diff --git a/.bazelrc b/.bazelrc
new file mode 100644
index 0000000..3a61f8c
--- /dev/null
+++ b/.bazelrc
@@ -0,0 +1,9 @@
+build --repository_cache=~/.gerritcodereview/bazel-cache/repository
+build --experimental_strict_action_env
+build --action_env=PATH
+build --disk_cache=~/.gerritcodereview/bazel-cache/cas
+build --java_toolchain //tools:error_prone_warnings_toolchain
+
+test --build_tests_only
+test --test_output=errors
+
diff --git a/README.md b/README.md
index 54133e1..091accd 100644
--- a/README.md
+++ b/README.md
@@ -1,15 +1,16 @@
-Java Git
-========
+# Java Git
 
 An implementation of the Git version control system in pure Java.
 
-This package is licensed under the EDL (Eclipse Distribution
+This project is licensed under the __EDL__ (Eclipse Distribution
 License).
 
-JGit can be imported straight into Eclipse, built and tested from
-there, but the automated builds use Maven.
+JGit can be imported straight into Eclipse and built and tested from
+there. It can be built from the command line using
+[Maven](https://maven.apache.org/) or [Bazel](https://bazel.build/).
+The CI builds use Maven and run on [Jenkins](https://ci.eclipse.org/jgit/).
 
-- org.eclipse.jgit
+- __org.eclipse.jgit__
 
     A pure Java library capable of being run standalone, with no
     additional support libraries. It provides classes to read and
@@ -18,63 +19,73 @@
     All portions of JGit are covered by the EDL. Absolutely no GPL,
     LGPL or EPL contributions are accepted within this package.
 
-- org.eclipse.jgit.ant
+- __org.eclipse.jgit.ant__
 
     Ant tasks based on JGit.
 
-- org.eclipse.jgit.archive
+- __org.eclipse.jgit.archive__
 
     Support for exporting to various archive formats (zip etc).
 
-- org.eclipse.jgit.http.apache
+- __org.eclipse.jgit.http.apache__
 
-    Apache httpclient support
+    [Apache httpclient](https://hc.apache.org/httpcomponents-client-ga/) support.
 
-- org.eclipse.jgit.http.server
+- __org.eclipse.jgit.http.server__
 
-    Server for the smart and dumb Git HTTP protocol.
+    Server for the smart and dumb
+    [Git HTTP protocol](https://github.com/git/git/blob/master/Documentation/technical/http-protocol.txt).
 
-- org.eclipse.jgit.pgm
+- __org.eclipse.jgit.lfs__
 
-    Command-line interface Git commands implemented using JGit
-    ("pgm" stands for program).
+    Support for [LFS](https://git-lfs.github.com/) (Large File Storage).
 
-- org.eclipse.jgit.packaging
+- __org.eclipse.jgit.lfs.server__
+
+    Basic LFS server support.
+
+- __org.eclipse.jgit.packaging__
 
     Production of Eclipse features and p2 repository for JGit. See the JGit
     Wiki on why and how to use this module.
 
-Tests
------
+- __org.eclipse.jgit.pgm__
 
-- org.eclipse.jgit.junit
+    Command-line interface Git commands implemented using JGit
+    ("pgm" stands for program).
 
-    Helpers for unit testing
+- __org.eclipse.jgit.ssh.apache__
 
-- org.eclipse.jgit.test
+    Client support for the ssh protocol based on
+    [Apache Mina sshd](https://mina.apache.org/sshd-project/).
 
-    Unit tests for org.eclipse.jgit
+- __org.eclipse.jgit.ui__
 
-- org.eclipse.jgit.ant.test
-- org.eclipse.jgit.pgm.test
-- org.eclipse.jgit.http.test
-- org.eclipse.jgit.junit.test
+    Simple UI for displaying git log.
 
-    No further description needed
+## Tests
 
-Warnings/Caveats
-----------------
+- __org.eclipse.jgit.junit__, __org.eclipse.jgit.junit.http__,
+__org.eclipse.jgit.junit.ssh__: Helpers for unit testing
+- __org.eclipse.jgit.ant.test__: Unit tests for org.eclipse.jgit.ant
+- __org.eclipse.jgit.http.test__: Unit tests for org.eclipse.jgit.http.server
+- __org.eclipse.jgit.lfs.server.test__: Unit tests for org.eclipse.jgit.lfs.server
+- __org.eclipse.jgit.lfs.test__: Unit tests for org.eclipse.jgit.lfs
+- __org.eclipse.jgit.pgm.test__: Unit tests for org.eclipse.jgit.pgm
+- __org.eclipse.jgit.ssh.apache.test__: Unit tests for org.eclipse.jgit.ssh.apache
+- __org.eclipse.jgit.test__: Unit tests for org.eclipse.jgit
 
-- Native smbolic links are supported, provided the file system supports
-  them. For Windows you must have Windows Vista/Windows 2008 or newer,
-  use a non-administrator account and have the SeCreateSymbolicLinkPrivilege.
+## Warnings/Caveats
 
-- Only the timestamp of the index is used by jgit if the index is
+- Native symbolic links are supported, provided the file system supports
+  them. For Windows you must use a non-administrator account and have the SeCreateSymbolicLinkPrivilege.
+
+- Only the timestamp of the index is used by JGit if the index is
   dirty.
 
 - JGit requires at least a Java 8 JDK.
 
-- CRLF conversion is performed depending on the core.autocrlf setting,
+- CRLF conversion is performed depending on the `core.autocrlf` setting,
   however Git for Windows by default stores that setting during
   installation in the "system wide" configuration file. If Git is not
   installed, use the global or repository configuration for the
@@ -88,102 +99,69 @@
   is installed. Modifying PATH is the recommended option if C Git is
   installed.
 
-- We try to use the same notation of $HOME as C Git does. On Windows
-  this is often not the same value as the user.home system property.
+- We try to use the same notation of `$HOME` as C Git does. On Windows
+  this is often not the same value as the `user.home` system property.
 
+## Features
 
-Package Features
-----------------
-
-- org.eclipse.jgit/
-
-    * Read loose and packed commits, trees, blobs, including
-      deltafied objects.
-
-    * Read objects from shared repositories
-
-    * Write loose commits, trees, blobs.
-
-    * Write blobs from local files or Java InputStreams.
-
-    * Read blobs as Java InputStreams.
-
-    * Copy trees to local directory, or local directory to a tree.
-
-    * Lazily loads objects as necessary.
-
-    * Read and write .git/config files.
-
-    * Create a new repository.
-
-    * Read and write refs, including walking through symrefs.
-
-    * Read, update and write the Git index.
-
-    * Checkout in dirty working directory if trivial.
-
-    * Walk the history from a given set of commits looking for commits
+- __org.eclipse.jgit__
+  - Read loose and packed commits, trees, blobs, including
+    deltafied objects.
+  - Read objects from shared repositories
+  - Write loose commits, trees, blobs.
+  - Write blobs from local files or Java InputStreams.
+  - Read blobs as Java InputStreams.
+  - Copy trees to local directory, or local directory to a tree.
+  - Lazily loads objects as necessary.
+  - Read and write .git/config files.
+  - Create a new repository.
+  - Read and write refs, including walking through symrefs.
+  - Read, update and write the Git index.
+  - Checkout in dirty working directory if trivial.
+  - Walk the history from a given set of commits looking for commits
       introducing changes in files under a specified path.
+  - Object transport
 
-    * Object transport
       Fetch via ssh, git, http, Amazon S3 and bundles.
       Push via ssh, git and Amazon S3. JGit does not yet deltify
       the pushed packs so they may be a lot larger than C Git packs.
 
-    * Garbage collection
+  - Garbage collection
+  - Merge
+  - Rebase
+  - And much more
 
-    * Merge
-
-    * Rebase
-
-    * And much more
-
-- org.eclipse.jgit.pgm/
-
-    * Assorted set of command line utilities. Mostly for ad-hoc testing of jgit
+- __org.eclipse.jgit.pgm__
+  - Assorted set of command line utilities. Mostly for ad-hoc testing of jgit
       log, glog, fetch etc.
+- __org.eclipse.jgit.ant__
+  - Ant tasks
+- __org.eclipse.jgit.archive__
+  - Support for Zip/Tar and other formats
+- __org.eclipse.http__
+  - HTTP client and server support
 
-- org.eclipse.jgit.ant/
-
-    * Ant tasks
-
-- org.eclipse.jgit.archive/
-
-    * Support for Zip/Tar and other formats
-
-- org.eclipse.http.*/
-
-    * HTTP client and server support
-
-Missing Features
-----------------
+## Missing Features
 
 There are some missing features:
 
-- gitattributes support
+- verifying signed commits
+- signing tags
+- signing push
 
+## Support
 
-Support
--------
+Post questions, comments or discussions to the jgit-dev@eclipse.org mailing list.
+You need to be [subscribed](https://dev.eclipse.org/mailman/listinfo/jgit-dev)
+to post. File bugs and enhancement requests in
+[Bugzilla](https://wiki.eclipse.org/EGit/Contributor_Guide#Filing_Bugs).
 
-Post question, comments or patches to the jgit-dev@eclipse.org mailing list.
-You need to be subscribed to post, see here:
+## Contributing
 
-https://dev.eclipse.org/mailman/listinfo/jgit-dev
+See the [EGit Contributor Guide](http://wiki.eclipse.org/EGit/Contributor_Guide).
 
-
-Contributing
-------------
-
-See the EGit Contributor Guide:
-
-http://wiki.eclipse.org/EGit/Contributor_Guide
-
-
-About Git
----------
+## About Git
 
 More information about Git, its repository format, and the canonical
-C based implementation can be obtained from the Git website:
-
-http://git-scm.com/
+C based implementation can be obtained from the
+[Git website](http://git-scm.com/).
diff --git a/WORKSPACE b/WORKSPACE
index 9a4a9a9..8129ace 100644
--- a/WORKSPACE
+++ b/WORKSPACE
@@ -108,8 +108,8 @@
 
 maven_jar(
     name = "tukaani-xz",
-    artifact = "org.tukaani:xz:1.6",
-    sha1 = "05b6f921f1810bdf90e25471968f741f87168b64",
+    artifact = "org.tukaani:xz:1.8",
+    sha1 = "c4f7d054303948eb6a4066194253886c8af07128",
 )
 
 maven_jar(
@@ -168,46 +168,69 @@
     sha1 = "3edcfe49d2c6053a70a2a47e4e1c2f94998a49cf",
 )
 
-JETTY_VER = "9.4.11.v20180605"
+JETTY_VER = "9.4.14.v20181114"
 
 maven_jar(
     name = "jetty-servlet",
     artifact = "org.eclipse.jetty:jetty-servlet:" + JETTY_VER,
-    sha1 = "66d31900fcfc70e3666f0b3335b6660635154f98",
-    src_sha1 = "930c50de49b9c258d5f0329426cbcac4d3143497",
+    sha1 = "96f501462af425190ff7b63e387692c1aa3af2c8",
+    src_sha1 = "204b8a84adf3ce354138509c42638b5b2d223d1f",
 )
 
 maven_jar(
     name = "jetty-security",
     artifact = "org.eclipse.jetty:jetty-security:" + JETTY_VER,
-    sha1 = "926def86d31ee07ca4b4658833dc6ee6918b8e86",
-    src_sha1 = "019bc7c2a366cbb201950f24dd64d9d9a49b6840",
+    sha1 = "6cbeb2fe9b3cc4f88a7ea040b8a0c4f703cd72ce",
+    src_sha1 = "33555125c5988fca12273f60a0aa545d848de54a",
 )
 
 maven_jar(
     name = "jetty-server",
     artifact = "org.eclipse.jetty:jetty-server:" + JETTY_VER,
-    sha1 = "58353c2f27515b007fc83ae22002feb34fc24714",
-    src_sha1 = "e7d832d74df616137755996b41bc28bb82b3bc42",
+    sha1 = "b36a3d52d78a1df6406f6fa236a6eeff48cbfef6",
+    src_sha1 = "55db20ea68c9c1b0ed264d80e7d75b4988da87a6",
 )
 
 maven_jar(
     name = "jetty-http",
     artifact = "org.eclipse.jetty:jetty-http:" + JETTY_VER,
-    sha1 = "20c35f5336befe35b0bd5c4a63e07170fe7872d7",
-    src_sha1 = "5bc30d1f7e8c4456c22cc85999b8cafd3741bdff",
+    sha1 = "6d0c8ac42e9894ae7b5032438eb4579c2a47f4fe",
+    src_sha1 = "3c4f8a942909cabe6d029f835c185207eb91af75",
 )
 
 maven_jar(
     name = "jetty-io",
     artifact = "org.eclipse.jetty:jetty-io:" + JETTY_VER,
-    sha1 = "d164de1dac18c4ca80a1b783d879c97449909c3b",
-    src_sha1 = "02c0caba292b1cb74cec1d36c6f91dc863c89b5a",
+    sha1 = "a8c6a705ddb9f83a75777d89b0be59fcef3f7637",
+    src_sha1 = "06132108ccabbe181707af911e5a68fd8e8806ff",
 )
 
 maven_jar(
     name = "jetty-util",
     artifact = "org.eclipse.jetty:jetty-util:" + JETTY_VER,
-    sha1 = "f0f25aa2f27d618a04bc7356fa247ae4a05245b3",
-    src_sha1 = "4e5c4c483cfd9804c2fc5d5751866243bbb9d740",
+    sha1 = "5bb3d7a38f7ea54138336591d89dd5867b806c02",
+    src_sha1 = "94e89a8c9f82e38555e95b9f7f58344a247e862c",
+)
+
+BOUNCYCASTLE_VER = "1.60"
+
+maven_jar(
+    name = "bcpg-jdk15on",
+    artifact = "org.bouncycastle:bcpg-jdk15on:" + BOUNCYCASTLE_VER,
+    sha1 = "13c7a199c484127daad298996e95818478431a2c",
+    src_sha1 = "edcd9e86d95e39b4da39bb295efd93bc4f56266e",
+)
+
+maven_jar(
+    name = "bcprov-jdk15on",
+    artifact = "org.bouncycastle:bcprov-jdk15on:" + BOUNCYCASTLE_VER,
+    sha1 = "bd47ad3bd14b8e82595c7adaa143501e60842a84",
+    src_sha1 = "7c57a4d13fe53d9abb967bba600dd0b293dafd6a",
+)
+
+maven_jar(
+    name = "bcpkix-jdk15on",
+    artifact = "org.bouncycastle:bcpkix-jdk15on:" + BOUNCYCASTLE_VER,
+    sha1 = "d0c46320fbc07be3a24eb13a56cee4e3d38e0c75",
+    src_sha1 = "a25f041293f401af08efba63ff4bbdce98134a03",
 )
diff --git a/lib/BUILD b/lib/BUILD
index 7403ce2..47125ed 100644
--- a/lib/BUILD
+++ b/lib/BUILD
@@ -151,6 +151,33 @@
 )
 
