/** @return maximum depth of the index; 0 for unlimited. */
+	public int getMaxIndexLevels() {
+		return maxIndexLevels;
+	}
+
+	/**
+	 * @param levels
+	 *            maximum number of levels to use in indexes. Lower levels of
+	 *            the index respect {@link #getRefBlockSize()}, and the highest
+	 *            level may exceed that if the number of levels is limited.
+	 */
+	public void setMaxIndexLevels(int levels) {
+		maxIndexLevels = Math.max(0, levels);
+	}
+
+	/** @return {@code true} if the writer should align blocks. */
+	public boolean isAlignBlocks() {
+		return alignBlocks;
+	}
+
+	/**
+	 * @param align
+	 *            if {@code true} blocks are written aligned to multiples of
+	 *            {@link #getRefBlockSize()}. May increase file size due to NUL
+	 *            padding bytes added between blocks. Default is {@code true}.
+	 */
+	public void setAlignBlocks(boolean align) {
+		alignBlocks = align;
+	}
+
+	/** @return {@code true} if the writer should index object to ref. */
+	public boolean isIndexObjects() {
+		return indexObjects;
+	}
+
+	/**
+	 * @param index
+	 *            if {@code true} the reftable may include additional storage to
+	 *            efficiently map from {@code ObjectId} to reference names. By
+	 *            default, {@code true}.
+	 */
+	public void setIndexObjects(boolean index) {
+		indexObjects = index;
+	}
+
+	/**
+	 * Update properties by setting fields from the configuration.
+	 *
+	 * If a property's corresponding variable is not defined in the supplied
+	 * configuration, then it is left unmodified.
+	 *
+	 * @param rc
+	 *            configuration to read properties from.
+	 */
+	public void fromConfig(Config rc) {
+		refBlockSize = rc.getInt("reftable", "blockSize", refBlockSize); //$NON-NLS-1$ //$NON-NLS-2$
+		logBlockSize = rc.getInt("reftable", "logBlockSize", logBlockSize); //$NON-NLS-1$ //$NON-NLS-2$
+		restartInterval = rc.getInt("reftable", "restartInterval", restartInterval); //$NON-NLS-1$ //$NON-NLS-2$
+		maxIndexLevels = rc.getInt("reftable", "indexLevels", maxIndexLevels); //$NON-NLS-1$ //$NON-NLS-2$
+		alignBlocks = rc.getBoolean("reftable", "alignBlocks", alignBlocks); //$NON-NLS-1$ //$NON-NLS-2$
+		indexObjects = rc.getBoolean("reftable", "indexObjects", indexObjects); //$NON-NLS-1$ //$NON-NLS-2$
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableConstants.java
similarity index 60%
copy from org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
copy to org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableConstants.java
index 98a2a94..0b89327 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackKey.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableConstants.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2011, Google Inc.
+ * Copyright (C) 2017, Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -41,20 +41,45 @@
  * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.eclipse.jgit.internal.storage.dfs;
+package org.eclipse.jgit.internal.storage.reftable;
 
-import java.util.concurrent.atomic.AtomicLong;
+class ReftableConstants {
+	static final byte[] FILE_HEADER_MAGIC = { 'R', 'E', 'F', 'T' };
+	static final byte VERSION_1 = (byte) 1;
 
-final class DfsPackKey {
-	final int hash;
+	static final int FILE_HEADER_LEN = 24;
+	static final int FILE_FOOTER_LEN = 68;
 
-	final AtomicLong cachedSize;
+	static final byte FILE_BLOCK_TYPE = 'R';
+	static final byte REF_BLOCK_TYPE = 'r';
+	static final byte OBJ_BLOCK_TYPE = 'o';
+	static final byte LOG_BLOCK_TYPE = 'g';
+	static final byte INDEX_BLOCK_TYPE = 'i';
 
-	DfsPackKey() {
-		// Multiply by 31 here so we can more directly combine with another
-		// value without doing the multiply there.
-		//
-		hash = System.identityHashCode(this) * 31;
-		cachedSize = new AtomicLong();
+	static final int VALUE_NONE = 0x0;
+	static final int VALUE_1ID = 0x1;
+	static final int VALUE_2ID = 0x2;
+	static final int VALUE_SYMREF = 0x3;
+	static final int VALUE_TYPE_MASK = 0x7;
+
+	static final int LOG_NONE = 0x0;
+	static final int LOG_DATA = 0x1;
+
+	static final int MAX_BLOCK_SIZE = (1 << 24) - 1;
+	static final int MAX_RESTARTS = 65535;
+
+	static boolean isFileHeaderMagic(byte[] buf, int o, int n) {
+		return (n - o) >= FILE_HEADER_MAGIC.length
+				&& buf[o + 0] == FILE_HEADER_MAGIC[0]
+				&& buf[o + 1] == FILE_HEADER_MAGIC[1]
+				&& buf[o + 2] == FILE_HEADER_MAGIC[2]
+				&& buf[o + 3] == FILE_HEADER_MAGIC[3];
+	}
+
+	static long reverseUpdateIndex(long time) {
+		return 0xffffffffffffffffL - time;
+	}
+
+	private ReftableConstants() {
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableOutputStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableOutputStream.java
new file mode 100644
index 0000000..a24619b
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableOutputStream.java
@@ -0,0 +1,247 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.reftable;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.FILE_HEADER_LEN;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.INDEX_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.LOG_BLOCK_TYPE;
+import static org.eclipse.jgit.lib.Constants.OBJECT_ID_LENGTH;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.Arrays;
+import java.util.zip.Deflater;
+import java.util.zip.DeflaterOutputStream;
+
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.util.NB;
+import org.eclipse.jgit.util.io.CountingOutputStream;
+
+/**
+ * Wrapper to assist formatting a reftable to an {@link OutputStream}.
+ * <p>
+ * Internally buffers at block size boundaries, flushing only complete blocks to
+ * the {@code OutputStream}.
+ */
+class ReftableOutputStream extends OutputStream {
+	private final byte[] tmp = new byte[10];
+	private final CountingOutputStream out;
+	private final boolean alignBlocks;
+
+	private Deflater deflater;
+	private DeflaterOutputStream compressor;
+
+	private int blockType;
+	private int blockSize;
+	private int blockStart;
+	private byte[] blockBuf;
+	private int cur;
+	private long paddingUsed;
+
+	ReftableOutputStream(OutputStream os, int bs, boolean align) {
+		blockSize = bs;
+		blockBuf = new byte[bs];
+		alignBlocks = align;
+		out = new CountingOutputStream(os);
+	}
+
+	void setBlockSize(int bs) {
+		blockSize = bs;
+	}
+
+	@Override
+	public void write(int b) {
+		ensureBytesAvailableInBlockBuf(1);
+		blockBuf[cur++] = (byte) b;
+	}
+
+	@Override
+	public void write(byte[] b, int off, int cnt) {
+		ensureBytesAvailableInBlockBuf(cnt);
+		System.arraycopy(b, off, blockBuf, cur, cnt);
+		cur += cnt;
+	}
+
+	int bytesWrittenInBlock() {
+		return cur;
+	}
+
+	int bytesAvailableInBlock() {
+		return blockSize - cur;
+	}
+
+	long paddingUsed() {
+		return paddingUsed;
+	}
+
+	/** @return bytes flushed; excludes {@link #bytesWrittenInBlock()}. */
+	long size() {
+		return out.getCount();
+	}
+
+	static int computeVarintSize(long val) {
+		int n = 1;
+		for (; (val >>>= 7) != 0; n++) {
+			val--;
+		}
+		return n;
+	}
+
+	void writeVarint(long val) {
+		int n = tmp.length;
+		tmp[--n] = (byte) (val & 0x7f);
+		while ((val >>>= 7) != 0) {
+			tmp[--n] = (byte) (0x80 | (--val & 0x7F));
+		}
+		write(tmp, n, tmp.length - n);
+	}
+
+	void writeInt16(int val) {
+		ensureBytesAvailableInBlockBuf(2);
+		NB.encodeInt16(blockBuf, cur, val);
+		cur += 2;
+	}
+
+	void writeInt24(int val) {
+		ensureBytesAvailableInBlockBuf(3);
+		NB.encodeInt24(blockBuf, cur, val);
+		cur += 3;
+	}
+
+	void writeId(ObjectId id) {
+		ensureBytesAvailableInBlockBuf(OBJECT_ID_LENGTH);
+		id.copyRawTo(blockBuf, cur);
+		cur += OBJECT_ID_LENGTH;
+	}
+
+	void writeVarintString(String s) {
+		writeVarintString(s.getBytes(UTF_8));
+	}
+
+	void writeVarintString(byte[] msg) {
+		writeVarint(msg.length);
+		write(msg, 0, msg.length);
+	}
+
+	private void ensureBytesAvailableInBlockBuf(int cnt) {
+		if (cur + cnt > blockBuf.length) {
+			int n = Math.max(cur + cnt, blockBuf.length * 2);
+			blockBuf = Arrays.copyOf(blockBuf, n);
+		}
+	}
+
+	void flushFileHeader() throws IOException {
+		if (cur == FILE_HEADER_LEN && out.getCount() == 0) {
+			out.write(blockBuf, 0, cur);
+			cur = 0;
+		}
+	}
+
+	void beginBlock(byte type) {
+		blockType = type;
+		blockStart = cur;
+		cur += 4; // reserve space for 4-byte block header.
+	}
+
+	void flushBlock() throws IOException {
+		if (cur > blockSize && blockType != INDEX_BLOCK_TYPE) {
+			throw new IOException(JGitText.get().overflowedReftableBlock);
+		}
+		NB.encodeInt32(blockBuf, blockStart, (blockType << 24) | cur);
+
+		if (blockType == LOG_BLOCK_TYPE) {
+			// Log blocks are deflated after the block header.
+			out.write(blockBuf, 0, 4);
+			if (deflater != null) {
+				deflater.reset();
+			} else {
+				deflater = new Deflater(Deflater.BEST_COMPRESSION);
+				compressor = new DeflaterOutputStream(out, deflater);
+			}
+			compressor.write(blockBuf, 4, cur - 4);
+			compressor.finish();
+		} else {
+			// Other blocks are uncompressed.
+			out.write(blockBuf, 0, cur);
+		}
+
+		cur = 0;
+		blockType = 0;
+		blockStart = 0;
+	}
+
+	void padBetweenBlocksToNextBlock() throws IOException {
+		if (alignBlocks) {
+			long m = size() % blockSize;
+			if (m > 0) {
+				int pad = blockSize - (int) m;
+				ensureBytesAvailableInBlockBuf(pad);
+				Arrays.fill(blockBuf, 0, pad, (byte) 0);
+				out.write(blockBuf, 0, pad);
+				paddingUsed += pad;
+			}
+		}
+	}
+
+	int estimatePadBetweenBlocks(int currentBlockSize) {
+		if (alignBlocks) {
+			long m = (size() + currentBlockSize) % blockSize;
+			return m > 0 ? blockSize - (int) m : 0;
+		}
+		return 0;
+	}
+
+	void finishFile() throws IOException {
+		// File footer doesn't need patching for the block start.
+		// Just flush what has been buffered.
+		out.write(blockBuf, 0, cur);
+		cur = 0;
+
+		if (deflater != null) {
+			deflater.end();
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableReader.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableReader.java
new file mode 100644
index 0000000..407a77c
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableReader.java
@@ -0,0 +1,683 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.reftable;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.eclipse.jgit.internal.storage.reftable.BlockReader.decodeBlockLen;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.FILE_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.FILE_FOOTER_LEN;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.FILE_HEADER_LEN;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.INDEX_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.LOG_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.REF_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.VERSION_1;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.isFileHeaderMagic;
+import static org.eclipse.jgit.lib.Constants.OBJECT_ID_LENGTH;
+
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.text.MessageFormat;
+import java.util.Arrays;
+import java.util.zip.CRC32;
+
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.internal.storage.io.BlockSource;
+import org.eclipse.jgit.internal.storage.reftable.BlockWriter.LogEntry;
+import org.eclipse.jgit.lib.AnyObjectId;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.ReflogEntry;
+import org.eclipse.jgit.util.LongList;
+import org.eclipse.jgit.util.LongMap;
+import org.eclipse.jgit.util.NB;
+
+/**
+ * Reads a reftable formatted file.
+ * <p>
+ * {@code ReftableReader} is not thread-safe. Concurrent readers need their own
+ * instance to read from the same file.
+ */
+public class ReftableReader extends Reftable {
+	private final BlockSource src;
+
+	private int blockSize = -1;
+	private long minUpdateIndex;
+	private long maxUpdateIndex;
+
+	private long refEnd;
+	private long objPosition;
+	private long objEnd;
+	private long logPosition;
+	private long logEnd;
+	private int objIdLen;
+
+	private long refIndexPosition = -1;
+	private long objIndexPosition = -1;
+	private long logIndexPosition = -1;
+
+	private BlockReader refIndex;
+	private BlockReader objIndex;
+	private BlockReader logIndex;
+	private LongMap<BlockReader> indexCache;
+
+	/**
+	 * Initialize a new reftable reader.
+	 *
+	 * @param src
+	 *            the file content to read.
+	 */
+	public ReftableReader(BlockSource src) {
+		this.src = src;
+	}
+
+	/**
+	 * @return the block size in bytes chosen for this file by the writer. Most
+	 *         reads from the {@link BlockSource} will be aligned to the block
+	 *         size.
+	 * @throws IOException
+	 *             file cannot be read.
+	 */
+	public int blockSize() throws IOException {
+		if (blockSize == -1) {
+			readFileHeader();
+		}
+		return blockSize;
+	}
+
+	/**
+	 * @return the minimum update index for log entries that appear in this
+	 *         reftable. This should be 1 higher than the prior reftable's
+	 *         {@code maxUpdateIndex} if this table is used in a stack.
+	 * @throws IOException
+	 *             file cannot be read.
+	 */
+	public long minUpdateIndex() throws IOException {
+		if (blockSize == -1) {
+			readFileHeader();
+		}
+		return minUpdateIndex;
+	}
+
+	/**
+	 * @return the maximum update index for log entries that appear in this
+	 *         reftable. This should be 1 higher than the prior reftable's
+	 *         {@code maxUpdateIndex} if this table is used in a stack.
+	 * @throws IOException
+	 *             file cannot be read.
+	 */
+	public long maxUpdateIndex() throws IOException {
+		if (blockSize == -1) {
+			readFileHeader();
+		}
+		return maxUpdateIndex;
+	}
+
+	@Override
+	public RefCursor allRefs() throws IOException {
+		if (blockSize == -1) {
+			readFileHeader();
+		}
+
+		long end = refEnd > 0 ? refEnd : (src.size() - FILE_FOOTER_LEN);
+		src.adviseSequentialRead(0, end);
+
+		RefCursorImpl i = new RefCursorImpl(end, null, false);
+		i.block = readBlock(0, end);
+		return i;
+	}
+
+	@Override
+	public RefCursor seekRef(String refName) throws IOException {
+		initRefIndex();
+
+		byte[] key = refName.getBytes(UTF_8);
+		boolean prefix = key[key.length - 1] == '/';
+
+		RefCursorImpl i = new RefCursorImpl(refEnd, key, prefix);
+		i.block = seek(REF_BLOCK_TYPE, key, refIndex, 0, refEnd);
+		return i;
+	}
+
+	@Override
+	public RefCursor byObjectId(AnyObjectId id) throws IOException {
+		initObjIndex();
+		ObjCursorImpl i = new ObjCursorImpl(refEnd, id);
+		if (objIndex != null) {
+			i.initSeek();
+		} else {
+			i.initScan();
+		}
+		return i;
+	}
+
+	@Override
+	public LogCursor allLogs() throws IOException {
+		initLogIndex();
+		if (logPosition > 0) {
+			src.adviseSequentialRead(logPosition, logEnd);
+			LogCursorImpl i = new LogCursorImpl(logEnd, null);
+			i.block = readBlock(logPosition, logEnd);
+			return i;
+		}
+		return new EmptyLogCursor();
+	}
+
+	@Override
+	public LogCursor seekLog(String refName, long updateIndex)
+			throws IOException {
+		initLogIndex();
+		if (logPosition > 0) {
+			byte[] key = LogEntry.key(refName, updateIndex);
+			byte[] match = refName.getBytes(UTF_8);
+			LogCursorImpl i = new LogCursorImpl(logEnd, match);
+			i.block = seek(LOG_BLOCK_TYPE, key, logIndex, logPosition, logEnd);
+			return i;
+		}
+		return new EmptyLogCursor();
+	}
+
+	private BlockReader seek(byte blockType, byte[] key, BlockReader idx,
+			long startPos, long endPos) throws IOException {
+		if (idx != null) {
+			// Walk through a possibly multi-level index to a leaf block.
+			BlockReader block = idx;
+			do {
+				if (block.seekKey(key) > 0) {
+					return null;
+				}
+				long pos = block.readPositionFromIndex();
+				block = readBlock(pos, endPos);
+			} while (block.type() == INDEX_BLOCK_TYPE);
+			block.seekKey(key);
+			return block;
+		}
+		return binarySearch(blockType, key, startPos, endPos);
+	}
+
+	private BlockReader binarySearch(byte blockType, byte[] key,
+			long startPos, long endPos) throws IOException {
+		if (blockSize == 0) {
+			BlockReader b = readBlock(startPos, endPos);
+			if (blockType != b.type()) {
+				return null;
+			}
+			b.seekKey(key);
+			return b;
+		}
+
+		int low = (int) (startPos / blockSize);
+		int end = blocksIn(startPos, endPos);
+		BlockReader block = null;
+		do {
+			int mid = (low + end) >>> 1;
+			block = readBlock(((long) mid) * blockSize, endPos);
+			if (blockType != block.type()) {
+				return null;
+			}
+			int cmp = block.seekKey(key);
+			if (cmp < 0) {
+				end = mid;
+			} else if (cmp == 0) {
+				break;
+			} else /* if (cmp > 0) */ {
+				low = mid + 1;
+			}
+		} while (low < end);
+		return block;
+	}
+
+	private void readFileHeader() throws IOException {
+		readHeaderOrFooter(0, FILE_HEADER_LEN);
+	}
+
+	private void readFileFooter() throws IOException {
+		int ftrLen = FILE_FOOTER_LEN;
+		byte[] ftr = readHeaderOrFooter(src.size() - ftrLen, ftrLen);
+
+		CRC32 crc = new CRC32();
+		crc.update(ftr, 0, ftrLen - 4);
+		if (crc.getValue() != NB.decodeUInt32(ftr, ftrLen - 4)) {
+			throw new IOException(JGitText.get().invalidReftableCRC);
+		}
+
+		refIndexPosition = NB.decodeInt64(ftr, 24);
+		long p = NB.decodeInt64(ftr, 32);
+		objPosition = p >>> 5;
+		objIdLen = (int) (p & 0x1f);
+		objIndexPosition = NB.decodeInt64(ftr, 40);
+		logPosition = NB.decodeInt64(ftr, 48);
+		logIndexPosition = NB.decodeInt64(ftr, 56);
+
+		if (refIndexPosition > 0) {
+			refEnd = refIndexPosition;
+		} else if (objPosition > 0) {
+			refEnd = objPosition;
+		} else if (logPosition > 0) {
+			refEnd = logPosition;
+		} else {
+			refEnd = src.size() - ftrLen;
+		}
+
+		if (objPosition > 0) {
+			if (objIndexPosition > 0) {
+				objEnd = objIndexPosition;
+			} else if (logPosition > 0) {
+				objEnd = logPosition;
+			} else {
+				objEnd = src.size() - ftrLen;
+			}
+		}
+
+		if (logPosition > 0) {
+			if (logIndexPosition > 0) {
+				logEnd = logIndexPosition;
+			} else {
+				logEnd = src.size() - ftrLen;
+			}
+		}
+	}
+
+	private byte[] readHeaderOrFooter(long pos, int len) throws IOException {
+		ByteBuffer buf = src.read(pos, len);
+		if (buf.position() != len) {
+			throw new IOException(JGitText.get().shortReadOfBlock);
+		}
+
+		byte[] tmp = new byte[len];
+		buf.flip();
+		buf.get(tmp);
+		if (!isFileHeaderMagic(tmp, 0, len)) {
+			throw new IOException(JGitText.get().invalidReftableFile);
+		}
+
+		int v = NB.decodeInt32(tmp, 4);
+		int version = v >>> 24;
+		if (VERSION_1 != version) {
+			throw new IOException(MessageFormat.format(
+					JGitText.get().unsupportedReftableVersion,
+					Integer.valueOf(version)));
+		}
+		if (blockSize == -1) {
+			blockSize = v & 0xffffff;
+		}
+		minUpdateIndex = NB.decodeInt64(tmp, 8);
+		maxUpdateIndex = NB.decodeInt64(tmp, 16);
+		return tmp;
+	}
+
+	private void initRefIndex() throws IOException {
+		if (refIndexPosition < 0) {
+			readFileFooter();
+		}
+		if (refIndex == null && refIndexPosition > 0) {
+			refIndex = readIndex(refIndexPosition);
+		}
+	}
+
+	private void initObjIndex() throws IOException {
+		if (objIndexPosition < 0) {
+			readFileFooter();
+		}
+		if (objIndex == null && objIndexPosition > 0) {
+			objIndex = readIndex(objIndexPosition);
+		}
+	}
+
+	private void initLogIndex() throws IOException {
+		if (logIndexPosition < 0) {
+			readFileFooter();
+		}
+		if (logIndex == null && logIndexPosition > 0) {
+			logIndex = readIndex(logIndexPosition);
+		}
+	}
+
+	private BlockReader readIndex(long pos) throws IOException {
+		int sz = readBlockLen(pos);
+		BlockReader i = new BlockReader();
+		i.readBlock(src, pos, sz);
+		i.verifyIndex();
+		return i;
+	}
+
+	private int readBlockLen(long pos) throws IOException {
+		int sz = pos == 0 ? FILE_HEADER_LEN + 4 : 4;
+		ByteBuffer tmp = src.read(pos, sz);
+		if (tmp.position() < sz) {
+			throw new IOException(JGitText.get().invalidReftableFile);
+		}
+		byte[] buf;
+		if (tmp.hasArray() && tmp.arrayOffset() == 0) {
+			buf = tmp.array();
+		} else {
+			buf = new byte[sz];
+			tmp.flip();
+			tmp.get(buf);
+		}
+		if (pos == 0 && buf[FILE_HEADER_LEN] == FILE_BLOCK_TYPE) {
+			return FILE_HEADER_LEN;
+		}
+		int p = pos == 0 ? FILE_HEADER_LEN : 0;
+		return decodeBlockLen(NB.decodeInt32(buf, p));
+	}
+
+	private BlockReader readBlock(long pos, long end) throws IOException {
+		if (indexCache != null) {
+			BlockReader b = indexCache.get(pos);
+			if (b != null) {
+				return b;
+			}
+		}
+
+		int sz = blockSize;
+		if (sz == 0) {
+			sz = readBlockLen(pos);
+		} else if (pos + sz > end) {
+			sz = (int) (end - pos); // last block may omit padding.
+		}
+
+		BlockReader b = new BlockReader();
+		b.readBlock(src, pos, sz);
+		if (b.type() == INDEX_BLOCK_TYPE && !b.truncated()) {
+			if (indexCache == null) {
+				indexCache = new LongMap<>();
+			}
+			indexCache.put(pos, b);
+		}
+		return b;
+	}
+
+	private int blocksIn(long pos, long end) {
+		int blocks = (int) ((end - pos) / blockSize);
+		return end % blockSize == 0 ? blocks : (blocks + 1);
+	}
+
+	/**
+	 * Get size of the reftable, in bytes.
+	 *
+	 * @return size of the reftable, in bytes.
+	 * @throws IOException
+	 *             size cannot be obtained.
+	 */
+	public long size() throws IOException {
+		return src.size();
+	}
+
+	@Override
+	public void close() throws IOException {
+		src.close();
+	}
+
+	private class RefCursorImpl extends RefCursor {
+		private final long scanEnd;
+		private final byte[] match;
+		private final boolean prefix;
+
+		private Ref ref;
+		private long updateIndex;
+		BlockReader block;
+
+		RefCursorImpl(long scanEnd, byte[] match, boolean prefix) {
+			this.scanEnd = scanEnd;
+			this.match = match;
+			this.prefix = prefix;
+		}
+
+		@Override
+		public boolean next() throws IOException {
+			for (;;) {
+				if (block == null || block.type() != REF_BLOCK_TYPE) {
+					return false;
+				} else if (!block.next()) {
+					long pos = block.endPosition();
+					if (pos >= scanEnd) {
+						return false;
+					}
+					block = readBlock(pos, scanEnd);
+					continue;
+				}
+
+				block.parseKey();
+				if (match != null && !block.match(match, prefix)) {
+					block.skipValue();
+					return false;
+				}
+
+				updateIndex = minUpdateIndex + block.readUpdateIndexDelta();
+				ref = block.readRef();
+				if (!includeDeletes && wasDeleted()) {
+					continue;
+				}
+				return true;
+			}
+		}
+
+		@Override
+		public Ref getRef() {
+			return ref;
+		}
+
+		@Override
+		public long getUpdateIndex() {
+			return updateIndex;
+		}
+
+		@Override
+		public void close() {
+			// Do nothing.
+		}
+	}
+
+	private class LogCursorImpl extends LogCursor {
+		private final long scanEnd;
+		private final byte[] match;
+
+		private String refName;
+		private long updateIndex;
+		private ReflogEntry entry;
+		BlockReader block;
+
+		LogCursorImpl(long scanEnd, byte[] match) {
+			this.scanEnd = scanEnd;
+			this.match = match;
+		}
+
+		@Override
+		public boolean next() throws IOException {
+			for (;;) {
+				if (block == null || block.type() != LOG_BLOCK_TYPE) {
+					return false;
+				} else if (!block.next()) {
+					long pos = block.endPosition();
+					if (pos >= scanEnd) {
+						return false;
+					}
+					block = readBlock(pos, scanEnd);
+					continue;
+				}
+
+				block.parseKey();
+				if (match != null && !block.match(match, false)) {
+					block.skipValue();
+					return false;
+				}
+
+				refName = block.name();
+				updateIndex = block.readLogUpdateIndex();
+				entry = block.readLogEntry();
+				if (entry == null && !includeDeletes) {
+					continue;
+				}
+				return true;
+			}
+		}
+
+		@Override
+		public String getRefName() {
+			return refName;
+		}
+
+		@Override
+		public long getUpdateIndex() {
+			return updateIndex;
+		}
+
+		@Override
+		public ReflogEntry getReflogEntry() {
+			return entry;
+		}
+
+		@Override
+		public void close() {
+			// Do nothing.
+		}
+	}
+
+	static final LongList EMPTY_LONG_LIST = new LongList(0);
+
+	private class ObjCursorImpl extends RefCursor {
+		private final long scanEnd;
+		private final ObjectId match;
+
+		private Ref ref;
+		private long updateIndex;
+		private int listIdx;
+
+		private LongList blockPos;
+		private BlockReader block;
+
+		ObjCursorImpl(long scanEnd, AnyObjectId id) {
+			this.scanEnd = scanEnd;
+			this.match = id.copy();
+		}
+
+		void initSeek() throws IOException {
+			byte[] rawId = new byte[OBJECT_ID_LENGTH];
+			match.copyRawTo(rawId, 0);
+			byte[] key = Arrays.copyOf(rawId, objIdLen);
+
+			BlockReader b = objIndex;
+			do {
+				if (b.seekKey(key) > 0) {
+					blockPos = EMPTY_LONG_LIST;
+					return;
+				}
+				long pos = b.readPositionFromIndex();
+				b = readBlock(pos, objEnd);
+			} while (b.type() == INDEX_BLOCK_TYPE);
+			b.seekKey(key);
+			while (b.next()) {
+				b.parseKey();
+				if (b.match(key, false)) {
+					blockPos = b.readBlockPositionList();
+					if (blockPos == null) {
+						initScan();
+						return;
+					}
+					break;
+				}
+				b.skipValue();
+			}
+			if (blockPos == null) {
+				blockPos = EMPTY_LONG_LIST;
+			}
+			if (blockPos.size() > 0) {
+				long pos = blockPos.get(listIdx++);
+				block = readBlock(pos, scanEnd);
+			}
+		}
+
+		void initScan() throws IOException {
+			block = readBlock(0, scanEnd);
+		}
+
+		@Override
+		public boolean next() throws IOException {
+			for (;;) {
+				if (block == null || block.type() != REF_BLOCK_TYPE) {
+					return false;
+				} else if (!block.next()) {
+					long pos;
+					if (blockPos != null) {
+						if (listIdx >= blockPos.size()) {
+							return false;
+						}
+						pos = blockPos.get(listIdx++);
+					} else {
+						pos = block.endPosition();
+					}
+					if (pos >= scanEnd) {
+						return false;
+					}
+					block = readBlock(pos, scanEnd);
+					continue;
+				}
+
+				block.parseKey();
+				updateIndex = minUpdateIndex + block.readUpdateIndexDelta();
+				ref = block.readRef();
+				ObjectId id = ref.getObjectId();
+				if (id != null && match.equals(id)
+						&& (includeDeletes || !wasDeleted())) {
+					return true;
+				}
+			}
+		}
+
+		@Override
+		public Ref getRef() {
+			return ref;
+		}
+
+		@Override
+		public long getUpdateIndex() {
+			return updateIndex;
+		}
+
+		@Override
+		public void close() {
+			// Do nothing.
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableWriter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableWriter.java
new file mode 100644
index 0000000..0ac2445
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/ReftableWriter.java
@@ -0,0 +1,813 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.reftable;
+
+import static java.lang.Math.log;
+import static org.eclipse.jgit.internal.storage.reftable.BlockWriter.padBetweenBlocks;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.FILE_FOOTER_LEN;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.FILE_HEADER_LEN;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.FILE_HEADER_MAGIC;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.INDEX_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.LOG_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.MAX_BLOCK_SIZE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.MAX_RESTARTS;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.OBJ_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.REF_BLOCK_TYPE;
+import static org.eclipse.jgit.internal.storage.reftable.ReftableConstants.VERSION_1;
+import static org.eclipse.jgit.lib.Constants.OBJECT_ID_LENGTH;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+import java.util.zip.CRC32;
+
+import org.eclipse.jgit.annotations.Nullable;
+import org.eclipse.jgit.internal.storage.reftable.BlockWriter.DeleteLogEntry;
+import org.eclipse.jgit.internal.storage.reftable.BlockWriter.Entry;
+import org.eclipse.jgit.internal.storage.reftable.BlockWriter.IndexEntry;
+import org.eclipse.jgit.internal.storage.reftable.BlockWriter.LogEntry;
+import org.eclipse.jgit.internal.storage.reftable.BlockWriter.ObjEntry;
+import org.eclipse.jgit.internal.storage.reftable.BlockWriter.RefEntry;
+import org.eclipse.jgit.lib.AbbreviatedObjectId;
+import org.eclipse.jgit.lib.AnyObjectId;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectIdOwnerMap;
+import org.eclipse.jgit.lib.ObjectIdSubclassMap;
+import org.eclipse.jgit.lib.PersonIdent;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.util.LongList;
+import org.eclipse.jgit.util.NB;
+
+/**
+ * Writes a reftable formatted file.
+ * <p>
+ * A reftable can be written in a streaming fashion, provided the caller sorts
+ * all references. A {@link ReftableWriter} is single-use, and not thread-safe.
+ */
+public class ReftableWriter {
+	private ReftableConfig config;
+	private int refBlockSize;
+	private int logBlockSize;
+	private int restartInterval;
+	private int maxIndexLevels;
+	private boolean alignBlocks;
+	private boolean indexObjects;
+
+	private long minUpdateIndex;
+	private long maxUpdateIndex;
+
+	private ReftableOutputStream out;
+	private ObjectIdSubclassMap<RefList> obj2ref;
+
+	private BlockWriter cur;
+	private Section refs;
+	private Section objs;
+	private Section logs;
+	private int objIdLen;
+	private Stats stats;
+
+	/** Initialize a writer with a default configuration. */
+	public ReftableWriter() {
+		this(new ReftableConfig());
+	}
+
+	/**
+	 * Initialize a writer with a specific configuration.
+	 *
+	 * @param cfg
+	 *            configuration for the writer.
+	 */
+	public ReftableWriter(ReftableConfig cfg) {
+		config = cfg;
+	}
+
+	/**
+	 * @param cfg
+	 *            configuration for the writer.
+	 * @return {@code this}
+	 */
+	public ReftableWriter setConfig(ReftableConfig cfg) {
+		this.config = cfg != null ? cfg : new ReftableConfig();
+		return this;
+	}
+
+	/**
+	 * @param min
+	 *            the minimum update index for log entries that appear in this
+	 *            reftable. This should be 1 higher than the prior reftable's
+	 *            {@code maxUpdateIndex} if this table will be used in a stack.
+	 * @return {@code this}
+	 */
+	public ReftableWriter setMinUpdateIndex(long min) {
+		minUpdateIndex = min;
+		return this;
+	}
+
+	/**
+	 * @param max
+	 *            the maximum update index for log entries that appear in this
+	 *            reftable. This should be at least 1 higher than the prior
+	 *            reftable's {@code maxUpdateIndex} if this table will be used
+	 *            in a stack.
+	 * @return {@code this}
+	 */
+	public ReftableWriter setMaxUpdateIndex(long max) {
+		maxUpdateIndex = max;
+		return this;
+	}
+
+	/**
+	 * Begin writing the reftable.
+	 *
+	 * @param os
+	 *            stream to write the table to. Caller is responsible for
+	 *            closing the stream after invoking {@link #finish()}.
+	 * @return {@code this}
+	 * @throws IOException
+	 *             if reftable header cannot be written.
+	 */
+	public ReftableWriter begin(OutputStream os) throws IOException {
+		refBlockSize = config.getRefBlockSize();
+		logBlockSize = config.getLogBlockSize();
+		restartInterval = config.getRestartInterval();
+		maxIndexLevels = config.getMaxIndexLevels();
+		alignBlocks = config.isAlignBlocks();
+		indexObjects = config.isIndexObjects();
+
+		if (refBlockSize <= 0) {
+			refBlockSize = 4 << 10;
+		} else if (refBlockSize > MAX_BLOCK_SIZE) {
+			throw new IllegalArgumentException();
+		}
+		if (logBlockSize <= 0) {
+			logBlockSize = 2 * refBlockSize;
+		}
+		if (restartInterval <= 0) {
+			restartInterval = refBlockSize < (60 << 10) ? 16 : 64;
+		}
+
+		out = new ReftableOutputStream(os, refBlockSize, alignBlocks);
+		refs = new Section(REF_BLOCK_TYPE);
+		if (indexObjects) {
+			obj2ref = new ObjectIdSubclassMap<>();
+		}
+		writeFileHeader();
+		return this;
+	}
+
+	/**
+	 * Sort a collection of references and write them to the reftable.
+	 *
+	 * @param refsToPack
+	 *            references to sort and write.
+	 * @return {@code this}
+	 * @throws IOException
+	 *             if reftable cannot be written.
+	 */
+	public ReftableWriter sortAndWriteRefs(Collection<Ref> refsToPack)
+			throws IOException {
+		Iterator<RefEntry> itr = refsToPack.stream()
+				.map(r -> new RefEntry(r, maxUpdateIndex - minUpdateIndex))
+				.sorted(Entry::compare)
+				.iterator();
+		while (itr.hasNext()) {
+			RefEntry entry = itr.next();
+			long blockPos = refs.write(entry);
+			indexRef(entry.ref, blockPos);
+		}
+		return this;
+	}
+
+	/**
+	 * Write one reference to the reftable.
+	 * <p>
+	 * References must be passed in sorted order.
+	 *
+	 * @param ref
+	 *            the reference to store.
+	 * @throws IOException
+	 *             if reftable cannot be written.
+	 */
+	public void writeRef(Ref ref) throws IOException {
+		writeRef(ref, maxUpdateIndex);
+	}
+
+	/**
+	 * Write one reference to the reftable.
+	 * <p>
+	 * References must be passed in sorted order.
+	 *
+	 * @param ref
+	 *            the reference to store.
+	 * @param updateIndex
+	 *            the updateIndex that modified this reference. Must be
+	 *            {@code >= minUpdateIndex} for this file.
+	 * @throws IOException
+	 *             if reftable cannot be written.
+	 */
+	public void writeRef(Ref ref, long updateIndex) throws IOException {
+		if (updateIndex < minUpdateIndex) {
+			throw new IllegalArgumentException();
+		}
+		long d = updateIndex - minUpdateIndex;
+		long blockPos = refs.write(new RefEntry(ref, d));
+		indexRef(ref, blockPos);
+	}
+
+	private void indexRef(Ref ref, long blockPos) {
+		if (indexObjects && !ref.isSymbolic()) {
+			indexId(ref.getObjectId(), blockPos);
+			indexId(ref.getPeeledObjectId(), blockPos);
+		}
+	}
+
+	private void indexId(ObjectId id, long blockPos) {
+		if (id != null) {
+			RefList l = obj2ref.get(id);
+			if (l == null) {
+				l = new RefList(id);
+				obj2ref.add(l);
+			}
+			l.addBlock(blockPos);
+		}
+	}
+
+	/**
+	 * Write one reflog entry to the reftable.
+	 * <p>
+	 * Reflog entries must be written in reference name and descending
+	 * {@code updateIndex} (highest first) order.
+	 *
+	 * @param ref
+	 *            name of the reference.
+	 * @param updateIndex
+	 *            identifier of the transaction that created the log record. The
+	 *            {@code updateIndex} must be unique within the scope of
+	 *            {@code ref}, and must be within the bounds defined by
+	 *            {@code minUpdateIndex <= updateIndex <= maxUpdateIndex}.
+	 * @param who
+	 *            committer of the reflog entry.
+	 * @param oldId
+	 *            prior id; pass {@link ObjectId#zeroId()} for creations.
+	 * @param newId
+	 *            new id; pass {@link ObjectId#zeroId()} for deletions.
+	 * @param message
+	 *            optional message (may be null).
+	 * @throws IOException
+	 *             if reftable cannot be written.
+	 */
+	public void writeLog(String ref, long updateIndex, PersonIdent who,
+			ObjectId oldId, ObjectId newId, @Nullable String message)
+					throws IOException {
+		String msg = message != null ? message : ""; //$NON-NLS-1$
+		beginLog();
+		logs.write(new LogEntry(ref, updateIndex, who, oldId, newId, msg));
+	}
+
+	/**
+	 * Record deletion of one reflog entry in this reftable.
+	 *
+	 * <p>
+	 * The deletion can shadow an entry stored in a lower table in the stack.
+	 * This is useful for {@code refs/stash} and dropping an entry from its
+	 * reflog.
+	 * <p>
+	 * Deletion must be properly interleaved in sorted updateIndex order with
+	 * any other logs written by
+	 * {@link #writeLog(String, long, PersonIdent, ObjectId, ObjectId, String)}.
+	 *
+	 * @param ref
+	 *            the ref to delete (hide) a reflog entry from.
+	 * @param updateIndex
+	 *            the update index that must be hidden.
+	 * @throws IOException
+	 *             if reftable cannot be written.
+	 */
+	public void deleteLog(String ref, long updateIndex) throws IOException {
+		beginLog();
+		logs.write(new DeleteLogEntry(ref, updateIndex));
+	}
+
+	private void beginLog() throws IOException {
+		if (logs == null) {
+			finishRefAndObjSections(); // close prior ref blocks and their index, if present.
+			out.flushFileHeader();
+			out.setBlockSize(logBlockSize);
+			logs = new Section(LOG_BLOCK_TYPE);
+		}
+	}
+
+	/**
+	 * @return an estimate of the current size in bytes of the reftable, if it
+	 *         was finished right now. Estimate is only accurate if
+	 *         {@link ReftableConfig#setIndexObjects(boolean)} is {@code false}
+	 *         and {@link ReftableConfig#setMaxIndexLevels(int)} is {@code 1}.
+	 */
+	public long estimateTotalBytes() {
+		long bytes = out.size();
+		if (bytes == 0) {
+			bytes += FILE_HEADER_LEN;
+		}
+		if (cur != null) {
+			long curBlockPos = out.size();
+			int sz = cur.currentSize();
+			bytes += sz;
+
+			IndexBuilder idx = null;
+			if (cur.blockType() == REF_BLOCK_TYPE) {
+				idx = refs.idx;
+			} else if (cur.blockType() == LOG_BLOCK_TYPE) {
+				idx = logs.idx;
+			}
+			if (idx != null && shouldHaveIndex(idx)) {
+				if (idx == refs.idx) {
+					bytes += out.estimatePadBetweenBlocks(sz);
+				}
+				bytes += idx.estimateBytes(curBlockPos);
+			}
+		}
+		bytes += FILE_FOOTER_LEN;
+		return bytes;
+	}
+
+	/**
+	 * Finish writing the reftable by writing its trailer.
+	 *
+	 * @return {@code this}
+	 * @throws IOException
+	 *             if reftable cannot be written.
+	 */
+	public ReftableWriter finish() throws IOException {
+		finishRefAndObjSections();
+		finishLogSection();
+		writeFileFooter();
+		out.finishFile();
+
+		stats = new Stats(this, out);
+		out = null;
+		obj2ref = null;
+		cur = null;
+		refs = null;
+		objs = null;
+		logs = null;
+		return this;
+	}
+
+	private void finishRefAndObjSections() throws IOException {
+		if (cur != null && cur.blockType() == REF_BLOCK_TYPE) {
+			refs.finishSectionMaybeWriteIndex();
+			if (indexObjects && !obj2ref.isEmpty() && refs.idx.bytes > 0) {
+				writeObjBlocks();
+			}
+			obj2ref = null;
+		}
+	}
+
+	private void writeObjBlocks() throws IOException {
+		List<RefList> sorted = sortById(obj2ref);
+		obj2ref = null;
+		objIdLen = shortestUniqueAbbreviation(sorted);
+
+		out.padBetweenBlocksToNextBlock();
+		objs = new Section(OBJ_BLOCK_TYPE);
+		objs.entryCnt = sorted.size();
+		for (RefList l : sorted) {
+			objs.write(new ObjEntry(objIdLen, l, l.blockPos));
+		}
+		objs.finishSectionMaybeWriteIndex();
+	}
+
+	private void finishLogSection() throws IOException {
+		if (cur != null && cur.blockType() == LOG_BLOCK_TYPE) {
+			logs.finishSectionMaybeWriteIndex();
+		}
+	}
+
+	private boolean shouldHaveIndex(IndexBuilder idx) {
+		int threshold;
+		if (idx == refs.idx && alignBlocks) {
+			threshold = 4;
+		} else {
+			threshold = 1;
+		}
+		return idx.entries.size() + (cur != null ? 1 : 0) > threshold;
+	}
+
+	private void writeFileHeader() {
+		byte[] hdr = new byte[FILE_HEADER_LEN];
+		encodeHeader(hdr);
+		out.write(hdr, 0, FILE_HEADER_LEN);
+	}
+
+	private void encodeHeader(byte[] hdr) {
+		System.arraycopy(FILE_HEADER_MAGIC, 0, hdr, 0, 4);
+		int bs = alignBlocks ? refBlockSize : 0;
+		NB.encodeInt32(hdr, 4, (VERSION_1 << 24) | bs);
+		NB.encodeInt64(hdr, 8, minUpdateIndex);
+		NB.encodeInt64(hdr, 16, maxUpdateIndex);
+	}
+
+	private void writeFileFooter() {
+		int ftrLen = FILE_FOOTER_LEN;
+		byte[] ftr = new byte[ftrLen];
+		encodeHeader(ftr);
+
+		NB.encodeInt64(ftr, 24, indexPosition(refs));
+		NB.encodeInt64(ftr, 32, (firstBlockPosition(objs) << 5) | objIdLen);
+		NB.encodeInt64(ftr, 40, indexPosition(objs));
+		NB.encodeInt64(ftr, 48, firstBlockPosition(logs));
+		NB.encodeInt64(ftr, 56, indexPosition(logs));
+
+		CRC32 crc = new CRC32();
+		crc.update(ftr, 0, ftrLen - 4);
+		NB.encodeInt32(ftr, ftrLen - 4, (int) crc.getValue());
+
+		out.write(ftr, 0, ftrLen);
+	}
+
+	private static long firstBlockPosition(@Nullable Section s) {
+		return s != null ? s.firstBlockPosition : 0;
+	}
+
+	private static long indexPosition(@Nullable Section s) {
+		return s != null && s.idx != null ? s.idx.rootPosition : 0;
+	}
+
+	/** @return statistics of the last written reftable. */
+	public Stats getStats() {
+		return stats;
+	}
+
+	/** Statistics about a written reftable. */
+	public static class Stats {
+		private final int refBlockSize;
+		private final int logBlockSize;
+		private final int restartInterval;
+
+		private final long minUpdateIndex;
+		private final long maxUpdateIndex;
+
+		private final long refCnt;
+		private final long objCnt;
+		private final int objIdLen;
+		private final long logCnt;
+		private final long refBytes;
+		private final long objBytes;
+		private final long logBytes;
+		private final long paddingUsed;
+		private final long totalBytes;
+
+		private final int refIndexSize;
+		private final int refIndexLevels;
+		private final int objIndexSize;
+		private final int objIndexLevels;
+
+		Stats(ReftableWriter w, ReftableOutputStream o) {
+			refBlockSize = w.refBlockSize;
+			logBlockSize = w.logBlockSize;
+			restartInterval = w.restartInterval;
+
+			minUpdateIndex = w.minUpdateIndex;
+			maxUpdateIndex = w.maxUpdateIndex;
+			paddingUsed = o.paddingUsed();
+			totalBytes = o.size();
+
+			refCnt = w.refs.entryCnt;
+			refBytes = w.refs.bytes;
+
+			objCnt = w.objs != null ? w.objs.entryCnt : 0;
+			objBytes = w.objs != null ? w.objs.bytes : 0;
+			objIdLen = w.objIdLen;
+
+			logCnt = w.logs != null ? w.logs.entryCnt : 0;
+			logBytes = w.logs != null ? w.logs.bytes : 0;
+
+			IndexBuilder refIdx = w.refs.idx;
+			refIndexSize = refIdx.bytes;
+			refIndexLevels = refIdx.levels;
+
+			IndexBuilder objIdx = w.objs != null ? w.objs.idx : null;
+			objIndexSize = objIdx != null ? objIdx.bytes : 0;
+			objIndexLevels = objIdx != null ? objIdx.levels : 0;
+		}
+
+		/** @return number of bytes in a ref block. */
+		public int refBlockSize() {
+			return refBlockSize;
+		}
+
+		/** @return number of bytes to compress into a log block. */
+		public int logBlockSize() {
+			return logBlockSize;
+		}
+
+		/** @return number of references between binary search markers. */
+		public int restartInterval() {
+			return restartInterval;
+		}
+
+		/** @return smallest update index contained in this reftable. */
+		public long minUpdateIndex() {
+			return minUpdateIndex;
+		}
+
+		/** @return largest update index contained in this reftable. */
+		public long maxUpdateIndex() {
+			return maxUpdateIndex;
+		}
+
+		/** @return total number of references in the reftable. */
+		public long refCount() {
+			return refCnt;
+		}
+
+		/** @return number of unique objects in the reftable. */
+		public long objCount() {
+			return objCnt;
+		}
+
+		/** @return total number of log records in the reftable. */
+		public long logCount() {
+			return logCnt;
+		}
+
+		/** @return number of bytes for references, including ref index. */
+		public long refBytes() {
+			return refBytes;
+		}
+
+		/** @return number of bytes for objects, including object index. */
+		public long objBytes() {
+			return objBytes;
+		}
+
+		/** @return number of bytes for log, including log index. */
+		public long logBytes() {
+			return logBytes;
+		}
+
+		/** @return total number of bytes in the reftable. */
+		public long totalBytes() {
+			return totalBytes;
+		}
+
+		/** @return bytes of padding used to maintain block alignment. */
+		public long paddingBytes() {
+			return paddingUsed;
+		}
+
+		/** @return number of bytes in the ref index; 0 if no index was used. */
+		public int refIndexSize() {
+			return refIndexSize;
+		}
+
+		/** @return number of levels in the ref index. */
+		public int refIndexLevels() {
+			return refIndexLevels;
+		}
+
+		/** @return number of bytes in the object index; 0 if no index. */
+		public int objIndexSize() {
+			return objIndexSize;
+		}
+
+		/** @return number of levels in the object index. */
+		public int objIndexLevels() {
+			return objIndexLevels;
+		}
+
+		/**
+		 * @return number of bytes required to uniquely identify all objects in
+		 *         the reftable. Unique abbreviations in hex would be
+		 *         {@code 2 * objIdLength()}.
+		 */
+		public int objIdLength() {
+			return objIdLen;
+		}
+	}
+
+	private static List<RefList> sortById(ObjectIdSubclassMap<RefList> m) {
+		List<RefList> s = new ArrayList<>(m.size());
+		for (RefList l : m) {
+			s.add(l);
+		}
+		Collections.sort(s);
+		return s;
+	}
+
+	private static int shortestUniqueAbbreviation(List<RefList> in) {
+		// Estimate minimum number of bytes necessary for unique abbreviations.
+		int bytes = Math.max(2, (int) (log(in.size()) / log(8)));
+		Set<AbbreviatedObjectId> tmp = new HashSet<>((int) (in.size() * 0.75f));
+		retry: for (;;) {
+			int hexLen = bytes * 2;
+			for (ObjectId id : in) {
+				AbbreviatedObjectId a = id.abbreviate(hexLen);
+				if (!tmp.add(a)) {
+					if (++bytes >= OBJECT_ID_LENGTH) {
+						return OBJECT_ID_LENGTH;
+					}
+					tmp.clear();
+					continue retry;
+				}
+			}
+			return bytes;
+		}
+	}
+
+	private static class RefList extends ObjectIdOwnerMap.Entry {
+		final LongList blockPos = new LongList(2);
+
+		RefList(AnyObjectId id) {
+			super(id);
+		}
+
+		void addBlock(long pos) {
+			if (!blockPos.contains(pos)) {
+				blockPos.add(pos);
+			}
+		}
+	}
+
+	private class Section {
+		final IndexBuilder idx;
+		final long firstBlockPosition;
+
+		long entryCnt;
+		long bytes;
+
+		Section(byte keyType) {
+			idx = new IndexBuilder(keyType);
+			firstBlockPosition = out.size();
+		}
+
+		long write(BlockWriter.Entry entry) throws IOException {
+			if (cur == null) {
+				beginBlock(entry);
+			} else if (!cur.tryAdd(entry)) {
+				flushCurBlock();
+				if (cur.padBetweenBlocks()) {
+					out.padBetweenBlocksToNextBlock();
+				}
+				beginBlock(entry);
+			}
+			entryCnt++;
+			return out.size();
+		}
+
+		private void beginBlock(BlockWriter.Entry entry)
+				throws BlockSizeTooSmallException {
+			byte blockType = entry.blockType();
+			int bs = out.bytesAvailableInBlock();
+			cur = new BlockWriter(blockType, idx.keyType, bs, restartInterval);
+			cur.mustAdd(entry);
+		}
+
+		void flushCurBlock() throws IOException {
+			idx.entries.add(new IndexEntry(cur.lastKey(), out.size()));
+			cur.writeTo(out);
+		}
+
+		void finishSectionMaybeWriteIndex() throws IOException {
+			flushCurBlock();
+			cur = null;
+			if (shouldHaveIndex(idx)) {
+				idx.writeIndex();
+			}
+			bytes = out.size() - firstBlockPosition;
+		}
+	}
+
+	private class IndexBuilder {
+		final byte keyType;
+		List<IndexEntry> entries = new ArrayList<>();
+		long rootPosition;
+		int bytes;
+		int levels;
+
+		IndexBuilder(byte kt) {
+			keyType = kt;
+		}
+
+		int estimateBytes(long curBlockPos) {
+			BlockWriter b = new BlockWriter(
+					INDEX_BLOCK_TYPE, keyType,
+					MAX_BLOCK_SIZE,
+					Math.max(restartInterval, entries.size() / MAX_RESTARTS));
+			try {
+				for (Entry e : entries) {
+					b.mustAdd(e);
+				}
+				if (cur != null) {
+					b.mustAdd(new IndexEntry(cur.lastKey(), curBlockPos));
+				}
+			} catch (BlockSizeTooSmallException e) {
+				return b.currentSize();
+			}
+			return b.currentSize();
+		}
+
+		void writeIndex() throws IOException {
+			if (padBetweenBlocks(keyType)) {
+				out.padBetweenBlocksToNextBlock();
+			}
+			long startPos = out.size();
+			writeMultiLevelIndex(entries);
+			bytes = (int) (out.size() - startPos);
+			entries = null;
+		}
+
+		private void writeMultiLevelIndex(List<IndexEntry> keys)
+				throws IOException {
+			levels = 1;
+			while (maxIndexLevels == 0 || levels < maxIndexLevels) {
+				keys = writeOneLevel(keys);
+				if (keys == null) {
+					return;
+				}
+				levels++;
+			}
+
+			// When maxIndexLevels has restricted the writer, write one
+			// index block with the entire remaining set of keys.
+			BlockWriter b = new BlockWriter(
+					INDEX_BLOCK_TYPE, keyType,
+					MAX_BLOCK_SIZE,
+					Math.max(restartInterval, keys.size() / MAX_RESTARTS));
+			for (Entry e : keys) {
+				b.mustAdd(e);
+			}
+			rootPosition = out.size();
+			b.writeTo(out);
+		}
+
+		private List<IndexEntry> writeOneLevel(List<IndexEntry> keys)
+				throws IOException {
+			Section thisLevel = new Section(keyType);
+			for (Entry e : keys) {
+				thisLevel.write(e);
+			}
+			if (!thisLevel.idx.entries.isEmpty()) {
+				thisLevel.flushCurBlock();
+				if (cur.padBetweenBlocks()) {
+					out.padBetweenBlocksToNextBlock();
+				}
+				cur = null;
+				return thisLevel.idx.entries;
+			}
+
+			// The current block fit entire level; make it the root.
+			rootPosition = out.size();
+			cur.writeTo(out);
+			cur = null;
+			return null;
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/AbbreviatedObjectId.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/AbbreviatedObjectId.java
index 29a379e..0567051 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/AbbreviatedObjectId.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/AbbreviatedObjectId.java
@@ -336,7 +336,7 @@ private int mask(final int word, final int v) {
 