 java_library(
+    name = "bcpg",
+    visibility = [
+        "//org.eclipse.jgit:__pkg__",
+        "//org.eclipse.jgit.test:__pkg__",
+    ],
+    exports = ["@bcpg-jdk15on//jar"],
+)
+
+java_library(
+    name = "bcprov",
+    visibility = [
+        "//org.eclipse.jgit:__pkg__",
+        "//org.eclipse.jgit.test:__pkg__",
+    ],
+    exports = ["@bcprov-jdk15on//jar"],
+)
+
+java_library(
+    name = "bcpkix",
+    visibility = [
+        "//org.eclipse.jgit:__pkg__",
+        "//org.eclipse.jgit.test:__pkg__",
+    ],
+    exports = ["@bcpkix-jdk15on//jar"],
+)
+
+java_library(
     name = "jzlib",
     visibility = [
         "//org.eclipse.jgit:__pkg__",
diff --git a/org.eclipse.jgit.ant.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.ant.test/META-INF/MANIFEST.MF
index ad64078..00bfaeb 100644
--- a/org.eclipse.jgit.ant.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.ant.test/META-INF/MANIFEST.MF
@@ -4,13 +4,13 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.ant.test
 Bundle-SymbolicName: org.eclipse.jgit.ant.test
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: org.apache.tools.ant,
- org.eclipse.jgit.ant.tasks;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.junit;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)",
+ org.eclipse.jgit.ant.tasks;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.junit;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)",
  org.hamcrest.core;version="[1.1.0,2.0.0)",
  org.junit;version="[4.12,5.0.0)"
diff --git a/org.eclipse.jgit.ant.test/pom.xml b/org.eclipse.jgit.ant.test/pom.xml
index d75acdb..5e02ccf 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.ant.test</artifactId>
@@ -105,7 +105,7 @@
       <plugin>
         <artifactId>maven-surefire-plugin</artifactId>
         <configuration>
-          <argLine>-Xmx256m -Dfile.encoding=UTF-8 -Djava.io.tmpdir=${project.build.directory}</argLine>
+          <argLine>@{argLine} -Xmx256m -Dfile.encoding=UTF-8 -Djava.io.tmpdir=${project.build.directory}</argLine>
         </configuration>
       </plugin>
     </plugins>
diff --git a/org.eclipse.jgit.ant/META-INF/MANIFEST.MF b/org.eclipse.jgit.ant/META-INF/MANIFEST.MF
index f0bbb7e..4d0c52c 100644
--- a/org.eclipse.jgit.ant/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.ant/META-INF/MANIFEST.MF
@@ -3,11 +3,11 @@
 Bundle-Name: %Bundle-Name
 Automatic-Module-Name: org.eclipse.jgit.ant
 Bundle-SymbolicName: org.eclipse.jgit.ant
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: org.apache.tools.ant,
-  org.eclipse.jgit.storage.file;version="[5.2.3,5.3.0)"
+  org.eclipse.jgit.storage.file;version="[5.3.6,5.4.0)"
 Bundle-Localization: plugin
 Bundle-Vendor: %Provider-Name
-Export-Package: org.eclipse.jgit.ant.tasks;version="5.2.3";
+Export-Package: org.eclipse.jgit.ant.tasks;version="5.3.6";
  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 f68a015..47c5b63 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>5.2.3-SNAPSHOT</version>
+		<version>5.3.6-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>org.eclipse.jgit.ant</artifactId>
diff --git a/org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitCheckoutTask.java b/org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitCheckoutTask.java
index 0b27cc2..5f80d00 100644
--- a/org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitCheckoutTask.java
+++ b/org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitCheckoutTask.java
@@ -123,7 +123,7 @@ public void execute() throws BuildException {
 		}
 
 		try {
-			checkout.setCreateBranch(createBranch).setForce(force)
+			checkout.setCreateBranch(createBranch).setForceRefUpdate(force)
 					.setName(branch);
 			checkout.call();
 		} catch (Exception e) {
diff --git a/org.eclipse.jgit.archive/META-INF/MANIFEST.MF b/org.eclipse.jgit.archive/META-INF/MANIFEST.MF
index 8c854b8..22f7549 100644
--- a/org.eclipse.jgit.archive/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.archive/META-INF/MANIFEST.MF
@@ -3,7 +3,7 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.archive
 Bundle-SymbolicName: org.eclipse.jgit.archive
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-Localization: plugin
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
@@ -13,15 +13,15 @@
  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="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.nls;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)",
+ org.eclipse.jgit.api;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.nls;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)",
  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="5.2.3";
+Export-Package: org.eclipse.jgit.archive;version="5.3.6";
   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 aab58a6..0985163 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: 5.2.3.qualifier
-Eclipse-SourceBundle: org.eclipse.jgit.archive;version="5.2.3.qualifier";roots="."
+Bundle-Version: 5.3.6.qualifier
+Eclipse-SourceBundle: org.eclipse.jgit.archive;version="5.3.6.qualifier";roots="."
diff --git a/org.eclipse.jgit.archive/pom.xml b/org.eclipse.jgit.archive/pom.xml
index f36a3a6..41403d8 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.archive</artifactId>
diff --git a/org.eclipse.jgit.coverage/.classpath b/org.eclipse.jgit.coverage/.classpath
new file mode 100644
index 0000000..248406b
--- /dev/null
+++ b/org.eclipse.jgit.coverage/.classpath
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/org.eclipse.jgit.coverage/.gitignore b/org.eclipse.jgit.coverage/.gitignore
new file mode 100644
index 0000000..b83d222
--- /dev/null
+++ b/org.eclipse.jgit.coverage/.gitignore
@@ -0,0 +1 @@
+/target/
diff --git a/org.eclipse.jgit.coverage/.project b/org.eclipse.jgit.coverage/.project
new file mode 100644
index 0000000..6306b5c
--- /dev/null
+++ b/org.eclipse.jgit.coverage/.project
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>org.eclipse.jgit.coverage</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>
diff --git a/org.eclipse.jgit.coverage/.settings/org.eclipse.core.resources.prefs b/org.eclipse.jgit.coverage/.settings/org.eclipse.core.resources.prefs
new file mode 100644
index 0000000..99f26c0
--- /dev/null
+++ b/org.eclipse.jgit.coverage/.settings/org.eclipse.core.resources.prefs
@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+encoding/<project>=UTF-8
diff --git a/org.eclipse.jgit.coverage/.settings/org.eclipse.m2e.core.prefs b/org.eclipse.jgit.coverage/.settings/org.eclipse.m2e.core.prefs
new file mode 100644
index 0000000..f897a7f
--- /dev/null
+++ b/org.eclipse.jgit.coverage/.settings/org.eclipse.m2e.core.prefs
@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1
diff --git a/org.eclipse.jgit.coverage/pom.xml b/org.eclipse.jgit.coverage/pom.xml
new file mode 100644
index 0000000..b4334f5
--- /dev/null
+++ b/org.eclipse.jgit.coverage/pom.xml
@@ -0,0 +1,143 @@
+<?xml version="1.0"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <parent>
+    <groupId>org.eclipse.jgit</groupId>
+    <artifactId>org.eclipse.jgit-parent</artifactId>
+    <version>5.3.6-SNAPSHOT</version>
+  </parent>
+  <modelVersion>4.0.0</modelVersion>
+
+  <artifactId>org.eclipse.jgit.coverage</artifactId>
+  <packaging>pom</packaging>
+
+  <name>JGit - Test Coverage</name>
+
+  <dependencies>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.ant</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.archive</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.http.apache</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.http.server</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.lfs</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.lfs.server</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.pgm</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.ui</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.ssh.apache</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.test</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.ant.test</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.http.test</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.pgm.test</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.lfs.test</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.lfs.server.test</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.ssh.apache.test</artifactId>
+      <version>5.3.6-SNAPSHOT</version>
+    </dependency>
+  </dependencies>
+
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>org.jacoco</groupId>
+        <artifactId>jacoco-maven-plugin</artifactId>
+        <executions>
+          <execution>
+            <id>aggregate-reports-all</id>
+            <phase>verify</phase>
+            <goals>
+              <goal>report-aggregate</goal>
+            </goals>
+            <configuration>
+              <title>JGit Test Coverage </title>
+              <outputDirectory>${project.reporting.outputDirectory}/jacoco-aggregate</outputDirectory>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+  <reporting>
+    <plugins>
+      <plugin>
+        <groupId>org.jacoco</groupId>
+        <artifactId>jacoco-maven-plugin</artifactId>
+        <reportSets>
+          <reportSet>
+            <id>aggregate</id>
+            <reports>
+              <report>report-aggregate</report>
+            </reports>
+          </reportSet>
+        </reportSets>
+      </plugin>
+    </plugins>
+  </reporting>
+</project>
diff --git a/org.eclipse.jgit.http.apache/META-INF/MANIFEST.MF b/org.eclipse.jgit.http.apache/META-INF/MANIFEST.MF
index fb3dec7..c3ca912 100644
--- a/org.eclipse.jgit.http.apache/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.http.apache/META-INF/MANIFEST.MF
@@ -3,7 +3,7 @@
 Bundle-Name: %Bundle-Name
 Automatic-Module-Name: org.eclipse.jgit.http.apache
 Bundle-SymbolicName: org.eclipse.jgit.http.apache
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Localization: plugin
 Bundle-Vendor: %Provider-Name
@@ -23,11 +23,11 @@
  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.annotations;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.nls;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.http;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)"
-Export-Package: org.eclipse.jgit.transport.http.apache;version="5.2.3";
+ org.eclipse.jgit.annotations;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.nls;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.http;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)"
+Export-Package: org.eclipse.jgit.transport.http.apache;version="5.3.6";
   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 a1cb74c..5c8095a 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>5.2.3-SNAPSHOT</version>
+		<version>5.3.6-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>org.eclipse.jgit.http.apache</artifactId>
diff --git a/org.eclipse.jgit.http.server/META-INF/MANIFEST.MF b/org.eclipse.jgit.http.server/META-INF/MANIFEST.MF
index b65ee84..04be08e 100644
--- a/org.eclipse.jgit.http.server/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.http.server/META-INF/MANIFEST.MF
@@ -3,13 +3,13 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.http.server
 Bundle-SymbolicName: org.eclipse.jgit.http.server
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
-Export-Package: org.eclipse.jgit.http.server;version="5.2.3",
- org.eclipse.jgit.http.server.glue;version="5.2.3";
+Export-Package: org.eclipse.jgit.http.server;version="5.3.6",
+ org.eclipse.jgit.http.server.glue;version="5.3.6";
   uses:="javax.servlet,javax.servlet.http",
- org.eclipse.jgit.http.server.resolver;version="5.2.3";
+ org.eclipse.jgit.http.server.resolver;version="5.3.6";
   uses:="org.eclipse.jgit.transport.resolver,
    org.eclipse.jgit.lib,
    org.eclipse.jgit.transport,
@@ -18,13 +18,13 @@
 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="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.dfs;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.transport.parser;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.nls;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.resolver;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)"
+ org.eclipse.jgit.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.dfs;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.transport.parser;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.nls;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.resolver;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)"
diff --git a/org.eclipse.jgit.http.server/pom.xml b/org.eclipse.jgit.http.server/pom.xml
index 78191ef..45da828 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-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 ee4b32e..5e09d01 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
@@ -63,6 +63,7 @@
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import org.eclipse.jgit.internal.transport.parser.FirstCommand;
 import org.eclipse.jgit.internal.transport.parser.FirstWant;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.transport.PacketLineIn;
@@ -287,7 +288,7 @@ private static boolean isReceivePackSideBand(HttpServletRequest req) {
 			// not have a ReceivePack, or it might not have read any of the request.
 			// So, cheat and read the first line.
 			String line = new PacketLineIn(req.getInputStream()).readString();
-			ReceivePack.FirstLine parsed = new ReceivePack.FirstLine(line);
+			FirstCommand parsed = FirstCommand.fromLine(line);
 			return parsed.getCapabilities().contains(CAPABILITY_SIDE_BAND_64K);
 		} catch (IOException e) {
 			// Probably the connection is closed and a subsequent write will fail, but
@@ -298,10 +299,11 @@ private static boolean isReceivePackSideBand(HttpServletRequest req) {
 
 	private static void writeSideBand(OutputStream out, String textForGit)
 			throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		OutputStream msg = new SideBandOutputStream(CH_ERROR, SMALL_BUF, out);
-		msg.write(Constants.encode("error: " + textForGit));
-		msg.flush();
+		try (OutputStream msg = new SideBandOutputStream(CH_ERROR, SMALL_BUF,
+				out)) {
+			msg.write(Constants.encode("error: " + textForGit));
+			msg.flush();
+		}
 	}
 
 	private static void writePacket(PacketLineOut pckOut, String textForGit)
diff --git a/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF
index 495d36d..9202566 100644
--- a/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF
@@ -3,7 +3,7 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.http.test
 Bundle-SymbolicName: org.eclipse.jgit.http.test
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-Localization: plugin
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
@@ -28,25 +28,25 @@
  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="[5.2.3,5.3.0)",
- org.eclipse.jgit.http.server;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.http.server.glue;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.http.server.resolver;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.dfs;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.reftable;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.junit;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.junit.http;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.nls;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.http;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.http.apache;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.resolver;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)",
+ org.eclipse.jgit.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.http.server;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.http.server.glue;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.http.server.resolver;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.dfs;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.reftable;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.junit;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.junit.http;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.nls;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.http;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.http.apache;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.resolver;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)",
  org.hamcrest;version="[1.1.0,2.0.0)",
  org.hamcrest.core;version="[1.1.0,2.0.0)",
  org.junit;version="[4.12,5.0.0)",
diff --git a/org.eclipse.jgit.http.test/pom.xml b/org.eclipse.jgit.http.test/pom.xml
index e8e697e..151574e 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.http.test</artifactId>
@@ -71,13 +71,6 @@
     </dependency>
 
     <dependency>
-      <groupId>org.hamcrest</groupId>
-      <artifactId>hamcrest-library</artifactId>
-      <scope>test</scope>
-      <version>[1.1.0,2.0.0)</version>
-    </dependency>
-
-    <dependency>
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit</artifactId>
       <version>${project.version}</version>
@@ -91,6 +84,13 @@
     </dependency>
 
     <dependency>
+      <groupId>org.hamcrest</groupId>
+      <artifactId>hamcrest-library</artifactId>
+      <scope>test</scope>
+      <version>[1.1.0,2.0.0)</version>
+    </dependency>
+
+    <dependency>
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit.junit.http</artifactId>
       <version>${project.version}</version>
@@ -139,7 +139,7 @@
       <plugin>
         <artifactId>maven-surefire-plugin</artifactId>
         <configuration>
-          <argLine>-Djava.io.tmpdir=${project.build.directory}  -Xmx300m</argLine>
+          <argLine>@{argLine} -Djava.io.tmpdir=${project.build.directory}  -Xmx300m</argLine>
           <includes>
             <include>**/*Test.java</include>
             <include>**/*Tests.java</include>
diff --git a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DumbClientDumbServerTest.java b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DumbClientDumbServerTest.java
index ab6dc35..c1e55cb 100644
--- a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DumbClientDumbServerTest.java
+++ b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DumbClientDumbServerTest.java
@@ -194,13 +194,13 @@ public void testListRemote() throws IOException {
 	@Test
 	public void testInitialClone_Loose() throws Exception {
 		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
+		assertFalse(dst.getObjectDatabase().has(A_txt));
 
 		try (Transport t = Transport.open(dst, remoteURI)) {
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
 		}
 
-		assertTrue(dst.hasObject(A_txt));
+		assertTrue(dst.getObjectDatabase().has(A_txt));
 		assertEquals(B, dst.exactRef(master).getObjectId());
 		fsck(dst, B);
 