 	@Override
 	public int hashCode() {
-		return w2;
+		return w1;
 	}
 
 	@Override
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BaseRepositoryBuilder.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BaseRepositoryBuilder.java
index de1003b..825c1f7 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BaseRepositoryBuilder.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BaseRepositoryBuilder.java
@@ -738,4 +738,4 @@ protected FS safeFS() {
 	protected final B self() {
 		return (B) this;
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BatchRefUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BatchRefUpdate.java
index 3f6995d..bcf9065 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BatchRefUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BatchRefUpdate.java
@@ -58,6 +58,8 @@
 import java.util.List;
 import java.util.concurrent.TimeoutException;
 
+import org.eclipse.jgit.annotations.Nullable;
+import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.RefUpdate.Result;
 import org.eclipse.jgit.revwalk.RevWalk;
@@ -80,8 +82,10 @@ public class BatchRefUpdate {
 	 * clock skew between machines on the same LAN using an NTP server also on
 	 * the same LAN should be under 5 seconds. 5 seconds is also not that long
 	 * for a large `git push` operation to complete.
+	 *
+	 * @since 4.9
 	 */
-	private static final Duration MAX_WAIT = Duration.ofSeconds(5);
+	protected static final Duration MAX_WAIT = Duration.ofSeconds(5);
 
 	private final RefDatabase refdb;
 
@@ -100,6 +104,12 @@ public class BatchRefUpdate {
 	/** Should the result value be appended to {@link #refLogMessage}. */
 	private boolean refLogIncludeResult;
 
+	/**
+	 * Should reflogs be written even if the configured default for this ref is
+	 * not to write it.
+	 */
+	private boolean forceRefLog;
+
 	/** Push certificate associated with this update. */
 	private PushCertificate pushCert;
 
@@ -173,25 +183,42 @@ public BatchRefUpdate setRefLogIdent(final PersonIdent pi) {
 	 * @return message the caller wants to include in the reflog; null if the
 	 *         update should not be logged.
 	 */
+	@Nullable
 	public String getRefLogMessage() {
 		return refLogMessage;
 	}
 
-	/** @return {@code true} if the ref log message should show the result. */
+	/**
+	 * Check whether the reflog message should include the result of the update,
+	 * such as fast-forward or force-update.
+	 * <p>
+	 * Describes the default for commands in this batch that do not override it
+	 * with {@link ReceiveCommand#setRefLogMessage(String, boolean)}.
+	 *
+	 * @return true if the message should include the result.
+	 */
 	public boolean isRefLogIncludingResult() {
 		return refLogIncludeResult;
 	}
 
 	/**
 	 * Set the message to include in the reflog.
+	 * <p>
+	 * Repository implementations may limit which reflogs are written by default,
+	 * based on the project configuration. If a repo is not configured to write
+	 * logs for this ref by default, setting the message alone may have no effect.
+	 * To indicate that the repo should write logs for this update in spite of
+	 * configured defaults, use {@link #setForceRefLog(boolean)}.
+	 * <p>
+	 * Describes the default for commands in this batch that do not override it
+	 * with {@link ReceiveCommand#setRefLogMessage(String, boolean)}.
 	 *
 	 * @param msg
-	 *            the message to describe this change. It may be null if
-	 *            appendStatus is null in order not to append to the reflog
+	 *            the message to describe this change. If null and appendStatus is
+	 *            false, the reflog will not be updated.
 	 * @param appendStatus
 	 *            true if the status of the ref change (fast-forward or
-	 *            forced-update) should be appended to the user supplied
-	 *            message.
+	 *            forced-update) should be appended to the user supplied message.
 	 * @return {@code this}.
 	 */
 	public BatchRefUpdate setRefLogMessage(String msg, boolean appendStatus) {
@@ -209,6 +236,8 @@ else if (msg == null && appendStatus) {
 
 	/**
 	 * Don't record this update in the ref's associated reflog.
+	 * <p>
+	 * Equivalent to {@code setRefLogMessage(null, false)}.
 	 *
 	 * @return {@code this}.
 	 */
@@ -218,12 +247,38 @@ public BatchRefUpdate disableRefLog() {
 		return this;
 	}
 
-	/** @return true if log has been disabled by {@link #disableRefLog()}. */
+	/**
+	 * Force writing a reflog for the updated ref.
+	 *
+	 * @param force whether to force.
+	 * @return {@code this}
+	 * @since 4.9
+	 */
+	public BatchRefUpdate setForceRefLog(boolean force) {
+		forceRefLog = force;
+		return this;
+	}
+
+	/**
+	 * Check whether log has been disabled by {@link #disableRefLog()}.
+	 *
+	 * @return true if disabled.
+	 */
 	public boolean isRefLogDisabled() {
 		return refLogMessage == null;
 	}
 
 	/**
+	 * Check whether the reflog should be written regardless of repo defaults.
+	 *
+	 * @return whether force writing is enabled.
+	 * @since 4.9
+	 */
+	protected boolean isForceRefLog() {
+		return forceRefLog;
+	}
+
+	/**
 	 * Request that all updates in this batch be performed atomically.
 	 * <p>
 	 * When atomic updates are used, either all commands apply successfully, or
@@ -323,14 +378,29 @@ public BatchRefUpdate addCommand(Collection<ReceiveCommand> cmd) {
 	/**
 	 * Gets the list of option strings associated with this update.
 	 *
-	 * @return pushOptions
+	 * @return push options that were passed to {@link #execute}; prior to calling
+	 *         {@link #execute}, always returns null.
 	 * @since 4.5
 	 */
+	@Nullable
 	public List<String> getPushOptions() {
 		return pushOptions;
 	}
 
 	/**
+	 * Set push options associated with this update.
+	 * <p>
+	 * Implementations must call this at the top of {@link #execute(RevWalk,
+	 * ProgressMonitor, List)}.
+	 *
+	 * @param options options passed to {@code execute}.
+	 * @since 4.9
+	 */
+	protected void setPushOptions(List<String> options) {
+		pushOptions = options;
+	}
+
+	/**
 	 * @return list of timestamps the batch must wait for.
 	 * @since 4.6
 	 */
@@ -396,7 +466,7 @@ public void execute(RevWalk walk, ProgressMonitor monitor,
 		}
 
 		if (options != null) {
-			pushOptions = options;
+			setPushOptions(options);
 		}
 
 		monitor.beginTask(JGitText.get().updatingReferences, commands.size());
@@ -407,6 +477,11 @@ public void execute(RevWalk walk, ProgressMonitor monitor,
 		for (ReceiveCommand cmd : commands) {
 			try {
 				if (cmd.getResult() == NOT_ATTEMPTED) {
+					if (isMissing(walk, cmd.getOldId())
+							|| isMissing(walk, cmd.getNewId())) {
+						cmd.setResult(ReceiveCommand.Result.REJECTED_MISSING_OBJECT);
+						continue;
+					}
 					cmd.updateType(walk);
 					switch (cmd.getType()) {
 					case CREATE:
@@ -462,7 +537,7 @@ public void execute(RevWalk walk, ProgressMonitor monitor,
 								break SWITCH;
 							}
 							ru.setCheckConflicting(false);
-							addRefToPrefixes(takenPrefixes, cmd.getRefName());
+							takenPrefixes.addAll(getPrefixes(cmd.getRefName()));
 							takenNames.add(cmd.getRefName());
 							cmd.setResult(ru.update(walk));
 						}
@@ -478,6 +553,19 @@ public void execute(RevWalk walk, ProgressMonitor monitor,
 		monitor.endTask();
 	}
 
+	private static boolean isMissing(RevWalk walk, ObjectId id)
+			throws IOException {
+		if (id.equals(ObjectId.zeroId())) {
+			return false; // Explicit add or delete is not missing.
+		}
+		try {
+			walk.parseAny(id);
+			return false;
+		} catch (MissingObjectException e) {
+			return true;
+		}
+	}
+
 	/**
 	 * Wait for timestamps to be in the past, aborting commands on timeout.
 	 *
@@ -523,29 +611,45 @@ public void execute(RevWalk walk, ProgressMonitor monitor)
 		execute(walk, monitor, null);
 	}
 
-	private static Collection<String> getTakenPrefixes(
-			final Collection<String> names) {
+	private static Collection<String> getTakenPrefixes(Collection<String> names) {
 		Collection<String> ref = new HashSet<>();
-		for (String name : names)
-			ref.addAll(getPrefixes(name));
+		for (String name : names) {
+			addPrefixesTo(name, ref);
+		}
 		return ref;
 	}
 
-	private static void addRefToPrefixes(Collection<String> prefixes,
-			String name) {
-		for (String prefix : getPrefixes(name)) {
-			prefixes.add(prefix);
-		}
+	/**
+	 * Get all path prefixes of a ref name.
+	 *
+	 * @param name
+	 *            ref name.
+	 * @return path prefixes of the ref name. For {@code refs/heads/foo}, returns
+	 *         {@code refs} and {@code refs/heads}.
+	 * @since 4.9
+	 */
+	protected static Collection<String> getPrefixes(String name) {
+		Collection<String> ret = new HashSet<>();
+		addPrefixesTo(name, ret);
+		return ret;
 	}
 
-	static Collection<String> getPrefixes(String s) {
-		Collection<String> ret = new HashSet<>();
-		int p1 = s.indexOf('/');
+	/**
+	 * Add prefixes of a ref name to an existing collection.
+	 *
+	 * @param name
+	 *            ref name.
+	 * @param out
+	 *            path prefixes of the ref name. For {@code refs/heads/foo},
+	 *            returns {@code refs} and {@code refs/heads}.
+	 * @since 4.9
+	 */
+	protected static void addPrefixesTo(String name, Collection<String> out) {
+		int p1 = name.indexOf('/');
 		while (p1 > 0) {
-			ret.add(s.substring(0, p1));
-			p1 = s.indexOf('/', p1 + 1);
+			out.add(name.substring(0, p1));
+			p1 = name.indexOf('/', p1 + 1);
 		}
-		return ret;
 	}
 
 	/**
@@ -560,11 +664,12 @@ static Collection<String> getPrefixes(String s) {
 	 */
 	protected RefUpdate newUpdate(ReceiveCommand cmd) throws IOException {
 		RefUpdate ru = refdb.newUpdate(cmd.getRefName(), false);
-		if (isRefLogDisabled())
+		if (isRefLogDisabled(cmd)) {
 			ru.disableRefLog();
-		else {
+		} else {
 			ru.setRefLogIdent(refLogIdent);
-			ru.setRefLogMessage(refLogMessage, refLogIncludeResult);
+			ru.setRefLogMessage(getRefLogMessage(cmd), isRefLogIncludingResult(cmd));
+			ru.setForceRefLog(isForceRefLog(cmd));
 		}
 		ru.setPushCertificate(pushCert);
 		switch (cmd.getType()) {
@@ -585,6 +690,62 @@ protected RefUpdate newUpdate(ReceiveCommand cmd) throws IOException {
 		}
 	}
 
+	/**
+	 * Check whether reflog is disabled for a command.
+	 *
+	 * @param cmd
+	 *            specific command.
+	 * @return whether the reflog is disabled, taking into account the state from
+	 *         this instance as well as overrides in the given command.
+	 * @since 4.9
+	 */
+	protected boolean isRefLogDisabled(ReceiveCommand cmd) {
+		return cmd.hasCustomRefLog() ? cmd.isRefLogDisabled() : isRefLogDisabled();
+	}
+
+	/**
+	 * Get reflog message for a command.
+	 *
+	 * @param cmd
+	 *            specific command.
+	 * @return reflog message, taking into account the state from this instance as
+	 *         well as overrides in the given command.
+	 * @since 4.9
+	 */
+	protected String getRefLogMessage(ReceiveCommand cmd) {
+		return cmd.hasCustomRefLog() ? cmd.getRefLogMessage() : getRefLogMessage();
+	}
+
+	/**
+	 * Check whether the reflog message for a command should include the result.
+	 *
+	 * @param cmd
+	 *            specific command.
+	 * @return whether the reflog message should show the result, taking into
+	 *         account the state from this instance as well as overrides in the
+	 *         given command.
+	 * @since 4.9
+	 */
+	protected boolean isRefLogIncludingResult(ReceiveCommand cmd) {
+		return cmd.hasCustomRefLog()
+				? cmd.isRefLogIncludingResult() : isRefLogIncludingResult();
+	}
+
+	/**
+	 * Check whether the reflog for a command should be written regardless of repo
+	 * defaults.
+	 *
+	 * @param cmd
+	 *            specific command.
+	 * @return whether force writing is enabled.
+	 * @since 4.9
+	 */
+	protected boolean isForceRefLog(ReceiveCommand cmd) {
+		Boolean isForceRefLog = cmd.isForceRefLog();
+		return isForceRefLog != null ? isForceRefLog.booleanValue()
+				: isForceRefLog();
+	}
+
 	@Override
 	public String toString() {
 		StringBuilder r = new StringBuilder();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BitmapObject.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BitmapObject.java
index 345016c..4e0dc2c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BitmapObject.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BitmapObject.java
@@ -62,4 +62,4 @@ public abstract class BitmapObject {
 	 * @return unique hash of this object.
 	 */
 	public abstract ObjectId getObjectId();
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BlobObjectChecker.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BlobObjectChecker.java
new file mode 100644
index 0000000..0fe63ae
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BlobObjectChecker.java
@@ -0,0 +1,92 @@
+/*
+ * Copyright (C) 2017, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.lib;
+
+import org.eclipse.jgit.errors.CorruptObjectException;
+
+/**
+ * Verifies that a blob object is a valid object.
+ * <p>
+ * Unlike trees, commits and tags, there's no validity of blobs. Implementers
+ * can optionally implement this blob checker to reject certain blobs.
+ *
+ * @since 4.9
+ */
+public interface BlobObjectChecker {
+	/** No-op implementation of {@link BlobObjectChecker}. */
+	public static final BlobObjectChecker NULL_CHECKER =
+			new BlobObjectChecker() {
+				@Override
+				public void update(byte[] in, int p, int len) {
+					// Empty implementation.
+				}
+
+				@Override
+				public void endBlob(AnyObjectId id) {
+					// Empty implementation.
+				}
+			};
+
+	/**
+	 * Check a new fragment of the blob.
+	 *
+	 * @param in
+	 *            input array of bytes.
+	 * @param offset
+	 *            offset to start at from {@code in}.
+	 * @param len
+	 *            length of the fragment to check.
+	 */
+	void update(byte[] in, int offset, int len);
+
+	/**
+	 * Finalize the blob checking.
+	 *
+	 * @param id
+	 *            identity of the object being checked.
+	 * @throws CorruptObjectException
+	 *             if any error was detected.
+	 */
+	void endBlob(AnyObjectId id) throws CorruptObjectException;
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/CheckoutEntry.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/CheckoutEntry.java
index d6608cd..34d0b14 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/CheckoutEntry.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/CheckoutEntry.java
@@ -17,4 +17,4 @@ public interface CheckoutEntry {
 	 */
 	public abstract String getToBranch();
 
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
index f45c71c..b0f5c2c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
@@ -51,9 +51,6 @@
 
 package org.eclipse.jgit.lib;
 
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
 import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -62,8 +59,6 @@
 import java.util.Set;
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.atomic.AtomicReference;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.events.ConfigChangedEvent;
@@ -71,21 +66,24 @@
 import org.eclipse.jgit.events.ListenerHandle;
 import org.eclipse.jgit.events.ListenerList;
 import org.eclipse.jgit.internal.JGitText;
-import org.eclipse.jgit.util.IO;
-import org.eclipse.jgit.util.RawParseUtils;
-import org.eclipse.jgit.util.StringUtils;
-
+import org.eclipse.jgit.transport.RefSpec;
 
 /**
  * Git style {@code .config}, {@code .gitconfig}, {@code .gitmodules} file.
  */
 public class Config {
+
 	private static final String[] EMPTY_STRING_ARRAY = {};
-	private static final long KiB = 1024;
-	private static final long MiB = 1024 * KiB;
-	private static final long GiB = 1024 * MiB;
+
+	static final long KiB = 1024;
+	static final long MiB = 1024 * KiB;
+	static final long GiB = 1024 * MiB;
 	private static final int MAX_DEPTH = 10;
 
+	private static final TypedConfigGetter DEFAULT_GETTER = new DefaultTypedConfigGetter();
+
+	private static TypedConfigGetter typedGetter = DEFAULT_GETTER;
+
 	/** the change listeners */
 	private final ListenerList listeners = new ListenerList();
 
@@ -106,7 +104,7 @@ public class Config {
 	 * must ensure it is a special copy of the empty string.  It also must
 	 * be treated like the empty string.
 	 */
-	private static final String MAGIC_EMPTY_VALUE = new String();
+	static final String MAGIC_EMPTY_VALUE = new String();
 
 	/** Create a configuration with no default fallback. */
 	public Config() {
@@ -126,6 +124,18 @@ public Config(Config defaultConfig) {
 	}
 
 	/**
+	 * Globally sets a {@link TypedConfigGetter} that is subsequently used to
+	 * read typed values from all git configs.
+	 *
+	 * @param getter
+	 *            to use; if {@code null} use the default getter.
+	 * @since 4.9
+	 */
+	public static void setTypedConfigGetter(TypedConfigGetter getter) {
+		typedGetter = getter == null ? DEFAULT_GETTER : getter;
+	}
+
+	/**
 	 * Escape the value before saving
 	 *
 	 * @param x
@@ -206,7 +216,7 @@ private static String escapeValue(final String x) {
 	 */
 	public int getInt(final String section, final String name,
 			final int defaultValue) {
-		return getInt(section, null, name, defaultValue);
+		return typedGetter.getInt(this, section, null, name, defaultValue);
 	}
 
 	/**
@@ -224,11 +234,8 @@ public int getInt(final String section, final String name,
 	 */
 	public int getInt(final String section, String subsection,
 			final String name, final int defaultValue) {
-		final long val = getLong(section, subsection, name, defaultValue);
-		if (Integer.MIN_VALUE <= val && val <= Integer.MAX_VALUE)
-			return (int) val;
-		throw new IllegalArgumentException(MessageFormat.format(JGitText.get().integerValueOutOfRange
-				, section, name));
+		return typedGetter.getInt(this, section, subsection, name,
+				defaultValue);
 	}
 
 	/**
@@ -243,7 +250,7 @@ public int getInt(final String section, String subsection,
 	 * @return an integer value from the configuration, or defaultValue.
 	 */
 	public long getLong(String section, String name, long defaultValue) {
-		return getLong(section, null, name, defaultValue);
+		return typedGetter.getLong(this, section, null, name, defaultValue);
 	}
 
 	/**
@@ -261,37 +268,8 @@ public long getLong(String section, String name, long defaultValue) {
 	 */
 	public long getLong(final String section, String subsection,
 			final String name, final long defaultValue) {
-		final String str = getString(section, subsection, name);
-		if (str == null)
-			return defaultValue;
-
-		String n = str.trim();
-		if (n.length() == 0)
-			return defaultValue;
-
-		long mul = 1;
-		switch (StringUtils.toLowerCase(n.charAt(n.length() - 1))) {
-		case 'g':
-			mul = GiB;
-			break;
-		case 'm':
-			mul = MiB;
-			break;
-		case 'k':
-			mul = KiB;
-			break;
-		}
-		if (mul > 1)
-			n = n.substring(0, n.length() - 1).trim();
-		if (n.length() == 0)
-			return defaultValue;
-
-		try {
-			return mul * Long.parseLong(n);
-		} catch (NumberFormatException nfe) {
-			throw new IllegalArgumentException(MessageFormat.format(JGitText.get().invalidIntegerValue
-					, section, name, str));
-		}
+		return typedGetter.getLong(this, section, subsection, name,
+				defaultValue);
 	}
 