@@ -213,16 +213,19 @@ public void testInitialClone_Loose() throws Exception {
 
 	@Test
 	public void testInitialClone_Packed() throws Exception {
-		new TestRepository<>(remoteRepository).packAndPrune();
+		try (TestRepository<Repository> tr = new TestRepository<>(
+				remoteRepository)) {
+			tr.packAndPrune();
+		}
 
 		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
+		assertFalse(dst.getObjectDatabase().has(A_txt));
 
 		try (Transport t = Transport.open(dst, remoteURI)) {
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
 		}
 
-		assertTrue(dst.hasObject(A_txt));
+		assertTrue(dst.getObjectDatabase().has(A_txt));
 		assertEquals(B, dst.exactRef(master).getObjectId());
 		fsck(dst, B);
 
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 4ff81c5..2d22baf 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
@@ -193,14 +193,14 @@ public void testListRemote() throws IOException {
 	@Test
 	public void testInitialClone_Small() throws Exception {
 		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
+		assertFalse(dst.getObjectDatabase().has(A_txt));
 
 		try (Transport t = Transport.open(dst, remoteURI)) {
 		((TransportHttp) t).setUseSmartHttp(false);
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
 		}
 
-		assertTrue(dst.hasObject(A_txt));
+		assertTrue(dst.getObjectDatabase().has(A_txt));
 		assertEquals(B, dst.exactRef(master).getObjectId());
 		fsck(dst, B);
 
@@ -215,17 +215,20 @@ public void testInitialClone_Small() throws Exception {
 
 	@Test
 	public void testInitialClone_Packed() throws Exception {
-		new TestRepository<>(remoteRepository).packAndPrune();
+		try (TestRepository<Repository> tr = new TestRepository<>(
+				remoteRepository)) {
+			tr.packAndPrune();
+		}
 
 		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
+		assertFalse(dst.getObjectDatabase().has(A_txt));
 
 		try (Transport t = Transport.open(dst, remoteURI)) {
 			((TransportHttp) t).setUseSmartHttp(false);
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
 		}
 
-		assertTrue(dst.hasObject(A_txt));
+		assertTrue(dst.getObjectDatabase().has(A_txt));
 		assertEquals(B, dst.exactRef(master).getObjectId());
 		fsck(dst, B);
 
diff --git a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/HookMessageTest.java b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/HookMessageTest.java
index 7795658..5a5ff1a 100644
--- a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/HookMessageTest.java
+++ b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/HookMessageTest.java
@@ -163,7 +163,7 @@ public void testPush_CreateBranch() throws Exception {
 					.singleton(update));
 		}
 
-		assertTrue(remoteRepository.hasObject(Q_txt));
+		assertTrue(remoteRepository.getObjectDatabase().has(Q_txt));
 		assertNotNull("has " + dstName, remoteRepository.exactRef(dstName));
 		assertEquals(Q, remoteRepository.exactRef(dstName).getObjectId());
 		fsck(remoteRepository, Q);
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
index 7deb0d8..30501df 100644
--- 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
@@ -275,13 +275,13 @@ public void destroy() {
 	@Test
 	public void testInitialClone_ViaHttps() throws Exception {
 		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
+		assertFalse(dst.getObjectDatabase().has(A_txt));
 
 		try (Transport t = Transport.open(dst, secureURI)) {
 			t.setCredentialsProvider(testCredentials);
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
 		}
-		assertTrue(dst.hasObject(A_txt));
+		assertTrue(dst.getObjectDatabase().has(A_txt));
 		assertEquals(B, dst.exactRef(master).getObjectId());
 		fsck(dst, B);
 
@@ -292,14 +292,14 @@ public void testInitialClone_ViaHttps() throws Exception {
 	@Test
 	public void testInitialClone_RedirectToHttps() throws Exception {
 		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
+		assertFalse(dst.getObjectDatabase().has(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));
+		assertTrue(dst.getObjectDatabase().has(A_txt));
 		assertEquals(B, dst.exactRef(master).getObjectId());
 		fsck(dst, B);
 
@@ -310,7 +310,7 @@ public void testInitialClone_RedirectToHttps() throws Exception {
 	@Test
 	public void testInitialClone_RedirectBackToHttp() throws Exception {
 		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
+		assertFalse(dst.getObjectDatabase().has(A_txt));
 
 		URIish cloneFrom = extendPath(secureURI, "/back");
 		try (Transport t = Transport.open(dst, cloneFrom)) {
@@ -325,7 +325,7 @@ public void testInitialClone_RedirectBackToHttp() throws Exception {
 	@Test
 	public void testInitialClone_SslFailure() throws Exception {
 		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
+		assertFalse(dst.getObjectDatabase().has(A_txt));
 
 		try (Transport t = Transport.open(dst, secureURI)) {
 			// Set a credentials provider that doesn't handle questions
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 78bf778..017e2c7 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
@@ -206,7 +206,7 @@ public UploadPack create(HttpServletRequest req, Repository db)
 
 		ServletContextHandler app = addNormalContext(gs, src, srcName);
 
-		ServletContextHandler broken = addBrokenContext(gs, src, srcName);
+		ServletContextHandler broken = addBrokenContext(gs, srcName);
 
 		ServletContextHandler redirect = addRedirectContext(gs);
 
@@ -285,8 +285,8 @@ public void destroy() {
 		return app;
 	}
 
-	@SuppressWarnings("unused")
-	private ServletContextHandler addBrokenContext(GitServlet gs, TestRepository<Repository> src, String srcName) {
+	private ServletContextHandler addBrokenContext(GitServlet gs,
+			String srcName) {
 		ServletContextHandler broken = server.addContext("/bad");
 		broken.addFilter(new FilterHolder(new Filter() {
 
@@ -414,12 +414,11 @@ public void destroy() {
 
 	@Test
 	public void testListRemote() throws IOException {
-		Repository dst = createBareRepository();
-
 		assertEquals("http", remoteURI.getScheme());
 
 		Map<String, Ref> map;
-		try (Transport t = Transport.open(dst, remoteURI)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, remoteURI)) {
 			// I didn't make up these public interface names, I just
 			// approved them for inclusion into the code base. Sorry.
 			// --spearce
@@ -457,9 +456,9 @@ public void testListRemote() throws IOException {
 
 	@Test
 	public void testListRemote_BadName() throws IOException, URISyntaxException {
-		Repository dst = createBareRepository();
 		URIish uri = new URIish(this.remoteURI.toString() + ".invalid");
-		try (Transport t = Transport.open(dst, uri)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, uri)) {
 			try {
 				t.openFetch();
 				fail("fetch connection opened");
@@ -484,23 +483,20 @@ public void testListRemote_BadName() throws IOException, URISyntaxException {
 
 	@Test
 	public void testFetchBySHA1() throws Exception {
-		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
-
-		try (Transport t = Transport.open(dst, remoteURI)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, remoteURI)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			t.fetch(NullProgressMonitor.INSTANCE,
 					Collections.singletonList(new RefSpec(B.name())));
+			assertTrue(dst.getObjectDatabase().has(A_txt));
 		}
-
-		assertTrue(dst.hasObject(A_txt));
 	}
 
 	@Test
 	public void testFetchBySHA1Unreachable() throws Exception {
-		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
-
-		try (Transport t = Transport.open(dst, remoteURI)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, remoteURI)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			thrown.expect(TransportException.class);
 			thrown.expectMessage(Matchers.containsString(
 					"want " + unreachableCommit.name() + " not valid"));
@@ -512,9 +508,6 @@ public void testFetchBySHA1Unreachable() throws Exception {
 	@Test
 	public void testFetchBySHA1UnreachableByAdvertiseRefsHook()
 			throws Exception {
-		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
-
 		advertiseRefsHook = new AbstractAdvertiseRefsHook() {
 			@Override
 			protected Map<String, Ref> getAdvertisedRefs(Repository repository,
@@ -523,7 +516,9 @@ protected Map<String, Ref> getAdvertisedRefs(Repository repository,
 			}
 		};
 
-		try (Transport t = Transport.open(dst, remoteURI)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, remoteURI)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			thrown.expect(TransportException.class);
 			thrown.expectMessage(Matchers.containsString(
 					"want " + A.name() + " not valid"));
@@ -534,17 +529,15 @@ protected Map<String, Ref> getAdvertisedRefs(Repository repository,
 
 	@Test
 	public void testInitialClone_Small() throws Exception {
-		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
-
-		try (Transport t = Transport.open(dst, remoteURI)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, remoteURI)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			assertTrue(dst.getObjectDatabase().has(A_txt));
+			assertEquals(B, dst.exactRef(master).getObjectId());
+			fsck(dst, B);
 		}
 
-		assertTrue(dst.hasObject(A_txt));
-		assertEquals(B, dst.exactRef(master).getObjectId());
-		fsck(dst, B);
-
 		List<AccessEvent> requests = getRequests();
 		assertEquals(2, requests.size());
 
@@ -574,21 +567,20 @@ public void testInitialClone_Small() throws Exception {
 
 	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);
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, cloneFrom)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
+			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			assertTrue(dst.getObjectDatabase().has(A_txt));
+			assertEquals(B, dst.exactRef(master).getObjectId());
+			fsck(dst, B);
+		}
 
 		List<AccessEvent> requests = getRequests();
 		assertEquals(2 + nofRedirects, requests.size());
@@ -663,12 +655,12 @@ public void testInitialClone_RedirectTooOften() throws Exception {
 				.getUserConfig();
 		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)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, cloneFrom)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
 			fail("Should have failed (too many redirects)");
 		} catch (TransportException e) {
@@ -685,11 +677,10 @@ public void testInitialClone_RedirectTooOften() throws Exception {
 
 	@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)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, cloneFrom)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
 			fail("Should have failed (redirect loop)");
 		} catch (TransportException e) {
@@ -703,18 +694,17 @@ public void testInitialClone_RedirectOnPostAllowed() throws Exception {
 				.getUserConfig();
 		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)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, cloneFrom)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			assertTrue(dst.getObjectDatabase().has(A_txt));
+			assertEquals(B, dst.exactRef(master).getObjectId());
+			fsck(dst, B);
 		}
 
-		assertTrue(dst.hasObject(A_txt));
-		assertEquals(B, dst.exactRef(master).getObjectId());
-		fsck(dst, B);
-
 		List<AccessEvent> requests = getRequests();
 		assertEquals(3, requests.size());
 
@@ -748,11 +738,10 @@ public void testInitialClone_RedirectOnPostAllowed() throws Exception {
 
 	@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)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, cloneFrom)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
 			fail("Should have failed (redirect on POST)");
 		} catch (TransportException e) {
@@ -767,10 +756,9 @@ public void testInitialClone_RedirectForbidden() throws Exception {
 		userConfig.setString("http", null, "followRedirects", "false");
 		userConfig.save();
 
-		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
-
-		try (Transport t = Transport.open(dst, redirectURI)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, redirectURI)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
 			fail("Should have failed (redirects forbidden)");
 		} catch (TransportException e) {
@@ -781,18 +769,16 @@ public void testInitialClone_RedirectForbidden() throws Exception {
 
 	@Test
 	public void testInitialClone_WithAuthentication() throws Exception {
-		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
-
-		try (Transport t = Transport.open(dst, authURI)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, authURI)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			t.setCredentialsProvider(testCredentials);
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			assertTrue(dst.getObjectDatabase().has(A_txt));
+			assertEquals(B, dst.exactRef(master).getObjectId());
+			fsck(dst, B);
 		}
 
-		assertTrue(dst.hasObject(A_txt));
-		assertEquals(B, dst.exactRef(master).getObjectId());
-		fsck(dst, B);
-
 		List<AccessEvent> requests = getRequests();
 		assertEquals(3, requests.size());
 
@@ -827,10 +813,9 @@ public void testInitialClone_WithAuthentication() throws Exception {
 	@Test
 	public void testInitialClone_WithAuthenticationNoCredentials()
 			throws Exception {
-		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
-
-		try (Transport t = Transport.open(dst, authURI)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, authURI)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
 			fail("Should not have succeeded -- no authentication");
 		} catch (TransportException e) {
@@ -849,10 +834,9 @@ public void testInitialClone_WithAuthenticationNoCredentials()
 	@Test
 	public void testInitialClone_WithAuthenticationWrongCredentials()
 			throws Exception {
-		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
-
-		try (Transport t = Transport.open(dst, authURI)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, authURI)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			t.setCredentialsProvider(new UsernamePasswordCredentialsProvider(
 					AppServer.username, "wrongpassword"));
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
@@ -875,9 +859,6 @@ public void testInitialClone_WithAuthenticationWrongCredentials()
 	@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") {
@@ -895,15 +876,16 @@ public boolean get(URIish uri, CredentialItem... items)
 				return super.get(uri, items);
 			}
 		};
-		try (Transport t = Transport.open(dst, cloneFrom)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, cloneFrom)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			t.setCredentialsProvider(uriSpecificCredentialsProvider);
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			assertTrue(dst.getObjectDatabase().has(A_txt));
+			assertEquals(B, dst.exactRef(master).getObjectId());
+			fsck(dst, B);
 		}
 
-		assertTrue(dst.hasObject(A_txt));
-		assertEquals(B, dst.exactRef(master).getObjectId());
-		fsck(dst, B);
-
 		List<AccessEvent> requests = getRequests();
 		assertEquals(4, requests.size());
 
@@ -944,18 +926,16 @@ public boolean get(URIish uri, CredentialItem... items)
 	@Test
 	public void testInitialClone_WithAuthenticationOnPostOnly()
 			throws Exception {
-		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
-
-		try (Transport t = Transport.open(dst, authOnPostURI)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, authOnPostURI)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			t.setCredentialsProvider(testCredentials);
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
+			assertTrue(dst.getObjectDatabase().has(A_txt));
+			assertEquals(B, dst.exactRef(master).getObjectId());
+			fsck(dst, B);
 		}
 
-		assertTrue(dst.hasObject(A_txt));
-		assertEquals(B, dst.exactRef(master).getObjectId());
-		fsck(dst, B);
-
 		List<AccessEvent> requests = getRequests();
 		assertEquals(3, requests.size());
 
@@ -1006,8 +986,12 @@ public void testFetch_FewLocalCommits() throws Exception {
 
 		// Create a new commit on the remote.
 		//
-		b = new TestRepository<>(remoteRepository).branch(master);
-		RevCommit Z = b.commit().message("Z").create();
+		RevCommit Z;
+		try (TestRepository<Repository> tr = new TestRepository<>(
+				remoteRepository)) {
+			b = tr.branch(master);
+			Z = b.commit().message("Z").create();
+		}
 
 		// Now incrementally update.
 		//
@@ -1066,8 +1050,12 @@ public void testFetch_TooManyLocalCommits() throws Exception {
 
 		// Create a new commit on the remote.
 		//
-		b = new TestRepository<>(remoteRepository).branch(master);
-		RevCommit Z = b.commit().message("Z").create();
+		RevCommit Z;
+		try (TestRepository<Repository> tr = new TestRepository<>(
+				remoteRepository)) {
+			b = tr.branch(master);
+			Z = b.commit().message("Z").create();
+		}
 
 		// Now incrementally update.
 		//
@@ -1121,10 +1109,9 @@ public void testFetch_TooManyLocalCommits() throws Exception {
 
 	@Test
 	public void testInitialClone_BrokenServer() throws Exception {
-		Repository dst = createBareRepository();
-		assertFalse(dst.hasObject(A_txt));
-
-		try (Transport t = Transport.open(dst, brokenURI)) {
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, brokenURI)) {
+			assertFalse(dst.getObjectDatabase().has(A_txt));
 			try {
 				t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
 				fail("fetch completed despite upload-pack being broken");
@@ -1159,12 +1146,14 @@ public void testInitialClone_BrokenServer() throws Exception {
 
 	@Test
 	public void testInvalidWant() throws Exception {
-		@SuppressWarnings("resource")
-		ObjectId id = new ObjectInserter.Formatter().idFor(Constants.OBJ_BLOB,
-				"testInvalidWant".getBytes(UTF_8));
+		ObjectId id;
+		try (ObjectInserter.Formatter formatter = new ObjectInserter.Formatter()) {
+			id = formatter.idFor(Constants.OBJ_BLOB,
+					"testInvalidWant".getBytes(UTF_8));
+		}
 
-		Repository dst = createBareRepository();
-		try (Transport t = Transport.open(dst, remoteURI);
+		try (Repository dst = createBareRepository();
+				Transport t = Transport.open(dst, remoteURI);
 				FetchConnection c = t.openFetch()) {
 			Ref want = new ObjectIdRef.Unpeeled(Ref.Storage.NETWORK, id.name(),
 					id);
@@ -1201,8 +1190,8 @@ public void testFetch_RefsUnreadableOnUpload() throws Exception {
 			URIish badRefsURI = new URIish(noRefServer.getURI()
 					.resolve(app.getContextPath() + "/" + repoName).toString());
 
-			Repository dst = createBareRepository();
-			try (Transport t = Transport.open(dst, badRefsURI);
+			try (Repository dst = createBareRepository();
+					Transport t = Transport.open(dst, badRefsURI);
 					FetchConnection c = t.openFetch()) {
 				// We start failing here to exercise the post-advertisement
 				// upload pack handler.
@@ -1281,7 +1270,7 @@ public void testPush_CreateBranch() throws Exception {
 			t.push(NullProgressMonitor.INSTANCE, Collections.singleton(u));
 		}
 
-		assertTrue(remoteRepository.hasObject(Q_txt));
+		assertTrue(remoteRepository.getObjectDatabase().has(Q_txt));
 		assertNotNull("has " + dstName, remoteRepository.exactRef(dstName));
 		assertEquals(Q, remoteRepository.exactRef(dstName).getObjectId());
 		fsck(remoteRepository, Q);
@@ -1355,7 +1344,7 @@ public void testPush_ChunkedEncoding() throws Exception {
 			t.push(NullProgressMonitor.INSTANCE, Collections.singleton(u));
 		}
 
-		assertTrue(remoteRepository.hasObject(Q_bin));
+		assertTrue(remoteRepository.getObjectDatabase().has(Q_bin));
 		assertNotNull("has " + dstName, remoteRepository.exactRef(dstName));
 		assertEquals(Q, remoteRepository.exactRef(dstName).getObjectId());
 		fsck(remoteRepository, Q);
diff --git a/org.eclipse.jgit.junit.http/META-INF/MANIFEST.MF b/org.eclipse.jgit.junit.http/META-INF/MANIFEST.MF
index 8432c45..1286fc3 100644
--- a/org.eclipse.jgit.junit.http/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.junit.http/META-INF/MANIFEST.MF
@@ -3,7 +3,7 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.junit.http
 Bundle-SymbolicName: org.eclipse.jgit.junit.http
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
@@ -22,16 +22,16 @@
  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.ssl;version="[9.4.5,10.0.0)",
- org.eclipse.jgit.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.http.server;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.junit;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.resolver;version="[5.2.3,5.3.0)",
+ org.eclipse.jgit.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.http.server;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.junit;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.resolver;version="[5.3.6,5.4.0)",
  org.junit;version="[4.12,5.0.0)"
-Export-Package: org.eclipse.jgit.junit.http;version="5.2.3";
+Export-Package: org.eclipse.jgit.junit.http;version="5.3.6";
   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 b766974..646cfd2 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.junit.http</artifactId>
diff --git a/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/HttpTestCase.java b/org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/HttpTestCase.java
index a133ca6..41bc97d 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
@@ -186,9 +186,10 @@ protected List<AccessEvent> getRequests(String path) {
 	 */
 	protected static void fsck(Repository db, RevObject... tips)
 			throws Exception {
-		TestRepository<? extends Repository> tr =
-				new TestRepository<>(db);
-		tr.fsck(tips);
+		try (TestRepository<? extends Repository> tr =
+				new TestRepository<>(db)) {
+			tr.fsck(tips);
+		}
 	}
 
 	/**
diff --git a/org.eclipse.jgit.junit.ssh/META-INF/MANIFEST.MF b/org.eclipse.jgit.junit.ssh/META-INF/MANIFEST.MF
index 1467499..d5ad11c 100644
--- a/org.eclipse.jgit.junit.ssh/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.junit.ssh/META-INF/MANIFEST.MF
@@ -3,7 +3,7 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.junit.ssh
 Bundle-SymbolicName: org.eclipse.jgit.junit.ssh
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
@@ -29,8 +29,8 @@
  org.apache.sshd.server.shell;version="[2.0.0,2.1.0)",
  org.apache.sshd.server.subsystem;version="[2.0.0,2.1.0)",
  org.apache.sshd.server.subsystem.sftp;version="[2.0.0,2.1.0)",
- org.eclipse.jgit.annotations;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport;version="[5.2.3,5.3.0)",
+ org.eclipse.jgit.annotations;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport;version="[5.3.6,5.4.0)",
  org.slf4j;version="[1.7.0,2.0.0)"
-Export-Package: org.eclipse.jgit.junit.ssh;version="5.2.3"
+Export-Package: org.eclipse.jgit.junit.ssh;version="5.3.6"
diff --git a/org.eclipse.jgit.junit.ssh/pom.xml b/org.eclipse.jgit.junit.ssh/pom.xml
index 4cd68eb..46e3ff7 100644
--- a/org.eclipse.jgit.junit.ssh/pom.xml
+++ b/org.eclipse.jgit.junit.ssh/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.junit.ssh</artifactId>
diff --git a/org.eclipse.jgit.junit/META-INF/MANIFEST.MF b/org.eclipse.jgit.junit/META-INF/MANIFEST.MF
index a416ae7..762a1da 100644
--- a/org.eclipse.jgit.junit/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.junit/META-INF/MANIFEST.MF
@@ -3,34 +3,34 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.junit
 Bundle-SymbolicName: org.eclipse.jgit.junit
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Import-Package: org.eclipse.jgit.annotations;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.api;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.api.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.dircache;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.pack;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.merge;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport;version="5.2.3",
- org.eclipse.jgit.treewalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.treewalk.filter;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util.io;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util.time;version="[5.2.3,5.3.0)",
+Import-Package: org.eclipse.jgit.annotations;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.api;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.api.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.dircache;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.pack;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.merge;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport;version="5.3.6",
+ org.eclipse.jgit.treewalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.treewalk.filter;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util.io;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util.time;version="[5.3.6,5.4.0)",
  org.junit;version="[4.12,5.0.0)",
  org.junit.rules;version="[4.12,5.0.0)",
  org.junit.runner;version="[4.12,5.0.0)",
  org.junit.runners.model;version="[4.12,5.0.0)",
  org.slf4j;version="[1.7.0,2.0.0)"
-Export-Package: org.eclipse.jgit.junit;version="5.2.3";
+Export-Package: org.eclipse.jgit.junit;version="5.3.6";
   uses:="org.eclipse.jgit.dircache,
    org.eclipse.jgit.lib,
    org.eclipse.jgit.revwalk,
@@ -43,4 +43,4 @@
    org.junit.runners.model,
    org.junit.runner,
    org.eclipse.jgit.util.time",
- org.eclipse.jgit.junit.time;version="5.2.3";uses:="org.eclipse.jgit.util.time"
+ org.eclipse.jgit.junit.time;version="5.3.6";uses:="org.eclipse.jgit.util.time"
diff --git a/org.eclipse.jgit.junit/pom.xml b/org.eclipse.jgit.junit/pom.xml
index e198193..5ec7bd7 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.junit</artifactId>
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java
index 29579d0..3b7cdde 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java
@@ -401,10 +401,11 @@ protected FileRepository createWorkRepository() throws IOException {
 	 * @return the newly created repository, opened for access
 	 * @throws IOException
 	 *             the repository could not be created in the temporary area
+	 * @since 5.3
 	 */
-	private FileRepository createRepository(boolean bare)
+	protected FileRepository createRepository(boolean bare)
 			throws IOException {
-		return createRepository(bare, true /* auto close */);
+		return createRepository(bare, false /* auto close */);
 	}
 
 	/**
@@ -414,11 +415,13 @@ private FileRepository createRepository(boolean bare)
 	 *            true to create a bare repository; false to make a repository
 	 *            within its working directory
 	 * @param autoClose
-	 *            auto close the repository in #tearDown
+	 *            auto close the repository in {@link #tearDown()}
 	 * @return the newly created repository, opened for access
 	 * @throws IOException
 	 *             the repository could not be created in the temporary area
+	 * @deprecated use {@link #createRepository(boolean)} instead
 	 */
+	@Deprecated
 	public FileRepository createRepository(boolean bare, boolean autoClose)
 			throws IOException {
 		File gitdir = createUniqueTestGitDir(bare);
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java
index 49a2b20..02ffe4f 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java
@@ -112,7 +112,7 @@
  * @param <R>
  *            type of Repository the test data is stored on.
  */
-public class TestRepository<R extends Repository> {
+public class TestRepository<R extends Repository> implements AutoCloseable {
 
 	/** Constant <code>AUTHOR="J. Author"</code> */
 	public static final String AUTHOR = "J. Author";
@@ -933,6 +933,23 @@ public void packAndPrune() throws Exception {
 		}
 	}
 
+	/**
+	 * Closes the underlying {@link Repository} object and any other internal
+	 * resources.
+	 * <p>
+	 * {@link AutoCloseable} resources that may escape this object, such as
+	 * those returned by the {@link #git} and {@link #getRevWalk()} methods are
+	 * not closed.
+	 */
+	@Override
+	public void close() {
+		try {
+			inserter.close();
+		} finally {
+			db.close();
+		}
+	}
+
 	private static void prunePacked(ObjectDirectory odb) throws IOException {
 		for (PackFile p : odb.getPacks()) {
 			for (MutableEntry e : p)
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 32bdf98..8712bce 100644
--- a/org.eclipse.jgit.lfs.server.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.lfs.server.test/META-INF/MANIFEST.MF
@@ -3,7 +3,7 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.lfs.server.test
 Bundle-SymbolicName: org.eclipse.jgit.lfs.server.test
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-Localization: plugin
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
@@ -28,24 +28,24 @@
  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.api;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.api.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.junit;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.junit.http;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.server;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.server.fs;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.test;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.treewalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.treewalk.filter;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)",
+ org.eclipse.jgit.api;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.api.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.junit;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.junit.http;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.server;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.server.fs;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.test;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.treewalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.treewalk.filter;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)",
  org.hamcrest.core;version="[1.1.0,2.0.0)",
  org.junit;version="[4.12,5.0.0)",
  org.junit.rules;version="[4.12,5.0.0)",
diff --git a/org.eclipse.jgit.lfs.server.test/pom.xml b/org.eclipse.jgit.lfs.server.test/pom.xml
index 1e26b0a..ee717ab 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.lfs.server.test</artifactId>
@@ -137,7 +137,7 @@
       <plugin>
         <artifactId>maven-surefire-plugin</artifactId>
         <configuration>
-          <argLine>-Djava.io.tmpdir=${project.build.directory}  -Xmx300m</argLine>
+          <argLine>@{argLine} -Djava.io.tmpdir=${project.build.directory}  -Xmx300m</argLine>
         </configuration>
       </plugin>
     </plugins>
diff --git a/org.eclipse.jgit.lfs.server/META-INF/MANIFEST.MF b/org.eclipse.jgit.lfs.server/META-INF/MANIFEST.MF
index 7bed133..b1ab4f5 100644
--- a/org.eclipse.jgit.lfs.server/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.lfs.server/META-INF/MANIFEST.MF
@@ -3,19 +3,19 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.lfs.server
 Bundle-SymbolicName: org.eclipse.jgit.lfs.server
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
-Export-Package: org.eclipse.jgit.lfs.server;version="5.2.3";
+Export-Package: org.eclipse.jgit.lfs.server;version="5.3.6";
   uses:="javax.servlet.http,
    org.eclipse.jgit.lfs.lib",
- org.eclipse.jgit.lfs.server.fs;version="5.2.3";
+ org.eclipse.jgit.lfs.server.fs;version="5.3.6";
   uses:="javax.servlet,
    javax.servlet.http,
    org.eclipse.jgit.lfs.server,
    org.eclipse.jgit.lfs.lib",
- org.eclipse.jgit.lfs.server.internal;version="5.2.3";x-internal:=true,
- org.eclipse.jgit.lfs.server.s3;version="5.2.3";
+ org.eclipse.jgit.lfs.server.internal;version="5.3.6";x-internal:=true,
+ org.eclipse.jgit.lfs.server.s3;version="5.3.6";
   uses:="org.eclipse.jgit.lfs.server,
    org.eclipse.jgit.lfs.lib"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
@@ -25,15 +25,15 @@
  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="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.internal;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.nls;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.http;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.http.apache;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)",
+ org.eclipse.jgit.annotations;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.internal;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.nls;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.http;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.http.apache;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)",
  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 4a2b38a..8305d60 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.lfs.server</artifactId>
diff --git a/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/internal/LfsGson.java b/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/internal/LfsGson.java
index 7974b24..3f6b780 100644
--- a/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/internal/LfsGson.java
+++ b/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/internal/LfsGson.java
@@ -53,8 +53,6 @@
 