 	/**
@@ -308,7 +286,7 @@ public long getLong(final String section, String subsection,
 	 */
 	public boolean getBoolean(final String section, final String name,
 			final boolean defaultValue) {
-		return getBoolean(section, null, name, defaultValue);
+		return typedGetter.getBoolean(this, section, null, name, defaultValue);
 	}
 
 	/**
@@ -327,17 +305,8 @@ public boolean getBoolean(final String section, final String name,
 	 */
 	public boolean getBoolean(final String section, String subsection,
 			final String name, final boolean defaultValue) {
-		String n = getRawString(section, subsection, name);
-		if (n == null)
-			return defaultValue;
-		if (MAGIC_EMPTY_VALUE == n)
-			return true;
-		try {
-			return StringUtils.toBoolean(n);
-		} catch (IllegalArgumentException err) {
-			throw new IllegalArgumentException(MessageFormat.format(JGitText.get().invalidBooleanValue
-					, section, name, n));
-		}
+		return typedGetter.getBoolean(this, section, subsection, name,
+				defaultValue);
 	}
 
 	/**
@@ -358,7 +327,8 @@ public boolean getBoolean(final String section, String subsection,
 	public <T extends Enum<?>> T getEnum(final String section,
 			final String subsection, final String name, final T defaultValue) {
 		final T[] all = allValuesOf(defaultValue);
-		return getEnum(all, section, subsection, name, defaultValue);
+		return typedGetter.getEnum(this, all, section, subsection, name,
+				defaultValue);
 	}
 
 	@SuppressWarnings("unchecked")
@@ -393,55 +363,8 @@ public <T extends Enum<?>> T getEnum(final String section,
 	 */
 	public <T extends Enum<?>> T getEnum(final T[] all, final String section,
 			final String subsection, final String name, final T defaultValue) {
-		String value = getString(section, subsection, name);
-		if (value == null)
-			return defaultValue;
-
-		if (all[0] instanceof ConfigEnum) {
-			for (T t : all) {
-				if (((ConfigEnum) t).matchConfigValue(value))
-					return t;
-			}
-		}
-
-		String n = value.replace(' ', '_');
-
-		// Because of c98abc9c0586c73ef7df4172644b7dd21c979e9d being used in
-		// the real world before its breakage was fully understood, we must
-		// also accept '-' as though it were ' '.
-		n = n.replace('-', '_');
-
-		T trueState = null;
-		T falseState = null;
-		for (T e : all) {
-			if (StringUtils.equalsIgnoreCase(e.name(), n))
-				return e;
-			else if (StringUtils.equalsIgnoreCase(e.name(), "TRUE")) //$NON-NLS-1$
-				trueState = e;
-			else if (StringUtils.equalsIgnoreCase(e.name(), "FALSE")) //$NON-NLS-1$
-				falseState = e;
-		}
-
-		// This is an odd little fallback. C Git sometimes allows boolean
-		// values in a tri-state with other things. If we have both a true
-		// and a false value in our enumeration, assume its one of those.
-		//
-		if (trueState != null && falseState != null) {
-			try {
-				return StringUtils.toBoolean(n) ? trueState : falseState;
-			} catch (IllegalArgumentException err) {
-				// Fall through and use our custom error below.
-			}
-		}
-
-		if (subsection != null)
-			throw new IllegalArgumentException(MessageFormat.format(
-					JGitText.get().enumValueNotSupported3, section, subsection,
-					name, value));
-		else
-			throw new IllegalArgumentException(
-					MessageFormat.format(JGitText.get().enumValueNotSupported2,
-							section, name, value));
+		return typedGetter.getEnum(this, all, section, subsection, name,
+				defaultValue);
 	}
 
 	/**
@@ -515,100 +438,25 @@ public String getString(final String section, String subsection,
 	 */
 	public long getTimeUnit(String section, String subsection, String name,
 			long defaultValue, TimeUnit wantUnit) {
-		String valueString = getString(section, subsection, name);
-
-		if (valueString == null) {
-			return defaultValue;
-		}
-
-		String s = valueString.trim();
-		if (s.length() == 0) {
-			return defaultValue;
-		}
-
-		if (s.startsWith("-")/* negative */) { //$NON-NLS-1$
-			throw notTimeUnit(section, subsection, name, valueString);
-		}
-
-		Matcher m = Pattern.compile("^(0|[1-9][0-9]*)\\s*(.*)$") //$NON-NLS-1$
-				.matcher(valueString);
-		if (!m.matches()) {
-			return defaultValue;
-		}
-
-		String digits = m.group(1);
-		String unitName = m.group(2).trim();
-
-		TimeUnit inputUnit;
-		int inputMul;
-
-		if (unitName.isEmpty()) {
-			inputUnit = wantUnit;
-			inputMul = 1;
-
-		} else if (match(unitName, "ms", "milliseconds")) { //$NON-NLS-1$ //$NON-NLS-2$
-			inputUnit = TimeUnit.MILLISECONDS;
-			inputMul = 1;
-
-		} else if (match(unitName, "s", "sec", "second", "seconds")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
-			inputUnit = TimeUnit.SECONDS;
-			inputMul = 1;
-
-		} else if (match(unitName, "m", "min", "minute", "minutes")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
-			inputUnit = TimeUnit.MINUTES;
-			inputMul = 1;
-
-		} else if (match(unitName, "h", "hr", "hour", "hours")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
-			inputUnit = TimeUnit.HOURS;
-			inputMul = 1;
-
-		} else if (match(unitName, "d", "day", "days")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
-			inputUnit = TimeUnit.DAYS;
-			inputMul = 1;
-
-		} else if (match(unitName, "w", "week", "weeks")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
-			inputUnit = TimeUnit.DAYS;
-			inputMul = 7;
-
-		} else if (match(unitName, "mon", "month", "months")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
-			inputUnit = TimeUnit.DAYS;
-			inputMul = 30;
-
-		} else if (match(unitName, "y", "year", "years")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
-			inputUnit = TimeUnit.DAYS;
-			inputMul = 365;
-
-		} else {
-			throw notTimeUnit(section, subsection, name, valueString);
-		}
-
-		try {
-			return wantUnit.convert(Long.parseLong(digits) * inputMul,
-					inputUnit);
-		} catch (NumberFormatException nfe) {
-			throw notTimeUnit(section, subsection, unitName, valueString);
-		}
+		return typedGetter.getTimeUnit(this, section, subsection, name,
+				defaultValue, wantUnit);
 	}
 
-	private static boolean match(final String a, final String... cases) {
-		for (final String b : cases) {
-			if (b != null && b.equalsIgnoreCase(a)) {
-				return true;
-			}
-		}
-		return false;
-	}
-
-	private IllegalArgumentException notTimeUnit(String section,
-			String subsection, String name, String valueString) {
-		if (subsection != null) {
-			return new IllegalArgumentException(
-					MessageFormat.format(JGitText.get().invalidTimeUnitValue3,
-							section, subsection, name, valueString));
-		}
-		return new IllegalArgumentException(
-				MessageFormat.format(JGitText.get().invalidTimeUnitValue2,
-						section, name, valueString));
+	/**
+	 * Parse a list of {@link RefSpec}s from the configuration.
+	 *
+	 * @param section
+	 *            section the key is in.
+	 * @param subsection
+	 *            subsection the key is in, or null if not in a subsection.
+	 * @param name
+	 *            the key name.
+	 * @return a possibly empty list of {@link RefSpec}s
+	 * @since 4.9
+	 */
+	public List<RefSpec> getRefSpecs(String section, String subsection,
+			String name) {
+		return typedGetter.getRefSpecs(this, section, subsection, name);
 	}
 
 	/**
@@ -757,7 +605,7 @@ protected void fireConfigChangedEvent() {
 		listeners.dispatch(new ConfigChangedEvent());
 	}
 
-	private String getRawString(final String section, final String subsection,
+	String getRawString(final String section, final String subsection,
 			final String name) {
 		String[] lst = getRawStringList(section, subsection, name);
 		if (lst != null) {
@@ -1220,10 +1068,6 @@ private List<ConfigLine> fromTextRecurse(final String text, int depth)
 					e.value = MAGIC_EMPTY_VALUE;
 				} else
 					e.value = readValue(in, false, -1);
-
-				if (e.section.equals("include")) { //$NON-NLS-1$
-					addIncludedConfig(newEntries, e, depth);
-				}
 			} else
 				throw new ConfigInvalidException(JGitText.get().invalidLineInConfigFile);
 		}
@@ -1231,36 +1075,6 @@ private List<ConfigLine> fromTextRecurse(final String text, int depth)
 		return newEntries;
 	}
 
-	private void addIncludedConfig(final List<ConfigLine> newEntries,
-			ConfigLine line, int depth) throws ConfigInvalidException {
-		if (!line.name.equals("path") || //$NON-NLS-1$
-				line.value == null || line.value.equals(MAGIC_EMPTY_VALUE)) {
-			throw new ConfigInvalidException(
-					JGitText.get().invalidLineInConfigFile);
-		}
-		File path = new File(line.value);
-		try {
-			byte[] bytes = IO.readFully(path);
-			String decoded;
-			if (isUtf8(bytes)) {
-				decoded = RawParseUtils.decode(RawParseUtils.UTF8_CHARSET,
-						bytes, 3, bytes.length);
-			} else {
-				decoded = RawParseUtils.decode(bytes);
-			}
-			newEntries.addAll(fromTextRecurse(decoded, depth + 1));
-		} catch (FileNotFoundException fnfe) {
-			if (path.exists()) {
-				throw new ConfigInvalidException(MessageFormat
-						.format(JGitText.get().cannotReadFile, path), fnfe);
-			}
-		} catch (IOException ioe) {
-			throw new ConfigInvalidException(
-					MessageFormat.format(JGitText.get().cannotReadFile, path),
-					ioe);
-		}
-	}
-
 	private ConfigSnapshot newState() {
 		return new ConfigSnapshot(Collections.<ConfigLine> emptyList(),
 				getBaseState());
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
index 2618180..08c883a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
@@ -108,6 +108,12 @@ public class ConfigConstants {
 	public static final String CONFIG_PULL_SECTION = "pull";
 
 	/**
+	 * The "merge" section
+	 * @since 4.9
+	 */
+	public static final String CONFIG_MERGE_SECTION = "merge";
+
+	/**
 	 * The "filter" section
 	 * @since 4.6
 	 */
@@ -372,6 +378,13 @@ public class ConfigConstants {
 	public static final String CONFIG_KEY_RENAMES = "renames";
 
 	/**
+	 * The "inCoreLimit" key in the "merge section". It's a size limit (bytes) used to
+	 * control a file to be stored in {@code Heap} or {@code LocalFile} during the merge.
+	 * @since 4.9
+	 */
+	public static final String CONFIG_KEY_IN_CORE_LIMIT = "inCoreLimit";
+
+	/**
 	 * The "prune" key
 	 * @since 3.3
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java
index bda1a27..5bfccda 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java
@@ -1,7 +1,7 @@
 /*
  * Copyright (C) 2008, Google Inc.
  * Copyright (C) 2008, Robin Rosenberg <robin.rosenberg@dewire.com>
- * Copyright (C) 2006-2012, Shawn O. Pearce <spearce@spearce.org>
+ * Copyright (C) 2006-2017, Shawn O. Pearce <spearce@spearce.org>
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -429,6 +429,20 @@ public final class Constants {
 	public static final String HOOKS = "hooks";
 
 	/**
+	 * Merge attribute.
+	 *
+	 * @since 4.9
+	 */
+	public static final String ATTR_MERGE = "merge"; //$NON-NLS-1$
+
+	/**
+	 * Binary value for custom merger.
+	 *
+	 * @since 4.9
+	 */
+	public static final String ATTR_BUILTIN_BINARY_MERGER = "binary"; //$NON-NLS-1$
+
+	/**
 	 * Create a new digest function for objects.
 	 *
 	 * @return a new digest object.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/CoreConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/CoreConfig.java
index 40aba63..fdbbe39 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/CoreConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/CoreConfig.java
@@ -57,12 +57,7 @@
  */
 public class CoreConfig {
 	/** Key for {@link Config#get(SectionParser)}. */
-	public static final Config.SectionParser<CoreConfig> KEY = new SectionParser<CoreConfig>() {
-		@Override
-		public CoreConfig parse(final Config cfg) {
-			return new CoreConfig(cfg);
-		}
-	};
+	public static final Config.SectionParser<CoreConfig> KEY = CoreConfig::new;
 
 	/** Permissible values for {@code core.autocrlf}. */
 	public static enum AutoCRLF {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java
new file mode 100644
index 0000000..fd37747
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java
@@ -0,0 +1,299 @@
+/*
+ * Copyright (C) 2017, Thomas Wolf <thomas.wolf@paranor.ch>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.lib;
+
+import java.text.MessageFormat;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.eclipse.jgit.annotations.NonNull;
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.lib.Config.ConfigEnum;
+import org.eclipse.jgit.transport.RefSpec;
+import org.eclipse.jgit.util.StringUtils;
+
+/**
+ * An {@link TypedConfigGetter} that throws {@link IllegalArgumentException} on
+ * invalid values.
+ *
+ * @since 4.9
+ */
+public class DefaultTypedConfigGetter implements TypedConfigGetter {
+
+	@Override
+	public boolean getBoolean(Config config, String section, String subsection,
+			String name, boolean defaultValue) {
+		String n = config.getRawString(section, subsection, name);
+		if (n == null) {
+			return defaultValue;
+		}
+		if (Config.MAGIC_EMPTY_VALUE == n) {
+			return true;
+		}
+		try {
+			return StringUtils.toBoolean(n);
+		} catch (IllegalArgumentException err) {
+			throw new IllegalArgumentException(MessageFormat.format(
+					JGitText.get().invalidBooleanValue, section, name, n));
+		}
+	}
+
+	@Override
+	public <T extends Enum<?>> T getEnum(Config config, T[] all, String section,
+			String subsection, String name, T defaultValue) {
+		String value = config.getString(section, subsection, name);
+		if (value == null) {
+			return defaultValue;
+		}
+		if (all[0] instanceof ConfigEnum) {
+			for (T t : all) {
+				if (((ConfigEnum) t).matchConfigValue(value)) {
+					return t;
+				}
+			}
+		}
+
+		String n = value.replace(' ', '_');
+
+		// Because of c98abc9c0586c73ef7df4172644b7dd21c979e9d being used in
+		// the real world before its breakage was fully understood, we must
+		// also accept '-' as though it were ' '.
+		n = n.replace('-', '_');
+
+		T trueState = null;
+		T falseState = null;
+		for (T e : all) {
+			if (StringUtils.equalsIgnoreCase(e.name(), n)) {
+				return e;
+			} else if (StringUtils.equalsIgnoreCase(e.name(), "TRUE")) { //$NON-NLS-1$
+				trueState = e;
+			} else if (StringUtils.equalsIgnoreCase(e.name(), "FALSE")) { //$NON-NLS-1$
+				falseState = e;
+			}
+		}
+
+		// This is an odd little fallback. C Git sometimes allows boolean
+		// values in a tri-state with other things. If we have both a true
+		// and a false value in our enumeration, assume its one of those.
+		//
+		if (trueState != null && falseState != null) {
+			try {
+				return StringUtils.toBoolean(n) ? trueState : falseState;
+			} catch (IllegalArgumentException err) {
+				// Fall through and use our custom error below.
+			}
+		}
+
+		if (subsection != null) {
+			throw new IllegalArgumentException(
+					MessageFormat.format(JGitText.get().enumValueNotSupported3,
+							section, subsection, name, value));
+		} else {
+			throw new IllegalArgumentException(
+					MessageFormat.format(JGitText.get().enumValueNotSupported2,
+							section, name, value));
+		}
+	}
+
+	@Override
+	public int getInt(Config config, String section, String subsection,
+			String name, int defaultValue) {
+		long val = config.getLong(section, subsection, name, defaultValue);
+		if (Integer.MIN_VALUE <= val && val <= Integer.MAX_VALUE) {
+			return (int) val;
+		}
+		throw new IllegalArgumentException(MessageFormat
+				.format(JGitText.get().integerValueOutOfRange, section, name));
+	}
+
+	@Override
+	public long getLong(Config config, String section, String subsection,
+			String name, long defaultValue) {
+		final String str = config.getString(section, subsection, name);
+		if (str == null) {
+			return defaultValue;
+		}
+		String n = str.trim();
+		if (n.length() == 0) {
+			return defaultValue;
+		}
+		long mul = 1;
+		switch (StringUtils.toLowerCase(n.charAt(n.length() - 1))) {
+		case 'g':
+			mul = Config.GiB;
+			break;
+		case 'm':
+			mul = Config.MiB;
+			break;
+		case 'k':
+			mul = Config.KiB;
+			break;
+		}
+		if (mul > 1) {
+			n = n.substring(0, n.length() - 1).trim();
+		}
+		if (n.length() == 0) {
+			return defaultValue;
+		}
+		try {
+			return mul * Long.parseLong(n);
+		} catch (NumberFormatException nfe) {
+			throw new IllegalArgumentException(MessageFormat.format(
+					JGitText.get().invalidIntegerValue, section, name, str));
+		}
+	}
+
+	@Override
+	public long getTimeUnit(Config config, String section, String subsection,
+			String name, long defaultValue, TimeUnit wantUnit) {
+		String valueString = config.getString(section, subsection, name);
+
+		if (valueString == null) {
+			return defaultValue;
+		}
+
+		String s = valueString.trim();
+		if (s.length() == 0) {
+			return defaultValue;
+		}
+
+		if (s.startsWith("-")/* negative */) { //$NON-NLS-1$
+			throw notTimeUnit(section, subsection, name, valueString);
+		}
+
+		Matcher m = Pattern.compile("^(0|[1-9][0-9]*)\\s*(.*)$") //$NON-NLS-1$
+				.matcher(valueString);
+		if (!m.matches()) {
+			return defaultValue;
+		}
+
+		String digits = m.group(1);
+		String unitName = m.group(2).trim();
+
+		TimeUnit inputUnit;
+		int inputMul;
+
+		if (unitName.isEmpty()) {
+			inputUnit = wantUnit;
+			inputMul = 1;
+
+		} else if (match(unitName, "ms", "milliseconds")) { //$NON-NLS-1$ //$NON-NLS-2$
+			inputUnit = TimeUnit.MILLISECONDS;
+			inputMul = 1;
+
+		} else if (match(unitName, "s", "sec", "second", "seconds")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
+			inputUnit = TimeUnit.SECONDS;
+			inputMul = 1;
+
+		} else if (match(unitName, "m", "min", "minute", "minutes")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
+			inputUnit = TimeUnit.MINUTES;
+			inputMul = 1;
+
+		} else if (match(unitName, "h", "hr", "hour", "hours")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
+			inputUnit = TimeUnit.HOURS;
+			inputMul = 1;
+
+		} else if (match(unitName, "d", "day", "days")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
+			inputUnit = TimeUnit.DAYS;
+			inputMul = 1;
+
+		} else if (match(unitName, "w", "week", "weeks")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
+			inputUnit = TimeUnit.DAYS;
+			inputMul = 7;
+
+		} else if (match(unitName, "mon", "month", "months")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
+			inputUnit = TimeUnit.DAYS;
+			inputMul = 30;
+
+		} else if (match(unitName, "y", "year", "years")) { //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
+			inputUnit = TimeUnit.DAYS;
+			inputMul = 365;
+
+		} else {
+			throw notTimeUnit(section, subsection, name, valueString);
+		}
+
+		try {
+			return wantUnit.convert(Long.parseLong(digits) * inputMul,
+					inputUnit);
+		} catch (NumberFormatException nfe) {
+			throw notTimeUnit(section, subsection, unitName, valueString);
+		}
+	}
+
+	private static boolean match(final String a, final String... cases) {
+		for (final String b : cases) {
+			if (b != null && b.equalsIgnoreCase(a)) {
+				return true;
+			}
+		}
+		return false;
+	}
+
+	private static IllegalArgumentException notTimeUnit(String section,
+			String subsection, String name, String valueString) {
+		if (subsection != null) {
+			return new IllegalArgumentException(
+					MessageFormat.format(JGitText.get().invalidTimeUnitValue3,
+							section, subsection, name, valueString));
+		}
+		return new IllegalArgumentException(
+				MessageFormat.format(JGitText.get().invalidTimeUnitValue2,
+						section, name, valueString));
+	}
+
+	@Override
+	public @NonNull List<RefSpec> getRefSpecs(Config config, String section,
+			String subsection, String name) {
+		String[] values = config.getStringList(section, subsection, name);
+		List<RefSpec> result = new ArrayList<>(values.length);
+		for (String spec : values) {
+			result.add(new RefSpec(spec));
+		}
+		return result;
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/FileMode.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/FileMode.java
index a489461..edbc709 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/FileMode.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/FileMode.java
@@ -83,7 +83,6 @@ public abstract class FileMode {
 	public static final int TYPE_MISSING = 0000000;
 
 	/** Mode indicating an entry is a tree (aka directory). */
-	@SuppressWarnings("synthetic-access")
 	public static final FileMode TREE = new FileMode(TYPE_TREE,
 			Constants.OBJ_TREE) {
 		@Override
@@ -93,7 +92,6 @@ public boolean equals(final int modeBits) {
 	};
 
 	/** Mode indicating an entry is a symbolic link. */
-	@SuppressWarnings("synthetic-access")
 	public static final FileMode SYMLINK = new FileMode(TYPE_SYMLINK,
 			Constants.OBJ_BLOB) {
 		@Override
@@ -103,7 +101,6 @@ public boolean equals(final int modeBits) {
 	};
 
 	/** Mode indicating an entry is a non-executable file. */
-	@SuppressWarnings("synthetic-access")
 	public static final FileMode REGULAR_FILE = new FileMode(0100644,
 			Constants.OBJ_BLOB) {
 		@Override
@@ -113,7 +110,6 @@ public boolean equals(final int modeBits) {
 	};
 
 	/** Mode indicating an entry is an executable file. */
-	@SuppressWarnings("synthetic-access")
 	public static final FileMode EXECUTABLE_FILE = new FileMode(0100755,
 			Constants.OBJ_BLOB) {
 		@Override
@@ -123,7 +119,6 @@ public boolean equals(final int modeBits) {
 	};
 
 	/** Mode indicating an entry is a submodule commit in another repository. */
-	@SuppressWarnings("synthetic-access")
 	public static final FileMode GITLINK = new FileMode(TYPE_GITLINK,
 			Constants.OBJ_COMMIT) {
 		@Override
@@ -133,7 +128,6 @@ public boolean equals(final int modeBits) {
 	};
 
 	/** Mode indicating an entry is missing during parallel walks. */
-	@SuppressWarnings("synthetic-access")
 	public static final FileMode MISSING = new FileMode(TYPE_MISSING,
 			Constants.OBJ_BAD) {
 		@Override
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java
index e544b72..ea573a4 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java
@@ -513,14 +513,10 @@ public boolean diff(final ProgressMonitor monitor, int estWorkTreeSize,
 					}
 				}
 
-				for (int i = 0; i < treeWalk.getTreeCount(); i++) {
-					Set<String> values = fileModes.get(treeWalk.getFileMode(i));
-					String path = treeWalk.getPathString();
-					if (path != null) {
-						if (values == null)
-							values = new HashSet<>();
-						values.add(path);
-						fileModes.put(treeWalk.getFileMode(i), values);
+				String path = treeWalk.getPathString();
+				if (path != null) {
+					for (int i = 0; i < treeWalk.getTreeCount(); i++) {
+						recordFileMode(path, treeWalk.getFileMode(i));
 					}
 				}
 			}
@@ -545,19 +541,21 @@ public boolean diff(final ProgressMonitor monitor, int estWorkTreeSize,
 				}
 				Repository subRepo = smw.getRepository();
 				if (subRepo != null) {
+					String subRepoPath = smw.getPath();
 					try {
 						ObjectId subHead = subRepo.resolve("HEAD"); //$NON-NLS-1$
 						if (subHead != null
-								&& !subHead.equals(smw.getObjectId()))
-							modified.add(smw.getPath());
-						else if (ignoreSubmoduleMode != IgnoreSubmoduleMode.DIRTY) {
+								&& !subHead.equals(smw.getObjectId())) {
+							modified.add(subRepoPath);
+							recordFileMode(subRepoPath, FileMode.GITLINK);
+						} else if (ignoreSubmoduleMode != IgnoreSubmoduleMode.DIRTY) {
 							IndexDiff smid = submoduleIndexDiffs.get(smw
 									.getPath());
 							if (smid == null) {
 								smid = new IndexDiff(subRepo,
 										smw.getObjectId(),
 										wTreeIt.getWorkingTreeIterator(subRepo));
-								submoduleIndexDiffs.put(smw.getPath(), smid);
+								submoduleIndexDiffs.put(subRepoPath, smid);
 							}
 							if (smid.diff()) {
 								if (ignoreSubmoduleMode == IgnoreSubmoduleMode.UNTRACKED
@@ -569,7 +567,8 @@ else if (ignoreSubmoduleMode != IgnoreSubmoduleMode.DIRTY) {
 										&& smid.getRemoved().isEmpty()) {
 									continue;
 								}
-								modified.add(smw.getPath());
+								modified.add(subRepoPath);
+								recordFileMode(subRepoPath, FileMode.GITLINK);
 							}
 						}
 					} finally {
@@ -593,6 +592,17 @@ else if (ignoreSubmoduleMode != IgnoreSubmoduleMode.DIRTY) {
 			return true;
 	}
 
+	private void recordFileMode(String path, FileMode mode) {
+		Set<String> values = fileModes.get(mode);
+		if (path != null) {
+			if (values == null) {
+				values = new HashSet<>();
+				fileModes.put(mode, values);
+			}
+			values.add(path);
+		}
+	}
+
 	private boolean isEntryGitLink(AbstractTreeIterator ti) {
 		return ((ti != null) && (ti.getEntryRawMode() == FileMode.GITLINK
 				.getBits()));
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectChecker.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectChecker.java
index 9d3aee1..19c5c7e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectChecker.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectChecker.java
@@ -359,7 +359,13 @@ public void check(@Nullable AnyObjectId id, int objType, byte[] raw)
 			checkTree(id, raw);
 			break;
 		case OBJ_BLOB:
-			checkBlob(raw);
+			BlobObjectChecker checker = newBlobObjectChecker();
+			if (checker == null) {
+				checkBlob(raw);
+			} else {
+				checker.update(raw, 0, raw.length);
+				checker.endBlob(id);
+			}
 			break;
 		default:
 			report(UNKNOWN_TYPE, id, MessageFormat.format(
@@ -1067,8 +1073,22 @@ private static boolean isPositiveDigit(byte b) {
 	}
 
 	/**
+	 * Create a new {@link BlobObjectChecker}.
+	 *
+	 * @return new BlobObjectChecker or null if it's not provided.
+	 * @since 4.9
+	 */
+	@Nullable
+	public BlobObjectChecker newBlobObjectChecker() {
+		return null;
+	}
+
+	/**
 	 * Check a blob for errors.
 	 *
+	 * <p>This may not be called from PackParser in some cases. Use {@link
+	 * #newBlobObjectChecker} instead.
+	 *
 	 * @param raw
 	 *            the blob data. The array is never modified.
 	 * @throws CorruptObjectException
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectInserter.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectInserter.java
index 857ec9b..b2ffbe6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectInserter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectInserter.java
@@ -423,6 +423,13 @@ public abstract ObjectId insert(int objectType, long length, InputStream in)
 	 * <p>
 	 * The returned reader should return this inserter instance from {@link
 	 * ObjectReader#getCreatedFromInserter()}.
+	 * <p>
+	 * Behavior is undefined if an insert method is called on the inserter in the
+	 * middle of reading from an {@link ObjectStream} opened from this reader. For
+	 * example, reading the remainder of the object may fail, or newly written
+	 * data may even be corrupted. Interleaving whole object reads (including
+	 * streaming reads) with inserts is fine, just not interleaving streaming
+	 * <em>partial</em> object reads with inserts.
 	 *
 	 * @since 3.5
 	 * @return reader for any object, including an object recently inserted by
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefUpdate.java
index fc334f0..766b21d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefUpdate.java
@@ -58,7 +58,13 @@
  * Creates, updates or deletes any reference.
  */
 public abstract class RefUpdate {
-	/** Status of an update request. */
+	/**
+	 * Status of an update request.
+	 * <p>
+	 * New values may be added to this enum in the future. Callers may assume that
+	 * unknown values are failures, and may generally treat them the same as
+	 * {@link #REJECTED_OTHER_REASON}.
+	 */
 	public static enum Result {
 		/** The ref update/delete has not been attempted by the caller. */
 		NOT_ATTEMPTED,
@@ -114,6 +120,10 @@ public static enum Result {
 		 * merged into the new value. The configuration did not allow a forced
 		 * update/delete to take place, so ref still contains the old value. No
 		 * previous history was lost.
+		 * <p>
+		 * <em>Note:</em> Despite the general name, this result only refers to the
+		 * non-fast-forward case. For more general errors, see {@link
+		 * #REJECTED_OTHER_REASON}.
 		 */
 		REJECTED,
 
@@ -139,7 +149,25 @@ public static enum Result {
 		 * The ref was renamed from another name
 		 * <p>
 		 */
-		RENAMED
+		RENAMED,
+
+		/**
+		 * One or more objects aren't in the repository.
+		 * <p>
+		 * This is severe indication of either repository corruption on the
+		 * server side, or a bug in the client wherein the client did not supply
+		 * all required objects during the pack transfer.
+		 *
+		 * @since 4.9
+		 */
+		REJECTED_MISSING_OBJECT,
+
+		/**
+		 * Rejected for some other reason not covered by another enum value.
+		 *
+		 * @since 4.9
+		 */
+		REJECTED_OTHER_REASON;
 	}
 
 	/** New value the caller wants this ref to have. */
@@ -157,6 +185,12 @@ public static enum Result {
 	/** Should the Result value be appended to {@link #refLogMessage}. */
 	private boolean refLogIncludeResult;
 
+	/**
+	 * Should reflogs be written even if the configured default for this ref is
+	 * not to write it.
+	 */
+	private boolean forceRefLog;
+
 	/** Old value of the ref, obtained after we lock it. */
 	private ObjectId oldValue;
 
@@ -278,6 +312,16 @@ public void setDetachingSymbolicRef() {
 	}
 
 	/**
+	 * Return whether this update is actually detaching a symbolic ref.
+	 *
+	 * @return true if detaching a symref.
+	 * @since 4.9
+	 */
+	public boolean isDetachingSymbolicRef() {
+		return detachingSymbolicRef;
+	}
+
+	/**
 	 * Set the new value the ref will update to.
 	 *
 	 * @param id
@@ -365,6 +409,12 @@ protected boolean isRefLogIncludingResult() {
 
 	/**
 	 * Set the message to include in the reflog.
+	 * <p>
+	 * Repository implementations may limit which reflogs are written by default,
+	 * based on the project configuration. If a repo is not configured to write
+	 * logs for this ref by default, setting the message alone may have no effect.
+	 * To indicate that the repo should write logs for this update in spite of
+	 * configured defaults, use {@link #setForceRefLog(boolean)}.
 	 *
 	 * @param msg
 	 *            the message to describe this change. It may be null if
@@ -393,6 +443,26 @@ public void disableRefLog() {
 	}
 
 	/**
+	 * Force writing a reflog for the updated ref.
+	 *
+	 * @param force whether to force.
+	 * @since 4.9
+	 */
+	public void setForceRefLog(boolean force) {
+		forceRefLog = force;
+	}
+
+	/**
+	 * Check whether the reflog should be written regardless of repo defaults.
+	 *
+	 * @return whether force writing is enabled.
+	 * @since 4.9
+	 */
+	protected boolean isForceRefLog() {
+		return forceRefLog;
+	}
+
+	/**
 	 * The old value of the ref, prior to the update being attempted.
 	 * <p>
 	 * This value may differ before and after the update method. Initially it is
@@ -627,34 +697,47 @@ private Result updateImpl(final RevWalk walk, final Store store)
 		RevObject oldObj;
 
 		// don't make expensive conflict check if this is an existing Ref
-		if (oldValue == null && checkConflicting && getRefDatabase().isNameConflicting(getName()))
+		if (oldValue == null && checkConflicting
+				&& getRefDatabase().isNameConflicting(getName())) {
 			return Result.LOCK_FAILURE;
+		}
 		try {
 			// If we're detaching a symbolic reference, we should update the reference
 			// itself. Otherwise, we will update the leaf reference, which should be
 			// an ObjectIdRef.
-			if (!tryLock(!detachingSymbolicRef))
+			if (!tryLock(!detachingSymbolicRef)) {
 				return Result.LOCK_FAILURE;
+			}
 			if (expValue != null) {
 				final ObjectId o;
 				o = oldValue != null ? oldValue : ObjectId.zeroId();
-				if (!AnyObjectId.equals(expValue, o))
+				if (!AnyObjectId.equals(expValue, o)) {
 					return Result.LOCK_FAILURE;
+				}
 			}
-			if (oldValue == null)
+			try {
+				newObj = safeParseNew(walk, newValue);
+			} catch (MissingObjectException e) {
+				return Result.REJECTED_MISSING_OBJECT;
+			}
+
+			if (oldValue == null) {
 				return store.execute(Result.NEW);
+			}
 
-			newObj = safeParse(walk, newValue);
-			oldObj = safeParse(walk, oldValue);
-			if (newObj == oldObj && !detachingSymbolicRef)
+			oldObj = safeParseOld(walk, oldValue);
+			if (newObj == oldObj && !detachingSymbolicRef) {
 				return store.execute(Result.NO_CHANGE);
+			}
 
-			if (isForceUpdate())
+			if (isForceUpdate()) {
 				return store.execute(Result.FORCED);
+			}
 
 			if (newObj instanceof RevCommit && oldObj instanceof RevCommit) {
-				if (walk.isMergedInto((RevCommit) oldObj, (RevCommit) newObj))
+				if (walk.isMergedInto((RevCommit) oldObj, (RevCommit) newObj)) {
 					return store.execute(Result.FAST_FORWARD);
+				}
 			}
 
 			return Result.REJECTED;
@@ -674,16 +757,23 @@ public void setCheckConflicting(boolean check) {
 		checkConflicting = check;
 	}
 
-	private static RevObject safeParse(final RevWalk rw, final AnyObjectId id)
+	private static RevObject safeParseNew(RevWalk rw, AnyObjectId newId)
+			throws IOException {
+		if (newId == null || ObjectId.zeroId().equals(newId)) {
+			return null;
+		}
+		return rw.parseAny(newId);
+	}
+
+	private static RevObject safeParseOld(RevWalk rw, AnyObjectId oldId)
 			throws IOException {
 		try {
-			return id != null ? rw.parseAny(id) : null;
+			return oldId != null ? rw.parseAny(oldId) : null;
 		} catch (MissingObjectException e) {
-			// We can expect some objects to be missing, like if we are
-			// trying to force a deletion of a branch and the object it
-			// points to has been pruned from the database due to freak
-			// corruption accidents (it happens with 'git new-work-dir').
-			//
+			// We can expect some old objects to be missing, like if we are trying to
+			// force a deletion of a branch and the object it points to has been
+			// pruned from the database due to freak corruption accidents (it happens
+			// with 'git new-work-dir').
 			return null;
 		}
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ReflogEntry.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ReflogEntry.java
index 0504646..afa6521 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ReflogEntry.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ReflogEntry.java
@@ -50,6 +50,39 @@
 public interface ReflogEntry {
 
 	/**
+	 * Prefix used in reflog messages when the ref was first created.
+	 * <p>
+	 * Does not have a corresponding constant in C git, but is untranslated like
+	 * the other constants.
+	 *
+	 * @since 4.9
+	 */
+	public static final String PREFIX_CREATED = "created"; //$NON-NLS-1$
+
+	/**
+	 * Prefix used in reflog messages when the ref was updated with a fast
+	 * forward.
+	 * <p>
+	 * Untranslated, and exactly matches the
+	 * <a href="https://git.kernel.org/pub/scm/git/git.git/tree/builtin/fetch.c?id=f3da2b79be9565779e4f76dc5812c68e156afdf0#n680">
+	 * untranslated string in C git</a>.
+	 *
+	 * @since 4.9
+	 */
+	public static final String PREFIX_FAST_FORWARD = "fast-forward"; //$NON-NLS-1$
+
+	/**
+	 * Prefix used in reflog messages when the ref was force updated.
+	 * <p>
+	 * Untranslated, and exactly matches the
+	 * <a href="https://git.kernel.org/pub/scm/git/git.git/tree/builtin/fetch.c?id=f3da2b79be9565779e4f76dc5812c68e156afdf0#n695">
+	 * untranslated string in C git</a>.
+	 *
+	 * @since 4.9
+	 */
+	public static final String PREFIX_FORCED_UPDATE = "forced-update"; //$NON-NLS-1$
+
+	/**
 	 * @return the commit id before the change
 	 */
 	public abstract ObjectId getOldId();
@@ -75,4 +108,4 @@ public interface ReflogEntry {
 	 */
 	public abstract CheckoutEntry parseCheckout();
 