 /**
  * Wrapper for {@link com.google.gson.Gson} used by LFS servlets.
- *
- * @since 4.10.0
  */
 public class LfsGson {
 	private static final Gson gson = new GsonBuilder()
diff --git a/org.eclipse.jgit.lfs.test/BUILD b/org.eclipse.jgit.lfs.test/BUILD
index 504e2df..ee2402a 100644
--- a/org.eclipse.jgit.lfs.test/BUILD
+++ b/org.eclipse.jgit.lfs.test/BUILD
@@ -1,11 +1,10 @@
-load("@rules_java//java:defs.bzl", "java_library")
-
-package(default_visibility = ["//visibility:public"])
-
 load(
     "@com_googlesource_gerrit_bazlets//tools:junit.bzl",
     "junit_tests",
 )
+load("@rules_java//java:defs.bzl", "java_library")
+
+package(default_visibility = ["//visibility:public"])
 
 junit_tests(
     name = "lfs",
diff --git a/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF
index 2863967..e87ccb6 100644
--- a/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF
@@ -3,23 +3,23 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.lfs.test
 Bundle-SymbolicName: org.eclipse.jgit.lfs.test
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-Localization: plugin
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Import-Package: org.eclipse.jgit.internal.storage.dfs;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.junit;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.treewalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.treewalk.filter;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)",
+Import-Package: org.eclipse.jgit.internal.storage.dfs;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.junit;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.treewalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.treewalk.filter;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)",
  org.hamcrest.core;version="[1.1.0,2.0.0)",
  org.junit;version="[4.12,5.0.0)",
  org.junit.runner;version="[4.12,5.0.0)",
  org.junit.runners;version="[4.12,5.0.0)"
-Export-Package: org.eclipse.jgit.lfs.test;version="5.2.3";x-friends:="org.eclipse.jgit.lfs.server.test"
+Export-Package: org.eclipse.jgit.lfs.test;version="5.3.6";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 37d11f9..1f05af8 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.lfs.test</artifactId>
@@ -111,7 +111,7 @@
       <plugin>
         <artifactId>maven-surefire-plugin</artifactId>
         <configuration>
-          <argLine>-Djava.io.tmpdir=${project.build.directory}  -Xmx300m</argLine>
+          <argLine>@{argLine} -Djava.io.tmpdir=${project.build.directory}  -Xmx300m</argLine>
         </configuration>
       </plugin>
     </plugins>
diff --git a/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF b/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF
index 209b2b2..ee9dec9 100644
--- a/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF
@@ -3,33 +3,33 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.lfs
 Bundle-SymbolicName: org.eclipse.jgit.lfs
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
-Export-Package: org.eclipse.jgit.lfs;version="5.2.3",
- org.eclipse.jgit.lfs.errors;version="5.2.3",
- org.eclipse.jgit.lfs.internal;version="5.2.3";x-friends:="org.eclipse.jgit.lfs.test,org.eclipse.jgit.lfs.server.fs,org.eclipse.jgit.lfs.server",
- org.eclipse.jgit.lfs.lib;version="5.2.3"
+Export-Package: org.eclipse.jgit.lfs;version="5.3.6",
+ org.eclipse.jgit.lfs.errors;version="5.3.6",
+ org.eclipse.jgit.lfs.internal;version="5.3.6";x-friends:="org.eclipse.jgit.lfs.test,org.eclipse.jgit.lfs.server.fs,org.eclipse.jgit.lfs.server",
+ org.eclipse.jgit.lfs.lib;version="5.3.6"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: com.google.gson;version="[2.8.2,3.0.0)",
  com.google.gson.stream;version="[2.8.2,3.0.0)",
  org.apache.http.impl.client;version="[4.2.6,5.0.0)",
  org.apache.http.impl.conn;version="[4.2.6,5.0.0)",
- org.eclipse.jgit.annotations;version="[5.2.3,5.3.0)";resolution:=optional,
- org.eclipse.jgit.api.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.attributes;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.diff;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.hooks;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.nls;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.storage.pack;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.http;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.treewalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.treewalk.filter;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util.io;version="[5.2.3,5.3.0)"
+ org.eclipse.jgit.annotations;version="[5.3.6,5.4.0)";resolution:=optional,
+ org.eclipse.jgit.api.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.attributes;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.diff;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.hooks;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.nls;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.storage.pack;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.http;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.treewalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.treewalk.filter;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util.io;version="[5.3.6,5.4.0)"
diff --git a/org.eclipse.jgit.lfs/pom.xml b/org.eclipse.jgit.lfs/pom.xml
index f7cad33..b0f849e 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.lfs</artifactId>
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 ad4da8c..7182e4f 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="5.2.3.qualifier"
+      version="5.3.6.qualifier"
       provider-name="%providerName">
 
    <description url="http://www.eclipse.org/jgit/">
@@ -86,4 +86,25 @@
          version="0.0.0"
          unpack="false"/>
 
+   <plugin
+         id="org.bouncycastle.bcpg"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         unpack="false"/>
+
+   <plugin
+         id="org.bouncycastle.bcpkix"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         unpack="false"/>
+
+   <plugin
+         id="org.bouncycastle.bcprov"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         unpack="false"/>
+
 </feature>
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 576756b..8a5d9df 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-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 e721ddc..6d5c864 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="5.2.3.qualifier"
+      version="5.3.6.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 c356b34..368d69f 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-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 0abc1ac..8fd9e66 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="5.2.3.qualifier"
+      version="5.3.6.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 da11f32..0fce4b1 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-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 d287505..cab1729 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="5.2.3.qualifier"
+      version="5.3.6.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 7957600..240ae30 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-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 c74326e..73db815 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="5.2.3.qualifier"
+      version="5.3.6.qualifier"
       provider-name="%providerName">
 
    <description url="http://www.eclipse.org/jgit/">
@@ -31,9 +31,9 @@
          version="0.0.0"/>
 
    <requires>
-      <import feature="org.eclipse.jgit" version="5.2.3" match="equivalent"/>
-      <import feature="org.eclipse.jgit.lfs" version="5.2.3" match="equivalent"/>
-      <import feature="org.eclipse.jgit.ssh.apache" version="5.2.3" match="equivalent"/>
+      <import feature="org.eclipse.jgit" version="5.3.6" match="equivalent"/>
+      <import feature="org.eclipse.jgit.lfs" version="5.3.6" match="equivalent"/>
+      <import feature="org.eclipse.jgit.ssh.apache" version="5.3.6" 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 e45d79d..464a3f8 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-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 2179699..e5050d9 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="5.2.3.qualifier"
+      version="5.3.6.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 221f031..85dfd20 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-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 e258eb2..67f0552 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-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 cee8946..44bc737 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="5.2.3.qualifier"
+      version="5.3.6.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 60b2c5e..e1d53a9 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.feature/feature.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.feature/feature.xml
index 2ce712c..b2d2e59 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.feature/feature.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.eclipse.jgit.ssh.apache"
       label="%featureName"
-      version="5.2.3.qualifier"
+      version="5.3.6.qualifier"
       provider-name="%providerName">
 
    <description url="http://www.eclipse.org/jgit/">
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.feature/pom.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.feature/pom.xml
index 869fb17..efacfc6 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.feature/pom.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.feature/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>jgit.tycho.parent</artifactId>
-    <version>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.source.feature/feature.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.source.feature/feature.xml
index 0877744..797f0fd 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.source.feature/feature.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.source.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.eclipse.jgit.ssh.apache.source"
       label="%featureName"
-      version="5.2.3.qualifier"
+      version="5.3.6.qualifier"
       provider-name="%providerName">
 
    <description url="http://www.eclipse.org/jgit/">
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.source.feature/pom.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.source.feature/pom.xml
index 6fd255a..76a3b3e 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.source.feature/pom.xml
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.ssh.apache.source.feature/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>jgit.tycho.parent</artifactId>
-    <version>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/.project b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/.project
index 18caf2c..48c2bd1 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/.project
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/.project
@@ -6,6 +6,11 @@
 	</projects>
 	<buildSpec>
 		<buildCommand>
+			<name>org.eclipse.xtext.ui.shared.xtextBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
 			<name>org.eclipse.pde.ManifestBuilder</name>
 			<arguments>
 			</arguments>
@@ -13,5 +18,6 @@
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.pde.PluginNature</nature>
+		<nature>org.eclipse.xtext.ui.shared.xtextNature</nature>
 	</natures>
 </projectDescription>
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 b869d8d..2f0c557 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: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.10-staging.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.10-staging.tpd
deleted file mode 100644
index 98bbc2d..0000000
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.10-staging.tpd
+++ /dev/null
@@ -1,8 +0,0 @@
-target "jgit-4.9-staging" with source configurePhase
-
-include "projects/jetty-9.4.11.tpd"
-include "orbit/R20190602212107-2019-06.tpd"
-
-location "http://download.eclipse.org/staging/2018-12/" {
-	org.eclipse.osgi lazy
-}
\ No newline at end of file
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-4.10.target
similarity index 72%
rename from org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.target
rename to org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.10.target
index 7820a13..86653be 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.target
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.10.target
@@ -1,26 +1,26 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.5" sequenceNumber="1566229356">
+<target name="jgit-4.10" sequenceNumber="1566244557">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
-      <unit id="org.eclipse.jetty.client" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.client.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.continuation" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.continuation.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.http" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.http.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.io" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.io.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.security" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.security.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.server" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.server.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.servlet" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.servlet.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.util" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.util.source" version="9.4.11.v20180605"/>
-      <repository id="jetty-9.4.11" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.client" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.client.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.continuation" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.continuation.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.http" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.http.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.io" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.io.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.security" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.security.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.server" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.server.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.servlet" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.servlet.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.util" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.util.source" version="9.4.14.v20181114"/>
+      <repository id="jetty-9.4.14" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.14.v20181114"/>
     </location>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.apache.ant" version="1.10.5.v20190526-1402"/>
@@ -37,6 +37,12 @@
       <unit id="org.apache.httpcomponents.httpcore.source" version="4.4.10.v20190123-2214"/>
       <unit id="org.apache.log4j" version="1.2.15.v201012070815"/>
       <unit id="org.apache.log4j.source" version="1.2.15.v201012070815"/>
+      <unit id="org.bouncycastle.bcpg" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpg.source" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpkix" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpkix.source" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcprov" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcprov.source" version="1.60.0.v20181210-2057"/>
       <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" version="1.1.0.v20090501071000"/>
@@ -62,8 +68,8 @@
       <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="1.6.0.v20170629-1752"/>
-      <unit id="org.tukaani.xz.source" version="1.6.0.v20170629-1752"/>
+      <unit id="org.tukaani.xz" version="1.8.0.v20180207-1613"/>
+      <unit id="org.tukaani.xz.source" version="1.8.0.v20180207-1613"/>
       <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"/>
@@ -80,7 +86,7 @@
     </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/mars/"/>
+      <repository location="http://download.eclipse.org/releases/2018-12/"/>
     </location>
   </locations>
 </target>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.10.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.10.tpd
new file mode 100644
index 0000000..6beb42e
--- /dev/null
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.10.tpd
@@ -0,0 +1,8 @@
+target "jgit-4.10" with source configurePhase
+
+include "projects/jetty-9.4.14.tpd"
+include "orbit/R20190602212107-2019-06.tpd"
+
+location "http://download.eclipse.org/releases/2018-12/" {
+	org.eclipse.osgi lazy
+}
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.10-staging.target b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.11-staging.target
similarity index 72%
rename from org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.10-staging.target
rename to org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.11-staging.target
index 55e44b8..0857af3 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.10-staging.target
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.11-staging.target
@@ -1,26 +1,26 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.9-staging" sequenceNumber="1566229361">
+<target name="jgit-4.11-staging" sequenceNumber="1566244434">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
-      <unit id="org.eclipse.jetty.client" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.client.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.continuation" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.continuation.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.http" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.http.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.io" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.io.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.security" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.security.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.server" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.server.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.servlet" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.servlet.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.util" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.util.source" version="9.4.11.v20180605"/>
-      <repository id="jetty-9.4.11" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.client" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.client.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.continuation" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.continuation.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.http" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.http.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.io" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.io.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.security" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.security.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.server" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.server.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.servlet" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.servlet.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.util" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.util.source" version="9.4.14.v20181114"/>
+      <repository id="jetty-9.4.14" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.14.v20181114"/>
     </location>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.apache.ant" version="1.10.5.v20190526-1402"/>
@@ -37,6 +37,12 @@
       <unit id="org.apache.httpcomponents.httpcore.source" version="4.4.10.v20190123-2214"/>
       <unit id="org.apache.log4j" version="1.2.15.v201012070815"/>
       <unit id="org.apache.log4j.source" version="1.2.15.v201012070815"/>
+      <unit id="org.bouncycastle.bcpg" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpg.source" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpkix" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpkix.source" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcprov" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcprov.source" version="1.60.0.v20181210-2057"/>
       <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" version="1.1.0.v20090501071000"/>
@@ -62,8 +68,8 @@
       <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="1.6.0.v20170629-1752"/>
-      <unit id="org.tukaani.xz.source" version="1.6.0.v20170629-1752"/>
+      <unit id="org.tukaani.xz" version="1.8.0.v20180207-1613"/>
+      <unit id="org.tukaani.xz.source" version="1.8.0.v20180207-1613"/>
       <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"/>
@@ -80,7 +86,7 @@
     </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/staging/2018-12/"/>
+      <repository location="http://download.eclipse.org/staging/2019-03/"/>
     </location>
   </locations>
 </target>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.11-staging.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.11-staging.tpd
new file mode 100644
index 0000000..4fc23ed
--- /dev/null
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.11-staging.tpd
@@ -0,0 +1,8 @@
+target "jgit-4.11-staging" with source configurePhase
+
+include "projects/jetty-9.4.14.tpd"
+include "orbit/R20190602212107-2019-06.tpd"
+
+location "http://download.eclipse.org/staging/2019-03/" {
+	org.eclipse.osgi lazy
+}
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.tpd
deleted file mode 100644
index 7a5feb0..0000000
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.tpd
+++ /dev/null
@@ -1,8 +0,0 @@
-target "jgit-4.5" with source configurePhase
-
-include "projects/jetty-9.4.11.tpd"
-include "orbit/R20190602212107-2019-06.tpd"
-
-location "http://download.eclipse.org/releases/mars/" {
-	org.eclipse.osgi lazy
-}
\ No newline at end of file
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 997d9c9..05488b9 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
@@ -1,26 +1,26 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.6" sequenceNumber="1566229352">
+<target name="jgit-4.6" sequenceNumber="1566244561">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
-      <unit id="org.eclipse.jetty.client" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.client.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.continuation" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.continuation.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.http" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.http.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.io" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.io.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.security" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.security.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.server" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.server.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.servlet" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.servlet.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.util" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.util.source" version="9.4.11.v20180605"/>
-      <repository id="jetty-9.4.11" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.client" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.client.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.continuation" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.continuation.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.http" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.http.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.io" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.io.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.security" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.security.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.server" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.server.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.servlet" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.servlet.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.util" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.util.source" version="9.4.14.v20181114"/>
+      <repository id="jetty-9.4.14" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.14.v20181114"/>
     </location>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.apache.ant" version="1.10.5.v20190526-1402"/>
@@ -37,6 +37,12 @@
       <unit id="org.apache.httpcomponents.httpcore.source" version="4.4.10.v20190123-2214"/>
       <unit id="org.apache.log4j" version="1.2.15.v201012070815"/>
       <unit id="org.apache.log4j.source" version="1.2.15.v201012070815"/>
+      <unit id="org.bouncycastle.bcpg" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpg.source" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpkix" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpkix.source" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcprov" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcprov.source" version="1.60.0.v20181210-2057"/>
       <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" version="1.1.0.v20090501071000"/>
@@ -62,8 +68,8 @@
       <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="1.6.0.v20170629-1752"/>
-      <unit id="org.tukaani.xz.source" version="1.6.0.v20170629-1752"/>
+      <unit id="org.tukaani.xz" version="1.8.0.v20180207-1613"/>
+      <unit id="org.tukaani.xz.source" version="1.8.0.v20180207-1613"/>
       <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"/>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.tpd
index 8b3dd0b..1a2c9a3 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.tpd
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.tpd
@@ -1,6 +1,6 @@
 target "jgit-4.6" with source configurePhase
 