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ReflogReader.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ReflogReader.java
index fdab883..d3f2536 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ReflogReader.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ReflogReader.java
@@ -86,4 +86,4 @@ public interface ReflogReader {
 	public abstract List<ReflogEntry> getReverseEntries(int max)
 			throws IOException;
 
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
index bd23ab9..fdf5966 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
@@ -108,7 +108,13 @@
  * A repository holds all objects and refs used for managing source code (could
  * be any type of file, but source code is what SCM's are typically used for).
  * <p>
- * This class is thread-safe.
+ * The thread-safety of a {@link Repository} very much depends on the concrete
+ * implementation. Applications working with a generic {@code Repository} type
+ * must not assume the instance is thread-safe.
+ * <ul>
+ * <li>{@code FileRepository} is thread-safe.
+ * <li>{@code DfsRepository} thread-safety is determined by its subclass.
+ * </ul>
  */
 public abstract class Repository implements AutoCloseable {
 	private static final Logger LOG = LoggerFactory.getLogger(Repository.class);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryBuilder.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryBuilder.java
index e989caf..95be2d1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryBuilder.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryBuilder.java
@@ -55,7 +55,7 @@
  * <p>
  * Single repository applications trying to be compatible with other Git
  * implementations are encouraged to use a model such as:
- * 
+ *
  * <pre>
  * new RepositoryBuilder() //
  * 		.setGitDir(gitDirArgument) // --git-dir if supplied, no-op if null
@@ -63,7 +63,7 @@
  * 		.findGitDir() // scan up the file system tree
  * 		.build()
  * </pre>
- * 
+ *
  * @see org.eclipse.jgit.storage.file.FileRepositoryBuilder
  */
 public class RepositoryBuilder extends
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/SubmoduleConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/SubmoduleConfig.java
index 12f7b82..1267506 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/SubmoduleConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/SubmoduleConfig.java
@@ -43,8 +43,6 @@
 
 package org.eclipse.jgit.lib;
 
-import java.util.Locale;
-
 import org.eclipse.jgit.util.StringUtils;
 
 /**
@@ -79,7 +77,7 @@ private FetchRecurseSubmodulesMode(String configValue) {
 
 		@Override
 		public String toConfigValue() {
-			return name().toLowerCase(Locale.ROOT).replace('_', '-');
+			return configValue;
 		}
 
 		@Override
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/TypedConfigGetter.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/TypedConfigGetter.java
new file mode 100644
index 0000000..594edef
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/TypedConfigGetter.java
@@ -0,0 +1,179 @@
+/*
+ * Copyright (C) 2017, Thomas Wolf <thomas.wolf@paranor.ch>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.lib;
+
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+import org.eclipse.jgit.annotations.NonNull;
+import org.eclipse.jgit.transport.RefSpec;
+
+/**
+ * Something that knows how to convert plain strings from a git {@link Config}
+ * to typed values.
+ *
+ * @since 4.9
+ */
+public interface TypedConfigGetter {
+
+	/**
+	 * Get a boolean value from a git {@link Config}.
+	 *
+	 * @param config
+	 *            to get the value from
+	 * @param section
+	 *            section the key is grouped within.
+	 * @param subsection
+	 *            subsection name, such a remote or branch name.
+	 * @param name
+	 *            name of the key to get.
+	 * @param defaultValue
+	 *            default value to return if no value was present.
+	 * @return true if any value or defaultValue is true, false for missing or
+	 *         explicit false
+	 */
+	boolean getBoolean(Config config, String section, String subsection,
+			String name, boolean defaultValue);
+
+	/**
+	 * Parse an enumeration from a git {@link Config}.
+	 *
+	 * @param <T>
+	 *            type of the enumeration object.
+	 * @param config
+	 *            to get the value from
+	 * @param all
+	 *            all possible values in the enumeration which should be
+	 *            recognized. Typically {@code EnumType.values()}.
+	 * @param section
+	 *            section the key is grouped within.
+	 * @param subsection
+	 *            subsection name, such a remote or branch name.
+	 * @param name
+	 *            name of the key to get.
+	 * @param defaultValue
+	 *            default value to return if no value was present.
+	 * @return the selected enumeration value, or {@code defaultValue}.
+	 */
+	<T extends Enum<?>> T getEnum(Config config, T[] all, String section,
+			String subsection, String name, T defaultValue);
+
+	/**
+	 * Obtain an integer value from a git {@link Config}.
+	 *
+	 * @param config
+	 *            to get the value from
+	 * @param section
+	 *            section the key is grouped within.
+	 * @param subsection
+	 *            subsection name, such a remote or branch name.
+	 * @param name
+	 *            name of the key to get.
+	 * @param defaultValue
+	 *            default value to return if no value was present.
+	 * @return an integer value from the configuration, or defaultValue.
+	 */
+	int getInt(Config config, String section, String subsection, String name,
+			int defaultValue);
+
+	/**
+	 * Obtain a long value from a git {@link Config}.
+	 *
+	 * @param config
+	 *            to get the value from
+	 * @param section
+	 *            section the key is grouped within.
+	 * @param subsection
+	 *            subsection name, such a remote or branch name.
+	 * @param name
+	 *            name of the key to get.
+	 * @param defaultValue
+	 *            default value to return if no value was present.
+	 * @return a long value from the configuration, or defaultValue.
+	 */
+	long getLong(Config config, String section, String subsection, String name,
+			long defaultValue);
+
+	/**
+	 * Parse a numerical time unit, such as "1 minute", from a git
+	 * {@link Config}.
+	 *
+	 * @param config
+	 *            to get the value from
+	 * @param section
+	 *            section the key is in.
+	 * @param subsection
+	 *            subsection the key is in, or null if not in a subsection.
+	 * @param name
+	 *            the key name.
+	 * @param defaultValue
+	 *            default value to return if no value was present.
+	 * @param wantUnit
+	 *            the units of {@code defaultValue} and the return value, as
+	 *            well as the units to assume if the value does not contain an
+	 *            indication of the units.
+	 * @return the value, or {@code defaultValue} if not set, expressed in
+	 *         {@code units}.
+	 */
+	long getTimeUnit(Config config, String section, String subsection,
+			String name, long defaultValue, TimeUnit wantUnit);
+
+
+	/**
+	 * Parse a list of {@link RefSpec}s from a git {@link Config}.
+	 *
+	 * @param config
+	 *            to get the list from
+	 * @param section
+	 *            section the key is in.
+	 * @param subsection
+	 *            subsection the key is in, or null if not in a subsection.
+	 * @param name
+	 *            the key name.
+	 * @return a possibly empty list of {@link RefSpec}s
+	 */
+	@NonNull
+	List<RefSpec> getRefSpecs(Config config, String section, String subsection,
+			String name);
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/UserConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/UserConfig.java
index bd393dd..102a451 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/UserConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/UserConfig.java
@@ -51,12 +51,7 @@
 /** The standard "user" configuration parameters. */
 public class UserConfig {
 	/** Key for {@link Config#get(SectionParser)}. */
-	public static final Config.SectionParser<UserConfig> KEY = new SectionParser<UserConfig>() {
-		@Override
-		public UserConfig parse(final Config cfg) {
-			return new UserConfig(cfg);
-		}
-	};
+	public static final Config.SectionParser<UserConfig> KEY = UserConfig::new;
 
 	private String authorName;
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeFormatterPass.java b/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeFormatterPass.java
index 0345921..060f068 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeFormatterPass.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeFormatterPass.java
@@ -143,4 +143,4 @@ private void writeLine(RawText seq, int i) throws IOException {
 		if (out.isBeginln())
 			out.write('\n');
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java b/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
index 86003e9..246121b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
@@ -2,6 +2,7 @@
  * Copyright (C) 2010, Christian Halstrick <christian.halstrick@sap.com>,
  * Copyright (C) 2010-2012, Matthias Sohn <matthias.sohn@sap.com>
  * Copyright (C) 2012, Research In Motion Limited
+ * Copyright (C) 2017, Obeo (mathieu.cartaud@obeo.fr)
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -67,6 +68,7 @@
 import java.util.List;
 import java.util.Map;
 
+import org.eclipse.jgit.attributes.Attributes;
 import org.eclipse.jgit.diff.DiffAlgorithm;
 import org.eclipse.jgit.diff.DiffAlgorithm.SupportedAlgorithm;
 import org.eclipse.jgit.diff.RawText;
@@ -83,6 +85,7 @@
 import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.errors.NoWorkTreeException;
 import org.eclipse.jgit.lib.Config;
+import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectInserter;
@@ -270,6 +273,12 @@ public enum MergeFailureReason {
 	 */
 	protected MergeAlgorithm mergeAlgorithm;
 
+	/**
+	 * The size limit (bytes) which controls a file to be stored in {@code Heap} or
+	 * {@code LocalFile} during the merge.
+	 */
+	private int inCoreLimit;
+
 	private static MergeAlgorithm getMergeAlgorithm(Config config) {
 		SupportedAlgorithm diffAlg = config.getEnum(
 				CONFIG_DIFF_SECTION, null, CONFIG_KEY_ALGORITHM,
@@ -277,6 +286,11 @@ private static MergeAlgorithm getMergeAlgorithm(Config config) {
 		return new MergeAlgorithm(DiffAlgorithm.getAlgorithm(diffAlg));
 	}
 
+	private static int getInCoreLimit(Config config) {
+		return config.getInt(
+				ConfigConstants.CONFIG_MERGE_SECTION, ConfigConstants.CONFIG_KEY_IN_CORE_LIMIT, 10 << 20);
+	}
+
 	private static String[] defaultCommitNames() {
 		return new String[] { "BASE", "OURS", "THEIRS" }; //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
 	}
@@ -287,7 +301,9 @@ private static MergeAlgorithm getMergeAlgorithm(Config config) {
 	 */
 	protected ResolveMerger(Repository local, boolean inCore) {
 		super(local);
-		mergeAlgorithm = getMergeAlgorithm(local.getConfig());
+		Config config = local.getConfig();
+		mergeAlgorithm = getMergeAlgorithm(config);
+		inCoreLimit = getInCoreLimit(config);
 		commitNames = defaultCommitNames();
 		this.inCore = inCore;
 
@@ -429,9 +445,10 @@ private DirCacheEntry keep(DirCacheEntry e) {
 	}
 
 	/**
-	 * Processes one path and tries to merge. This method will do all do all
-	 * trivial (not content) merges and will also detect if a merge will fail.
-	 * The merge will fail when one of the following is true
+	 * Processes one path and tries to merge taking git attributes in account.
+	 * This method will do all trivial (not content) merges and will also detect
+	 * if a merge will fail. The merge will fail when one of the following is
+	 * true
 	 * <ul>
 	 * <li>the index entry does not match the entry in ours. When merging one
 	 * branch into the current HEAD, ours will point to HEAD and theirs will
@@ -471,11 +488,69 @@ private DirCacheEntry keep(DirCacheEntry e) {
 	 * @throws CorruptObjectException
 	 * @throws IOException
 	 * @since 3.5
+	 * @deprecated
+	 */
+	@Deprecated
+	protected boolean processEntry(CanonicalTreeParser base,
+			CanonicalTreeParser ours, CanonicalTreeParser theirs,
+			DirCacheBuildIterator index, WorkingTreeIterator work,
+			boolean ignoreConflicts) throws MissingObjectException,
+			IncorrectObjectTypeException, CorruptObjectException, IOException {
+		return processEntry(base, ours, theirs, index, work, ignoreConflicts,
+				null);
+	}
+
+	/**
+	 * Processes one path and tries to merge taking git attributes in account.
+	 * This method will do all trivial (not content) merges and will also detect
+	 * if a merge will fail. The merge will fail when one of the following is
+	 * true
+	 * <ul>
+	 * <li>the index entry does not match the entry in ours. When merging one
+	 * branch into the current HEAD, ours will point to HEAD and theirs will
+	 * point to the other branch. It is assumed that the index matches the HEAD
+	 * because it will only not match HEAD if it was populated before the merge
+	 * operation. But the merge commit should not accidentally contain
+	 * modifications done before the merge. Check the <a href=
+	 * "http://www.kernel.org/pub/software/scm/git/docs/git-read-tree.html#_3_way_merge"
+	 * >git read-tree</a> documentation for further explanations.</li>
+	 * <li>A conflict was detected and the working-tree file is dirty. When a
+	 * conflict is detected the content-merge algorithm will try to write a
+	 * merged version into the working-tree. If the file is dirty we would
+	 * override unsaved data.</li>
+	 * </ul>
+	 *
+	 * @param base
+	 *            the common base for ours and theirs
+	 * @param ours
+	 *            the ours side of the merge. When merging a branch into the
+	 *            HEAD ours will point to HEAD
+	 * @param theirs
+	 *            the theirs side of the merge. When merging a branch into the
+	 *            current HEAD theirs will point to the branch which is merged
+	 *            into HEAD.
+	 * @param index
+	 *            the index entry
+	 * @param work
+	 *            the file in the working tree
+	 * @param ignoreConflicts
+	 *            see
+	 *            {@link ResolveMerger#mergeTrees(AbstractTreeIterator, RevTree, RevTree, boolean)}
+	 * @param attributes
+	 *            the attributes defined for this entry
+	 * @return <code>false</code> if the merge will fail because the index entry
+	 *         didn't match ours or the working-dir file was dirty and a
+	 *         conflict occurred
+	 * @throws MissingObjectException
+	 * @throws IncorrectObjectTypeException
+	 * @throws CorruptObjectException
+	 * @throws IOException
+	 * @since 4.9
 	 */
 	protected boolean processEntry(CanonicalTreeParser base,
 			CanonicalTreeParser ours, CanonicalTreeParser theirs,
 			DirCacheBuildIterator index, WorkingTreeIterator work,
-			boolean ignoreConflicts)
+			boolean ignoreConflicts, Attributes attributes)
 			throws MissingObjectException, IncorrectObjectTypeException,
 			CorruptObjectException, IOException {
 		enterSubtree = true;
@@ -627,7 +702,8 @@ protected boolean processEntry(CanonicalTreeParser base,
 				return false;
 
 			// Don't attempt to resolve submodule link conflicts
-			if (isGitLink(modeO) || isGitLink(modeT)) {
+			if (isGitLink(modeO) || isGitLink(modeT)
+					|| !attributes.canBeContentMerged()) {
 				add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, 0, 0);
 				add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, 0, 0);
 				add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, 0, 0);
@@ -636,8 +712,9 @@ protected boolean processEntry(CanonicalTreeParser base,
 			}
 
 			MergeResult<RawText> result = contentMerge(base, ours, theirs);
-			if (ignoreConflicts)
+			if (ignoreConflicts) {
 				result.setContainsConflicts(false);
+			}
 			updateIndex(base, ours, theirs, result);
 			if (result.containsConflicts() && !ignoreConflicts)
 				unmergedPaths.add(tw.getPathString());
@@ -760,6 +837,7 @@ private void updateIndex(CanonicalTreeParser base,
 			MergeResult<RawText> result) throws FileNotFoundException,
 			IOException {
 		File mergedFile = !inCore ? writeMergedFile(result) : null;
+
 		if (result.containsConflicts()) {
 			// A conflict occurred, the file will contain conflict markers
 			// the index will be populated with the three stages and the
@@ -827,7 +905,7 @@ private File writeMergedFile(MergeResult<RawText> result)
 	private ObjectId insertMergeResult(MergeResult<RawText> result)
 			throws IOException {
 		TemporaryBuffer.LocalFile buf = new TemporaryBuffer.LocalFile(
-				db != null ? nonNullRepo().getDirectory() : null, 10 << 20);
+				db != null ? nonNullRepo().getDirectory() : null, inCoreLimit);
 		try {
 			new MergeFormatter().formatMerge(buf, result,
 					Arrays.asList(commitNames), CHARACTER_ENCODING);
@@ -1091,6 +1169,8 @@ protected boolean mergeTrees(AbstractTreeIterator baseTree,
 	protected boolean mergeTreeWalk(TreeWalk treeWalk, boolean ignoreConflicts)
 			throws IOException {
 		boolean hasWorkingTreeIterator = tw.getTreeCount() > T_FILE;
+		boolean hasAttributeNodeProvider = treeWalk
+				.getAttributesNodeProvider() != null;
 		while (treeWalk.next()) {
 			if (!processEntry(
 					treeWalk.getTree(T_BASE, CanonicalTreeParser.class),
@@ -1098,7 +1178,9 @@ protected boolean mergeTreeWalk(TreeWalk treeWalk, boolean ignoreConflicts)
 					treeWalk.getTree(T_THEIRS, CanonicalTreeParser.class),
 					treeWalk.getTree(T_INDEX, DirCacheBuildIterator.class),
 					hasWorkingTreeIterator ? treeWalk.getTree(T_FILE,
-							WorkingTreeIterator.class) : null, ignoreConflicts)) {
+							WorkingTreeIterator.class) : null,
+					ignoreConflicts, hasAttributeNodeProvider
+							? treeWalk.getAttributes() : new Attributes())) {
 				cleanUp();
 				return false;
 			}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/nls/TranslationBundle.java b/org.eclipse.jgit/src/org/eclipse/jgit/nls/TranslationBundle.java
index c85c179..bde69c0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/nls/TranslationBundle.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/nls/TranslationBundle.java
@@ -184,4 +184,4 @@ void load(Locale locale)
 			}
 		}
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/filter/SkipRevFilter.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/filter/SkipRevFilter.java
index e230c9b..51dd2ed 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/filter/SkipRevFilter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/filter/SkipRevFilter.java
@@ -91,4 +91,4 @@ public boolean include(RevWalk walker, RevCommit cmit)
 	public RevFilter clone() {
 		return new SkipRevFilter(skip);
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/pack/PackConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/pack/PackConfig.java
index c64aa2d..4f2374f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/pack/PackConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/pack/PackConfig.java
@@ -260,6 +260,8 @@ public class PackConfig {
 
 	private boolean cutDeltaChains;
 
+	private boolean singlePack;
+
 	/** Create a default configuration. */
 	public PackConfig() {
 		// Fields are initialized to defaults.
@@ -320,6 +322,7 @@ public PackConfig(PackConfig cfg) {
 		this.bitmapExcessiveBranchCount = cfg.bitmapExcessiveBranchCount;
 		this.bitmapInactiveBranchAgeInDays = cfg.bitmapInactiveBranchAgeInDays;
 		this.cutDeltaChains = cfg.cutDeltaChains;
+		this.singlePack = cfg.singlePack;
 	}
 
 	/**
@@ -555,6 +558,30 @@ public void setCutDeltaChains(boolean cut) {
 	}
 
 	/**
+	 * @return true if all of refs/* should be packed in a single pack. Default
+	 *        is false, packing a separate GC_REST pack for references outside
+	 *        of refs/heads/* and refs/tags/*.
+	 * @since 4.9
+	 */
+	public boolean getSinglePack() {
+		return singlePack;
+	}
+
+	/**
+	 * If {@code true}, packs a single GC pack for all objects reachable from
+	 * refs/*. Otherwise packs the GC pack with objects reachable from
+	 * refs/heads/* and refs/tags/*, and a GC_REST pack with the remaining
+	 * reachable objects. Disabled by default, packing GC and GC_REST.
+	 *
+	 * @param single
+	 *            true to pack a single GC pack rather than GC and GC_REST packs
+	 * @since 4.9
+	 */
+	public void setSinglePack(boolean single) {
+		singlePack = single;
+	}
+
+	/**
 	 * Get the number of objects to try when looking for a delta base.
 	 *
 	 * This limit is per thread, if 4 threads are used the actual memory used
@@ -1026,6 +1053,8 @@ public void fromConfig(final Config rc) {
 				rc.getBoolean("pack", "deltacompression", isDeltaCompress())); //$NON-NLS-1$ //$NON-NLS-2$
 		setCutDeltaChains(
 				rc.getBoolean("pack", "cutdeltachains", getCutDeltaChains())); //$NON-NLS-1$ //$NON-NLS-2$
+		setSinglePack(
+				rc.getBoolean("pack", "singlepack", getSinglePack())); //$NON-NLS-1$ //$NON-NLS-2$
 		setBuildBitmaps(
 				rc.getBoolean("pack", "buildbitmaps", isBuildBitmaps())); //$NON-NLS-1$ //$NON-NLS-2$
 		setBitmapContiguousCommitCount(
@@ -1073,6 +1102,7 @@ public String toString() {
 				.append(getBitmapExcessiveBranchCount());
 		b.append(", bitmapInactiveBranchAge=") //$NON-NLS-1$
 				.append(getBitmapInactiveBranchAgeInDays());
+		b.append(", singlePack=").append(getSinglePack()); //$NON-NLS-1$
 		return b.toString();
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/submodule/SubmoduleWalk.java b/org.eclipse.jgit/src/org/eclipse/jgit/submodule/SubmoduleWalk.java
index a10f3d7..56784f7 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/submodule/SubmoduleWalk.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/submodule/SubmoduleWalk.java
@@ -45,7 +45,8 @@
 import java.io.File;
 import java.io.IOException;
 import java.text.MessageFormat;
-import java.util.Locale;
+import java.util.HashMap;
+import java.util.Map;
 
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheIterator;
@@ -330,6 +331,8 @@ else if (submoduleUrl.startsWith("../")) { //$NON-NLS-1$
 
 	private String path;
 
+	private Map<String, String> pathToName;
+
 	/**
 	 * Create submodule generator
 	 *
@@ -355,6 +358,7 @@ public SubmoduleWalk(final Repository repository) throws IOException {
 	 */
 	public SubmoduleWalk setModulesConfig(final Config config) {
 		modulesConfig = config;
+		loadPathNames();
 		return this;
 	}
 
@@ -374,6 +378,7 @@ public SubmoduleWalk setModulesConfig(final Config config) {
 	public SubmoduleWalk setRootTree(final AbstractTreeIterator tree) {
 		rootTree = tree;
 		modulesConfig = null;
+		pathToName = null;
 		return this;
 	}
 
@@ -396,6 +401,7 @@ public SubmoduleWalk setRootTree(final AnyObjectId id) throws IOException {
 		p.reset(walk.getObjectReader(), id);
 		rootTree = p;
 		modulesConfig = null;
+		pathToName = null;
 		return this;
 	}
 
@@ -419,6 +425,7 @@ public SubmoduleWalk loadModulesConfig() throws IOException, ConfigInvalidExcept
 					repository.getFS());
 			config.load();
 			modulesConfig = config;
+			loadPathNames();
 		} else {
 			try (TreeWalk configWalk = new TreeWalk(repository)) {
 				configWalk.addTree(rootTree);
@@ -438,10 +445,12 @@ public SubmoduleWalk loadModulesConfig() throws IOException, ConfigInvalidExcept
 						if (filter.isDone(configWalk)) {
 							modulesConfig = new BlobBasedConfig(null, repository,
 									configWalk.getObjectId(0));
+							loadPathNames();
 							return this;
 						}
 					}
 					modulesConfig = new Config();
+					pathToName = null;
 				} finally {
 					if (idx > 0)
 						rootTree.next(idx);
@@ -451,6 +460,20 @@ public SubmoduleWalk loadModulesConfig() throws IOException, ConfigInvalidExcept
 		return this;
 	}
 
+	private void loadPathNames() {
+		pathToName = null;
+		if (modulesConfig != null) {
+			HashMap<String, String> pathNames = new HashMap<>();
+			for (String name : modulesConfig
+					.getSubsections(ConfigConstants.CONFIG_SUBMODULE_SECTION)) {
+				pathNames.put(modulesConfig.getString(
+						ConfigConstants.CONFIG_SUBMODULE_SECTION, name,
+						ConfigConstants.CONFIG_KEY_PATH), name);
+			}
+			pathToName = pathNames;
+		}
+	}
+
 	/**
 	 * Checks whether the working tree contains a .gitmodules file. That's a
 	 * hint that the repo contains submodules.
@@ -475,8 +498,14 @@ public static boolean containsGitModulesFile(Repository repository)
 	}
 
 	private void lazyLoadModulesConfig() throws IOException, ConfigInvalidException {
-		if (modulesConfig == null)
+		if (modulesConfig == null) {
 			loadModulesConfig();
+		}
+	}
+
+	private String getModuleName(String modulePath) {
+		String name = pathToName != null ? pathToName.get(modulePath) : null;
+		return name != null ? name : modulePath;
 	}
 
 	/**
@@ -525,6 +554,7 @@ public SubmoduleWalk setTree(final AnyObjectId treeId) throws IOException {
 	public SubmoduleWalk reset() {
 		repoConfig = repository.getConfig();
 		modulesConfig = null;
+		pathToName = null;
 		walk.reset();
 		return this;
 	}
@@ -586,9 +616,8 @@ public ObjectId getObjectId() {
 	 */
 	public String getModulesPath() throws IOException, ConfigInvalidException {
 		lazyLoadModulesConfig();
-		return modulesConfig.getString(
-				ConfigConstants.CONFIG_SUBMODULE_SECTION, path,
-				ConfigConstants.CONFIG_KEY_PATH);
+		return modulesConfig.getString(ConfigConstants.CONFIG_SUBMODULE_SECTION,
+				getModuleName(path), ConfigConstants.CONFIG_KEY_PATH);
 	}
 
 	/**
@@ -600,6 +629,10 @@ public String getModulesPath() throws IOException, ConfigInvalidException {
 	 * @throws IOException
 	 */
 	public String getConfigUrl() throws IOException, ConfigInvalidException {
+		// SubmoduleInitCommand copies the submodules.*.url and
+		// submodules.*.update values from .gitmodules to the config, and
+		// does so using the path defined in .gitmodules as the subsection
+		// name. So no path-to-name translation is necessary here.
 		return repoConfig.getString(ConfigConstants.CONFIG_SUBMODULE_SECTION,
 				path, ConfigConstants.CONFIG_KEY_URL);
 	}
@@ -614,9 +647,8 @@ public String getConfigUrl() throws IOException, ConfigInvalidException {
 	 */
 	public String getModulesUrl() throws IOException, ConfigInvalidException {
 		lazyLoadModulesConfig();
-		return modulesConfig.getString(
-				ConfigConstants.CONFIG_SUBMODULE_SECTION, path,
-				ConfigConstants.CONFIG_KEY_URL);
+		return modulesConfig.getString(ConfigConstants.CONFIG_SUBMODULE_SECTION,
+				getModuleName(path), ConfigConstants.CONFIG_KEY_URL);
 	}
 
 	/**
@@ -642,9 +674,8 @@ public String getConfigUpdate() throws IOException, ConfigInvalidException {
 	 */
 	public String getModulesUpdate() throws IOException, ConfigInvalidException {
 		lazyLoadModulesConfig();
-		return modulesConfig.getString(
-				ConfigConstants.CONFIG_SUBMODULE_SECTION, path,
-				ConfigConstants.CONFIG_KEY_UPDATE);
+		return modulesConfig.getString(ConfigConstants.CONFIG_SUBMODULE_SECTION,
+				getModuleName(path), ConfigConstants.CONFIG_KEY_UPDATE);
 	}
 
 	/**
@@ -659,13 +690,9 @@ public String getModulesUpdate() throws IOException, ConfigInvalidException {
 	public IgnoreSubmoduleMode getModulesIgnore() throws IOException,
 			ConfigInvalidException {
 		lazyLoadModulesConfig();
-		String name = modulesConfig.getString(
-				ConfigConstants.CONFIG_SUBMODULE_SECTION, path,
-				ConfigConstants.CONFIG_KEY_IGNORE);
-		if (name == null)
-			return null;
-		return IgnoreSubmoduleMode
-				.valueOf(name.trim().toUpperCase(Locale.ROOT));
+		return modulesConfig.getEnum(IgnoreSubmoduleMode.values(),
+				ConfigConstants.CONFIG_SUBMODULE_SECTION, getModuleName(path),
+				ConfigConstants.CONFIG_KEY_IGNORE, IgnoreSubmoduleMode.NONE);
 	}
 
 	/**
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackFetchConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackFetchConnection.java
index e8d1881..61c4c4b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackFetchConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackFetchConnection.java
@@ -63,7 +63,6 @@
 import org.eclipse.jgit.internal.storage.file.PackLock;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Config;
-import org.eclipse.jgit.lib.Config.SectionParser;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.MutableObjectId;
 import org.eclipse.jgit.lib.NullProgressMonitor;
@@ -250,7 +249,7 @@ public BasePackFetchConnection(final PackTransport packTransport) {
 		super(packTransport);
 
 		if (local != null) {
-			final FetchConfig cfg = local.getConfig().get(FetchConfig.KEY);
+			final FetchConfig cfg = local.getConfig().get(FetchConfig::new);
 			allowOfsDelta = cfg.allowOfsDelta;
 		} else {
 			allowOfsDelta = true;
@@ -279,13 +278,6 @@ public BasePackFetchConnection(final PackTransport packTransport) {
 	}
 
 	private static class FetchConfig {
-		static final SectionParser<FetchConfig> KEY = new SectionParser<FetchConfig>() {
-			@Override
-			public FetchConfig parse(final Config cfg) {
-				return new FetchConfig(cfg);
-			}
-		};
-
 		final boolean allowOfsDelta;
 
 		FetchConfig(final Config c) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java
index 6f94dbb..44abcd5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java
@@ -78,7 +78,6 @@
 import org.eclipse.jgit.internal.storage.file.PackLock;
 import org.eclipse.jgit.lib.BatchRefUpdate;
 import org.eclipse.jgit.lib.Config;
-import org.eclipse.jgit.lib.Config.SectionParser;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.NullProgressMonitor;
 import org.eclipse.jgit.lib.ObjectChecker;
@@ -314,7 +313,7 @@ protected BaseReceivePack(final Repository into) {
 		TransferConfig tc = db.getConfig().get(TransferConfig.KEY);
 		objectChecker = tc.newReceiveObjectChecker();
 
-		ReceiveConfig rc = db.getConfig().get(ReceiveConfig.KEY);
+		ReceiveConfig rc = db.getConfig().get(ReceiveConfig::new);
 		allowCreates = rc.allowCreates;
 		allowAnyDeletes = true;
 		allowBranchDeletes = rc.allowDeletes;
@@ -332,13 +331,6 @@ protected BaseReceivePack(final Repository into) {
 
 	/** Configuration for receive operations. */
 	protected static class ReceiveConfig {
-		static final SectionParser<ReceiveConfig> KEY = new SectionParser<ReceiveConfig>() {
-			@Override
-			public ReceiveConfig parse(final Config cfg) {
-				return new ReceiveConfig(cfg);
-			}
-		};
-
 		final boolean allowCreates;
 		final boolean allowDeletes;
 		final boolean allowNonFastForwards;
@@ -455,6 +447,7 @@ public final Map<String, Ref> getAdvertisedRefs() {
 	public void setAdvertisedRefs(Map<String, Ref> allRefs, Set<ObjectId> additionalHaves) {
 		refs = allRefs != null ? allRefs : db.getAllRefs();
 		refs = refFilter.filter(refs);
+		advertisedHaves.clear();
 
 		Ref head = refs.get(Constants.HEAD);
 		if (head != null && head.isSymbolic())
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/Daemon.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/Daemon.java
index 40b2c47..896b10a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/Daemon.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/Daemon.java
@@ -45,13 +45,14 @@
 
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.InterruptedIOException;
 import java.io.OutputStream;
 import java.net.InetAddress;
 import java.net.InetSocketAddress;
 import java.net.ServerSocket;
 import java.net.Socket;
 import java.net.SocketAddress;
+import java.net.SocketException;
+import java.util.concurrent.atomic.AtomicBoolean;
 
 import org.eclipse.jgit.errors.RepositoryNotFoundException;
 import org.eclipse.jgit.internal.JGitText;
@@ -77,9 +78,7 @@ public class Daemon {
 
 	private final ThreadGroup processors;
 
-	private boolean run;
-
-	Thread acceptThread;
+	private Acceptor acceptThread;
 
 	private int timeout;
 
@@ -281,6 +280,56 @@ public void setReceivePackFactory(ReceivePackFactory<DaemonClient> factory) {
 			receivePackFactory = (ReceivePackFactory<DaemonClient>) ReceivePackFactory.DISABLED;
 	}
 
+	private class Acceptor extends Thread {
+
+		private final ServerSocket listenSocket;
+
+		private final AtomicBoolean running = new AtomicBoolean(true);
+
+		public Acceptor(ThreadGroup group, String name, ServerSocket socket) {
+			super(group, name);
+			this.listenSocket = socket;
+		}
+
+		@Override
+		public void run() {
+			setUncaughtExceptionHandler((thread, throwable) -> terminate());
+			while (isRunning()) {
+				try {
+					startClient(listenSocket.accept());
+				} catch (SocketException e) {
+					// Test again to see if we should keep accepting.
+				} catch (IOException e) {
+					break;
+				}
+			}
+
+			terminate();
+		}
+
+		private void terminate() {
+			try {
+				shutDown();
+			} finally {
+				clearThread();
+			}
+		}
+
+		public boolean isRunning() {
+			return running.get();
+		}
+
+		public void shutDown() {
+			running.set(false);
+			try {
+				listenSocket.close();
+			} catch (IOException err) {
+				//
+			}
+		}
+
+	}
+
 	/**
 	 * Start this daemon on a background thread.
 	 *
@@ -290,52 +339,56 @@ public void setReceivePackFactory(ReceivePackFactory<DaemonClient> factory) {
 	 *             the daemon is already running.
 	 */
 	public synchronized void start() throws IOException {
-		if (acceptThread != null)
+		if (acceptThread != null) {
 			throw new IllegalStateException(JGitText.get().daemonAlreadyRunning);
+		}
+		ServerSocket socket = new ServerSocket();
+		socket.setReuseAddress(true);
+		if (myAddress != null) {
+			socket.bind(myAddress, BACKLOG);
+		} else {
+			socket.bind(new InetSocketAddress((InetAddress) null, 0), BACKLOG);
+		}
+		myAddress = (InetSocketAddress) socket.getLocalSocketAddress();
 
-		final ServerSocket listenSock = new ServerSocket(
-				myAddress != null ? myAddress.getPort() : 0, BACKLOG,
-				myAddress != null ? myAddress.getAddress() : null);
-		myAddress = (InetSocketAddress) listenSock.getLocalSocketAddress();
-
-		run = true;
-		acceptThread = new Thread(processors, "Git-Daemon-Accept") { //$NON-NLS-1$
-			@Override
-			public void run() {
-				while (isRunning()) {
-					try {
-						startClient(listenSock.accept());
-					} catch (InterruptedIOException e) {
-						// Test again to see if we should keep accepting.
-					} catch (IOException e) {
-						break;
-					}
-				}
-
-				try {
-					listenSock.close();
-				} catch (IOException err) {
-					//
-				} finally {
-					synchronized (Daemon.this) {
-						acceptThread = null;
-					}
-				}
-			}
-		};
+		acceptThread = new Acceptor(processors, "Git-Daemon-Accept", socket); //$NON-NLS-1$
 		acceptThread.start();
 	}
 
+	private synchronized void clearThread() {
+		acceptThread = null;
+	}
+
 	/** @return true if this daemon is receiving connections. */
 	public synchronized boolean isRunning() {
-		return run;
+		return acceptThread != null && acceptThread.isRunning();
 	}
 
-	/** Stop this daemon. */
+	/**
+	 * Stop this daemon.
+	 */
 	public synchronized void stop() {
 		if (acceptThread != null) {
-			run = false;
-			acceptThread.interrupt();
+			acceptThread.shutDown();
+		}
+	}
+
+	/**
+	 * Stops this daemon and waits until it's acceptor thread has finished.
+	 *
+	 * @throws InterruptedException
+	 *             if waiting for the acceptor thread is interrupted
+	 *
+	 * @since 4.9
+	 */
+	public void stopAndWait() throws InterruptedException {
+		Thread acceptor = null;
+		synchronized (this) {
+			acceptor = acceptThread;
+			stop();
+		}
+		if (acceptor != null) {
+			acceptor.join();
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/DaemonService.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/DaemonService.java
index 80b2cae..566153a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/DaemonService.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/DaemonService.java
@@ -64,12 +64,7 @@ public abstract class DaemonService {
 
 	DaemonService(final String cmdName, final String cfgName) {
 		command = cmdName.startsWith("git-") ? cmdName : "git-" + cmdName; //$NON-NLS-1$ //$NON-NLS-2$
-		configKey = new SectionParser<ServiceConfig>() {
-			@Override
-			public ServiceConfig parse(final Config cfg) {
-				return new ServiceConfig(DaemonService.this, cfg, cfgName);
-			}
-		};
+		configKey = cfg -> new ServiceConfig(DaemonService.this, cfg, cfgName);
 		overridable = true;
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
index 280e6d4..ed10f44 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
@@ -74,6 +74,7 @@
 import org.eclipse.jgit.lib.BatchingProgressMonitor;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectIdRef;
 import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.RefDatabase;
@@ -202,12 +203,10 @@ else if (tagopt == TagOpt.FETCH_TAGS)
 				((BatchingProgressMonitor) monitor).setDelayStart(
 						250, TimeUnit.MILLISECONDS);
 			}
-			if (transport.isRemoveDeletedRefs())
+			if (transport.isRemoveDeletedRefs()) {
 				deleteStaleTrackingRefs(result, batch);
-			for (TrackingRefUpdate u : localUpdates) {
-				result.add(u);
-				batch.addCommand(u.asReceiveCommand());
 			}
+			addUpdateBatchCommands(result, batch);
 			for (ReceiveCommand cmd : batch.getCommands()) {
 				cmd.updateType(walk);
 				if (cmd.getType() == UPDATE_NONFASTFORWARD
@@ -220,8 +219,11 @@ else if (tagopt == TagOpt.FETCH_TAGS)
 					if (cmd.getResult() == NOT_ATTEMPTED)
 						cmd.setResult(OK);
 				}
-			} else
+			} else {
 				batch.execute(walk, monitor);
+			}
+		} catch (TransportException e) {
+			throw e;
 		} catch (IOException err) {
 			throw new TransportException(MessageFormat.format(
 					JGitText.get().failureUpdatingTrackingRef,
@@ -238,6 +240,23 @@ else if (tagopt == TagOpt.FETCH_TAGS)
 		}
 	}
 
+	private void addUpdateBatchCommands(FetchResult result,
+			BatchRefUpdate batch) throws TransportException {
+		Map<String, ObjectId> refs = new HashMap<>();
+		for (TrackingRefUpdate u : localUpdates) {
+			// Try to skip duplicates if they'd update to the same object ID
+			ObjectId existing = refs.get(u.getLocalName());
+			if (existing == null) {
+				refs.put(u.getLocalName(), u.getNewObjectId());
+				result.add(u);
+				batch.addCommand(u.asReceiveCommand());
+			} else if (!existing.equals(u.getNewObjectId())) {
+				throw new TransportException(MessageFormat
+						.format(JGitText.get().duplicateRef, u.getLocalName()));
+			}
+		}
+	}
+
 	private void fetchObjects(final ProgressMonitor monitor)
 			throws TransportException {
 		try {
@@ -360,12 +379,19 @@ private void expandWildcard(final RefSpec spec, final Set<Ref> matched)
 
 	private void expandSingle(final RefSpec spec, final Set<Ref> matched)
 			throws TransportException {
-		final Ref src = conn.getRef(spec.getSource());
-		if (src == null) {
-			throw new TransportException(MessageFormat.format(JGitText.get().remoteDoesNotHaveSpec, spec.getSource()));
+		String want = spec.getSource();
+		if (ObjectId.isId(want)) {
+			want(ObjectId.fromString(want));
+			return;
 		}
-		if (matched.add(src))
+
+		Ref src = conn.getRef(want);
+		if (src == null) {
+			throw new TransportException(MessageFormat.format(JGitText.get().remoteDoesNotHaveSpec, want));
+		}
+		if (matched.add(src)) {
 			want(src, spec);
+		}
 	}
 
 	private Collection<Ref> expandAutoFollowTags() throws TransportException {
@@ -440,6 +466,11 @@ private void want(final Ref src, final RefSpec spec)
 		fetchHeadUpdates.add(fhr);
 	}
 
+	private void want(ObjectId id) {
+		askFor.put(id,
+				new ObjectIdRef.Unpeeled(Ref.Storage.NETWORK, id.name(), id));
+	}
+
 	private TrackingRefUpdate createUpdate(RefSpec spec, ObjectId newId)
 			throws TransportException {
 		Ref ref = localRefs().get(spec.getDestination());
@@ -468,12 +499,14 @@ private Map<String, Ref> localRefs() throws TransportException {
 
 	private void deleteStaleTrackingRefs(FetchResult result,
 			BatchRefUpdate batch) throws IOException {
+		final Set<Ref> processed = new HashSet<>();
 		for (final Ref ref : localRefs().values()) {
 			final String refname = ref.getName();
 			for (final RefSpec spec : toFetch) {
 				if (spec.matchDestination(refname)) {
 					final RefSpec s = spec.expandFromDestination(refname);
-					if (result.getAdvertisedRef(s.getSource()) == null) {
+					if (result.getAdvertisedRef(s.getSource()) == null
+							&& processed.add(ref)) {
 						deleteTrackingRef(result, batch, s, ref);
 					}
 				}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpConfig.java
new file mode 100644
index 0000000..db59a54
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpConfig.java
@@ -0,0 +1,412 @@
+/*
+ * Copyright (C) 2008, 2010, Google Inc.
+ * Copyright (C) 2017, Thomas Wolf <thomas.wolf@paranor.ch>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.transport;
+
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.text.MessageFormat;
+import java.util.Set;
+import java.util.function.Supplier;
+
+import org.eclipse.jgit.errors.ConfigInvalidException;
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.lib.Config;
+import org.eclipse.jgit.storage.file.FileBasedConfig;
+import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.util.StringUtils;
+import org.eclipse.jgit.util.SystemReader;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * A representation of the "http.*" config values in a git {@link Config}. git
+ * provides for setting values for specific URLs through "http.<url>.*
+ * subsections. git always considers only the initial original URL for such
+ * settings, not any redirected URL.
+ *
+ * @since 4.9
+ */
+public class HttpConfig {
+
+	private static final Logger LOG = LoggerFactory.getLogger(HttpConfig.class);
+
+	private static final String FTP = "ftp"; //$NON-NLS-1$
+
+	/** git config section key for http settings. */
+	public static final String HTTP = "http"; //$NON-NLS-1$
+
+	/** git config key for the "followRedirects" setting. */
+	public static final String FOLLOW_REDIRECTS_KEY = "followRedirects"; //$NON-NLS-1$
+
+	/** git config key for the "maxRedirects" setting. */
+	public static final String MAX_REDIRECTS_KEY = "maxRedirects"; //$NON-NLS-1$
+
+	/** git config key for the "postBuffer" setting. */
+	public static final String POST_BUFFER_KEY = "postBuffer"; //$NON-NLS-1$
+
+	/** git config key for the "sslVerify" setting. */
+	public static final String SSL_VERIFY_KEY = "sslVerify"; //$NON-NLS-1$
+
+	private static final String MAX_REDIRECT_SYSTEM_PROPERTY = "http.maxRedirects"; //$NON-NLS-1$
+
+	private static final int DEFAULT_MAX_REDIRECTS = 5;
+
+	private static final int MAX_REDIRECTS = (new Supplier<Integer>() {
+
+		@Override
+		public Integer get() {
+			String rawValue = SystemReader.getInstance()
+					.getProperty(MAX_REDIRECT_SYSTEM_PROPERTY);
+			Integer value = Integer.valueOf(DEFAULT_MAX_REDIRECTS);
+			if (rawValue != null) {
+				try {
+					value = Integer.valueOf(Integer.parseUnsignedInt(rawValue));
+				} catch (NumberFormatException e) {
+					LOG.warn(MessageFormat.format(
+							JGitText.get().invalidSystemProperty,
+							MAX_REDIRECT_SYSTEM_PROPERTY, rawValue, value));
+				}
+			}
+			return value;
+		}
+	}).get().intValue();
+
+	/**
+	 * Config values for http.followRedirect.
+	 */
+	public enum HttpRedirectMode implements Config.ConfigEnum {
+
+		/** Always follow redirects (up to the http.maxRedirects limit). */
+		TRUE("true"), //$NON-NLS-1$
+		/**
+		 * Only follow redirects on the initial GET request. This is the
+		 * default.
+		 */
+		INITIAL("initial"), //$NON-NLS-1$
+		/** Never follow redirects. */
+		FALSE("false"); //$NON-NLS-1$
+
+		private final String configValue;
+
+		private HttpRedirectMode(String configValue) {
+			this.configValue = configValue;
+		}
+
+		@Override
+		public String toConfigValue() {
+			return configValue;
+		}
+
+		@Override
+		public boolean matchConfigValue(String s) {
+			return configValue.equals(s);
+		}
+	}
+
+	private int postBuffer;
+
+	private boolean sslVerify;
+
+	private HttpRedirectMode followRedirects;
+
+	private int maxRedirects;
+
+	/**
+	 * @return the value of the "http.postBuffer" setting
+	 */
+	public int getPostBuffer() {
+		return postBuffer;
+	}
+
+	/**
+	 * @return the value of the "http.sslVerify" setting
+	 */
+	public boolean isSslVerify() {
+		return sslVerify;
+	}
+
+	/**
+	 * @return the value of the "http.followRedirects" setting
+	 */
+	public HttpRedirectMode getFollowRedirects() {
+		return followRedirects;
+	}
+
+	/**
+	 * @return the value of the "http.maxRedirects" setting
+	 */
+	public int getMaxRedirects() {
+		return maxRedirects;
+	}
+
+	/**
+	 * Creates a new {@link HttpConfig} tailored to the given {@link URIish}.
+	 *
+	 * @param config
+	 *            to read the {@link HttpConfig} from
+	 * @param uri
+	 *            to get the configuration values for
+	 */
+	public HttpConfig(Config config, URIish uri) {
+		init(config, uri);
+	}
+
+	/**
+	 * Creates a {@link HttpConfig} that reads values solely from the user
+	 * config.
+	 *
+	 * @param uri
+	 *            to get the configuration values for
+	 */
+	public HttpConfig(URIish uri) {
+		FileBasedConfig userConfig = SystemReader.getInstance()
+				.openUserConfig(null, FS.DETECTED);
+		try {
+			userConfig.load();
+		} catch (IOException | ConfigInvalidException e) {
+			// Log it and then work with default values.
+			LOG.error(MessageFormat.format(JGitText.get().userConfigFileInvalid,
+					userConfig.getFile().getAbsolutePath(), e));
+			init(new Config(), uri);
+			return;
+		}
+		init(userConfig, uri);
+	}
+
+	private void init(Config config, URIish uri) {
+		// Set defaults from the section first
+		int postBufferSize = config.getInt(HTTP, POST_BUFFER_KEY,
+				1 * 1024 * 1024);
+		boolean sslVerifyFlag = config.getBoolean(HTTP, SSL_VERIFY_KEY, true);
+		HttpRedirectMode followRedirectsMode = config.getEnum(
+				HttpRedirectMode.values(), HTTP, null,
+				FOLLOW_REDIRECTS_KEY, HttpRedirectMode.INITIAL);
+		int redirectLimit = config.getInt(HTTP, MAX_REDIRECTS_KEY,
+				MAX_REDIRECTS);
+		if (redirectLimit < 0) {
+			redirectLimit = MAX_REDIRECTS;
+		}
+		String match = findMatch(config.getSubsections(HTTP), uri);
+		if (match != null) {
+			// Override with more specific items
+			postBufferSize = config.getInt(HTTP, match, POST_BUFFER_KEY,
+					postBufferSize);
+			sslVerifyFlag = config.getBoolean(HTTP, match, SSL_VERIFY_KEY,
+					sslVerifyFlag);
+			followRedirectsMode = config.getEnum(HttpRedirectMode.values(),
+					HTTP, match, FOLLOW_REDIRECTS_KEY, followRedirectsMode);
+			int newMaxRedirects = config.getInt(HTTP, match, MAX_REDIRECTS_KEY,
+					redirectLimit);
+			if (newMaxRedirects >= 0) {
+				redirectLimit = newMaxRedirects;
+			}
+		}
+		postBuffer = postBufferSize;
+		sslVerify = sslVerifyFlag;
+		followRedirects = followRedirectsMode;
+		maxRedirects = redirectLimit;
+	}
+
+	/**
+	 * Determines the best match from a set of subsection names (representing
+	 * prefix URLs) for the given {@link URIish}.
+	 *
+	 * @param names
+	 *            to match against the {@code uri}
+	 * @param uri
+	 *            to find a match for
+	 * @return the best matching subsection name, or {@code null} if no
+	 *         subsection matches
+	 */
+	private String findMatch(Set<String> names, URIish uri) {
+		String bestMatch = null;
+		int bestMatchLength = -1;
+		boolean withUser = false;
+		String uPath = uri.getPath();
+		boolean hasPath = !StringUtils.isEmptyOrNull(uPath);
+		if (hasPath) {
+			uPath = normalize(uPath);
+			if (uPath == null) {
+				// Normalization failed; warning was logged.
+				return null;
+			}
+		}
+		for (String s : names) {
+			try {
+				URIish candidate = new URIish(s);
+				// Scheme and host must match case-insensitively
+				if (!compare(uri.getScheme(), candidate.getScheme())
+						|| !compare(uri.getHost(), candidate.getHost())) {
+					continue;
+				}
+				// Ports must match after default ports have been substituted
+				if (defaultedPort(uri.getPort(),
+						uri.getScheme()) != defaultedPort(candidate.getPort(),
+								candidate.getScheme())) {
+					continue;
+				}
+				// User: if present in candidate, must match
+				boolean hasUser = false;
+				if (candidate.getUser() != null) {
+					if (!candidate.getUser().equals(uri.getUser())) {
+						continue;
+					}
+					hasUser = true;
+				}
+				// Path: prefix match, longer is better
+				String cPath = candidate.getPath();
+				int matchLength = -1;
+				if (StringUtils.isEmptyOrNull(cPath)) {
+					matchLength = 0;
+				} else {
+					if (!hasPath) {
+						continue;
+					}
+					// Paths can match only on segments
+					matchLength = segmentCompare(uPath, cPath);
+					if (matchLength < 0) {
+						continue;
+					}
+				}
+				// A longer path match is always preferred even over a user
+				// match. If the path matches are equal, a match with user wins
+				// over a match without user.
+				if (matchLength > bestMatchLength || !withUser && hasUser
+						&& matchLength >= 0 && matchLength == bestMatchLength) {
+					bestMatch = s;
+					bestMatchLength = matchLength;
+					withUser = hasUser;
+				}
+			} catch (URISyntaxException e) {
+				LOG.warn(MessageFormat
+						.format(JGitText.get().httpConfigInvalidURL, s));
+			}
+		}
+		return bestMatch;
+	}
+
+	private boolean compare(String a, String b) {
+		if (a == null) {
+			return b == null;
+		}
+		return a.equalsIgnoreCase(b);
+	}
+
+	private int defaultedPort(int port, String scheme) {
+		if (port >= 0) {
+			return port;
+		}
+		if (FTP.equalsIgnoreCase(scheme)) {
+			return 21;
+		} else if (HTTP.equalsIgnoreCase(scheme)) {
+			return 80;
+		} else {
+			return 443; // https
+		}
+	}
+
+	static int segmentCompare(String uriPath, String m) {
+		// Precondition: !uriPath.isEmpty() && !m.isEmpty(),and u must already
+		// be normalized
+		String matchPath = normalize(m);
+		if (matchPath == null || !uriPath.startsWith(matchPath)) {
+			return -1;
+		}
+		// We can match only on a segment boundary: either both paths are equal,
+		// or if matchPath does not end in '/', there is a '/' in uriPath right
+		// after the match.
+		int uLength = uriPath.length();
+		int mLength = matchPath.length();
+		if (mLength == uLength || matchPath.charAt(mLength - 1) == '/'
+				|| mLength < uLength && uriPath.charAt(mLength) == '/') {
+			return mLength;
+		}
+		return -1;
+	}
+
+	static String normalize(String path) {
+		// C-git resolves . and .. segments
+		int i = 0;
+		int length = path.length();
+		StringBuilder builder = new StringBuilder(length);
+		builder.append('/');
+		if (length > 0 && path.charAt(0) == '/') {
+			i = 1;
+		}
+		while (i < length) {
+			int slash = path.indexOf('/', i);
+			if (slash < 0) {
+				slash = length;
+			}
+			if (slash == i || slash == i + 1 && path.charAt(i) == '.') {
+				// Skip /. or also double slashes
+			} else if (slash == i + 2 && path.charAt(i) == '.'
+					&& path.charAt(i + 1) == '.') {
+				// Remove previous segment if we have "/.."
+				int l = builder.length() - 2; // Skip terminating slash.
+				while (l >= 0 && builder.charAt(l) != '/') {
+					l--;
+				}
+				if (l < 0) {
+					LOG.warn(MessageFormat.format(
+							JGitText.get().httpConfigCannotNormalizeURL, path));
+					return null;
+				}
+				builder.setLength(l + 1);
+			} else {
+				// Include the slash, if any
+				builder.append(path, i, Math.min(length, slash + 1));
+			}
+			i = slash + 1;
+		}
+		if (builder.length() > 1 && builder.charAt(builder.length() - 1) == '/'
+				&& length > 0 && path.charAt(length - 1) != '/') {
+			// . or .. normalization left a trailing slash when the original
+			// path had none at the end
+			builder.setLength(builder.length() - 1);
+		}
+		return builder.toString();
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschConfigSessionFactory.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschConfigSessionFactory.java
index ce14183..0cc40f3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschConfigSessionFactory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschConfigSessionFactory.java
@@ -53,15 +53,23 @@
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
 import java.net.ConnectException;
 import java.net.UnknownHostException;
+import java.text.MessageFormat;
 import java.util.HashMap;
+import java.util.Locale;
 import java.util.Map;
+import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.errors.TransportException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.util.FS;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
+import com.jcraft.jsch.ConfigRepository;
 import com.jcraft.jsch.JSch;
 import com.jcraft.jsch.JSchException;
 import com.jcraft.jsch.Session;
@@ -80,6 +88,18 @@
  * to supply appropriate {@link UserInfo} to the session.
  */
 public abstract class JschConfigSessionFactory extends SshSessionFactory {
+
+	private static final Logger LOG = LoggerFactory
+			.getLogger(JschConfigSessionFactory.class);
+
+	/**
+	 * We use different Jsch instances for hosts that have an IdentityFile
+	 * configured in ~/.ssh/config. Jsch by default would cache decrypted keys
+	 * only per session, which results in repeated password prompts. Using
+	 * different Jsch instances, we can cache the keys on these instances so
+	 * that they will be re-used for successive sessions, and thus the user is
+	 * prompted for a key password only once while Eclipse runs.
+	 */
 	private final Map<String, JSch> byIdentityFile = new HashMap<>();
 
 	private JSch defaultJSch;
@@ -101,7 +121,6 @@ public synchronized RemoteSession getSession(URIish uri,
 				config = OpenSshConfig.get(fs);
 
 			final OpenSshConfig.Host hc = config.lookup(host);
-			host = hc.getHostName();
 			if (port <= 0)
 				port = hc.getPort();
 			if (user == null)
@@ -153,10 +172,13 @@ public synchronized RemoteSession getSession(URIish uri,
 
 		} catch (JSchException je) {
 			final Throwable c = je.getCause();
-			if (c instanceof UnknownHostException)
-				throw new TransportException(uri, JGitText.get().unknownHost);
-			if (c instanceof ConnectException)
-				throw new TransportException(uri, c.getMessage());
+			if (c instanceof UnknownHostException) {
+				throw new TransportException(uri, JGitText.get().unknownHost,
+						je);
+			}
+			if (c instanceof ConnectException) {
+				throw new TransportException(uri, c.getMessage(), je);
+			}
 			throw new TransportException(uri, je.getMessage(), je);
 		}
 
@@ -170,10 +192,18 @@ private static boolean isAuthenticationCanceled(JSchException e) {
 		return e.getCause() == null && e.getMessage().equals("Auth cancel"); //$NON-NLS-1$
 	}
 
-	private Session createSession(CredentialsProvider credentialsProvider,
+	// Package visibility for tests
+	Session createSession(CredentialsProvider credentialsProvider,
 			FS fs, String user, final String pass, String host, int port,
 			final OpenSshConfig.Host hc) throws JSchException {
 		final Session session = createSession(hc, user, host, port, fs);
+		// Jsch will have overridden the explicit user by the one from the SSH
+		// config file...
+		setUserName(session, user);
+		// Jsch will also have overridden the port.
+		if (port > 0 && port != session.getPort()) {
+			session.setPort(port);
+		}
 		// We retry already in getSession() method. JSch must not retry
 		// on its own.
 		session.setConfig("MaxAuthTries", "1"); //$NON-NLS-1$ //$NON-NLS-2$
@@ -196,6 +226,28 @@ private Session createSession(CredentialsProvider credentialsProvider,
 		return session;
 	}
 
+	private void setUserName(Session session, String userName) {
+		// Jsch 0.1.54 picks up the user name from the ssh config, even if an
+		// explicit user name was given! We must correct that if ~/.ssh/config
+		// has a different user name.
+		if (userName == null || userName.isEmpty()
+				|| userName.equals(session.getUserName())) {
+			return;
+		}
+		try {
+			Class<?>[] parameterTypes = { String.class };
+			Method method = Session.class.getDeclaredMethod("setUserName", //$NON-NLS-1$
+					parameterTypes);
+			method.setAccessible(true);
+			method.invoke(session, userName);
+		} catch (NullPointerException | IllegalAccessException
+				| IllegalArgumentException | InvocationTargetException
+				| NoSuchMethodException | SecurityException e) {
+			LOG.error(MessageFormat.format(JGitText.get().sshUserNameError,
+					userName, session.getUserName()), e);
+		}
+	}
+
 	/**
 	 * Create a new remote session for the requested address.
 	 *
@@ -259,6 +311,10 @@ protected void configureJSch(JSch jsch) {
 	protected JSch getJSch(final OpenSshConfig.Host hc, FS fs) throws JSchException {
 		if (defaultJSch == null) {
 			defaultJSch = createDefaultJSch(fs);
+			if (defaultJSch.getConfigRepository() == null) {
+				defaultJSch.setConfigRepository(
+						new JschBugFixingConfigRepository(config));
+			}
 			for (Object name : defaultJSch.getIdentityNames())
 				byIdentityFile.put((String) name, defaultJSch);
 		}
@@ -272,6 +328,9 @@ protected JSch getJSch(final OpenSshConfig.Host hc, FS fs) throws JSchException
 		if (jsch == null) {
 			jsch = new JSch();
 			configureJSch(jsch);
+			if (jsch.getConfigRepository() == null) {
+				jsch.setConfigRepository(defaultJSch.getConfigRepository());
+			}
 			jsch.setHostKeyRepository(defaultJSch.getHostKeyRepository());
 			jsch.addIdentity(identityKey);
 			byIdentityFile.put(identityKey, jsch);
@@ -335,4 +394,101 @@ private static void loadIdentity(final JSch sch, final File priv) {
 			}
 		}
 	}
+
+	private static class JschBugFixingConfigRepository
+			implements ConfigRepository {
+
+		private final ConfigRepository base;
+
+		public JschBugFixingConfigRepository(ConfigRepository base) {
+			this.base = base;
+		}
+
+		@Override
+		public Config getConfig(String host) {
+			return new JschBugFixingConfig(base.getConfig(host));
+		}
+
+		/**
+		 * A {@link com.jcraft.jsch.ConfigRepository.Config} that transforms
+		 * some values from the config file into the format Jsch 0.1.54 expects.
+		 * This is a work-around for bugs in Jsch.
+		 * <p>
+		 * Additionally, this config hides the IdentityFile config entries from
+		 * Jsch; we manage those ourselves. Otherwise Jsch would cache passwords
+		 * (or rather, decrypted keys) only for a single session, resulting in
+		 * multiple password prompts for user operations that use several Jsch
+		 * sessions.
+		 */
+		private static class JschBugFixingConfig implements Config {
+
+			private static final String[] NO_IDENTITIES = {};
+
+			private final Config real;
+
+			public JschBugFixingConfig(Config delegate) {
+				real = delegate;
+			}
+
+			@Override
+			public String getHostname() {
+				return real.getHostname();
+			}
+
+			@Override
+			public String getUser() {
+				return real.getUser();
+			}
+
+			@Override
+			public int getPort() {
+				return real.getPort();
+			}
+
+			@Override
+			public String getValue(String key) {
+				String k = key.toUpperCase(Locale.ROOT);
+				if ("IDENTITYFILE".equals(k)) { //$NON-NLS-1$
+					return null;
+				}
+				String result = real.getValue(key);
+				if (result != null) {
+					if ("SERVERALIVEINTERVAL".equals(k) //$NON-NLS-1$
+							|| "CONNECTTIMEOUT".equals(k)) { //$NON-NLS-1$
+						// These values are in seconds. Jsch 0.1.54 passes them
+						// on as is to java.net.Socket.setSoTimeout(), which
+						// expects milliseconds. So convert here to
+						// milliseconds.
+						try {
+							int timeout = Integer.parseInt(result);
+							result = Long.toString(
+									TimeUnit.SECONDS.toMillis(timeout));
+						} catch (NumberFormatException e) {
+							// Ignore
+						}
+					}
+				}
+				return result;
+			}
+
+			@Override
+			public String[] getValues(String key) {
+				String k = key.toUpperCase(Locale.ROOT);
+				if ("IDENTITYFILE".equals(k)) { //$NON-NLS-1$
+					return NO_IDENTITIES;
+				}
+				return real.getValues(key);
+			}
+		}
+	}
+
+	/**
+	 * Set the {@link OpenSshConfig} to use. Intended for use in tests.
+	 *
+	 * @param config
+	 *            to use
+	 */
+	void setConfig(OpenSshConfig config) {
+		this.config = config;
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschSession.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschSession.java
index f445bcb..a8cc032 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschSession.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschSession.java
@@ -220,6 +220,7 @@ private boolean isRunning() {
 		public void destroy() {
 			if (channel.isConnected())
 				channel.disconnect();
+			closeOutputStream();
 		}
 
 		@Override
@@ -229,4 +230,4 @@ public int waitFor() throws InterruptedException {
 			return exitValue();
 		}
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java
index bab5bf0..5727b03 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java
@@ -317,4 +317,4 @@ private void parse() {
 			}
 		}
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java
index 8b7b60d..b5d5099 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2008, 2014, Google Inc.
+ * Copyright (C) 2008, 2017, Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -46,32 +46,90 @@
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.security.AccessController;
 import java.security.PrivilegedAction;
 import java.util.ArrayList;
-import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
+import java.util.Set;
 
 import org.eclipse.jgit.errors.InvalidPatternException;
 import org.eclipse.jgit.fnmatch.FileNameMatcher;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.StringUtils;
+import org.eclipse.jgit.util.SystemReader;
+
+import com.jcraft.jsch.ConfigRepository;
 
 /**
- * Simple configuration parser for the OpenSSH ~/.ssh/config file.
+ * Fairly complete configuration parser for the OpenSSH ~/.ssh/config file.
  * <p>
- * Since JSch does not (currently) have the ability to parse an OpenSSH
- * configuration file this is a simple parser to read that file and make the
- * critical options available to {@link SshSessionFactory}.
+ * JSch does have its own config file parser
+ * {@link com.jcraft.jsch.OpenSSHConfig} since version 0.1.50, but it has a
+ * number of problems:
+ * <ul>
+ * <li>it splits lines of the format "keyword = value" wrongly: you'd end up
+ * with the value "= value".
+ * <li>its "Host" keyword is not case insensitive.
+ * <li>it doesn't handle quoted values.
+ * <li>JSch's OpenSSHConfig doesn't monitor for config file changes.
+ * </ul>
+ * <p>
+ * Therefore implement our own parser to read an OpenSSH configuration file. It
+ * makes the critical options available to {@link SshSessionFactory} via
+ * {@link Host} objects returned by {@link #lookup(String)}, and implements a
+ * fully conforming {@link ConfigRepository} providing
+ * {@link com.jcraft.jsch.ConfigRepository.Config}s via
+ * {@link #getConfig(String)}.
+ * </p>
+ * <p>
+ * Limitations compared to the full OpenSSH 7.5 parser:
+ * </p>
+ * <ul>
+ * <li>This parser does not handle Match or Include keywords.
+ * <li>This parser does not do host name canonicalization (Jsch ignores it
+ * anyway).
+ * </ul>
+ * <p>
+ * Note that OpenSSH's readconf.c is a validating parser; Jsch's
+ * ConfigRepository OTOH treats all option values as plain strings, so any
+ * validation must happen in Jsch outside of the parser. Thus this parser does
+ * not validate option values, except for a few options when constructing a
+ * {@link Host} object.
+ * </p>
+ * <p>
+ * This config does %-substitutions for the following tokens:
+ * </p>
+ * <ul>
+ * <li>%% - single %
+ * <li>%C - short-hand for %l%h%p%r. See %p and %r below; the replacement may be
+ * done partially only and may leave %p or %r or both unreplaced.
+ * <li>%d - home directory path
+ * <li>%h - remote host name
+ * <li>%L - local host name without domain
+ * <li>%l - FQDN of the local host
+ * <li>%n - host name as specified in {@link #lookup(String)}
+ * <li>%p - port number; replaced only if set in the config
+ * <li>%r - remote user name; replaced only if set in the config
+ * <li>%u - local user name
+ * </ul>
+ * <p>
+ * If the config doesn't set the port or the remote user name, %p and %r remain
+ * un-substituted. It's the caller's responsibility to replace them with values
+ * obtained from the connection URI. %i is not handled; Java has no concept of a
+ * "user ID".
+ * </p>
  */
-public class OpenSshConfig {
+public class OpenSshConfig implements ConfigRepository {
+
 	/** IANA assigned port number for SSH. */
 	static final int SSH_PORT = 22;
 
@@ -105,16 +163,31 @@ public static OpenSshConfig get(FS fs) {
 	/** The .ssh/config file we read and monitor for updates. */
 	private final File configFile;
 
-	/** Modification time of {@link #configFile} when {@link #hosts} loaded. */
+	/** Modification time of {@link #configFile} when it was last loaded. */
 	private long lastModified;
 
-	/** Cached entries read out of the configuration file. */
-	private Map<String, Host> hosts;
+	/**
+	 * Encapsulates entries read out of the configuration file, and
+	 * {@link Host}s created from that.
+	 */
+	private static class State {
+		Map<String, HostEntry> entries = new LinkedHashMap<>();
+		Map<String, Host> hosts = new HashMap<>();
+
+		@Override
+		@SuppressWarnings("nls")
+		public String toString() {
+			return "State [entries=" + entries + ", hosts=" + hosts + "]";
+		}
+	}
+
+	/** State read from the config file, plus {@link Host}s created from it. */
+	private State state;
 
 	OpenSshConfig(final File h, final File cfg) {
 		home = h;
 		configFile = cfg;
-		hosts = Collections.emptyMap();
+		state = new State();
 	}
 
 	/**
@@ -127,75 +200,81 @@ public static OpenSshConfig get(FS fs) {
 	 * @return r configuration for the requested name. Never null.
 	 */
 	public Host lookup(final String hostName) {
-		final Map<String, Host> cache = refresh();
-		Host h = cache.get(hostName);
-		if (h == null)
-			h = new Host();
-		if (h.patternsApplied)
+		final State cache = refresh();
+		Host h = cache.hosts.get(hostName);
+		if (h != null) {
 			return h;
-
-		for (final Map.Entry<String, Host> e : cache.entrySet()) {
-			if (!isHostPattern(e.getKey()))
-				continue;
-			if (!isHostMatch(e.getKey(), hostName))
-				continue;
-			h.copyFrom(e.getValue());
 		}
-
-		if (h.hostName == null)
-			h.hostName = hostName;
-		if (h.user == null)
-			h.user = OpenSshConfig.userName();
-		if (h.port == 0)
-			h.port = OpenSshConfig.SSH_PORT;
-		if (h.connectionAttempts == 0)
-			h.connectionAttempts = 1;
-		h.patternsApplied = true;
+		HostEntry fullConfig = new HostEntry();
+		// Initialize with default entries at the top of the file, before the
+		// first Host block.
+		fullConfig.merge(cache.entries.get(HostEntry.DEFAULT_NAME));
+		for (final Map.Entry<String, HostEntry> e : cache.entries.entrySet()) {
+			String key = e.getKey();
+			if (isHostMatch(key, hostName)) {
+				fullConfig.merge(e.getValue());
+			}
+		}
+		fullConfig.substitute(hostName, home);
+		h = new Host(fullConfig, hostName, home);
+		cache.hosts.put(hostName, h);
 		return h;
 	}
 
-	private synchronized Map<String, Host> refresh() {
+	private synchronized State refresh() {
 		final long mtime = configFile.lastModified();
 		if (mtime != lastModified) {
-			try {
-				final FileInputStream in = new FileInputStream(configFile);
-				try {
-					hosts = parse(in);
-				} finally {
-					in.close();
-				}
-			} catch (FileNotFoundException none) {
-				hosts = Collections.emptyMap();
-			} catch (IOException err) {
-				hosts = Collections.emptyMap();
+			State newState = new State();
+			try (FileInputStream in = new FileInputStream(configFile)) {
+				newState.entries = parse(in);
+			} catch (IOException none) {
+				// Ignore -- we'll set and return an empty state
 			}
 			lastModified = mtime;
+			state = newState;
 		}
-		return hosts;
+		return state;
 	}
 
-	private Map<String, Host> parse(final InputStream in) throws IOException {
-		final Map<String, Host> m = new LinkedHashMap<>();
+	private Map<String, HostEntry> parse(final InputStream in)
+			throws IOException {
+		final Map<String, HostEntry> m = new LinkedHashMap<>();
 		final BufferedReader br = new BufferedReader(new InputStreamReader(in));
-		final List<Host> current = new ArrayList<>(4);
+		final List<HostEntry> current = new ArrayList<>(4);
 		String line;
 
+		// The man page doesn't say so, but the OpenSSH parser (readconf.c)
+		// starts out in active mode and thus always applies any lines that
+		// occur before the first host block. We gather those options in a
+		// HostEntry for DEFAULT_NAME.
+		HostEntry defaults = new HostEntry();
+		current.add(defaults);
+		m.put(HostEntry.DEFAULT_NAME, defaults);
+
 		while ((line = br.readLine()) != null) {
 			line = line.trim();
-			if (line.length() == 0 || line.startsWith("#")) //$NON-NLS-1$
+			if (line.isEmpty() || line.startsWith("#")) { //$NON-NLS-1$
 				continue;
-
-			final String[] parts = line.split("[ \t]*[= \t]", 2); //$NON-NLS-1$
-			final String keyword = parts[0].trim();
-			final String argValue = parts[1].trim();
+			}
+			String[] parts = line.split("[ \t]*[= \t]", 2); //$NON-NLS-1$
+			// Although the ssh-config man page doesn't say so, the OpenSSH
+			// parser does allow quoted keywords.
+			String keyword = dequote(parts[0].trim());
+			// man 5 ssh-config says lines had the format "keyword arguments",
+			// with no indication that arguments were optional. However, let's
+			// not crap out on missing arguments. See bug 444319.
+			String argValue = parts.length > 1 ? parts[1].trim() : ""; //$NON-NLS-1$
 
 			if (StringUtils.equalsIgnoreCase("Host", keyword)) { //$NON-NLS-1$
 				current.clear();
-				for (final String pattern : argValue.split("[ \t]")) { //$NON-NLS-1$
-					final String name = dequote(pattern);
-					Host c = m.get(name);
+				for (String name : HostEntry.parseList(argValue)) {
+					if (name == null || name.isEmpty()) {
+						// null should not occur, but better be safe than sorry.
+						continue;
+					}
+					HostEntry c = m.get(name);
 					if (c == null) {
-						c = new Host();
+						c = new HostEntry();
 						m.put(name, c);
 					}
 					current.add(c);
@@ -206,57 +285,18 @@ private Map<String, Host> parse(final InputStream in) throws IOException {
 			if (current.isEmpty()) {
 				// We received an option outside of a Host block. We
 				// don't know who this should match against, so skip.
-				//
 				continue;
 			}
 