-include "projects/jetty-9.4.11.tpd"
+include "projects/jetty-9.4.14.tpd"
 include "orbit/R20190602212107-2019-06.tpd"
 
 location "http://download.eclipse.org/releases/neon/" {
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 03c9a8b..e82222a 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
@@ -1,26 +1,26 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.7" sequenceNumber="1566229348">
+<target name="jgit-4.7" sequenceNumber="1566244564">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
-      <unit id="org.eclipse.jetty.client" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.client.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.continuation" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.continuation.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.http" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.http.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.io" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.io.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.security" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.security.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.server" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.server.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.servlet" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.servlet.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.util" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.util.source" version="9.4.11.v20180605"/>
-      <repository id="jetty-9.4.11" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.client" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.client.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.continuation" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.continuation.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.http" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.http.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.io" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.io.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.security" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.security.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.server" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.server.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.servlet" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.servlet.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.util" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.util.source" version="9.4.14.v20181114"/>
+      <repository id="jetty-9.4.14" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.14.v20181114"/>
     </location>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.apache.ant" version="1.10.5.v20190526-1402"/>
@@ -37,6 +37,12 @@
       <unit id="org.apache.httpcomponents.httpcore.source" version="4.4.10.v20190123-2214"/>
       <unit id="org.apache.log4j" version="1.2.15.v201012070815"/>
       <unit id="org.apache.log4j.source" version="1.2.15.v201012070815"/>
+      <unit id="org.bouncycastle.bcpg" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpg.source" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpkix" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpkix.source" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcprov" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcprov.source" version="1.60.0.v20181210-2057"/>
       <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" version="1.1.0.v20090501071000"/>
@@ -62,8 +68,8 @@
       <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="1.6.0.v20170629-1752"/>
-      <unit id="org.tukaani.xz.source" version="1.6.0.v20170629-1752"/>
+      <unit id="org.tukaani.xz" version="1.8.0.v20180207-1613"/>
+      <unit id="org.tukaani.xz.source" version="1.8.0.v20180207-1613"/>
       <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"/>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.tpd
index e93fc46..fc1b046 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.tpd
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.tpd
@@ -1,6 +1,6 @@
 target "jgit-4.7" with source configurePhase
 
-include "projects/jetty-9.4.11.tpd"
+include "projects/jetty-9.4.14.tpd"
 include "orbit/R20190602212107-2019-06.tpd"
 
 location "http://download.eclipse.org/releases/oxygen/" {
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
index e29620c..0b353db 100644
--- 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
@@ -1,26 +1,26 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.8" sequenceNumber="1566229344">
+<target name="jgit-4.8" sequenceNumber="1566244569">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
-      <unit id="org.eclipse.jetty.client" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.client.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.continuation" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.continuation.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.http" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.http.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.io" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.io.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.security" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.security.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.server" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.server.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.servlet" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.servlet.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.util" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.util.source" version="9.4.11.v20180605"/>
-      <repository id="jetty-9.4.11" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.client" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.client.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.continuation" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.continuation.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.http" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.http.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.io" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.io.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.security" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.security.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.server" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.server.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.servlet" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.servlet.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.util" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.util.source" version="9.4.14.v20181114"/>
+      <repository id="jetty-9.4.14" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.14.v20181114"/>
     </location>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.apache.ant" version="1.10.5.v20190526-1402"/>
@@ -37,6 +37,12 @@
       <unit id="org.apache.httpcomponents.httpcore.source" version="4.4.10.v20190123-2214"/>
       <unit id="org.apache.log4j" version="1.2.15.v201012070815"/>
       <unit id="org.apache.log4j.source" version="1.2.15.v201012070815"/>
+      <unit id="org.bouncycastle.bcpg" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpg.source" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpkix" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpkix.source" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcprov" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcprov.source" version="1.60.0.v20181210-2057"/>
       <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" version="1.1.0.v20090501071000"/>
@@ -62,8 +68,8 @@
       <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="1.6.0.v20170629-1752"/>
-      <unit id="org.tukaani.xz.source" version="1.6.0.v20170629-1752"/>
+      <unit id="org.tukaani.xz" version="1.8.0.v20180207-1613"/>
+      <unit id="org.tukaani.xz.source" version="1.8.0.v20180207-1613"/>
       <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"/>
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
index ba6337d..a8f837e 100644
--- 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
@@ -1,6 +1,6 @@
 target "jgit-4.8" with source configurePhase
 
-include "projects/jetty-9.4.11.tpd"
+include "projects/jetty-9.4.14.tpd"
 include "orbit/R20190602212107-2019-06.tpd"
 
 location "http://download.eclipse.org/releases/photon/" {
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9.target b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9.target
index 82a64ce..94a752c 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9.target
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9.target
@@ -1,26 +1,26 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.9" sequenceNumber="1566229339">
+<target name="jgit-4.9" sequenceNumber="1566244572">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
-      <unit id="org.eclipse.jetty.client" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.client.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.continuation" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.continuation.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.http" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.http.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.io" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.io.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.security" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.security.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.server" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.server.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.servlet" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.servlet.source" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.util" version="9.4.11.v20180605"/>
-      <unit id="org.eclipse.jetty.util.source" version="9.4.11.v20180605"/>
-      <repository id="jetty-9.4.11" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.client" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.client.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.continuation" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.continuation.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.http" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.http.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.io" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.io.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.security" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.security.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.server" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.server.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.servlet" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.servlet.source" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.util" version="9.4.14.v20181114"/>
+      <unit id="org.eclipse.jetty.util.source" version="9.4.14.v20181114"/>
+      <repository id="jetty-9.4.14" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.14.v20181114"/>
     </location>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.apache.ant" version="1.10.5.v20190526-1402"/>
@@ -37,6 +37,12 @@
       <unit id="org.apache.httpcomponents.httpcore.source" version="4.4.10.v20190123-2214"/>
       <unit id="org.apache.log4j" version="1.2.15.v201012070815"/>
       <unit id="org.apache.log4j.source" version="1.2.15.v201012070815"/>
+      <unit id="org.bouncycastle.bcpg" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpg.source" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpkix" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcpkix.source" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcprov" version="1.60.0.v20181210-2057"/>
+      <unit id="org.bouncycastle.bcprov.source" version="1.60.0.v20181210-2057"/>
       <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" version="1.1.0.v20090501071000"/>
@@ -62,8 +68,8 @@
       <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="1.6.0.v20170629-1752"/>
-      <unit id="org.tukaani.xz.source" version="1.6.0.v20170629-1752"/>
+      <unit id="org.tukaani.xz" version="1.8.0.v20180207-1613"/>
+      <unit id="org.tukaani.xz.source" version="1.8.0.v20180207-1613"/>
       <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"/>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9.tpd
index d5beea3..f91f53e 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9.tpd
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9.tpd
@@ -1,6 +1,6 @@
 target "jgit-4.9" with source configurePhase
 
-include "projects/jetty-9.4.11.tpd"
+include "projects/jetty-9.4.14.tpd"
 include "orbit/R20190602212107-2019-06.tpd"
 
 location "http://download.eclipse.org/releases/2018-09/" {
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20181128170323-2018-12.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20181128170323-2018-12.tpd
index d5a257d..fd69da2 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20181128170323-2018-12.tpd
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20181128170323-2018-12.tpd
@@ -16,6 +16,12 @@
 	org.apache.httpcomponents.httpcore.source [4.4.9.v20180409-1525,4.4.9.v20180409-1525]
 	org.apache.log4j [1.2.15.v201012070815,1.2.15.v201012070815]
 	org.apache.log4j.source [1.2.15.v201012070815,1.2.15.v201012070815]
+	org.bouncycastle.bcpg [1.60.0.v20181107-1520,1.60.0.v20181107-1520]
+	org.bouncycastle.bcpg.source [1.60.0.v20181107-1520,1.60.0.v20181107-1520]
+	org.bouncycastle.bcpkix [1.60.0.v20181107-1520,1.60.0.v20181107-1520]
+	org.bouncycastle.bcpkix.source [1.60.0.v20181107-1520,1.60.0.v20181107-1520]
+	org.bouncycastle.bcprov [1.60.0.v20181107-1520,1.60.0.v20181107-1520]
+	org.bouncycastle.bcprov.source [1.60.0.v20181107-1520,1.60.0.v20181107-1520]
 	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 [1.1.0.v20090501071000,1.1.0.v20090501071000]
@@ -41,8 +47,8 @@
 	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 [1.6.0.v20170629-1752,1.6.0.v20170629-1752]
-	org.tukaani.xz.source [1.6.0.v20170629-1752,1.6.0.v20170629-1752]
+	org.tukaani.xz [1.8.0.v20180207-1613,1.8.0.v20180207-1613]
+	org.tukaani.xz.source [1.8.0.v20180207-1613,1.8.0.v20180207-1613]
 	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]
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20190226160451-2019-03.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20190226160451-2019-03.tpd
new file mode 100644
index 0000000..32aba68
--- /dev/null
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20190226160451-2019-03.tpd
@@ -0,0 +1,64 @@
+target "R20190226160451-2019-03" with source configurePhase
+// see http://download.eclipse.org/tools/orbit/downloads/
+
+location "http://download.eclipse.org/tools/orbit/downloads/drops/R20190226160451/repository" {
+	org.apache.ant [1.10.5.v20180808-0324,1.10.5.v20180808-0324]
+	org.apache.ant.source [1.10.5.v20180808-0324,1.10.5.v20180808-0324]
+	org.apache.commons.codec [1.10.0.v20180409-1845,1.10.0.v20180409-1845]
+	org.apache.commons.codec.source [1.10.0.v20180409-1845,1.10.0.v20180409-1845]
+	org.apache.commons.compress [1.18.0.v20181121-2221,1.18.0.v20181121-2221]
+	org.apache.commons.compress.source [1.18.0.v20181121-2221,1.18.0.v20181121-2221]
+	org.apache.commons.logging [1.2.0.v20180409-1502,1.2.0.v20180409-1502]
+	org.apache.commons.logging.source [1.2.0.v20180409-1502,1.2.0.v20180409-1502]
+	org.apache.httpcomponents.httpclient [4.5.6.v20190213-1430,4.5.6.v20190213-1430]
+	org.apache.httpcomponents.httpclient.source [4.5.6.v20190213-1430,4.5.6.v20190213-1430]
+	org.apache.httpcomponents.httpcore [4.4.10.v20190123-2214,4.4.10.v20190123-2214]
+	org.apache.httpcomponents.httpcore.source [4.4.10.v20190123-2214,4.4.10.v20190123-2214]
+	org.apache.log4j [1.2.15.v201012070815,1.2.15.v201012070815]
+	org.apache.log4j.source [1.2.15.v201012070815,1.2.15.v201012070815]
+	org.bouncycastle.bcpg [1.60.0.v20181210-2057,1.60.0.v20181210-2057]
+	org.bouncycastle.bcpg.source [1.60.0.v20181210-2057,1.60.0.v20181210-2057]
+	org.bouncycastle.bcpkix [1.60.0.v20181210-2057,1.60.0.v20181210-2057]
+	org.bouncycastle.bcpkix.source [1.60.0.v20181210-2057,1.60.0.v20181210-2057]
+	org.bouncycastle.bcprov [1.60.0.v20181210-2057,1.60.0.v20181210-2057]
+	org.bouncycastle.bcprov.source [1.60.0.v20181210-2057,1.60.0.v20181210-2057]
+	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 [1.1.0.v20090501071000,1.1.0.v20090501071000]
+	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 [2.6.0.v20180420-1519,2.6.0.v20180420-1519]
+	org.objenesis.source [2.6.0.v20180420-1519,2.6.0.v20180420-1519]
+	org.mockito [2.13.0.v20180426-1843,2.13.0.v20180426-1843]
+	org.mockito.source [2.13.0.v20180426-1843,2.13.0.v20180426-1843]
+	net.bytebuddy.byte-buddy [1.7.9.v20180420-1519,1.7.9.v20180420-1519]
+	net.bytebuddy.byte-buddy.source [1.7.9.v20180420-1519,1.7.9.v20180420-1519]
+	net.bytebuddy.byte-buddy-agent [1.7.9.v20180420-1519,1.7.9.v20180420-1519]
+	net.bytebuddy.byte-buddy-agent.source [1.7.9.v20180420-1519,1.7.9.v20180420-1519]
+	com.google.gson [2.8.2.v20180104-1110,2.8.2.v20180104-1110]
+	com.google.gson.source [2.8.2.v20180104-1110,2.8.2.v20180104-1110]
+	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 [1.8.0.v20180207-1613,1.8.0.v20180207-1613]
+	org.tukaani.xz.source [1.8.0.v20180207-1613,1.8.0.v20180207-1613]
+	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]
+	com.jcraft.jzlib [1.1.1.v201205102305,1.1.1.v201205102305]
+	com.jcraft.jzlib.source [1.1.1.v201205102305,1.1.1.v201205102305]
+	net.i2p.crypto.eddsa [0.3.0.v20181102-1323,0.3.0.v20181102-1323]
+	net.i2p.crypto.eddsa.source [0.3.0.v20181102-1323,0.3.0.v20181102-1323]
+	org.apache.sshd.core [2.0.0.v20181102-1323,2.0.0.v20181102-1323]
+	org.apache.sshd.core.source [2.0.0.v20181102-1323,2.0.0.v20181102-1323]
+	org.apache.sshd.sftp [2.0.0.v20181102-1323,2.0.0.v20181102-1323]
+	org.apache.sshd.sftp.source [2.0.0.v20181102-1323,2.0.0.v20181102-1323]
+}
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20190602212107-2019-06.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20190602212107-2019-06.tpd
index b503092..65d5c9f 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20190602212107-2019-06.tpd
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20190602212107-2019-06.tpd
@@ -16,6 +16,12 @@
 	org.apache.httpcomponents.httpcore.source [4.4.10.v20190123-2214,4.4.10.v20190123-2214]
 	org.apache.log4j [1.2.15.v201012070815,1.2.15.v201012070815]
 	org.apache.log4j.source [1.2.15.v201012070815,1.2.15.v201012070815]
+	org.bouncycastle.bcpg [1.60.0.v20181210-2057,1.60.0.v20181210-2057]
+	org.bouncycastle.bcpg.source [1.60.0.v20181210-2057,1.60.0.v20181210-2057]
+	org.bouncycastle.bcpkix [1.60.0.v20181210-2057,1.60.0.v20181210-2057]
+	org.bouncycastle.bcpkix.source [1.60.0.v20181210-2057,1.60.0.v20181210-2057]
+	org.bouncycastle.bcprov [1.60.0.v20181210-2057,1.60.0.v20181210-2057]
+	org.bouncycastle.bcprov.source [1.60.0.v20181210-2057,1.60.0.v20181210-2057]
 	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 [1.1.0.v20090501071000,1.1.0.v20090501071000]
@@ -41,8 +47,8 @@
 	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 [1.6.0.v20170629-1752,1.6.0.v20170629-1752]
-	org.tukaani.xz.source [1.6.0.v20170629-1752,1.6.0.v20170629-1752]
+	org.tukaani.xz [1.8.0.v20180207-1613,1.8.0.v20180207-1613]
+	org.tukaani.xz.source [1.8.0.v20180207-1613,1.8.0.v20180207-1613]
 	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]
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 dba70d3..43dc50d 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.target</artifactId>
@@ -82,4 +82,4 @@
       </plugin>
     </plugins>
   </build>
-</project>
+</project>
\ No newline at end of file
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/projects/jetty-9.4.11.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/projects/jetty-9.4.11.tpd
deleted file mode 100644
index d2fd901..0000000
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/projects/jetty-9.4.11.tpd
+++ /dev/null
@@ -1,20 +0,0 @@
-target "jetty-9.4.11" with source configurePhase
-
-location jetty-9.4.11 "http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.11.v20180605" {
-	org.eclipse.jetty.client [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.client.source [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.continuation [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.continuation.source [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.http [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.http.source [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.io [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.io.source [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.security [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.security.source [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.server [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.server.source [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.servlet [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.servlet.source [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.util [9.4.11.v20180605,9.4.11.v20180605]
-	org.eclipse.jetty.util.source [9.4.11.v20180605,9.4.11.v20180605]
-}
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/projects/jetty-9.4.14.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/projects/jetty-9.4.14.tpd
new file mode 100644
index 0000000..5372e77
--- /dev/null
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/projects/jetty-9.4.14.tpd
@@ -0,0 +1,20 @@
+target "jetty-9.4.14" with source configurePhase
+
+location jetty-9.4.14 "http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.14.v20181114" {
+	org.eclipse.jetty.client [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.client.source [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.continuation [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.continuation.source [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.http [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.http.source [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.io [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.io.source [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.security [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.security.source [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.server [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.server.source [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.servlet [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.servlet.source [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.util [9.4.14.v20181114,9.4.14.v20181114]
+	org.eclipse.jetty.util.source [9.4.14.v20181114,9.4.14.v20181114]
+}
diff --git a/org.eclipse.jgit.packaging/pom.xml b/org.eclipse.jgit.packaging/pom.xml
index cbb5ee5..cbda55f 100644
--- a/org.eclipse.jgit.packaging/pom.xml
+++ b/org.eclipse.jgit.packaging/pom.xml
@@ -49,7 +49,7 @@
 