-			if (StringUtils.equalsIgnoreCase("HostName", keyword)) { //$NON-NLS-1$
-				for (final Host c : current)
-					if (c.hostName == null)
-						c.hostName = dequote(argValue);
-			} else if (StringUtils.equalsIgnoreCase("User", keyword)) { //$NON-NLS-1$
-				for (final Host c : current)
-					if (c.user == null)
-						c.user = dequote(argValue);
-			} else if (StringUtils.equalsIgnoreCase("Port", keyword)) { //$NON-NLS-1$
-				try {
-					final int port = Integer.parseInt(dequote(argValue));
-					for (final Host c : current)
-						if (c.port == 0)
-							c.port = port;
-				} catch (NumberFormatException nfe) {
-					// Bad port number. Don't set it.
+			if (HostEntry.isListKey(keyword)) {
+				List<String> args = HostEntry.parseList(argValue);
+				for (HostEntry entry : current) {
+					entry.setValue(keyword, args);
 				}
-			} else if (StringUtils.equalsIgnoreCase("IdentityFile", keyword)) { //$NON-NLS-1$
-				for (final Host c : current)
-					if (c.identityFile == null)
-						c.identityFile = toFile(dequote(argValue));
-			} else if (StringUtils.equalsIgnoreCase(
-					"PreferredAuthentications", keyword)) { //$NON-NLS-1$
-				for (final Host c : current)
-					if (c.preferredAuthentications == null)
-						c.preferredAuthentications = nows(dequote(argValue));
-			} else if (StringUtils.equalsIgnoreCase("BatchMode", keyword)) { //$NON-NLS-1$
-				for (final Host c : current)
-					if (c.batchMode == null)
-						c.batchMode = yesno(dequote(argValue));
-			} else if (StringUtils.equalsIgnoreCase(
-					"StrictHostKeyChecking", keyword)) { //$NON-NLS-1$
-				String value = dequote(argValue);
-				for (final Host c : current)
-					if (c.strictHostKeyChecking == null)
-						c.strictHostKeyChecking = value;
-			} else if (StringUtils.equalsIgnoreCase(
-					"ConnectionAttempts", keyword)) { //$NON-NLS-1$
-				try {
-					final int connectionAttempts = Integer.parseInt(dequote(argValue));
-					if (connectionAttempts > 0) {
-						for (final Host c : current)
-							if (c.connectionAttempts == 0)
-								c.connectionAttempts = connectionAttempts;
-					}
-				} catch (NumberFormatException nfe) {
-					// ignore bad values
+			} else if (!argValue.isEmpty()) {
+				argValue = dequote(argValue);
+				for (HostEntry entry : current) {
+					entry.setValue(keyword, argValue);
 				}
 			}
 		}
@@ -264,23 +304,35 @@ private Map<String, Host> parse(final InputStream in) throws IOException {
 		return m;
 	}
 
-	private static boolean isHostPattern(final String s) {
-		return s.indexOf('*') >= 0 || s.indexOf('?') >= 0;
+	private static boolean isHostMatch(final String pattern,
+			final String name) {
+		if (pattern.startsWith("!")) { //$NON-NLS-1$
+			return !patternMatchesHost(pattern.substring(1), name);
+		} else {
+			return patternMatchesHost(pattern, name);
+		}
 	}
 
-	private static boolean isHostMatch(final String pattern, final String name) {
-		final FileNameMatcher fn;
-		try {
-			fn = new FileNameMatcher(pattern, null);
-		} catch (InvalidPatternException e) {
-			return false;
+	private static boolean patternMatchesHost(final String pattern,
+			final String name) {
+		if (pattern.indexOf('*') >= 0 || pattern.indexOf('?') >= 0) {
+			final FileNameMatcher fn;
+			try {
+				fn = new FileNameMatcher(pattern, null);
+			} catch (InvalidPatternException e) {
+				return false;
+			}
+			fn.append(name);
+			return fn.isMatch();
+		} else {
+			// Not a pattern but a full host name
+			return pattern.equals(name);
 		}
-		fn.append(name);
-		return fn.isMatch();
 	}
 
 	private static String dequote(final String value) {
-		if (value.startsWith("\"") && value.endsWith("\"")) //$NON-NLS-1$ //$NON-NLS-2$
+		if (value.startsWith("\"") && value.endsWith("\"") //$NON-NLS-1$ //$NON-NLS-2$
+				&& value.length() > 1)
 			return value.substring(1, value.length() - 1);
 		return value;
 	}
@@ -300,24 +352,453 @@ private static Boolean yesno(final String value) {
 		return Boolean.FALSE;
 	}
 
-	private File toFile(final String path) {
-		if (path.startsWith("~/")) //$NON-NLS-1$
+	private static File toFile(String path, File home) {
+		if (path.startsWith("~/")) { //$NON-NLS-1$
 			return new File(home, path.substring(2));
+		}
 		File ret = new File(path);
-		if (ret.isAbsolute())
+		if (ret.isAbsolute()) {
 			return ret;
+		}
 		return new File(home, path);
 	}
 
+	private static int positive(final String value) {
+		if (value != null) {
+			try {
+				return Integer.parseUnsignedInt(value);
+			} catch (NumberFormatException e) {
+				// Ignore
+			}
+		}
+		return -1;
+	}
+
 	static String userName() {
 		return AccessController.doPrivileged(new PrivilegedAction<String>() {
 			@Override
 			public String run() {
-				return System.getProperty("user.name"); //$NON-NLS-1$
+				return SystemReader.getInstance()
+						.getProperty(Constants.OS_USER_NAME_KEY);
 			}
 		});
 	}
 
+	private static class HostEntry implements ConfigRepository.Config {
+
+		/**
+		 * "Host name" of the HostEntry for the default options before the first
+		 * host block in a config file.
+		 */
+		public static final String DEFAULT_NAME = ""; //$NON-NLS-1$
+
+		// See com.jcraft.jsch.OpenSSHConfig. Translates some command-line keys
+		// to ssh-config keys.
+		private static final Map<String, String> KEY_MAP = new HashMap<>();
+
+		static {
+			KEY_MAP.put("kex", "KexAlgorithms"); //$NON-NLS-1$//$NON-NLS-2$
+			KEY_MAP.put("server_host_key", "HostKeyAlgorithms"); //$NON-NLS-1$ //$NON-NLS-2$
+			KEY_MAP.put("cipher.c2s", "Ciphers"); //$NON-NLS-1$ //$NON-NLS-2$
+			KEY_MAP.put("cipher.s2c", "Ciphers"); //$NON-NLS-1$ //$NON-NLS-2$
+			KEY_MAP.put("mac.c2s", "Macs"); //$NON-NLS-1$ //$NON-NLS-2$
+			KEY_MAP.put("mac.s2c", "Macs"); //$NON-NLS-1$ //$NON-NLS-2$
+			KEY_MAP.put("compression.s2c", "Compression"); //$NON-NLS-1$ //$NON-NLS-2$
+			KEY_MAP.put("compression.c2s", "Compression"); //$NON-NLS-1$ //$NON-NLS-2$
+			KEY_MAP.put("compression_level", "CompressionLevel"); //$NON-NLS-1$ //$NON-NLS-2$
+			KEY_MAP.put("MaxAuthTries", "NumberOfPasswordPrompts"); //$NON-NLS-1$ //$NON-NLS-2$
+		}
+
+		/**
+		 * Keys that can be specified multiple times, building up a list. (I.e.,
+		 * those are the keys that do not follow the general rule of "first
+		 * occurrence wins".)
+		 */
+		private static final Set<String> MULTI_KEYS = new HashSet<>();
+
+		static {
+			MULTI_KEYS.add("CERTIFICATEFILE"); //$NON-NLS-1$
+			MULTI_KEYS.add("IDENTITYFILE"); //$NON-NLS-1$
+			MULTI_KEYS.add("LOCALFORWARD"); //$NON-NLS-1$
+			MULTI_KEYS.add("REMOTEFORWARD"); //$NON-NLS-1$
+			MULTI_KEYS.add("SENDENV"); //$NON-NLS-1$
+		}
+
+		/**
+		 * Keys that take a whitespace-separated list of elements as argument.
+		 * Because the dequote-handling is different, we must handle those in
+		 * the parser. There are a few other keys that take comma-separated
+		 * lists as arguments, but for the parser those are single arguments
+		 * that must be quoted if they contain whitespace, and taking them apart
+		 * is the responsibility of the user of those keys.
+		 */
+		private static final Set<String> LIST_KEYS = new HashSet<>();
+
+		static {
+			LIST_KEYS.add("CANONICALDOMAINS"); //$NON-NLS-1$
+			LIST_KEYS.add("GLOBALKNOWNHOSTSFILE"); //$NON-NLS-1$
+			LIST_KEYS.add("SENDENV"); //$NON-NLS-1$
+			LIST_KEYS.add("USERKNOWNHOSTSFILE"); //$NON-NLS-1$
+		}
+
+		private Map<String, String> options;
+
+		private Map<String, List<String>> multiOptions;
+
+		private Map<String, List<String>> listOptions;
+
+		@Override
+		public String getHostname() {
+			return getValue("HOSTNAME"); //$NON-NLS-1$
+		}
+
+		@Override
+		public String getUser() {
+			return getValue("USER"); //$NON-NLS-1$
+		}
+
+		@Override
+		public int getPort() {
+			return positive(getValue("PORT")); //$NON-NLS-1$
+		}
+
+		private static String mapKey(String key) {
+			String k = KEY_MAP.get(key);
+			if (k == null) {
+				k = key;
+			}
+			return k.toUpperCase(Locale.ROOT);
+		}
+
+		private String findValue(String key) {
+			String k = mapKey(key);
+			String result = options != null ? options.get(k) : null;
+			if (result == null) {
+				// Also check the list and multi options. Modern OpenSSH treats
+				// UserKnownHostsFile and GlobalKnownHostsFile as list-valued,
+				// and so does this parser. Jsch 0.1.54 in general doesn't know
+				// about list-valued options (it _does_ know multi-valued
+				// options, though), and will ask for a single value for such
+				// options.
+				//
+				// Let's be lenient and return at least the first value from
+				// a list-valued or multi-valued key for which Jsch asks for a
+				// single value.
+				List<String> values = listOptions != null ? listOptions.get(k)
+						: null;
+				if (values == null) {
+					values = multiOptions != null ? multiOptions.get(k) : null;
+				}
+				if (values != null && !values.isEmpty()) {
+					result = values.get(0);
+				}
+			}
+			return result;
+		}
+
+		@Override
+		public String getValue(String key) {
+			// See com.jcraft.jsch.OpenSSHConfig.MyConfig.getValue() for this
+			// special case.
+			if (key.equals("compression.s2c") //$NON-NLS-1$
+					|| key.equals("compression.c2s")) { //$NON-NLS-1$
+				String foo = findValue(key);
+				if (foo == null || foo.equals("no")) { //$NON-NLS-1$
+					return "none,zlib@openssh.com,zlib"; //$NON-NLS-1$
+				}
+				return "zlib@openssh.com,zlib,none"; //$NON-NLS-1$
+			}
+			return findValue(key);
+		}
+
+		@Override
+		public String[] getValues(String key) {
+			String k = mapKey(key);
+			List<String> values = listOptions != null ? listOptions.get(k)
+					: null;
+			if (values == null) {
+				values = multiOptions != null ? multiOptions.get(k) : null;
+			}
+			if (values == null || values.isEmpty()) {
+				return new String[0];
+			}
+			return values.toArray(new String[values.size()]);
+		}
+
+		public void setValue(String key, String value) {
+			String k = key.toUpperCase(Locale.ROOT);
+			if (MULTI_KEYS.contains(k)) {
+				if (multiOptions == null) {
+					multiOptions = new HashMap<>();
+				}
+				List<String> values = multiOptions.get(k);
+				if (values == null) {
+					values = new ArrayList<>(4);
+					multiOptions.put(k, values);
+				}
+				values.add(value);
+			} else {
+				if (options == null) {
+					options = new HashMap<>();
+				}
+				if (!options.containsKey(k)) {
+					options.put(k, value);
+				}
+			}
+		}
+
+		public void setValue(String key, List<String> values) {
+			if (values.isEmpty()) {
+				// Can occur only on a missing argument: ignore.
+				return;
+			}
+			String k = key.toUpperCase(Locale.ROOT);
+			// Check multi-valued keys first; because of the replacement
+			// strategy, they must take precedence over list-valued keys
+			// which always follow the "first occurrence wins" strategy.
+			//
+			// Note that SendEnv is a multi-valued list-valued key. (It's
+			// rather immaterial for JGit, though.)
+			if (MULTI_KEYS.contains(k)) {
+				if (multiOptions == null) {
+					multiOptions = new HashMap<>(2 * MULTI_KEYS.size());
+				}
+				List<String> items = multiOptions.get(k);
+				if (items == null) {
+					items = new ArrayList<>(values);
+					multiOptions.put(k, items);
+				} else {
+					items.addAll(values);
+				}
+			} else {
+				if (listOptions == null) {
+					listOptions = new HashMap<>(2 * LIST_KEYS.size());
+				}
+				if (!listOptions.containsKey(k)) {
+					listOptions.put(k, values);
+				}
+			}
+		}
+
+		public static boolean isListKey(String key) {
+			return LIST_KEYS.contains(key.toUpperCase(Locale.ROOT));
+		}
+
+		/**
+		 * Splits the argument into a list of whitespace-separated elements.
+		 * Elements containing whitespace must be quoted and will be de-quoted.
+		 *
+		 * @param argument
+		 *            argument part of the configuration line as read from the
+		 *            config file
+		 * @return a {@link List} of elements, possibly empty and possibly
+		 *         containing empty elements
+		 */
+		public static List<String> parseList(String argument) {
+			List<String> result = new ArrayList<>(4);
+			int start = 0;
+			int length = argument.length();
+			while (start < length) {
+				// Skip whitespace
+				if (Character.isSpaceChar(argument.charAt(start))) {
+					start++;
+					continue;
+				}
+				if (argument.charAt(start) == '"') {
+					int stop = argument.indexOf('"', ++start);
+					if (stop < start) {
+						// No closing double quote: skip
+						break;
+					}
+					result.add(argument.substring(start, stop));
+					start = stop + 1;
+				} else {
+					int stop = start + 1;
+					while (stop < length
+							&& !Character.isSpaceChar(argument.charAt(stop))) {
+						stop++;
+					}
+					result.add(argument.substring(start, stop));
+					start = stop + 1;
+				}
+			}
+			return result;
+		}
+
+		protected void merge(HostEntry entry) {
+			if (entry == null) {
+				// Can occur if we could not read the config file
+				return;
+			}
+			if (entry.options != null) {
+				if (options == null) {
+					options = new HashMap<>();
+				}
+				for (Map.Entry<String, String> item : entry.options
+						.entrySet()) {
+					if (!options.containsKey(item.getKey())) {
+						options.put(item.getKey(), item.getValue());
+					}
+				}
+			}
+			if (entry.listOptions != null) {
+				if (listOptions == null) {
+					listOptions = new HashMap<>(2 * LIST_KEYS.size());
+				}
+				for (Map.Entry<String, List<String>> item : entry.listOptions
+						.entrySet()) {
+					if (!listOptions.containsKey(item.getKey())) {
+						listOptions.put(item.getKey(), item.getValue());
+					}
+				}
+
+			}
+			if (entry.multiOptions != null) {
+				if (multiOptions == null) {
+					multiOptions = new HashMap<>(2 * MULTI_KEYS.size());
+				}
+				for (Map.Entry<String, List<String>> item : entry.multiOptions
+						.entrySet()) {
+					List<String> values = multiOptions.get(item.getKey());
+					if (values == null) {
+						values = new ArrayList<>(item.getValue());
+						multiOptions.put(item.getKey(), values);
+					} else {
+						values.addAll(item.getValue());
+					}
+				}
+			}
+		}
+
+		private class Replacer {
+			private final Map<Character, String> replacements = new HashMap<>();
+
+			public Replacer(String originalHostName, File home) {
+				replacements.put(Character.valueOf('%'), "%"); //$NON-NLS-1$
+				replacements.put(Character.valueOf('d'), home.getPath());
+				// Needs special treatment...
+				String host = getValue("HOSTNAME"); //$NON-NLS-1$
+				replacements.put(Character.valueOf('h'), originalHostName);
+				if (host != null && host.indexOf('%') >= 0) {
+					host = substitute(host, "h"); //$NON-NLS-1$
+					options.put("HOSTNAME", host); //$NON-NLS-1$
+				}
+				if (host != null) {
+					replacements.put(Character.valueOf('h'), host);
+				}
+				String localhost = SystemReader.getInstance().getHostname();
+				replacements.put(Character.valueOf('l'), localhost);
+				int period = localhost.indexOf('.');
+				if (period > 0) {
+					localhost = localhost.substring(0, period);
+				}
+				replacements.put(Character.valueOf('L'), localhost);
+				replacements.put(Character.valueOf('n'), originalHostName);
+				replacements.put(Character.valueOf('p'), getValue("PORT")); //$NON-NLS-1$
+				replacements.put(Character.valueOf('r'), getValue("USER")); //$NON-NLS-1$
+				replacements.put(Character.valueOf('u'), userName());
+				replacements.put(Character.valueOf('C'),
+						substitute("%l%h%p%r", "hlpr")); //$NON-NLS-1$ //$NON-NLS-2$
+			}
+
+			public String substitute(String input, String allowed) {
+				if (input == null || input.length() <= 1
+						|| input.indexOf('%') < 0) {
+					return input;
+				}
+				StringBuilder builder = new StringBuilder();
+				int start = 0;
+				int length = input.length();
+				while (start < length) {
+					int percent = input.indexOf('%', start);
+					if (percent < 0 || percent + 1 >= length) {
+						builder.append(input.substring(start));
+						break;
+					}
+					String replacement = null;
+					char ch = input.charAt(percent + 1);
+					if (ch == '%' || allowed.indexOf(ch) >= 0) {
+						replacement = replacements.get(Character.valueOf(ch));
+					}
+					if (replacement == null) {
+						builder.append(input.substring(start, percent + 2));
+					} else {
+						builder.append(input.substring(start, percent))
+								.append(replacement);
+					}
+					start = percent + 2;
+				}
+				return builder.toString();
+			}
+		}
+
+		private List<String> substitute(List<String> values, String allowed,
+				Replacer r) {
+			List<String> result = new ArrayList<>(values.size());
+			for (String value : values) {
+				result.add(r.substitute(value, allowed));
+			}
+			return result;
+		}
+
+		private List<String> replaceTilde(List<String> values, File home) {
+			List<String> result = new ArrayList<>(values.size());
+			for (String value : values) {
+				result.add(toFile(value, home).getPath());
+			}
+			return result;
+		}
+
+		protected void substitute(String originalHostName, File home) {
+			Replacer r = new Replacer(originalHostName, home);
+			if (multiOptions != null) {
+				List<String> values = multiOptions.get("IDENTITYFILE"); //$NON-NLS-1$
+				if (values != null) {
+					values = substitute(values, "dhlru", r); //$NON-NLS-1$
+					values = replaceTilde(values, home);
+					multiOptions.put("IDENTITYFILE", values); //$NON-NLS-1$
+				}
+				values = multiOptions.get("CERTIFICATEFILE"); //$NON-NLS-1$
+				if (values != null) {
+					values = substitute(values, "dhlru", r); //$NON-NLS-1$
+					values = replaceTilde(values, home);
+					multiOptions.put("CERTIFICATEFILE", values); //$NON-NLS-1$
+				}
+			}
+			if (listOptions != null) {
+				List<String> values = listOptions.get("GLOBALKNOWNHOSTSFILE"); //$NON-NLS-1$
+				if (values != null) {
+					values = replaceTilde(values, home);
+					listOptions.put("GLOBALKNOWNHOSTSFILE", values); //$NON-NLS-1$
+				}
+				values = listOptions.get("USERKNOWNHOSTSFILE"); //$NON-NLS-1$
+				if (values != null) {
+					values = replaceTilde(values, home);
+					listOptions.put("USERKNOWNHOSTSFILE", values); //$NON-NLS-1$
+				}
+			}
+			if (options != null) {
+				// HOSTNAME already done in Replacer constructor
+				String value = options.get("IDENTITYAGENT"); //$NON-NLS-1$
+				if (value != null) {
+					value = r.substitute(value, "dhlru"); //$NON-NLS-1$
+					value = toFile(value, home).getPath();
+					options.put("IDENTITYAGENT", value); //$NON-NLS-1$
+				}
+			}
+			// Match is not implemented and would need to be done elsewhere
+			// anyway. ControlPath, LocalCommand, ProxyCommand, and
+			// RemoteCommand are not used by Jsch.
+		}
+
+		@Override
+		@SuppressWarnings("nls")
+		public String toString() {
+			return "HostEntry [options=" + options + ", multiOptions="
+					+ multiOptions + ", listOptions=" + listOptions + "]";
+		}
+	}
+
 	/**
 	 * Configuration of one "Host" block in the configuration file.
 	 * <p>
@@ -330,8 +811,6 @@ public String run() {
 	 * already merged into this block.
 	 */
 	public static class Host {
-		boolean patternsApplied;
-
 		String hostName;
 
 		int port;
@@ -348,23 +827,18 @@ public static class Host {
 
 		int connectionAttempts;
 
-		void copyFrom(final Host src) {
-			if (hostName == null)
-				hostName = src.hostName;
-			if (port == 0)
-				port = src.port;
-			if (identityFile == null)
-				identityFile = src.identityFile;
-			if (user == null)
-				user = src.user;
-			if (preferredAuthentications == null)
-				preferredAuthentications = src.preferredAuthentications;
-			if (batchMode == null)
-				batchMode = src.batchMode;
-			if (strictHostKeyChecking == null)
-				strictHostKeyChecking = src.strictHostKeyChecking;
-			if (connectionAttempts == 0)
-				connectionAttempts = src.connectionAttempts;
+		private Config config;
+
+		/**
+		 * Creates a new uninitialized {@link Host}.
+		 */
+		public Host() {
+			// For API backwards compatibility with pre-4.9 JGit
+		}
+
+		Host(Config config, String hostName, File homeDir) {
+			this.config = config;
+			complete(hostName, homeDir);
 		}
 
 		/**
@@ -432,5 +906,78 @@ public boolean isBatchMode() {
 		public int getConnectionAttempts() {
 			return connectionAttempts;
 		}
+
+
+		private void complete(String initialHostName, File homeDir) {
+			// Try to set values from the options.
+			hostName = config.getHostname();
+			user = config.getUser();
+			port = config.getPort();
+			connectionAttempts = positive(
+					config.getValue("ConnectionAttempts")); //$NON-NLS-1$
+			strictHostKeyChecking = config.getValue("StrictHostKeyChecking"); //$NON-NLS-1$
+			String value = config.getValue("BatchMode"); //$NON-NLS-1$
+			if (value != null) {
+				batchMode = yesno(value);
+			}
+			value = config.getValue("PreferredAuthentications"); //$NON-NLS-1$
+			if (value != null) {
+				preferredAuthentications = nows(value);
+			}
+			// Fill in defaults if still not set
+			if (hostName == null) {
+				hostName = initialHostName;
+			}
+			if (user == null) {
+				user = OpenSshConfig.userName();
+			}
+			if (port <= 0) {
+				port = OpenSshConfig.SSH_PORT;
+			}
+			if (connectionAttempts <= 0) {
+				connectionAttempts = 1;
+			}
+			String[] identityFiles = config.getValues("IdentityFile"); //$NON-NLS-1$
+			if (identityFiles != null && identityFiles.length > 0) {
+				identityFile = toFile(identityFiles[0], homeDir);
+			}
+		}
+
+		Config getConfig() {
+			return config;
+		}
+
+		@Override
+		@SuppressWarnings("nls")
+		public String toString() {
+			return "Host [hostName=" + hostName + ", port=" + port
+					+ ", identityFile=" + identityFile + ", user=" + user
+					+ ", preferredAuthentications=" + preferredAuthentications
+					+ ", batchMode=" + batchMode + ", strictHostKeyChecking="
+					+ strictHostKeyChecking + ", connectionAttempts="
+					+ connectionAttempts + ", config=" + config + "]";
+		}
+	}
+
+	/**
+	 * Retrieves the full {@link com.jcraft.jsch.ConfigRepository.Config Config}
+	 * for the given host name. Should be called only by Jsch and tests.
+	 *
+	 * @param hostName
+	 *            to get the config for
+	 * @return the configuration for the host
+	 * @since 4.9
+	 */
+	@Override
+	public Config getConfig(String hostName) {
+		Host host = lookup(hostName);
+		return host.getConfig();
+	}
+
+	@Override
+	@SuppressWarnings("nls")
+	public String toString() {
+		return "OpenSshConfig [home=" + home + ", configFile=" + configFile
+				+ ", lastModified=" + lastModified + ", state=" + state + "]";
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackParser.java
index c82b389..833d211 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackParser.java
@@ -66,6 +66,7 @@
 import org.eclipse.jgit.internal.storage.pack.BinaryDelta;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.BatchingProgressMonitor;
+import org.eclipse.jgit.lib.BlobObjectChecker;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.InflaterCache;
 import org.eclipse.jgit.lib.MutableObjectId;
@@ -82,6 +83,7 @@
 import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.util.BlockList;
 import org.eclipse.jgit.util.IO;
+import org.eclipse.jgit.util.LongMap;
 import org.eclipse.jgit.util.NB;
 import org.eclipse.jgit.util.sha1.SHA1;
 
@@ -143,7 +145,7 @@ public static enum Source {
 
 	private boolean expectDataAfterPackFooter;
 
-	private long objectCount;
+	private long expectedObjectCount;
 
 	private PackedObjectInfo[] entries;
 
@@ -173,8 +175,8 @@ public static enum Source {
 
 	private LongMap<UnresolvedDelta> baseByPos;
 
-	/** Blobs whose contents need to be double-checked after indexing. */
-	private BlockList<PackedObjectInfo> deferredCheckBlobs;
+	/** Objects need to be double-checked for collision after indexing. */
+	private BlockList<PackedObjectInfo> collisionCheckObjs;
 
 	private MessageDigest packDigest;
 
@@ -525,15 +527,15 @@ public PackLock parse(ProgressMonitor receiving, ProgressMonitor resolving)
 		try {
 			readPackHeader();
 
-			entries = new PackedObjectInfo[(int) objectCount];
+			entries = new PackedObjectInfo[(int) expectedObjectCount];
 			baseById = new ObjectIdOwnerMap<>();
 			baseByPos = new LongMap<>();
-			deferredCheckBlobs = new BlockList<>();
+			collisionCheckObjs = new BlockList<>();
 
 			receiving.beginTask(JGitText.get().receivingObjects,
-					(int) objectCount);
+					(int) expectedObjectCount);
 			try {
-				for (int done = 0; done < objectCount; done++) {
+				for (int done = 0; done < expectedObjectCount; done++) {
 					indexOneObject();
 					receiving.update(1);
 					if (receiving.isCancelled())
@@ -545,32 +547,12 @@ public PackLock parse(ProgressMonitor receiving, ProgressMonitor resolving)
 				receiving.endTask();
 			}
 
-			if (!deferredCheckBlobs.isEmpty())
-				doDeferredCheckBlobs();
+			if (!collisionCheckObjs.isEmpty()) {
+				checkObjectCollision();
+			}
+
 			if (deltaCount > 0) {
-				if (resolving instanceof BatchingProgressMonitor) {
-					((BatchingProgressMonitor) resolving).setDelayStart(
-							1000,
-							TimeUnit.MILLISECONDS);
-				}
-				resolving.beginTask(JGitText.get().resolvingDeltas, deltaCount);
-				resolveDeltas(resolving);
-				if (entryCount < objectCount) {
-					if (!isAllowThin()) {
-						throw new IOException(MessageFormat.format(
-								JGitText.get().packHasUnresolvedDeltas,
-								Long.valueOf(objectCount - entryCount)));
-					}
-
-					resolveDeltasWithExternalBases(resolving);
-
-					if (entryCount < objectCount) {
-						throw new IOException(MessageFormat.format(
-								JGitText.get().packHasUnresolvedDeltas,
-								Long.valueOf(objectCount - entryCount)));
-					}
-				}
-				resolving.endTask();
+				processDeltas(resolving);
 			}
 
 			packDigest = null;
@@ -593,6 +575,31 @@ public PackLock parse(ProgressMonitor receiving, ProgressMonitor resolving)
 		return null; // By default there is no locking.
 	}
 
+	private void processDeltas(ProgressMonitor resolving) throws IOException {
+		if (resolving instanceof BatchingProgressMonitor) {
+			((BatchingProgressMonitor) resolving).setDelayStart(1000,
+					TimeUnit.MILLISECONDS);
+		}
+		resolving.beginTask(JGitText.get().resolvingDeltas, deltaCount);
+		resolveDeltas(resolving);
+		if (entryCount < expectedObjectCount) {
+			if (!isAllowThin()) {
+				throw new IOException(MessageFormat.format(
+						JGitText.get().packHasUnresolvedDeltas,
+						Long.valueOf(expectedObjectCount - entryCount)));
+			}
+
+			resolveDeltasWithExternalBases(resolving);
+
+			if (entryCount < expectedObjectCount) {
+				throw new IOException(MessageFormat.format(
+						JGitText.get().packHasUnresolvedDeltas,
+						Long.valueOf(expectedObjectCount - entryCount)));
+			}
+		}
+		resolving.endTask();
+	}
+
 	private void resolveDeltas(final ProgressMonitor progress)
 			throws IOException {
 		final int last = entryCount;
@@ -675,10 +682,14 @@ private void resolveDeltas(DeltaVisit visit, final int type,
 			objectDigest.digest(tempObjectId);
 
 			verifySafeObject(tempObjectId, type, visit.data);
+			if (isCheckObjectCollisions() && readCurs.has(tempObjectId)) {
+				checkObjectCollision(tempObjectId, type, visit.data);
+			}
 
 			PackedObjectInfo oe;
 			oe = newInfo(tempObjectId, visit.delta, visit.parent.id);
 			oe.setOffset(visit.delta.position);
+			oe.setType(type);
 			onInflatedObjectData(oe, type, visit.data);
 			addObjectAndTrack(oe);
 			visit.id = oe;
@@ -849,10 +860,9 @@ private void resolveDeltasWithExternalBases(final ProgressMonitor progress)
 			visit.id = baseId;
 			final int typeCode = ldr.getType();
 			final PackedObjectInfo oe = newInfo(baseId, null, null);
-
+			oe.setType(typeCode);
 			if (onAppendBase(typeCode, visit.data, oe))
 				entries[entryCount++] = oe;
-
 			visit.nextChild = firstChildOf(oe);
 			resolveDeltas(visit.next(), typeCode,
 					new ObjectTypeAndSize(), progress);
@@ -873,7 +883,7 @@ private void resolveDeltasWithExternalBases(final ProgressMonitor progress)
 	private void growEntries(int extraObjects) {
 		final PackedObjectInfo[] ne;
 
-		ne = new PackedObjectInfo[(int) objectCount + extraObjects];
+		ne = new PackedObjectInfo[(int) expectedObjectCount + extraObjects];
 		System.arraycopy(entries, 0, ne, 0, entryCount);
 		entries = ne;
 	}
@@ -896,9 +906,9 @@ private void readPackHeader() throws IOException {
 		if (vers != 2 && vers != 3)
 			throw new IOException(MessageFormat.format(
 					JGitText.get().unsupportedPackVersion, Long.valueOf(vers)));
-		objectCount = NB.decodeUInt32(buf, p + 8);
+		final long objectCount = NB.decodeUInt32(buf, p + 8);
 		use(hdrln);
-
+		setExpectedObjectCount(objectCount);
 		onPackHeader(objectCount);
 	}
 
@@ -1031,24 +1041,29 @@ private void whole(final long pos, final int type, final long sz)
 		objectDigest.update((byte) 0);
 
 		final byte[] data;
-		boolean checkContentLater = false;
 		if (type == Constants.OBJ_BLOB) {
 			byte[] readBuffer = buffer();
 			InputStream inf = inflate(Source.INPUT, sz);
+			BlobObjectChecker checker = null;
+			if (objCheck != null) {
+				checker = objCheck.newBlobObjectChecker();
+			}
+			if (checker == null) {
+				checker = BlobObjectChecker.NULL_CHECKER;
+			}
 			long cnt = 0;
 			while (cnt < sz) {
 				int r = inf.read(readBuffer);
 				if (r <= 0)
 					break;
 				objectDigest.update(readBuffer, 0, r);
+				checker.update(readBuffer, 0, r);
 				cnt += r;
 			}
 			inf.close();
 			objectDigest.digest(tempObjectId);
-			checkContentLater = isCheckObjectCollisions()
-					&& readCurs.has(tempObjectId);
+			checker.endBlob(tempObjectId);
 			data = null;
-
 		} else {
 			data = inflateAndReturn(Source.INPUT, sz);
 			objectDigest.update(data);
@@ -1058,16 +1073,32 @@ private void whole(final long pos, final int type, final long sz)
 
 		PackedObjectInfo obj = newInfo(tempObjectId, null, null);
 		obj.setOffset(pos);
+		obj.setType(type);
 		onEndWholeObject(obj);
 		if (data != null)
 			onInflatedObjectData(obj, type, data);
 		addObjectAndTrack(obj);
-		if (checkContentLater)
-			deferredCheckBlobs.add(obj);
+
+		if (isCheckObjectCollisions()) {
+			collisionCheckObjs.add(obj);
+		}
 	}
 
-	private void verifySafeObject(final AnyObjectId id, final int type,
-			final byte[] data) throws IOException {
+	/**
+	 * Verify the integrity of the object.
+	 *
+	 * @param id
+	 *            identity of the object to be checked.
+	 * @param type
+	 *            the type of the object.
+	 * @param data
+	 *            raw content of the object.
+	 * @throws CorruptObjectException
+	 * @since 4.9
+	 *
+	 */
+	protected void verifySafeObject(final AnyObjectId id, final int type,
+			final byte[] data) throws CorruptObjectException {
 		if (objCheck != null) {
 			try {
 				objCheck.check(id, type, data);
@@ -1075,65 +1106,73 @@ private void verifySafeObject(final AnyObjectId id, final int type,
 				if (e.getErrorType() != null) {
 					throw e;
 				}
-				throw new CorruptObjectException(MessageFormat.format(
-						JGitText.get().invalidObject,
-						Constants.typeString(type),
-						readCurs.abbreviate(id, 10).name(),
-						e.getMessage()), e);
-			}
-		}
-
-		if (isCheckObjectCollisions()) {
-			try {
-				final ObjectLoader ldr = readCurs.open(id, type);
-				final byte[] existingData = ldr.getCachedBytes(data.length);
-				if (!Arrays.equals(data, existingData)) {
-					throw new IOException(MessageFormat.format(
-							JGitText.get().collisionOn, id.name()));
-				}
-			} catch (MissingObjectException notLocal) {
-				// This is OK, we don't have a copy of the object locally
-				// but the API throws when we try to read it as usually its
-				// an error to read something that doesn't exist.
+				throw new CorruptObjectException(
+						MessageFormat.format(JGitText.get().invalidObject,
+								Constants.typeString(type), id.name(),
+								e.getMessage()),
+						e);
 			}
 		}
 	}
 
-	private void doDeferredCheckBlobs() throws IOException {
+	private void checkObjectCollision() throws IOException {
+		for (PackedObjectInfo obj : collisionCheckObjs) {
+			if (!readCurs.has(obj)) {
+				continue;
+			}
+			checkObjectCollision(obj);
+		}
+	}
+
+	private void checkObjectCollision(PackedObjectInfo obj)
+			throws IOException {
+		ObjectTypeAndSize info = openDatabase(obj, new ObjectTypeAndSize());
 		final byte[] readBuffer = buffer();
 		final byte[] curBuffer = new byte[readBuffer.length];
-		ObjectTypeAndSize info = new ObjectTypeAndSize();
-
-		for (PackedObjectInfo obj : deferredCheckBlobs) {
-			info = openDatabase(obj, info);
-
-			if (info.type != Constants.OBJ_BLOB)
+		long sz = info.size;
+		InputStream pck = null;
+		try (ObjectStream cur = readCurs.open(obj, info.type).openStream()) {
+			if (cur.getSize() != sz) {
 				throw new IOException(MessageFormat.format(
-						JGitText.get().unknownObjectType,
-						Integer.valueOf(info.type)));
-
-			ObjectStream cur = readCurs.open(obj, info.type).openStream();
-			try {
-				long sz = info.size;
-				if (cur.getSize() != sz)
-					throw new IOException(MessageFormat.format(
-							JGitText.get().collisionOn, obj.name()));
-				InputStream pck = inflate(Source.DATABASE, sz);
-				while (0 < sz) {
-					int n = (int) Math.min(readBuffer.length, sz);
-					IO.readFully(cur, curBuffer, 0, n);
-					IO.readFully(pck, readBuffer, 0, n);
-					for (int i = 0; i < n; i++) {
-						if (curBuffer[i] != readBuffer[i])
-							throw new IOException(MessageFormat.format(JGitText
-									.get().collisionOn, obj.name()));
-					}
-					sz -= n;
-				}
-				pck.close();
-			} finally {
-				cur.close();
+						JGitText.get().collisionOn, obj.name()));
 			}
+			pck = inflate(Source.DATABASE, sz);
+			while (0 < sz) {
+				int n = (int) Math.min(readBuffer.length, sz);
+				IO.readFully(cur, curBuffer, 0, n);
+				IO.readFully(pck, readBuffer, 0, n);
+				for (int i = 0; i < n; i++) {
+					if (curBuffer[i] != readBuffer[i]) {
+						throw new IOException(MessageFormat.format(JGitText
+								.get().collisionOn, obj.name()));
+					}
+				}
+				sz -= n;
+			}
+		} catch (MissingObjectException notLocal) {
+			// This is OK, we don't have a copy of the object locally
+			// but the API throws when we try to read it as usually its
+			// an error to read something that doesn't exist.
+		} finally {
+			if (pck != null) {
+				pck.close();
+			}
+		}
+	}
+
+	private void checkObjectCollision(AnyObjectId obj, int type, byte[] data)
+			throws IOException {
+		try {
+			final ObjectLoader ldr = readCurs.open(obj, type);
+			final byte[] existingData = ldr.getCachedBytes(data.length);
+			if (!Arrays.equals(data, existingData)) {
+				throw new IOException(MessageFormat.format(
+						JGitText.get().collisionOn, obj.name()));
+			}
+		} catch (MissingObjectException notLocal) {
+			// This is OK, we don't have a copy of the object locally
+			// but the API throws when we try to read it as usually its
+			// an error to read something that doesn't exist.
 		}
 	}
 
@@ -1250,6 +1289,23 @@ protected PackedObjectInfo newInfo(AnyObjectId id, UnresolvedDelta delta,
 	}
 
 	/**
+	 * Set the expected number of objects in the pack stream.
+	 * <p>
+	 * The object count in the pack header is not always correct for some Dfs
+	 * pack files. e.g. INSERT pack always assume 1 object in the header since
+	 * the actual object count is unknown when the pack is written.
+	 * <p>
+	 * If external implementation wants to overwrite the expectedObjectCount,
+	 * they should call this method during {@link #onPackHeader(long)}.
+	 *
+	 * @param expectedObjectCount
+	 * @since 4.9
+	 */
+	protected void setExpectedObjectCount(long expectedObjectCount) {
+		this.expectedObjectCount = expectedObjectCount;
+	}
+
+	/**
 	 * Store bytes received from the raw stream.
 	 * <p>
 	 * This method is invoked during {@link #parse(ProgressMonitor)} as data is
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackedObjectInfo.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackedObjectInfo.java
index 6da1c57..381c228 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackedObjectInfo.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackedObjectInfo.java
@@ -45,6 +45,7 @@
 package org.eclipse.jgit.transport;
 
 import org.eclipse.jgit.lib.AnyObjectId;
+import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectIdOwnerMap;
 
 /**
@@ -59,6 +60,8 @@ public class PackedObjectInfo extends ObjectIdOwnerMap.Entry {
 
 	private int crc;
 
+	private int type = Constants.OBJ_BAD;
+
 	PackedObjectInfo(final long headerOffset, final int packedCRC,
 			final AnyObjectId id) {
 		super(id);
@@ -112,4 +115,24 @@ public int getCRC() {
 	public void setCRC(final int crc) {
 		this.crc = crc;
 	}
+
+	/**
+	 * @return the object type. The default type is OBJ_BAD, which is considered
+	 *         as unknown or invalid type.
+	 * @since 4.9
+	 */
+	public int getType() {
+		return type;
+	}
+
+	/**
+	 * Record the object type if applicable.
+	 *
+	 * @param type
+	 *            the object type.
+	 * @since 4.9
+	 */
+	public void setType(int type) {
+		this.type = type;
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushConfig.java
new file mode 100644
index 0000000..bff9c71
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushConfig.java
@@ -0,0 +1,95 @@
+/*
+ * Copyright (C) 2017, David Pursehouse <david.pursehouse@gmail.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.transport;
+
+import org.eclipse.jgit.lib.Config;
+import org.eclipse.jgit.util.StringUtils;
+
+/**
+ * Push section of a Git configuration file.
+ *
+ * @since 4.9
+ */
+public class PushConfig {
+	/**
+	 * Config values for push.recurseSubmodules.
+	 */
+	public enum PushRecurseSubmodulesMode implements Config.ConfigEnum {
+		/**
+		 * Verify that all submodule commits that changed in the revisions to be
+		 * pushed are available on at least one remote of the submodule.
+		 */
+		CHECK("check"), //$NON-NLS-1$
+
+		/**
+		 * All submodules that changed in the revisions to be pushed will be
+		 * pushed.
+		 */
+		ON_DEMAND("on-demand"), //$NON-NLS-1$
+
+		/** Default behavior of ignoring submodules when pushing is retained. */
+		NO("false"); //$NON-NLS-1$
+
+		private final String configValue;
+
+		private PushRecurseSubmodulesMode(String configValue) {
+			this.configValue = configValue;
+		}
+
+		@Override
+		public String toConfigValue() {
+			return configValue;
+		}
+
+		@Override
+		public boolean matchConfigValue(String s) {
+			if (StringUtils.isEmptyOrNull(s)) {
+				return false;
+			}
+			s = s.replace('-', '_');
+			return name().equalsIgnoreCase(s)
+					|| configValue.equalsIgnoreCase(s);
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceiveCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceiveCommand.java
index 2b21c4a..e9681b3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceiveCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceiveCommand.java
@@ -52,6 +52,7 @@
 import java.util.Collection;
 import java.util.List;
 
+import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.ObjectId;
@@ -190,6 +191,20 @@ public static void abort(Iterable<ReceiveCommand> commands) {
 		}
 	}
 
+	/**
+	 * Check whether a command failed due to transaction aborted.
+	 *
+	 * @param cmd
+	 *            command.
+	 * @return whether the command failed due to transaction aborted, as in {@link
+	 *         #abort(Iterable)}.
+	 * @since 4.9
+	 */
+	public static boolean isTransactionAborted(ReceiveCommand cmd) {
+		return cmd.getResult() == REJECTED_OTHER_REASON
+				&& cmd.getMessage().equals(JGitText.get().transactionAborted);
+	}
+
 	private final ObjectId oldId;
 
 	private final ObjectId newId;
@@ -204,13 +219,21 @@ public static void abort(Iterable<ReceiveCommand> commands) {
 
 	private String message;
 
+	private boolean customRefLog;
+
+	private String refLogMessage;
+
+	private boolean refLogIncludeResult;
+
+	private Boolean forceRefLog;
+
 	private boolean typeIsCorrect;
 
 	/**
 	 * Create a new command for {@link BaseReceivePack}.
 	 *
 	 * @param oldId
-	 *            the old object id; must not be null. Use
+	 *            the expected old object id; must not be null. Use
 	 *            {@link ObjectId#zeroId()} to indicate a ref creation.
 	 * @param newId
 	 *            the new object id; must not be null. Use
@@ -220,15 +243,23 @@ public static void abort(Iterable<ReceiveCommand> commands) {
 	 */
 	public ReceiveCommand(final ObjectId oldId, final ObjectId newId,
 			final String name) {
+		if (oldId == null) {
+			throw new IllegalArgumentException(JGitText.get().oldIdMustNotBeNull);
+		}
+		if (newId == null) {
+			throw new IllegalArgumentException(JGitText.get().newIdMustNotBeNull);
+		}
 		this.oldId = oldId;
 		this.newId = newId;
 		this.name = name;
 
 		type = Type.UPDATE;
-		if (ObjectId.zeroId().equals(oldId))
+		if (ObjectId.zeroId().equals(oldId)) {
 			type = Type.CREATE;
-		if (ObjectId.zeroId().equals(newId))
+		}
+		if (ObjectId.zeroId().equals(newId)) {
 			type = Type.DELETE;
+		}
 	}
 
 	/**
@@ -243,14 +274,45 @@ public ReceiveCommand(final ObjectId oldId, final ObjectId newId,
 	 * @param name
 	 *            name of the ref being affected.
 	 * @param type
-	 *            type of the command.
+	 *            type of the command. Must be {@link Type#CREATE} if {@code
+	 *            oldId} is zero, or {@link Type#DELETE} if {@code newId} is zero.
 	 * @since 2.0
 	 */
 	public ReceiveCommand(final ObjectId oldId, final ObjectId newId,
 			final String name, final Type type) {
+		if (oldId == null) {
+			throw new IllegalArgumentException(JGitText.get().oldIdMustNotBeNull);
+		}
+		if (newId == null) {
+			throw new IllegalArgumentException(JGitText.get().newIdMustNotBeNull);
+		}
 		this.oldId = oldId;
 		this.newId = newId;
 		this.name = name;
+		switch (type) {
+		case CREATE:
+			if (!ObjectId.zeroId().equals(oldId)) {
+				throw new IllegalArgumentException(
+						JGitText.get().createRequiresZeroOldId);
+			}
+			break;
+		case DELETE:
+			if (!ObjectId.zeroId().equals(newId)) {
+				throw new IllegalArgumentException(
+						JGitText.get().deleteRequiresZeroNewId);
+			}
+			break;
+		case UPDATE:
+		case UPDATE_NONFASTFORWARD:
+			if (ObjectId.zeroId().equals(newId)
+					|| ObjectId.zeroId().equals(oldId)) {
+				throw new IllegalArgumentException(
+						JGitText.get().updateRequiresOldIdAndNewId);
+			}
+			break;
+		default:
+			throw new IllegalStateException(JGitText.get().enumValueNotSupported0);
+		}
 		this.type = type;
 	}
 
@@ -290,6 +352,116 @@ public String getMessage() {
 	}
 
 	/**
+	 * Set the message to include in the reflog.
+	 * <p>
+	 * Overrides the default set by {@code setRefLogMessage} on any containing
+	 * {@link org.eclipse.jgit.lib.BatchRefUpdate}.
+	 *
+	 * @param msg
+	 *            the message to describe this change. If null and appendStatus is
+	 *            false, the reflog will not be updated.
+	 * @param appendStatus
+	 *            true if the status of the ref change (fast-forward or
+	 *            forced-update) should be appended to the user supplied message.
+	 * @since 4.9
+	 */
+	public void setRefLogMessage(String msg, boolean appendStatus) {
+		customRefLog = true;
+		if (msg == null && !appendStatus) {
+			disableRefLog();
+		} else if (msg == null && appendStatus) {
+			refLogMessage = ""; //$NON-NLS-1$
+			refLogIncludeResult = true;
+		} else {
+			refLogMessage = msg;
+			refLogIncludeResult = appendStatus;
+		}
+	}
+
+	/**
+	 * Don't record this update in the ref's associated reflog.
+	 * <p>
+	 * Equivalent to {@code setRefLogMessage(null, false)}.
+	 *
+	 * @since 4.9
+	 */
+	public void disableRefLog() {
+		customRefLog = true;
+		refLogMessage = null;
+		refLogIncludeResult = false;
+	}
+
+	/**
+	 * Force writing a reflog for the updated ref.
+	 *
+	 * @param force whether to force.
+	 * @since 4.9
+	 */
+	public void setForceRefLog(boolean force) {
+		forceRefLog = Boolean.valueOf(force);
+	}
+
+	/**
+	 * Check whether this command has a custom reflog message setting that should
+	 * override defaults in any containing
+	 * {@link org.eclipse.jgit.lib.BatchRefUpdate}.
+	 * <p>
+	 * Does not take into account whether {@code #setForceRefLog(boolean)} has
+	 * been called.
+	 *
+	 * @return whether a custom reflog is set.
+	 * @since 4.9
+	 */
+	public boolean hasCustomRefLog() {
+		return customRefLog;
+	}
+
+	/**
+	 * Check whether log has been disabled by {@link #disableRefLog()}.
+	 *
+	 * @return true if disabled.
+	 * @since 4.9
+	 */
+	public boolean isRefLogDisabled() {
+		return refLogMessage == null;
+	}
+
+	/**
+	 * Get the message to include in the reflog.
+	 *
+	 * @return message the caller wants to include in the reflog; null if the
+	 *         update should not be logged.
+	 * @since 4.9
+	 */
+	@Nullable
+	public String getRefLogMessage() {
+		return refLogMessage;
+	}
+
+	/**
+	 * Check whether the reflog message should include the result of the update,
+	 * such as fast-forward or force-update.
+	 *
+	 * @return true if the message should include the result.
+	 * @since 4.9
+	 */
+	public boolean isRefLogIncludingResult() {
+		return refLogIncludeResult;
+	}
+
+	/**
+	 * Check whether the reflog should be written regardless of repo defaults.
+	 *
+	 * @return whether force writing is enabled; null if {@code
+	 * #setForceRefLog(boolean)} was never called.
+	 * @since 4.9
+	 */
+	@Nullable
+	public Boolean isForceRefLog() {
+		return forceRefLog;
+	}
+
+	/**
 	 * Set the status of this command.
 	 *
 	 * @param s
@@ -355,6 +527,7 @@ public void execute(final BaseReceivePack rp) {
 		try {
 			final RefUpdate ru = rp.getRepository().updateRef(getRefName());
 			ru.setRefLogIdent(rp.getRefLogIdent());
+			ru.setRefLogMessage(refLogMessage, refLogIncludeResult);
 			switch (getType()) {
 			case DELETE:
 				if (!ObjectId.zeroId().equals(getOldId())) {
@@ -428,6 +601,14 @@ public void setResult(RefUpdate.Result r) {
 			setResult(Result.REJECTED_CURRENT_BRANCH);
 			break;
 
+		case REJECTED_MISSING_OBJECT:
+			setResult(Result.REJECTED_MISSING_OBJECT);
+			break;
+
+		case REJECTED_OTHER_REASON:
+			setResult(Result.REJECTED_OTHER_REASON);
+			break;
+
 		default:
 			setResult(Result.REJECTED_OTHER_REASON, r.name());
 			break;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteConfig.java
index d91684e..c968ba3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteConfig.java
@@ -170,38 +170,49 @@ public RemoteConfig(final Config rc, final String remoteName)
 		vlst = rc.getStringList(SECTION, name, KEY_URL);
 		Map<String, String> insteadOf = getReplacements(rc, KEY_INSTEADOF);
 		uris = new ArrayList<>(vlst.length);
-		for (final String s : vlst)
+		for (final String s : vlst) {
 			uris.add(new URIish(replaceUri(s, insteadOf)));
-
-		Map<String, String> pushInsteadOf = getReplacements(rc,
-				KEY_PUSHINSTEADOF);
-		vlst = rc.getStringList(SECTION, name, KEY_PUSHURL);
-		pushURIs = new ArrayList<>(vlst.length);
-		for (final String s : vlst)
-			pushURIs.add(new URIish(replaceUri(s, pushInsteadOf)));
-
-		vlst = rc.getStringList(SECTION, name, KEY_FETCH);
-		fetch = new ArrayList<>(vlst.length);
-		for (final String s : vlst)
-			fetch.add(new RefSpec(s));
-
-		vlst = rc.getStringList(SECTION, name, KEY_PUSH);
-		push = new ArrayList<>(vlst.length);
-		for (final String s : vlst)
-			push.add(new RefSpec(s));
-
+		}
+		String[] plst = rc.getStringList(SECTION, name, KEY_PUSHURL);
+		pushURIs = new ArrayList<>(plst.length);
+		for (final String s : plst) {
+			pushURIs.add(new URIish(s));
+		}
+		if (pushURIs.isEmpty()) {
+			// Would default to the uris. If we have pushinsteadof, we must
+			// supply rewritten push uris.
+			Map<String, String> pushInsteadOf = getReplacements(rc,
+					KEY_PUSHINSTEADOF);
+			if (!pushInsteadOf.isEmpty()) {
+				for (String s : vlst) {
+					String replaced = replaceUri(s, pushInsteadOf);
+					if (!s.equals(replaced)) {
+						pushURIs.add(new URIish(replaced));
+					}
+				}
+			}
+		}
+		fetch = rc.getRefSpecs(SECTION, name, KEY_FETCH);
+		push = rc.getRefSpecs(SECTION, name, KEY_PUSH);
 		val = rc.getString(SECTION, name, KEY_UPLOADPACK);
-		if (val == null)
+		if (val == null) {
 			val = DEFAULT_UPLOAD_PACK;
+		}
 		uploadpack = val;
 
 		val = rc.getString(SECTION, name, KEY_RECEIVEPACK);
-		if (val == null)
+		if (val == null) {
 			val = DEFAULT_RECEIVE_PACK;
+		}
 		receivepack = val;
 
-		val = rc.getString(SECTION, name, KEY_TAGOPT);
-		tagopt = TagOpt.fromOption(val);
+		try {
+			val = rc.getString(SECTION, name, KEY_TAGOPT);
+			tagopt = TagOpt.fromOption(val);
+		} catch (IllegalArgumentException e) {
+			// C git silently ignores invalid tagopt values.
+			tagopt = TagOpt.AUTO_FOLLOW;
+		}
 		mirror = rc.getBoolean(SECTION, name, KEY_MIRROR, DEFAULT_MIRROR);
 		timeout = rc.getInt(SECTION, name, KEY_TIMEOUT, 0);
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteSession.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteSession.java
index 5a73cf5..d6a2fe6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteSession.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteSession.java
@@ -83,4 +83,4 @@ public interface RemoteSession {
 	 * Disconnect the remote session
 	 */
 	public void disconnect();
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SignedPushConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SignedPushConfig.java
index 83b4aca..1ecbed9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SignedPushConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SignedPushConfig.java
@@ -54,12 +54,7 @@
 public class SignedPushConfig {
 	/** Key for {@link Config#get(SectionParser)}. */
 	public static final SectionParser<SignedPushConfig> KEY =
-			new SectionParser<SignedPushConfig>() {
-		@Override
-		public SignedPushConfig parse(Config cfg) {
-			return new SignedPushConfig(cfg);
-		}
-	};
+			SignedPushConfig::new;
 
 	private String certNonceSeed;
 	private int certNonceSlopLimit;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshSessionFactory.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshSessionFactory.java
index a1aeceb..2d5029a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshSessionFactory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshSessionFactory.java
@@ -66,7 +66,7 @@ public abstract class SshSessionFactory {
 	 * <p>
 	 * A factory is always available. By default the factory will read from the
 	 * user's <code>$HOME/.ssh</code> and assume OpenSSH compatibility.
-	 * 
+	 *
 	 * @return factory the current factory for this JVM.
 	 */
 	public static SshSessionFactory getInstance() {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshTransport.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshTransport.java
index 6f17ebf..74865dc 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshTransport.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshTransport.java
@@ -120,7 +120,7 @@ public SshSessionFactory getSshSessionFactory() {
 
 	/**
 	 * Get the default SSH session
-	 * 
+	 *
 	 * @return a remote session
 	 * @throws TransportException
 	 *             in case of error with opening SSH session
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransferConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransferConfig.java
index 2198b50..099629c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransferConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransferConfig.java
@@ -69,15 +69,27 @@ public class TransferConfig {
 	private static final String FSCK = "fsck"; //$NON-NLS-1$
 
 	/** Key for {@link Config#get(SectionParser)}. */
-	public static final Config.SectionParser<TransferConfig> KEY = new SectionParser<TransferConfig>() {
-		@Override
-		public TransferConfig parse(final Config cfg) {
-			return new TransferConfig(cfg);
-		}
-	};
+	public static final Config.SectionParser<TransferConfig> KEY =
+			TransferConfig::new;
 
-	enum FsckMode {
-		ERROR, WARN, IGNORE;
+	/**
+	 * A git configuration value for how to handle a fsck failure of a particular kind.
+	 * Used in e.g. fsck.missingEmail.
+	 * @since 4.9
+	 */
+	public enum FsckMode {
+		/**
+		 * Treat it as an error (the default).
+		 */
+		ERROR,
+		/**
+		 * Issue a warning (in fact, jgit treats this like IGNORE, but git itself does warn).
+		 */
+		WARN,
+		/**
+		 * Ignore the error.
+		 */
+		IGNORE;
 	}
 
 	private final boolean fetchFsck;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportGitSsh.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportGitSsh.java
index 9a40f47..b1b910e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportGitSsh.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportGitSsh.java
@@ -242,14 +242,7 @@ public Process exec(String command, int timeout)
 				args.add(getURI().getHost());
 			args.add(command);
 
-			ProcessBuilder pb = new ProcessBuilder();
-			pb.command(args);
-
-			File directory = local.getDirectory();
-			if (directory != null)
-				pb.environment().put(Constants.GIT_DIR_KEY,
-						directory.getPath());
-
+			ProcessBuilder pb = createProcess(args);
 			try {
 				return pb.start();
 			} catch (IOException err) {
@@ -257,6 +250,17 @@ public Process exec(String command, int timeout)
 			}
 		}
 
+		private ProcessBuilder createProcess(List<String> args) {
+			ProcessBuilder pb = new ProcessBuilder();
+			pb.command(args);
+			File directory = local != null ? local.getDirectory() : null;
+			if (directory != null) {
+				pb.environment().put(Constants.GIT_DIR_KEY,
+						directory.getPath());
+			}
+			return pb;
+		}
+
 		@Override
 		public void disconnect() {
 			// Nothing to do
@@ -285,7 +289,7 @@ class SshFetchConnection extends BasePackFetchConnection {
 			} catch (TransportException err) {
 				close();
 				throw err;
-			} catch (IOException err) {
+			} catch (Throwable err) {
 				close();
 				throw new TransportException(uri,
 						JGitText.get().remoteHungUpUnexpectedly, err);
@@ -341,10 +345,18 @@ class SshPushConnection extends BasePackPushConnection {
 				init(process.getInputStream(), process.getOutputStream());
 
 			} catch (TransportException err) {
-				close();
+				try {
+					close();
+				} catch (Exception e) {
+					// ignore
+				}
 				throw err;
-			} catch (IOException err) {
-				close();
+			} catch (Throwable err) {
+				try {
+					close();
+				} catch (Exception e) {
+					// ignore
+				}
 				throw new TransportException(uri,
 						JGitText.get().remoteHungUpUnexpectedly, err);
 			}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportHttp.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportHttp.java
index 26a254d..7c3f738 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportHttp.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportHttp.java
@@ -2,6 +2,7 @@
  * Copyright (C) 2008-2010, Google Inc.
  * Copyright (C) 2008, Shawn O. Pearce <spearce@spearce.org>
  * Copyright (C) 2013, Matthias Sohn <matthias.sohn@sap.com>
+ * Copyright (C) 2017, Thomas Wolf <thomas.wolf@paranor.ch>
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -69,7 +70,11 @@
 import java.net.MalformedURLException;
 import java.net.Proxy;
 import java.net.ProxySelector;
+import java.net.URISyntaxException;
 import java.net.URL;
+import java.security.cert.CertPathBuilderException;
+import java.security.cert.CertPathValidatorException;
+import java.security.cert.CertificateException;
 import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -78,35 +83,44 @@
 import java.util.EnumSet;
 import java.util.HashSet;
 import java.util.LinkedHashSet;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Set;
 import java.util.TreeMap;
 import java.util.zip.GZIPInputStream;
 import java.util.zip.GZIPOutputStream;
 
+import javax.net.ssl.SSLHandshakeException;
+
+import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.errors.NoRemoteRepositoryException;
 import org.eclipse.jgit.errors.NotSupportedException;
 import org.eclipse.jgit.errors.PackProtocolException;
 import org.eclipse.jgit.errors.TransportException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.internal.storage.file.RefDirectory;
-import org.eclipse.jgit.lib.Config;
-import org.eclipse.jgit.lib.Config.SectionParser;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectIdRef;
 import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.lib.SymbolicRef;
+import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.transport.HttpAuthMethod.Type;
+import org.eclipse.jgit.transport.HttpConfig.HttpRedirectMode;
 import org.eclipse.jgit.transport.http.HttpConnection;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.HttpSupport;
 import org.eclipse.jgit.util.IO;
 import org.eclipse.jgit.util.RawParseUtils;
+import org.eclipse.jgit.util.SystemReader;
 import org.eclipse.jgit.util.TemporaryBuffer;
 import org.eclipse.jgit.util.io.DisabledOutputStream;
 import org.eclipse.jgit.util.io.UnionInputStream;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Transport over HTTP and FTP protocols.
@@ -127,6 +141,9 @@
 public class TransportHttp extends HttpTransport implements WalkTransport,
 		PackTransport {
 
+	private static final Logger LOG = LoggerFactory
+			.getLogger(TransportHttp.class);
+
 	private static final String SVC_UPLOAD_PACK = "git-upload-pack"; //$NON-NLS-1$
 
 	private static final String SVC_RECEIVE_PACK = "git-receive-pack"; //$NON-NLS-1$
@@ -231,33 +248,18 @@ public Transport open(URIish uri, Repository local, String remoteName)
 		}
 	};
 
-	private static final Config.SectionParser<HttpConfig> HTTP_KEY = new SectionParser<HttpConfig>() {
-		@Override
-		public HttpConfig parse(final Config cfg) {
-			return new HttpConfig(cfg);
-		}
-	};
+	/**
+	 * The current URI we're talking to. The inherited (final) field
+	 * {@link #uri} stores the original URI; {@code currentUri} may be different
+	 * after redirects.
+	 */
+	private URIish currentUri;
 
-	private static class HttpConfig {
-		final int postBuffer;
+	private URL baseUrl;
 
-		final boolean sslVerify;
+	private URL objectsUrl;
 
-		HttpConfig(final Config rc) {
-			postBuffer = rc.getInt("http", "postbuffer", 1 * 1024 * 1024); //$NON-NLS-1$  //$NON-NLS-2$
-			sslVerify = rc.getBoolean("http", "sslVerify", true); //$NON-NLS-1$ //$NON-NLS-2$
-		}
-
-		HttpConfig() {
-			this(new Config());
-		}
-	}
-
-	final URL baseUrl;
-
-	private final URL objectsUrl;
-
-	final HttpConfig http;
+	private final HttpConfig http;
 
 	private final ProxySelector proxySelector;
 
@@ -267,20 +269,40 @@ private static class HttpConfig {
 
 	private Map<String, String> headers;
 
+	private boolean sslVerify;
+
+	private boolean sslFailure = false;
+
 	TransportHttp(final Repository local, final URIish uri)
 			throws NotSupportedException {
 		super(local, uri);
+		setURI(uri);
+		http = new HttpConfig(local.getConfig(), uri);
+		proxySelector = ProxySelector.getDefault();
+		sslVerify = http.isSslVerify();
+	}
+
+	private URL toURL(URIish urish) throws MalformedURLException {
+		String uriString = urish.toString();
+		if (!uriString.endsWith("/")) { //$NON-NLS-1$
+			uriString += '/';
+		}
+		return new URL(uriString);
+	}
+
+	/**
+	 * @param uri
+	 * @throws NotSupportedException
+	 * @since 4.9
+	 */
+	protected void setURI(final URIish uri) throws NotSupportedException {
 		try {
-			String uriString = uri.toString();
-			if (!uriString.endsWith("/")) //$NON-NLS-1$
-				uriString += "/"; //$NON-NLS-1$
-			baseUrl = new URL(uriString);
+			currentUri = uri;
+			baseUrl = toURL(uri);
 			objectsUrl = new URL(baseUrl, "objects/"); //$NON-NLS-1$
 		} catch (MalformedURLException e) {
 			throw new NotSupportedException(MessageFormat.format(JGitText.get().invalidURL, uri), e);
 		}
-		http = local.getConfig().get(HTTP_KEY);
-		proxySelector = ProxySelector.getDefault();
 	}
 
 	/**
@@ -291,17 +313,10 @@ private static class HttpConfig {
 	 */
 	TransportHttp(final URIish uri) throws NotSupportedException {
 		super(uri);
-		try {
-			String uriString = uri.toString();
-			if (!uriString.endsWith("/")) //$NON-NLS-1$
-				uriString += "/"; //$NON-NLS-1$
-			baseUrl = new URL(uriString);
-			objectsUrl = new URL(baseUrl, "objects/"); //$NON-NLS-1$
-		} catch (MalformedURLException e) {
-			throw new NotSupportedException(MessageFormat.format(JGitText.get().invalidURL, uri), e);
-		}
-		http = new HttpConfig();
+		setURI(uri);
+		http = new HttpConfig(uri);
 		proxySelector = ProxySelector.getDefault();
+		sslVerify = http.isSslVerify();
 	}
 
 	/**
@@ -469,28 +484,9 @@ public void setAdditionalHeaders(Map<String, String> headers) {
 
 	private HttpConnection connect(final String service)
 			throws TransportException, NotSupportedException {
-		final URL u;
-		try {
-			final StringBuilder b = new StringBuilder();
-			b.append(baseUrl);
-
-			if (b.charAt(b.length() - 1) != '/')
-				b.append('/');
-			b.append(Constants.INFO_REFS);
-
-			if (useSmartHttp) {
-				b.append(b.indexOf("?") < 0 ? '?' : '&'); //$NON-NLS-1$
-				b.append("service="); //$NON-NLS-1$
-				b.append(service);
-			}
-
-			u = new URL(b.toString());
-		} catch (MalformedURLException e) {
-			throw new NotSupportedException(MessageFormat.format(JGitText.get().invalidURL, uri), e);
-		}
-
-
+		URL u = getServiceURL(service);
 		int authAttempts = 1;
+		int redirects = 0;
 		Collection<Type> ignoreTypes = null;
 		for (;;) {
 			try {
@@ -527,9 +523,10 @@ private HttpConnection connect(final String service)
 						throw new TransportException(uri,
 								JGitText.get().noCredentialsProvider);
 					if (authAttempts > 1)
-						credentialsProvider.reset(uri);
+						credentialsProvider.reset(currentUri);
 					if (3 < authAttempts
-							|| !authMethod.authorize(uri, credentialsProvider)) {
+							|| !authMethod.authorize(currentUri,
+									credentialsProvider)) {
 						throw new TransportException(uri,
 								JGitText.get().notAuthorized);
 					}
@@ -538,8 +535,28 @@ private HttpConnection connect(final String service)
 
 				case HttpConnection.HTTP_FORBIDDEN:
 					throw new TransportException(uri, MessageFormat.format(
-							JGitText.get().serviceNotPermitted, service));
+							JGitText.get().serviceNotPermitted, baseUrl,
+							service));
 
+				case HttpConnection.HTTP_MOVED_PERM:
+				case HttpConnection.HTTP_MOVED_TEMP:
+				case HttpConnection.HTTP_SEE_OTHER:
+				case HttpConnection.HTTP_11_MOVED_TEMP:
+					// SEE_OTHER should actually never be sent by a git server,
+					// and in general should occur only on POST requests. But it
+					// doesn't hurt to accept it here as a redirect.
+					if (http.getFollowRedirects() == HttpRedirectMode.FALSE) {
+						throw new TransportException(uri,
+								MessageFormat.format(
+										JGitText.get().redirectsOff,
+										Integer.valueOf(status)));
+					}
+					URIish newUri = redirect(conn.getHeaderField(HDR_LOCATION),
+							Constants.INFO_REFS, redirects++);
+					setURI(newUri);
+					u = getServiceURL(service);
+					authAttempts = 1;
+					break;
 				default:
 					String err = status + " " + conn.getResponseMessage(); //$NON-NLS-1$
 					throw new TransportException(uri, err);
@@ -548,6 +565,9 @@ private HttpConnection connect(final String service)
 				throw e;
 			} catch (TransportException e) {
 				throw e;
+			} catch (SSLHandshakeException e) {
+				handleSslFailure(e);
+				continue; // Re-try
 			} catch (IOException e) {
 				if (authMethod.getType() != HttpAuthMethod.Type.NONE) {
 					if (ignoreTypes == null) {
@@ -568,6 +588,215 @@ private HttpConnection connect(final String service)
 		}
 	}
 
+	private static class CredentialItems {
+		CredentialItem.InformationalMessage message;
+
+		/** Trust the server for this git operation */
+		CredentialItem.YesNoType now;
+
+		/**
+		 * Trust the server for all git operations from this repository; may be
+		 * {@code null} if the transport was created via
+		 * {@link #TransportHttp(URIish)}.
+		 */
+		CredentialItem.YesNoType forRepo;
+
+		/** Always trust the server from now on. */
+		CredentialItem.YesNoType always;
+
+		public CredentialItem[] items() {
+			if (forRepo == null) {
+				return new CredentialItem[] { message, now, always };
+			} else {
+				return new CredentialItem[] { message, now, forRepo, always };
+			}
+		}
+	}
+
+	private void handleSslFailure(Throwable e) throws TransportException {
+		if (sslFailure || !trustInsecureSslConnection(e.getCause())) {
+			throw new TransportException(uri,
+					MessageFormat.format(
+							JGitText.get().sslFailureExceptionMessage,
+							currentUri.setPass(null)),
+					e);
+		}
+		sslFailure = true;
+	}
+
+	private boolean trustInsecureSslConnection(Throwable cause) {
+		if (cause instanceof CertificateException
+				|| cause instanceof CertPathBuilderException
+				|| cause instanceof CertPathValidatorException) {
+			// Certificate expired or revoked, PKIX path building not
+			// possible, self-signed certificate, host does not match ...
+			CredentialsProvider provider = getCredentialsProvider();
+			if (provider != null) {
+				CredentialItems trust = constructSslTrustItems(cause);
+				CredentialItem[] items = trust.items();
+				if (provider.supports(items)) {
+					boolean answered = provider.get(uri, items);
+					if (answered) {
+						// Not canceled
+						boolean trustNow = trust.now.getValue();
+						boolean trustLocal = trust.forRepo != null
+								&& trust.forRepo.getValue();
+						boolean trustAlways = trust.always.getValue();
+						if (trustNow || trustLocal || trustAlways) {
+							sslVerify = false;
+							if (trustAlways) {
+								updateSslVerifyUser(false);
+							} else if (trustLocal) {
+								updateSslVerify(local.getConfig(), false);
+							}
+							return true;
+						}
+					}
+				}
+			}
+		}
+		return false;
+	}
+
+	private CredentialItems constructSslTrustItems(Throwable cause) {
+		CredentialItems items = new CredentialItems();
+		String info = MessageFormat.format(JGitText.get().sslFailureInfo,
+				currentUri.setPass(null));
+		String sslMessage = cause.getLocalizedMessage();
+		if (sslMessage == null) {
+			sslMessage = cause.toString();
+		}
+		sslMessage = MessageFormat.format(JGitText.get().sslFailureCause,
+				sslMessage);
+		items.message = new CredentialItem.InformationalMessage(info + '\n'
+				+ sslMessage + '\n'
+				+ JGitText.get().sslFailureTrustExplanation);
+		items.now = new CredentialItem.YesNoType(JGitText.get().sslTrustNow);
+		if (local != null) {
+			items.forRepo = new CredentialItem.YesNoType(
+					MessageFormat.format(JGitText.get().sslTrustForRepo,
+					local.getDirectory()));
+		}
+		items.always = new CredentialItem.YesNoType(
+				JGitText.get().sslTrustAlways);
+		return items;
+	}
+
+	private void updateSslVerify(StoredConfig config, boolean value) {
+		// Since git uses the original URI for matching, we must also use the
+		// original URI and cannot use the current URI (which might be different
+		// after redirects).
+		String uriPattern = uri.getScheme() + "://" + uri.getHost(); //$NON-NLS-1$
+		int port = uri.getPort();
+		if (port > 0) {
+			uriPattern += ":" + port; //$NON-NLS-1$
+		}
+		config.setBoolean(HttpConfig.HTTP, uriPattern,
+				HttpConfig.SSL_VERIFY_KEY, value);
+		try {
+			config.save();
+		} catch (IOException e) {
+			LOG.error(JGitText.get().sslVerifyCannotSave, e);
+		}
+	}
+
+	private void updateSslVerifyUser(boolean value) {
+		FileBasedConfig userConfig = SystemReader.getInstance()
+				.openUserConfig(null, FS.DETECTED);
+		try {
+			userConfig.load();
+			updateSslVerify(userConfig, value);
+		} catch (IOException | ConfigInvalidException e) {
+			// Log it, but otherwise ignore here.
+			LOG.error(MessageFormat.format(JGitText.get().userConfigFileInvalid,
+					userConfig.getFile().getAbsolutePath(), e));
+		}
+	}
+
+	private URIish redirect(String location, String checkFor, int redirects)
+			throws TransportException {
+		if (location == null || location.isEmpty()) {
+			throw new TransportException(uri,
+					MessageFormat.format(JGitText.get().redirectLocationMissing,
+							baseUrl));
+		}
+		if (redirects >= http.getMaxRedirects()) {
+			throw new TransportException(uri,
+					MessageFormat.format(JGitText.get().redirectLimitExceeded,
+							Integer.valueOf(http.getMaxRedirects()), baseUrl,
+							location));
+		}
+		try {
+			if (!isValidRedirect(baseUrl, location, checkFor)) {
+				throw new TransportException(uri,
+						MessageFormat.format(JGitText.get().redirectBlocked,
+								baseUrl, location));
+			}
+			location = location.substring(0, location.indexOf(checkFor));
+			URIish result = new URIish(location);
+			if (LOG.isInfoEnabled()) {
+				LOG.info(MessageFormat.format(JGitText.get().redirectHttp,
+						uri.setPass(null),
+						Integer.valueOf(redirects), baseUrl, result));
+			}
+			return result;
+		} catch (URISyntaxException e) {
+			throw new TransportException(uri,
+					MessageFormat.format(JGitText.get().invalidRedirectLocation,
+							baseUrl, location),
+					e);
+		}
+	}
+
+	private boolean isValidRedirect(URL current, String next, String checkFor) {
+		// Protocols must be the same, or current is "http" and next "https". We
+		// do not follow redirects from https back to http.
+		String oldProtocol = current.getProtocol().toLowerCase(Locale.ROOT);
+		int schemeEnd = next.indexOf("://"); //$NON-NLS-1$
+		if (schemeEnd < 0) {
+			return false;
+		}
+		String newProtocol = next.substring(0, schemeEnd)
+				.toLowerCase(Locale.ROOT);
+		if (!oldProtocol.equals(newProtocol)) {
+			if (!"https".equals(newProtocol)) { //$NON-NLS-1$
+				return false;
+			}
+		}
+		// git allows only rewriting the root, i.e., everything before INFO_REFS
+		// or the service name
+		if (next.indexOf(checkFor) < 0) {
+			return false;
+		}
+		// Basically we should test here that whatever follows INFO_REFS is
+		// unchanged. But since we re-construct the query part
+		// anyway, it doesn't matter.
+		return true;
+	}
+
+	private URL getServiceURL(final String service)
+			throws NotSupportedException {
+		try {
+			final StringBuilder b = new StringBuilder();
+			b.append(baseUrl);
+
+			if (b.charAt(b.length() - 1) != '/') {
+				b.append('/');
+			}
+			b.append(Constants.INFO_REFS);
+
+			if (useSmartHttp) {
+				b.append(b.indexOf("?") < 0 ? '?' : '&'); //$NON-NLS-1$
+				b.append("service="); //$NON-NLS-1$
+				b.append(service);
+			}
+
+			return new URL(b.toString());
+		} catch (MalformedURLException e) {
+			throw new NotSupportedException(MessageFormat.format(JGitText.get().invalidURL, uri), e);
+		}
+	}
+
 	/**
 	 * Open an HTTP connection, setting the accept-encoding request header to gzip.
 	 *
@@ -602,10 +831,14 @@ protected HttpConnection httpOpen(String method, URL u,
 		final Proxy proxy = HttpSupport.proxyFor(proxySelector, u);
 		HttpConnection conn = connectionFactory.create(u, proxy);
 