   <groupId>org.eclipse.jgit</groupId>
   <artifactId>jgit.tycho.parent</artifactId>
-  <version>5.2.3-SNAPSHOT</version>
+  <version>5.3.6-SNAPSHOT</version>
   <packaging>pom</packaging>
 
   <name>JGit Tycho Parent</name>
diff --git a/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF
index 90398a9..b67e5d3 100644
--- a/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF
@@ -3,28 +3,28 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.pgm.test
 Bundle-SymbolicName: org.eclipse.jgit.pgm.test
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-Localization: plugin
 Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Import-Package: org.eclipse.jgit.api;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.api.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.diff;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.dircache;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.file;version="5.2.3",
- org.eclipse.jgit.junit;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.merge;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.pgm;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.pgm.internal;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.pgm.opt;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.treewalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util.io;version="[5.2.3,5.3.0)",
+Import-Package: org.eclipse.jgit.api;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.api.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.diff;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.dircache;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.file;version="5.3.6",
+ org.eclipse.jgit.junit;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.merge;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.pgm;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.pgm.internal;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.pgm.opt;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.treewalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util.io;version="[5.3.6,5.4.0)",
  org.hamcrest.core;bundle-version="[1.1.0,2.0.0)",
  org.junit;version="[4.12,5.0.0)",
  org.junit.rules;version="[4.12,5.0.0)",
diff --git a/org.eclipse.jgit.pgm.test/pom.xml b/org.eclipse.jgit.pgm.test/pom.xml
index ced7168..80c420a 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.pgm.test</artifactId>
@@ -109,7 +109,7 @@
       <plugin>
         <artifactId>maven-surefire-plugin</artifactId>
         <configuration>
-          <argLine>-Djava.io.tmpdir=${project.build.directory}</argLine>
+          <argLine>@{argLine} -Djava.io.tmpdir=${project.build.directory}</argLine>
         </configuration>
       </plugin>
     </plugins>
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 b2115a4..f0e2b38 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
@@ -58,6 +58,7 @@
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.CheckoutConflictException;
 import org.eclipse.jgit.diff.DiffEntry;
+import org.eclipse.jgit.junit.LocalDiskRepositoryTestCase;
 import org.eclipse.jgit.lib.CLIRepositoryTestCase;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.Ref;
@@ -684,4 +685,19 @@ public void testCheckoutLink() throws Exception {
 			assertTrue(Files.isSymbolicLink(path));
 		}
 	}
+
+	@Test
+	public void testCheckoutForce_Bug530771() throws Exception {
+		try (Git git = new Git(db)) {
+			File f = writeTrashFile("a", "Hello world");
+			git.add().addFilepattern("a").call();
+			git.commit().setMessage("create a").call();
+			writeTrashFile("a", "Goodbye world");
+			assertEquals("[]",
+					Arrays.toString(execute("git checkout -f HEAD")));
+			assertEquals("Hello world", read(f));
+			assertEquals("[a, mode:100644, content:Hello world]",
+					indexState(db, LocalDiskRepositoryTestCase.CONTENT));
+		}
+	}
 }
diff --git a/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF b/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF
index e10a772..a00dc54 100644
--- a/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF
@@ -3,7 +3,7 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.pgm
 Bundle-SymbolicName: org.eclipse.jgit.pgm
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
 Bundle-Localization: plugin
@@ -28,50 +28,50 @@
  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="[5.2.3,5.3.0)",
- org.eclipse.jgit.api.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.archive;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.awtui;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.blame;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.diff;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.dircache;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.gitrepo;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.ketch;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.dfs;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.io;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.pack;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.reftable;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.reftree;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.server;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.server.fs;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs.server.s3;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.merge;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.nls;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.notes;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revplot;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk.filter;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.storage.pack;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.http.apache;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.resolver;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.sshd;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.treewalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.treewalk.filter;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util.io;version="[5.2.3,5.3.0)",
+ org.eclipse.jgit.api;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.api.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.archive;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.awtui;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.blame;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.diff;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.dircache;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.gitrepo;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.ketch;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.dfs;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.io;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.pack;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.reftable;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.reftree;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.server;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.server.fs;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs.server.s3;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.merge;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.nls;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.notes;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revplot;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk.filter;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.storage.pack;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.http.apache;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.resolver;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.sshd;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.treewalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.treewalk.filter;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util.io;version="[5.3.6,5.4.0)",
  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="5.2.3";
+Export-Package: org.eclipse.jgit.console;version="5.3.6";
   uses:="org.eclipse.jgit.transport,
    org.eclipse.jgit.util",
- org.eclipse.jgit.pgm;version="5.2.3";
+ org.eclipse.jgit.pgm;version="5.3.6";
   uses:="org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.pgm.opt,
@@ -82,11 +82,11 @@
    org.eclipse.jgit.treewalk,
    javax.swing,
    org.eclipse.jgit.transport",
- org.eclipse.jgit.pgm.debug;version="5.2.3";
+ org.eclipse.jgit.pgm.debug;version="5.3.6";
   uses:="org.eclipse.jgit.util.io,
    org.eclipse.jgit.pgm",
- org.eclipse.jgit.pgm.internal;version="5.2.3";x-friends:="org.eclipse.jgit.pgm.test,org.eclipse.jgit.test",
- org.eclipse.jgit.pgm.opt;version="5.2.3";
+ org.eclipse.jgit.pgm.internal;version="5.3.6";x-friends:="org.eclipse.jgit.pgm.test,org.eclipse.jgit.test",
+ org.eclipse.jgit.pgm.opt;version="5.3.6";
   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 9831e13..858111e 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: 5.2.3.qualifier
-Eclipse-SourceBundle: org.eclipse.jgit.pgm;version="5.2.3.qualifier";roots="."
+Bundle-Version: 5.3.6.qualifier
+Eclipse-SourceBundle: org.eclipse.jgit.pgm;version="5.3.6.qualifier";roots="."
diff --git a/org.eclipse.jgit.pgm/jgit.sh b/org.eclipse.jgit.pgm/jgit.sh
index 8267147..e263782 100644
--- a/org.eclipse.jgit.pgm/jgit.sh
+++ b/org.eclipse.jgit.pgm/jgit.sh
@@ -110,9 +110,9 @@
 	LESS=${LESS:-FSRX}
 	export LESS
 
-	"$java" $java_args org.eclipse.jgit.pgm.Main "$@" | $use_pager
+	"$java" $java_args org.springframework.boot.loader.JarLauncher "$@" | $use_pager
 	exit
 else
-  exec "$java" $java_args org.eclipse.jgit.pgm.Main "$@"
+  exec "$java" $java_args org.springframework.boot.loader.JarLauncher "$@"
   exit 1
 fi
diff --git a/org.eclipse.jgit.pgm/pom.xml b/org.eclipse.jgit.pgm/pom.xml
index 81ef1b3..70e3d69 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.pgm</artifactId>
@@ -172,40 +172,19 @@
       </plugin>
 
       <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-shade-plugin</artifactId>
+        <groupId>org.springframework.boot</groupId>
+        <artifactId>spring-boot-maven-plugin</artifactId>
         <executions>
           <execution>
-            <phase>package</phase>
             <goals>
-              <goal>shade</goal>
+              <goal>repackage</goal>
             </goals>
             <configuration>
               <finalName>jgit-cli</finalName>
-              <createDependencyReducedPom>false</createDependencyReducedPom>
-              <transformers>
-                <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
-                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
-                  <manifestEntries>
-                    <Main-Class>org.eclipse.jgit.pgm.Main</Main-Class>
-                    <Implementation-Title>JGit Command Line Interface</Implementation-Title>
-                  </manifestEntries>
-                </transformer>
-              </transformers>
-              <filters>
-                <!-- exclude the signing data for individual jars, ueberjar will be signed again -->
-                <filter>
-                  <artifact>*:*</artifact>
-                  <excludes>
-                    <exclude>META-INF/*.SF</exclude>
-                    <exclude>META-INF/*.DSA</exclude>
-                    <exclude>META-INF/*.RSA</exclude>
-                    <exclude>OSGI-OPT/**</exclude>
-                  </excludes>
-                </filter>
-              </filters>
-              <shadedArtifactAttached>true</shadedArtifactAttached>
-              <shadedClassifierName>shaded</shadedClassifierName> <!-- Any name that makes sense -->
+              <attach>false</attach>
+              <mainClass>org.eclipse.jgit.pgm.Main</mainClass>
+              <executable>true</executable>
+              <embeddedLaunchScript>jgit.sh</embeddedLaunchScript>
             </configuration>
           </execution>
         </executions>
@@ -220,11 +199,13 @@
             <phase>package</phase>
             <configuration>
               <target>
-                <concat destfile="${basedir}/target/jgit" force="yes" binary="true">
-                  <fileset file="${basedir}/jgit.sh" />
-                  <fileset file="${basedir}/target/jgit-cli.jar" />
-                </concat>
-                <chmod file="${basedir}/target/jgit" perm="a+x"/>
+                <move
+                  file="${basedir}/target/jgit-cli.jar"
+                  force="yes"
+                  tofile="${basedir}/target/jgit" />
+                <chmod
+                  file="${basedir}/target/jgit"
+                  perm="a+x" />
               </target>
             </configuration>
             <goals>
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 bbf9366..aa2608d 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
@@ -49,6 +49,7 @@
 clonedEmptyRepository=warning: You appear to have cloned an empty repository.
 cloningInto=Cloning into ''{0}''...
 commitLabel=commit
+configOnlyListOptionSupported=only the --list option is currently supported
 configFileNotFound=configuration file {0} not found
 conflictingUsageOf_git_dir_andArguments=conflicting usage of --git-dir and arguments
 couldNotCreateBranch=Could not create branch {0}: {1}
@@ -129,6 +130,7 @@
 metaVar_paths=path ...
 metaVar_pattern=pattern
 metaVar_port=PORT
+metaVar_prefix=PREFIX
 metaVar_ref=REF
 metaVar_refs=REFS
 metaVar_refspec=refspec
@@ -171,7 +173,7 @@
 onBranch=On branch {0}
 onBranchToBeBorn=You are on a branch yet to be born
 onlyOneMetaVarExpectedIn=Only one {0} expected in {1}.
-onlyOneOfIncludeOnlyAllInteractiveCanBeUsed=Only one of --include/--only/--all/--interactive can be used.
+onlyOneCommitOptionAllowed=Only one of --include/--only/--all/--interactive can be used.
 password=Password:
 pathspecDidNotMatch=error: pathspec ''{0}'' did not match any file(s) known to git.
 pushTo=To {0}
@@ -182,6 +184,7 @@
 remoteSideDoesNotSupportDeletingRefs=remote side does not support deleting refs
 removing=Removing {0}
 repaint=Repaint
+resetNoMode=no reset mode set
 s3InvalidBucket=Invalid S3 bucket ''{0}''
 serviceNotSupported=Service ''{0}'' not supported
 skippingObject=skipping {0} {1}
@@ -337,7 +340,8 @@
 usage_filesToAddContentFrom=Files to add content from
 usage_fixAThinPackToBeComplete=fix a thin pack to be complete
 usage_forEachRefOutput=for-each-ref output
-usage_forceCheckout=when switching branches, proceed even if the index or the working tree differs from HEAD
+usage_forcedSwitchBranch=when switching branches do it forcefully. Succeed even if resetting an existing branch would cause commits to become unreachable
+usage_forceCheckout=when checking out a commit succeed even if the working tree or the index is dirty. Overwrite the working tree or index in such cases
 usage_forceClean=required to delete files or directories
 usage_forceCreateBranchEvenExists=force create branch even exists
 usage_forcedFetch=force ref update fetch option
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Add.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Add.java
index 08a9f48..9ecbbf1 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Add.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Add.java
@@ -48,6 +48,7 @@
 
 import org.eclipse.jgit.api.AddCommand;
 import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.Option;
 
@@ -69,6 +70,8 @@ protected void run() throws Exception {
 			for (String p : filepatterns)
 				addCmd.addFilepattern(p);
 			addCmd.call();
+		} catch (GitAPIException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 }
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Archive.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Archive.java
index 4721b3a..cb63a9a 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Archive.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Archive.java
@@ -96,11 +96,11 @@ protected void run() throws Exception {
 				if (output != null)
 					cmd.setFilename(output);
 				cmd.call();
-		} catch (GitAPIException e) {
-			throw die(e.getMessage());
-		}
+			} catch (GitAPIException e) {
+				throw die(e.getMessage(), e);
+			}
 		} catch (FileNotFoundException e) {
-			throw die(e.getMessage());
+			throw die(e.getMessage(), e);
 		} finally {
 			if (output != null && stream != null)
 				stream.close();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
index 13a38dd..3858b3d 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
@@ -65,6 +65,7 @@
 import org.eclipse.jgit.diff.RawText;
 import org.eclipse.jgit.diff.RawTextComparator;
 import org.eclipse.jgit.dircache.DirCache;
+import org.eclipse.jgit.errors.NoWorkTreeException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.PersonIdent;
@@ -122,8 +123,6 @@ void ignoreAllSpace(@SuppressWarnings("unused") boolean on) {
 	@Argument(index = 1, required = false, metaVar = "metaVar_file")
 	private String file;
 
-	private ObjectReader reader;
-
 	private final Map<RevCommit, String> abbreviatedCommits = new HashMap<>();
 
 	private SimpleDateFormat dateFmt;
@@ -136,29 +135,34 @@ void ignoreAllSpace(@SuppressWarnings("unused") boolean on) {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		if (file == null) {
-			if (revision == null)
+			if (revision == null) {
 				throw die(CLIText.get().fileIsRequired);
+			}
 			file = revision;
 			revision = null;
 		}
 
 		boolean autoAbbrev = abbrev == 0;
-		if (abbrev == 0)
+		if (abbrev == 0) {
 			abbrev = db.getConfig().getInt("core", "abbrev", 7); //$NON-NLS-1$ //$NON-NLS-2$
-		if (!showBlankBoundary)
+		}
+		if (!showBlankBoundary) {
 			root = db.getConfig().getBoolean("blame", "blankboundary", false); //$NON-NLS-1$ //$NON-NLS-2$
-		if (!root)
+		}
+		if (!root) {
 			root = db.getConfig().getBoolean("blame", "showroot", false); //$NON-NLS-1$ //$NON-NLS-2$
+		}
 