-		if (!http.sslVerify && "https".equals(u.getProtocol())) { //$NON-NLS-1$
+		if (!sslVerify && "https".equals(u.getProtocol())) { //$NON-NLS-1$
 			HttpSupport.disableSslVerify(conn);
 		}
 
+		// We must do our own redirect handling to implement git rules and to
+		// handle http->https redirects
+		conn.setInstanceFollowRedirects(false);
+
 		conn.setRequestMethod(method);
 		conn.setUseCaches(false);
 		if (acceptEncoding == AcceptEncoding.GZIP) {
@@ -914,13 +1147,7 @@ abstract class Service {
 		}
 
 		void openStream() throws IOException {
-			openStream(null);
-		}
-
-		void openStream(final String redirectUrl) throws IOException {
-			conn = httpOpen(
-					METHOD_POST,
-					redirectUrl == null ? new URL(baseUrl, serviceName) : new URL(redirectUrl),
+			conn = httpOpen(METHOD_POST, new URL(baseUrl, serviceName),
 					AcceptEncoding.GZIP);
 			conn.setInstanceFollowRedirects(false);
 			conn.setDoOutput(true);
@@ -929,12 +1156,9 @@ void openStream(final String redirectUrl) throws IOException {
 		}
 
 		void sendRequest() throws IOException {
-			sendRequest(null);
-		}
-
-		void sendRequest(final String redirectUrl) throws IOException {
 			// Try to compress the content, but only if that is smaller.
-			TemporaryBuffer buf = new TemporaryBuffer.Heap(http.postBuffer);
+			TemporaryBuffer buf = new TemporaryBuffer.Heap(
+					http.getPostBuffer());
 			try {
 				GZIPOutputStream gzip = new GZIPOutputStream(buf);
 				out.writeTo(gzip, null);
@@ -947,21 +1171,141 @@ void sendRequest(final String redirectUrl) throws IOException {
 				buf = out;
 			}
 
-			openStream(redirectUrl);
-			if (buf != out)
-				conn.setRequestProperty(HDR_CONTENT_ENCODING, ENCODING_GZIP);
-			conn.setFixedLengthStreamingMode((int) buf.length());
-			final OutputStream httpOut = conn.getOutputStream();
-			try {
-				buf.writeTo(httpOut, null);
-			} finally {
-				httpOut.close();
-			}
+			HttpAuthMethod authenticator = null;
+			Collection<Type> ignoreTypes = EnumSet.noneOf(Type.class);
+			// Counts number of repeated authentication attempts using the same
+			// authentication scheme
+			int authAttempts = 1;
+			int redirects = 0;
+			for (;;) {
+				try {
+					// The very first time we will try with the authentication
+					// method used on the initial GET request. This is a hint
+					// only; it may fail. If so, we'll then re-try with proper
+					// 401 handling, going through the available authentication
+					// schemes.
+					openStream();
+					if (buf != out) {
+						conn.setRequestProperty(HDR_CONTENT_ENCODING,
+								ENCODING_GZIP);
+					}
+					conn.setFixedLengthStreamingMode((int) buf.length());
+					try (OutputStream httpOut = conn.getOutputStream()) {
+						buf.writeTo(httpOut, null);
+					}
 
-			final int status = HttpSupport.response(conn);
-			if (status == HttpConnection.HTTP_MOVED_PERM) {
-				String locationHeader = HttpSupport.responseHeader(conn, HDR_LOCATION);
-				sendRequest(locationHeader);
+					final int status = HttpSupport.response(conn);
+					switch (status) {
+					case HttpConnection.HTTP_OK:
+						// We're done.
+						return;
+
+					case HttpConnection.HTTP_NOT_FOUND:
+						throw new NoRemoteRepositoryException(uri,
+								MessageFormat.format(JGitText.get().uriNotFound,
+										conn.getURL()));
+
+					case HttpConnection.HTTP_FORBIDDEN:
+						throw new TransportException(uri,
+								MessageFormat.format(
+										JGitText.get().serviceNotPermitted,
+										baseUrl, serviceName));
+
+					case HttpConnection.HTTP_MOVED_PERM:
+					case HttpConnection.HTTP_MOVED_TEMP:
+					case HttpConnection.HTTP_11_MOVED_TEMP:
+						// SEE_OTHER after a POST doesn't make sense for a git
+						// server, so we don't handle it here and thus we'll
+						// report an error in openResponse() later on.
+						if (http.getFollowRedirects() != HttpRedirectMode.TRUE) {
+							// Let openResponse() issue an error
+							return;
+						}
+						currentUri = redirect(conn.getHeaderField(HDR_LOCATION),
+								'/' + serviceName, redirects++);
+						try {
+							baseUrl = toURL(currentUri);
+						} catch (MalformedURLException e) {
+							throw new TransportException(uri,
+									MessageFormat.format(
+											JGitText.get().invalidRedirectLocation,
+											baseUrl, currentUri),
+									e);
+						}
+						continue;
+
+					case HttpConnection.HTTP_UNAUTHORIZED:
+						HttpAuthMethod nextMethod = HttpAuthMethod
+								.scanResponse(conn, ignoreTypes);
+						switch (nextMethod.getType()) {
+						case NONE:
+							throw new TransportException(uri,
+									MessageFormat.format(
+											JGitText.get().authenticationNotSupported,
+											conn.getURL()));
+						case NEGOTIATE:
+							// RFC 4559 states "When using the SPNEGO [...] with
+							// [...] POST, the authentication should be complete
+							// [...] before sending the user data." So in theory
+							// the initial GET should have been authenticated
+							// already. (Unless there was a redirect?)
+							//
+							// We try this only once:
+							ignoreTypes.add(HttpAuthMethod.Type.NEGOTIATE);
+							if (authenticator != null) {
+								ignoreTypes.add(authenticator.getType());
+							}
+							authAttempts = 1;
+							// We only do the Kerberos part of SPNEGO, which
+							// requires only one attempt. We do *not* to the
+							// NTLM part of SPNEGO; it's a multi-round
+							// negotiation and among other problems it would
+							// be unclear when to stop if no HTTP_OK is
+							// forthcoming. In theory a malicious server
+							// could keep sending requests for another NTLM
+							// round, keeping a client stuck here.
+							break;
+						default:
+							// DIGEST or BASIC. Let's be sure we ignore
+							// NEGOTIATE; if it was available, we have tried it
+							// before.
+							ignoreTypes.add(HttpAuthMethod.Type.NEGOTIATE);
+							if (authenticator == null || authenticator
+									.getType() != nextMethod.getType()) {
+								if (authenticator != null) {
+									ignoreTypes.add(authenticator.getType());
+								}
+								authAttempts = 1;
+							}
+							break;
+						}
+						authMethod = nextMethod;
+						authenticator = nextMethod;
+						CredentialsProvider credentialsProvider = getCredentialsProvider();
+						if (credentialsProvider == null) {
+							throw new TransportException(uri,
+									JGitText.get().noCredentialsProvider);
+						}
+						if (authAttempts > 1) {
+							credentialsProvider.reset(currentUri);
+						}
+						if (3 < authAttempts || !authMethod
+								.authorize(currentUri, credentialsProvider)) {
+							throw new TransportException(uri,
+									JGitText.get().notAuthorized);
+						}
+						authAttempts++;
+						continue;
+
+					default:
+						// Just return here; openResponse() will report an
+						// appropriate error.
+						return;
+					}
+				} catch (SSLHandshakeException e) {
+					handleSslFailure(e);
+					continue; // Re-try
+				}
 			}
 		}
 
@@ -1011,7 +1355,7 @@ public long skip(long n) throws IOException {
 
 		class HttpOutputStream extends TemporaryBuffer {
 			HttpOutputStream() {
-				super(http.postBuffer);
+				super(http.getPostBuffer());
 			}
 
 			@Override
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java
index 17af0b9..cf070c6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java
@@ -71,7 +71,6 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-
 import org.eclipse.jgit.errors.CorruptObjectException;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.MissingObjectException;
@@ -719,7 +718,7 @@ private Map<String, Ref> getAdvertisedOrDefaultRefs() throws IOException {
 	}
 
 	private void service() throws IOException {
-		boolean sendPack;
+		boolean sendPack = false;
 		// If it's a non-bidi request, we need to read the entire request before
 		// writing a response. Buffer the response until then.
 		try {
@@ -752,6 +751,17 @@ else if (requestValidator instanceof AnyRequestValidator)
 			if (!clientShallowCommits.isEmpty())
 				walk.assumeShallow(clientShallowCommits);
 			sendPack = negotiate();
+			if (sendPack && !biDirectionalPipe) {
+				// Ensure the request was fully consumed. Any remaining input must
+				// be a protocol error. If we aren't at EOF the implementation is broken.
+				int eof = rawIn.read();
+				if (0 <= eof) {
+					sendPack = false;
+					throw new CorruptObjectException(MessageFormat.format(
+							JGitText.get().expectedEOFReceived,
+							"\\x" + Integer.toHexString(eof))); //$NON-NLS-1$
+				}
+			}
 		} catch (ServiceMayNotContinueException err) {
 			if (!err.isOutput() && err.getMessage() != null) {
 				try {
@@ -778,6 +788,11 @@ else if (requestValidator instanceof AnyRequestValidator)
 			}
 			throw err;
 		} finally {
+			if (!sendPack && !biDirectionalPipe) {
+				while (0 < rawIn.skip(2048) || 0 <= rawIn.read()) {
+					// Discard until EOF.
+				}
+			}
 			rawOut.stopBuffering();
 		}
 
@@ -1245,7 +1260,7 @@ public static final class ReachableCommitRequestValidator
 		@Override
 		public void checkWants(UploadPack up, List<ObjectId> wants)
 				throws PackProtocolException, IOException {
-			checkNotAdvertisedWants(up.getRevWalk(), wants,
+			checkNotAdvertisedWants(up, wants,
 					refIdSet(up.getAdvertisedRefs().values()));
 		}
 	}
@@ -1282,7 +1297,7 @@ public static final class ReachableCommitTipRequestValidator
 		@Override
 		public void checkWants(UploadPack up, List<ObjectId> wants)
 				throws PackProtocolException, IOException {
-			checkNotAdvertisedWants(up.getRevWalk(), wants,
+			checkNotAdvertisedWants(up, wants,
 					refIdSet(up.getRepository().getRefDatabase().getRefs(ALL).values()));
 		}
 	}
@@ -1300,7 +1315,7 @@ public void checkWants(UploadPack up, List<ObjectId> wants)
 		}
 	}
 
-	private static void checkNotAdvertisedWants(RevWalk walk,
+	private static void checkNotAdvertisedWants(UploadPack up,
 			List<ObjectId> notAdvertisedWants, Set<ObjectId> reachableFrom)
 			throws MissingObjectException, IncorrectObjectTypeException, IOException {
 		// Walk the requested commits back to the provided set of commits. If any
@@ -1309,32 +1324,34 @@ private static void checkNotAdvertisedWants(RevWalk walk,
 		// into an advertised branch it will be marked UNINTERESTING and no commits
 		// return.
 
-		AsyncRevObjectQueue q = walk.parseAny(notAdvertisedWants, true);
-		try {
-			RevObject obj;
-			while ((obj = q.next()) != null) {
-				if (!(obj instanceof RevCommit))
-					throw new WantNotValidException(obj);
-				walk.markStart((RevCommit) obj);
-			}
-		} catch (MissingObjectException notFound) {
-			throw new WantNotValidException(notFound.getObjectId(), notFound);
-		} finally {
-			q.release();
-		}
-		for (ObjectId id : reachableFrom) {
+		try (RevWalk walk = new RevWalk(up.getRevWalk().getObjectReader())) {
+			AsyncRevObjectQueue q = walk.parseAny(notAdvertisedWants, true);
 			try {
-				walk.markUninteresting(walk.parseCommit(id));
-			} catch (IncorrectObjectTypeException notCommit) {
-				continue;
+				RevObject obj;
+				while ((obj = q.next()) != null) {
+					if (!(obj instanceof RevCommit))
+						throw new WantNotValidException(obj);
+					walk.markStart((RevCommit) obj);
+				}
+			} catch (MissingObjectException notFound) {
+				throw new WantNotValidException(notFound.getObjectId(),
+						notFound);
+			} finally {
+				q.release();
+			}
+			for (ObjectId id : reachableFrom) {
+				try {
+					walk.markUninteresting(walk.parseCommit(id));
+				} catch (IncorrectObjectTypeException notCommit) {
+					continue;
+				}
+			}
+
+			RevCommit bad = walk.next();
+			if (bad != null) {
+				throw new WantNotValidException(bad);
 			}
 		}
-
-		RevCommit bad = walk.next();
-		if (bad != null) {
-			throw new WantNotValidException(bad);
-		}
-		walk.reset();
 	}
 
 	private void addCommonBase(final RevObject o) {
@@ -1390,17 +1407,6 @@ private boolean wantSatisfied(final RevObject want) throws IOException {
 	private void sendPack() throws IOException {
 		final boolean sideband = options.contains(OPTION_SIDE_BAND)
 				|| options.contains(OPTION_SIDE_BAND_64K);
-
-		if (!biDirectionalPipe) {
-			// Ensure the request was fully consumed. Any remaining input must
-			// be a protocol error. If we aren't at EOF the implementation is broken.
-			int eof = rawIn.read();
-			if (0 <= eof)
-				throw new CorruptObjectException(MessageFormat.format(
-						JGitText.get().expectedEOFReceived,
-						"\\x" + Integer.toHexString(eof))); //$NON-NLS-1$
-		}
-
 		if (sideband) {
 			try {
 				sendPack(true);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/HttpConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/HttpConnection.java
index 58081c1..35a1ee1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/HttpConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/HttpConnection.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2013 Christian Halstrick <christian.halstrick@sap.com>
+ * Copyright (C) 2013, 2017 Christian Halstrick <christian.halstrick@sap.com>
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -79,6 +79,26 @@ public interface HttpConnection {
 	public static final int HTTP_MOVED_PERM = java.net.HttpURLConnection.HTTP_MOVED_PERM;
 
 	/**
+	 * @see HttpURLConnection#HTTP_MOVED_TEMP
+	 * @since 4.9
+	 */
+	public static final int HTTP_MOVED_TEMP = java.net.HttpURLConnection.HTTP_MOVED_TEMP;
+
+	/**
+	 * @see HttpURLConnection#HTTP_SEE_OTHER
+	 * @since 4.9
+	 */
+	public static final int HTTP_SEE_OTHER = java.net.HttpURLConnection.HTTP_SEE_OTHER;
+
+	/**
+	 * HTTP 1.1 additional MOVED_TEMP status code; value = 307.
+	 *
+	 * @see #HTTP_MOVED_TEMP
+	 * @since 4.9
+	 */
+	public static final int HTTP_11_MOVED_TEMP = 307;
+
+	/**
 	 * @see HttpURLConnection#HTTP_NOT_FOUND
 	 */
 	public static final int HTTP_NOT_FOUND = java.net.HttpURLConnection.HTTP_NOT_FOUND;
@@ -253,7 +273,7 @@ public void setRequestMethod(String method)
 
 	/**
 	 * Configure the connection so that it can be used for https communication.
-	 * 
+	 *
 	 * @param km
 	 *            the keymanager managing the key material used to authenticate
 	 *            the local SSLSocket to its peer
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/FileResolver.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/FileResolver.java
index 7654d46..8ab112e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/FileResolver.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/FileResolver.java
@@ -244,11 +244,11 @@ private static boolean isUnreasonableName(final String name) {
 			return true; // no absolute paths
 
 		if (name.startsWith("../")) //$NON-NLS-1$
-			return true; // no "l../etc/passwd" 
+			return true; // no "l../etc/passwd"
 		if (name.contains("/../")) //$NON-NLS-1$
-			return true; // no "foo/../etc/passwd" 
+			return true; // no "foo/../etc/passwd"
 		if (name.contains("/./")) //$NON-NLS-1$
-			return true; // "foo/./foo" is insane to ask 
+			return true; // "foo/./foo" is insane to ask
 		if (name.contains("//")) //$NON-NLS-1$
 			return true; // double slashes is sloppy, don't use it
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeOptions.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeOptions.java
index 7d2b33f..2b18904 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeOptions.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeOptions.java
@@ -55,12 +55,8 @@
 /** Options used by the {@link WorkingTreeIterator}. */
 public class WorkingTreeOptions {
 	/** Key for {@link Config#get(SectionParser)}. */
-	public static final Config.SectionParser<WorkingTreeOptions> KEY = new SectionParser<WorkingTreeOptions>() {
-		@Override
-		public WorkingTreeOptions parse(final Config cfg) {
-			return new WorkingTreeOptions(cfg);
-		}
-	};
+	public static final Config.SectionParser<WorkingTreeOptions> KEY =
+			WorkingTreeOptions::new;
 
 	private final boolean fileMode;
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/InterIndexDiffFilter.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/InterIndexDiffFilter.java
index 1719416..2ea8228 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/InterIndexDiffFilter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/InterIndexDiffFilter.java
@@ -102,4 +102,4 @@ public TreeFilter clone() {
 	public String toString() {
 		return "INTERINDEX_DIFF"; //$NON-NLS-1$
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
index 6f3877f..244d71f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
@@ -568,6 +568,10 @@ protected static String readPipe(File dir, String[] command,
 	}
 
 	private static class GobblerThread extends Thread {
+
+		/* The process has 5 seconds to exit after closing stderr */
+		private static final int PROCESS_EXIT_TIMEOUT = 5;
+
 		private final Process p;
 		private final String desc;
 		private final String dir;
@@ -590,15 +594,16 @@ public void run() {
 					err.append((char) ch);
 				}
 			} catch (IOException e) {
-				if (p.exitValue() != 0) {
-					setError(e, e.getMessage());
+				if (waitForProcessCompletion(e) && p.exitValue() != 0) {
+					setError(e, e.getMessage(), p.exitValue());
 					fail.set(true);
 				} else {
 					// ignore. command terminated faster and stream was just closed
+					// or the process didn't terminate within timeout
 				}
 			} finally {
-				if (err.length() > 0) {
-					setError(null, err.toString());
+				if (waitForProcessCompletion(null) && err.length() > 0) {
+					setError(null, err.toString(), p.exitValue());
 					if (p.exitValue() != 0) {
 						fail.set(true);
 					}
@@ -606,11 +611,27 @@ public void run() {
 			}
 		}
 
-		private void setError(IOException e, String message) {
+		@SuppressWarnings("boxing")
+		private boolean waitForProcessCompletion(IOException originalError) {
+			try {
+				if (!p.waitFor(PROCESS_EXIT_TIMEOUT, TimeUnit.SECONDS)) {
+					setError(originalError, MessageFormat.format(
+							JGitText.get().commandClosedStderrButDidntExit,
+							desc, PROCESS_EXIT_TIMEOUT), -1);
+					fail.set(true);
+				}
+			} catch (InterruptedException e) {
+				LOG.error(MessageFormat.format(
+						JGitText.get().threadInterruptedWhileRunning, desc), e);
+			}
+			return false;
+		}
+
+		private void setError(IOException e, String message, int exitCode) {
 			exception.set(e);
 			errorMessage.set(MessageFormat.format(
-					JGitText.get().exceptionCaughtDuringExcecutionOfCommand,
-					desc, dir, Integer.valueOf(p.exitValue()), message));
+					JGitText.get().exceptionCaughtDuringExecutionOfCommand,
+					desc, dir, Integer.valueOf(exitCode), message));
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java
index 607e078..d220030 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java
@@ -229,7 +229,7 @@ public boolean setExecute(File f, boolean canExecute) {
 		if (!isFile(f))
 			return false;
 		if (!canExecute)
-			return f.setExecutable(false);
+			return f.setExecutable(false, false);
 
 		try {
 			Path path = f.toPath();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/IntList.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/IntList.java
index 658dd06..0a3c846 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/IntList.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/IntList.java
@@ -71,6 +71,21 @@ public int size() {
 	}
 
 	/**
+	 * Check if an entry appears in this collection.
+	 *
+	 * @param value
+	 *            the value to search for.
+	 * @return true of {@code value} appears in this list.
+	 * @since 4.9
+	 */
+	public boolean contains(int value) {
+		for (int i = 0; i < count; i++)
+			if (entries[i] == value)
+				return true;
+		return false;
+	}
+
+	/**
 	 * @param i
 	 *            index to read, must be in the range [0, {@link #size()}).
 	 * @return the number at the specified index
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/LongMap.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/LongMap.java
similarity index 82%
rename from org.eclipse.jgit/src/org/eclipse/jgit/transport/LongMap.java
rename to org.eclipse.jgit/src/org/eclipse/jgit/util/LongMap.java
index 4d60202..7b0b0c7 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/LongMap.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/LongMap.java
@@ -41,15 +41,16 @@
  * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.eclipse.jgit.transport;
+package org.eclipse.jgit.util;
 
 /**
- * Simple Map<long,Object> helper for {@link PackParser}.
+ * Simple Map<long,Object>.
  *
  * @param <V>
  *            type of the value instance.
+ * @since 4.9
  */
-final class LongMap<V> {
+public class LongMap<V> {
 	private static final float LOAD_FACTOR = 0.75f;
 
 	private Node<V>[] table;
@@ -60,16 +61,27 @@ final class LongMap<V> {
 	/** Next {@link #size} to trigger a {@link #grow()}. */
 	private int growAt;
 
-	LongMap() {
+	/** Initialize an empty LongMap. */
+	public LongMap() {
 		table = createArray(64);
 		growAt = (int) (table.length * LOAD_FACTOR);
 	}
 
-	boolean containsKey(final long key) {
+	/**
+	 * @param key
+	 *            the key to find.
+	 * @return {@code true} if {@code key} is present in the map.
+	 */
+	public boolean containsKey(long key) {
 		return get(key) != null;
 	}
 
-	V get(final long key) {
+	/**
+	 * @param key
+	 *            the key to find.
+	 * @return stored value of the key, or {@code null}.
+	 */
+	public V get(long key) {
 		for (Node<V> n = table[index(key)]; n != null; n = n.next) {
 			if (n.key == key)
 				return n.value;
@@ -77,7 +89,12 @@ V get(final long key) {
 		return null;
 	}
 
-	V remove(final long key) {
+	/**
+	 * @param key
+	 *            key to remove from the map.
+	 * @return old value of the key, or {@code null}.
+	 */
+	public V remove(long key) {
 		Node<V> n = table[index(key)];
 		Node<V> prior = null;
 		while (n != null) {
@@ -95,7 +112,14 @@ V remove(final long key) {
 		return null;
 	}
 
-	V put(final long key, final V value) {
+	/**
+	 * @param key
+	 *            key to store {@code value} under.
+	 * @param value
+	 *            new value.
+	 * @return prior value, or null.
+	 */
+	public V put(long key, V value) {
 		for (Node<V> n = table[index(key)]; n != null; n = n.next) {
 			if (n.key == key) {
 				final V o = n.value;
@@ -145,9 +169,7 @@ private final int index(final long key) {
 
 	private static class Node<V> {
 		final long key;
-
 		V value;
-
 		Node<V> next;
 
 		Node(final long k, final V v) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/NB.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/NB.java
index 8536f1d..471a499 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/NB.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/NB.java
@@ -113,6 +113,24 @@ public static int decodeUInt16(final byte[] intbuf, final int offset) {
 	}
 
 	/**
+	 * Convert sequence of 3 bytes (network byte order) into unsigned value.
+	 *
+	 * @param intbuf
+	 *            buffer to acquire the 3 bytes of data from.
+	 * @param offset
+	 *            position within the buffer to begin reading from. This
+	 *            position and the next 2 bytes after it (for a total of 3
+	 *            bytes) will be read.
+	 * @return signed integer value that matches the 24 bits read.
+	 * @since 4.9
+	 */
+	public static int decodeUInt24(byte[] intbuf, int offset) {
+		int r = (intbuf[offset] & 0xff) << 8;
+		r |= intbuf[offset + 1] & 0xff;
+		return (r << 8) | (intbuf[offset + 2] & 0xff);
+	}
+
+	/**
 	 * Convert sequence of 4 bytes (network byte order) into signed value.
 	 *
 	 * @param intbuf
@@ -223,6 +241,29 @@ public static void encodeInt16(final byte[] intbuf, final int offset, int v) {
 	}
 
 	/**
+	 * Write a 24 bit integer as a sequence of 3 bytes (network byte order).
+	 *
+	 * @param intbuf
+	 *            buffer to write the 3 bytes of data into.
+	 * @param offset
+	 *            position within the buffer to begin writing to. This position
+	 *            and the next 2 bytes after it (for a total of 3 bytes) will be
+	 *            replaced.
+	 * @param v
+	 *            the value to write.
+	 * @since 4.9
+	 */
+	public static void encodeInt24(byte[] intbuf, int offset, int v) {
+		intbuf[offset + 2] = (byte) v;
+		v >>>= 8;
+
+		intbuf[offset + 1] = (byte) v;
+		v >>>= 8;
+
+		intbuf[offset] = (byte) v;
+	}
+
+	/**
 	 * Write a 32 bit integer as a sequence of 4 bytes (network byte order).
 	 *
 	 * @param intbuf
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/RawParseUtils.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/RawParseUtils.java
index 86777b9..ad138bb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/RawParseUtils.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/RawParseUtils.java
@@ -618,6 +618,10 @@ public static final int prevLF(final byte[] b, int ptr, final char chrA) {
 	 * <p>
 	 * The last element (index <code>map.size()-1</code>) always contains
 	 * <code>end</code>.
+	 * <p>
+	 * If the data contains a '\0' anywhere, the whole region is considered binary
+	 * and a LineMap corresponding to a single line is returned.
+	 * </p>
 	 *
 	 * @param buf
 	 *            buffer to scan.
@@ -629,14 +633,29 @@ public static final int prevLF(final byte[] b, int ptr, final char chrA) {
 	 * @return a line map indexing the start position of each line.
 	 */
 	public static final IntList lineMap(final byte[] buf, int ptr, int end) {
+		int start = ptr;
+
 		// Experimentally derived from multiple source repositories
 		// the average number of bytes/line is 36. Its a rough guess
 		// to initially size our map close to the target.
-		//
-		final IntList map = new IntList((end - ptr) / 36);
-		map.fillTo(1, Integer.MIN_VALUE);
-		for (; ptr < end; ptr = nextLF(buf, ptr))
-			map.add(ptr);
+		IntList map = new IntList((end - ptr) / 36);
+		map.add(Integer.MIN_VALUE);
+		boolean foundLF = true;
+		for (; ptr < end; ptr++) {
+			if (foundLF) {
+				map.add(ptr);
+			}
+
+			if (buf[ptr] == '\0') {
+				// binary data.
+				map = new IntList(3);
+				map.add(Integer.MIN_VALUE);
+				map.add(start);
+				break;
+			}
+
+			foundLF = (buf[ptr] == '\n');
+		}
 		map.add(end);
 		return map;
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/RefList.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/RefList.java
index 1597817..ce4b7c7 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/RefList.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/RefList.java
@@ -338,10 +338,11 @@ public Builder() {
 		 * Create an empty list with at least the specified capacity.
 		 *
 		 * @param capacity
-		 *            the new capacity.
+		 *            the new capacity; if zero or negative, behavior is the same as
+		 *            {@link #Builder()}.
 		 */
 		public Builder(int capacity) {
-			list = new Ref[capacity];
+			list = new Ref[Math.max(capacity, 16)];
 		}
 
 		/** @return number of items in this builder's internal collection. */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/RelativeDateFormatter.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/RelativeDateFormatter.java
index 3cb3749..a5df66e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/RelativeDateFormatter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/RelativeDateFormatter.java
@@ -114,10 +114,11 @@ public static String format(Date when) {
 
 		// up to 5 years use "year, months" rounded to months
 		if (ageMillis < 5 * YEAR_IN_MILLIS) {
-			long years = ageMillis / YEAR_IN_MILLIS;
+			long years = round(ageMillis, MONTH_IN_MILLIS) / 12;
 			String yearLabel = (years > 1) ? JGitText.get().years : //
 					JGitText.get().year;
-			long months = round(ageMillis % YEAR_IN_MILLIS, MONTH_IN_MILLIS);
+			long months = round(ageMillis - years * YEAR_IN_MILLIS,
+					MONTH_IN_MILLIS);
 			String monthLabel = (months > 1) ? JGitText.get().months : //
 					(months == 1 ? JGitText.get().month : ""); //$NON-NLS-1$
 			return MessageFormat.format(
@@ -140,4 +141,4 @@ private static long round(long n, long unit) {
 		long rounded = (n + unit / 2) / unit;
 		return rounded;
 	}
-}
\ No newline at end of file
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolStreamTypeUtil.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolStreamTypeUtil.java
index c95992f..727c1f4 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolStreamTypeUtil.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolStreamTypeUtil.java
@@ -144,6 +144,11 @@ public static OutputStream wrapOutputStream(OutputStream out,
 
 	private static EolStreamType checkInStreamType(WorkingTreeOptions options,
 			Attributes attrs) {
+		if (attrs.isUnset("text")) {//$NON-NLS-1$
+			// "binary" or "-text" (which is included in the binary expansion)
+			return EolStreamType.DIRECT;
+		}
+
 		// old git system
 		if (attrs.isSet("crlf")) {//$NON-NLS-1$
 			return EolStreamType.TEXT_LF;
@@ -154,9 +159,6 @@ private static EolStreamType checkInStreamType(WorkingTreeOptions options,
 		}
 
 		// new git system
-		if (attrs.isUnset("text")) {//$NON-NLS-1$
-			return EolStreamType.DIRECT;
-		}
 		String eol = attrs.getValue("eol"); //$NON-NLS-1$
 		if (eol != null)
 			// check-in is always normalized to LF
@@ -183,6 +185,11 @@ private static EolStreamType checkInStreamType(WorkingTreeOptions options,
 
 	private static EolStreamType checkOutStreamType(WorkingTreeOptions options,
 			Attributes attrs) {
+		if (attrs.isUnset("text")) {//$NON-NLS-1$
+			// "binary" or "-text" (which is included in the binary expansion)
+			return EolStreamType.DIRECT;
+		}
+
 		// old git system
 		if (attrs.isSet("crlf")) {//$NON-NLS-1$
 			return FORCE_EOL_LF_ON_CHECKOUT ? EolStreamType.TEXT_LF
@@ -194,9 +201,6 @@ private static EolStreamType checkOutStreamType(WorkingTreeOptions options,
 		}
 
 		// new git system
-		if (attrs.isUnset("text")) {//$NON-NLS-1$
-			return EolStreamType.DIRECT;
-		}
 		String eol = attrs.getValue("eol"); //$NON-NLS-1$
 		if (eol != null && "crlf".equals(eol)) //$NON-NLS-1$
 			return EolStreamType.TEXT_CRLF;
diff --git a/pom.xml b/pom.xml
index b74de4e..7ca479c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -51,7 +51,7 @@
   <groupId>org.eclipse.jgit</groupId>
   <artifactId>org.eclipse.jgit-parent</artifactId>
   <packaging>pom</packaging>
-  <version>4.8.1-SNAPSHOT</version>
+  <version>4.9.6-SNAPSHOT</version>
 
   <name>JGit - Parent</name>
   <url>${jgit-url}</url>
@@ -200,7 +200,7 @@
     <javaewah-version>1.1.6</javaewah-version>
     <junit-version>4.12</junit-version>
     <test-fork-count>1C</test-fork-count>
-    <args4j-version>2.0.15</args4j-version>
+    <args4j-version>2.33</args4j-version>
     <commons-compress-version>1.6</commons-compress-version>
     <osgi-core-version>4.3.1</osgi-core-version>
     <servlet-api-version>3.1.0</servlet-api-version>
@@ -212,7 +212,7 @@
     <maven-javadoc-plugin-version>2.10.4</maven-javadoc-plugin-version>
     <tycho-extras-version>1.0.0</tycho-extras-version>
     <gson-version>2.2.4</gson-version>
-    <findbugs-maven-plugin-version>3.0.4</findbugs-maven-plugin-version>
+    <spotbugs-maven-plugin-version>3.0.6</spotbugs-maven-plugin-version>
     <maven-surefire-report-plugin-version>2.20</maven-surefire-report-plugin-version>
 
     <!-- Properties to enable jacoco code coverage analysis -->
@@ -264,7 +264,7 @@
 
         <plugin>
           <artifactId>maven-compiler-plugin</artifactId>
-          <version>3.6.1</version>
+          <version>3.6.2</version>
           <configuration>
             <encoding>UTF-8</encoding>
             <source>1.8</source>
@@ -302,19 +302,19 @@
             <dependency>
               <groupId>org.codehaus.plexus</groupId>
               <artifactId>plexus-compiler-javac</artifactId>
-              <version>2.8.1</version>
+              <version>2.8.2</version>
             </dependency>
             <dependency>
               <groupId>org.codehaus.plexus</groupId>
               <artifactId>plexus-compiler-javac-errorprone</artifactId>
-              <version>2.8.1</version>
+              <version>2.8.2</version>
             </dependency>
             <!-- override plexus-compiler-javac-errorprone's dependency on
                  Error Prone with the latest version -->
             <dependency>
               <groupId>com.google.errorprone</groupId>
               <artifactId>error_prone_core</artifactId>
-              <version>2.0.19</version>
+              <version>2.1.1</version>
             </dependency>
           </dependencies>
         </plugin>
@@ -371,9 +371,9 @@
         </plugin>
 
         <plugin>
-          <groupId>org.codehaus.mojo</groupId>
-          <artifactId>findbugs-maven-plugin</artifactId>
-          <version>${findbugs-maven-plugin-version}</version>
+          <groupId>com.github.hazendaz.spotbugs</groupId>
+          <artifactId>spotbugs-maven-plugin</artifactId>
+          <version>${spotbugs-maven-plugin-version}</version>
           <configuration>
             <findbugsXmlOutput>true</findbugsXmlOutput>
             <failOnError>false</failOnError>
@@ -579,9 +579,9 @@
         <version>2.5</version>
       </plugin>
       <plugin>
-        <groupId>org.codehaus.mojo</groupId>
-        <artifactId>findbugs-maven-plugin</artifactId>
-        <version>${findbugs-maven-plugin-version}</version>
+        <groupId>com.github.hazendaz.spotbugs</groupId>
+        <artifactId>spotbugs-maven-plugin</artifactId>
+        <version>${spotbugs-maven-plugin-version}</version>
       </plugin>
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
@@ -751,8 +751,8 @@
       <build>
         <plugins>
           <plugin>
-            <groupId>org.codehaus.mojo</groupId>
-            <artifactId>findbugs-maven-plugin</artifactId>
+            <groupId>com.github.hazendaz.spotbugs</groupId>
+            <artifactId>spotbugs-maven-plugin</artifactId>
           </plugin>
           <plugin>
             <groupId>org.apache.maven.plugins</groupId>