-		if (showRawTimestamp)
+		if (showRawTimestamp) {
 			dateFmt = new SimpleDateFormat("ZZZZ"); //$NON-NLS-1$
-		else
+		} else {
 			dateFmt = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss ZZZZ"); //$NON-NLS-1$
+		}
 
-		reader = db.newObjectReader();
-		try (BlameGenerator generator = new BlameGenerator(db, file)) {
+		try (ObjectReader reader = db.newObjectReader();
+				BlameGenerator generator = new BlameGenerator(db, file)) {
 			RevFlag scanned = generator.newFlag("SCANNED"); //$NON-NLS-1$
 			generator.setTextComparator(comparator);
 
@@ -166,10 +170,11 @@ protected void run() throws Exception {
 				RevCommit rangeStart = null;
 				List<RevCommit> rangeEnd = new ArrayList<>(2);
 				for (RevCommit c : reverseRange) {
-					if (c.has(RevFlag.UNINTERESTING))
+					if (c.has(RevFlag.UNINTERESTING)) {
 						rangeStart = c;
-					else
+					} else {
 						rangeEnd.add(c);
+					}
 				}
 				generator.reverse(rangeStart, rangeEnd);
 			} else if (revision != null) {
@@ -179,20 +184,23 @@ protected void run() throws Exception {
 				if (!db.isBare()) {
 					DirCache dc = db.readDirCache();
 					int entry = dc.findEntry(file);
-					if (0 <= entry)
+					if (0 <= entry) {
 						generator.push(null, dc.getEntry(entry).getObjectId());
+					}
 
 					File inTree = new File(db.getWorkTree(), file);
-					if (db.getFS().isFile(inTree))
+					if (db.getFS().isFile(inTree)) {
 						generator.push(null, new RawText(inTree));
+					}
 				}
 			}
 
 			blame = BlameResult.create(generator);
 			begin = 0;
 			end = blame.getResultContents().size();
-			if (rangeString != null)
+			if (rangeString != null) {
 				parseLineRangeOption();
+			}
 			blame.computeRange(begin, end);
 
 			int authorWidth = 8;
@@ -203,14 +211,16 @@ protected void run() throws Exception {
 				RevCommit c = blame.getSourceCommit(line);
 				if (c != null && !c.has(scanned)) {
 					c.add(scanned);
-					if (autoAbbrev)
-						abbrev = Math.max(abbrev, uniqueAbbrevLen(c));
+					if (autoAbbrev) {
+						abbrev = Math.max(abbrev, uniqueAbbrevLen(reader, c));
+					}
 					authorWidth = Math.max(authorWidth, author(line).length());
 					dateWidth = Math.max(dateWidth, date(line).length());
 					pathWidth = Math.max(pathWidth, path(line).length());
 				}
-				while (line + 1 < end && blame.getSourceCommit(line + 1) == c)
+				while (line + 1 < end && blame.getSourceCommit(line + 1) == c) {
 					line++;
+				}
 				maxSourceLine = Math.max(maxSourceLine, blame.getSourceLine(line));
 			}
 
@@ -224,7 +234,7 @@ protected void run() throws Exception {
 
 			for (int line = begin; line < end;) {
 				RevCommit c = blame.getSourceCommit(line);
-				String commit = abbreviate(c);
+				String commit = abbreviate(reader, c);
 				String author = null;
 				String date = null;
 				if (!noAuthor) {
@@ -233,12 +243,15 @@ protected void run() throws Exception {
 				}
 				do {
 					outw.print(commit);
-					if (showSourcePath)
+					if (showSourcePath) {
 						outw.format(pathFmt, path(line));
-					if (showSourceLine)
+					}
+					if (showSourceLine) {
 						outw.format(numFmt, valueOf(blame.getSourceLine(line) + 1));
-					if (!noAuthor)
+					}
+					if (!noAuthor) {
 						outw.format(authorFmt, author, date);
+					}
 					outw.format(lineFmt, valueOf(line + 1));
 					outw.flush();
 					blame.getResultContents().writeLine(outs, line);
@@ -246,12 +259,13 @@ protected void run() throws Exception {
 					outw.print('\n');
 				} while (++line < end && blame.getSourceCommit(line) == c);
 			}
-		} finally {
-			reader.close();
+		} catch (NoWorkTreeException | IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 
-	private int uniqueAbbrevLen(RevCommit commit) throws IOException {
+	private int uniqueAbbrevLen(ObjectReader reader, RevCommit commit)
+			throws IOException {
 		return reader.abbreviate(commit, abbrev).length();
 	}
 
@@ -345,7 +359,8 @@ private String date(int line) {
 				dateFmt.format(author.getWhen()));
 	}
 
-	private String abbreviate(RevCommit commit) throws IOException {
+	private String abbreviate(ObjectReader reader, RevCommit commit)
+			throws IOException {
 		String r = abbreviatedCommits.get(commit);
 		if (r != null)
 			return r;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java
index a88354d..bac697f 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java
@@ -54,6 +54,7 @@
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.ListBranchCommand;
 import org.eclipse.jgit.api.ListBranchCommand.ListMode;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectReader;
@@ -182,15 +183,17 @@ public void moveRename(List<String> currentAndNew) {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
-		if (delete != null || deleteForce != null) {
-			if (delete != null) {
-				delete(delete, false);
+	protected void run() {
+		try {
+			if (delete != null || deleteForce != null) {
+				if (delete != null) {
+					delete(delete, false);
+				}
+				if (deleteForce != null) {
+					delete(deleteForce, true);
+				}
+				return;
 			}
-			if (deleteForce != null) {
-				delete(deleteForce, true);
-			}
-		} else {
 			if (rename) {
 				String src, dst;
 				if (otherBranch == null) {
@@ -204,22 +207,27 @@ protected void run() throws Exception {
 				} else {
 					src = branch;
 					final Ref old = db.findRef(src);
-					if (old == null)
+					if (old == null) {
 						throw die(MessageFormat.format(CLIText.get().doesNotExist, src));
-					if (!old.getName().startsWith(Constants.R_HEADS))
+					}
+					if (!old.getName().startsWith(Constants.R_HEADS)) {
 						throw die(MessageFormat.format(CLIText.get().notABranch, src));
+					}
 					src = old.getName();
 					dst = otherBranch;
 				}
 
-				if (!dst.startsWith(Constants.R_HEADS))
+				if (!dst.startsWith(Constants.R_HEADS)) {
 					dst = Constants.R_HEADS + dst;
-				if (!Repository.isValidRefName(dst))
+				}
+				if (!Repository.isValidRefName(dst)) {
 					throw die(MessageFormat.format(CLIText.get().notAValidRefName, dst));
+				}
 
 				RefRename r = db.renameRef(src, dst);
-				if (r.rename() != Result.RENAMED)
+				if (r.rename() != Result.RENAMED) {
 					throw die(MessageFormat.format(CLIText.get().cannotBeRenamed, src));
+				}
 
 			} else if (createForce || branch != null) {
 				String newHead = branch;
@@ -264,10 +272,12 @@ protected void run() throws Exception {
 				}
 				list();
 			}
+		} catch (IOException | GitAPIException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 
-	private void list() throws Exception {
+	private void list() throws IOException, GitAPIException {
 		Ref head = db.exactRef(Constants.HEAD);
 		// This can happen if HEAD is stillborn
 		if (head != null) {
@@ -316,7 +326,7 @@ private void addRef(String name, Ref ref) {
 	}
 
 	private void printHead(final ObjectReader reader, final String ref,
-			final boolean isCurrent, final Ref refObj) throws Exception {
+			final boolean isCurrent, final Ref refObj) throws IOException {
 		outw.print(isCurrent ? '*' : ' ');
 		outw.print(' ');
 		outw.print(ref);
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 6ff39fa..7e1737f 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
@@ -69,8 +69,11 @@ class Checkout extends TextBuiltin {
 	@Option(name = "-b", usage = "usage_createBranchAndCheckout")
 	private boolean createBranch = false;
 
+	@Option(name = "-B", usage = "usage_forcedSwitchBranch")
+	private boolean forceSwitchBranch = false;
+
 	@Option(name = "--force", aliases = { "-f" }, usage = "usage_forceCheckout")
-	private boolean force = false;
+	private boolean forced = false;
 
 	@Option(name = "--orphan", usage = "usage_orphan")
 	private boolean orphan = false;
@@ -103,7 +106,8 @@ protected void run() throws Exception {
 			} else {
 				command.setCreateBranch(createBranch);
 				command.setName(name);
-				command.setForce(force);
+				command.setForceRefUpdate(forceSwitchBranch);
+				command.setForced(forced);
 				command.setOrphan(orphan);
 			}
 			try {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clean.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clean.java
index 6ae078c..db9e959 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clean.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clean.java
@@ -43,10 +43,13 @@
 
 package org.eclipse.jgit.pgm;
 
+import java.io.IOException;
 import java.text.MessageFormat;
 import java.util.Set;
 
 import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.errors.NoWorkTreeException;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.kohsuke.args4j.Option;
 
@@ -64,7 +67,7 @@ class Clean extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		try (Git git = new Git(db)) {
 			boolean requireForce = git.getRepository().getConfig()
 					.getBoolean("clean", "requireForce", true); //$NON-NLS-1$ //$NON-NLS-2$
@@ -82,6 +85,8 @@ protected void run() throws Exception {
 				outw.println(MessageFormat.format(CLIText.get().removing,
 						removedFile));
 			}
+		} catch (NoWorkTreeException | GitAPIException | IOException e) {
+			throw die(e.getMessage(), 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 393c607..fe24620 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
@@ -110,7 +110,7 @@ protected void run() throws Exception {
 						Constants.OS_USER_DIR), localName);
 			} catch (IllegalArgumentException e) {
 				throw die(MessageFormat.format(
-						CLIText.get().cannotGuessLocalNameFrom, sourceUri));
+						CLIText.get().cannotGuessLocalNameFrom, sourceUri), e);
 			}
 		} else
 			localNameF = new File(localName);
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Commit.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Commit.java
index 2e67c02..b0713f7 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Commit.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Commit.java
@@ -37,18 +37,18 @@
  */
 package org.eclipse.jgit.pgm;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
 import org.eclipse.jgit.api.CommitCommand;
 import org.eclipse.jgit.api.Git;
-import org.eclipse.jgit.api.errors.ConcurrentRefUpdateException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
-import org.eclipse.jgit.api.errors.NoHeadException;
-import org.eclipse.jgit.api.errors.NoMessageException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.pgm.internal.CLIText;
+import org.eclipse.jgit.pgm.opt.GpgSignHandler;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.util.RawParseUtils;
 import org.kohsuke.args4j.Argument;
@@ -74,26 +74,46 @@ class Commit extends TextBuiltin {
 	@Option(name = "--amend", usage = "usage_CommitAmend")
 	private boolean amend;
 
+	@Option(name = "--gpg-sign", aliases = { "-S" }, forbids = {
+			"--no-gpg-sign" }, handler = GpgSignHandler.class)
+	private String gpgSigningKey;
+
+	@Option(name = "--no-gpg-sign", forbids = { "--gpg-sign" })
+	private boolean noGpgSign;
+
 	@Argument(metaVar = "metaVar_commitPaths", usage = "usage_CommitPaths")
 	private List<String> paths = new ArrayList<>();
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws NoHeadException, NoMessageException,
-			ConcurrentRefUpdateException, JGitInternalException, Exception {
+	protected void run() {
 		try (Git git = new Git(db)) {
 			CommitCommand commitCmd = git.commit();
-			if (author != null)
+			if (author != null) {
 				commitCmd.setAuthor(RawParseUtils.parsePersonIdent(author));
-			if (message != null)
+			}
+			if (message != null) {
 				commitCmd.setMessage(message);
-			if (only && paths.isEmpty())
+			}
+			if (noGpgSign) {
+				commitCmd.setSign(Boolean.FALSE);
+			} else if (gpgSigningKey != null) {
+				commitCmd.setSign(Boolean.TRUE);
+				if (!gpgSigningKey.equals(GpgSignHandler.DEFAULT)) {
+					commitCmd.setSigningKey(gpgSigningKey);
+				}
+			}
+			if (only && paths.isEmpty()) {
 				throw die(CLIText.get().pathsRequired);
-			if (only && all)
-				throw die(CLIText.get().onlyOneOfIncludeOnlyAllInteractiveCanBeUsed);
-			if (!paths.isEmpty())
-				for (String p : paths)
+			}
+			if (only && all) {
+				throw die(CLIText.get().onlyOneCommitOptionAllowed);
+			}
+			if (!paths.isEmpty()) {
+				for (String p : paths) {
 					commitCmd.setOnly(p);
+				}
+			}
 			commitCmd.setAmend(amend);
 			commitCmd.setAll(all);
 			Ref head = db.exactRef(Constants.HEAD);
@@ -103,20 +123,24 @@ protected void run() throws NoHeadException, NoMessageException,
 			RevCommit commit;
 			try {
 				commit = commitCmd.call();
-			} catch (JGitInternalException e) {
-				throw die(e.getMessage());
+			} catch (JGitInternalException | GitAPIException e) {
+				throw die(e.getMessage(), e);
 			}
 
 			String branchName;
-			if (!head.isSymbolic())
+			if (!head.isSymbolic()) {
 				branchName = CLIText.get().branchDetachedHEAD;
-			else {
+			} else {
 				branchName = head.getTarget().getName();
-				if (branchName.startsWith(Constants.R_HEADS))
-					branchName = branchName.substring(Constants.R_HEADS.length());
+				if (branchName.startsWith(Constants.R_HEADS)) {
+					branchName = branchName
+							.substring(Constants.R_HEADS.length());
+				}
 			}
-			outw.println("[" + branchName + " " + commit.name() + "] " //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
+			outw.println('[' + branchName + ' ' + commit.name() + "] " //$NON-NLS-1$
 					+ commit.getShortMessage());
+		} catch (IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 }
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 f762c0d..979c6fa 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
@@ -42,9 +42,9 @@
 import java.util.Set;
 
 import org.eclipse.jgit.errors.ConfigInvalidException;
-import org.eclipse.jgit.errors.NotSupportedException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.StoredConfig;
+import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.StringUtils;
@@ -70,12 +70,15 @@ class Config extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
-		if (list)
+	protected void run() {
+		if (!list) {
+			throw die(CLIText.get().configOnlyListOptionSupported);
+		}
+		try {
 			list();
-		else
-			throw new NotSupportedException(
-					"only --list option is currently supported"); //$NON-NLS-1$
+		} catch (IOException | ConfigInvalidException e) {
+			throw die(e.getMessage(), e);
+		}
 	}
 
 	private void list() throws IOException, ConfigInvalidException {
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 f914748..d89fee6 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
@@ -42,12 +42,15 @@
  */
 package org.eclipse.jgit.pgm;
 
+import java.io.IOException;
 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.GitAPIException;
 import org.eclipse.jgit.api.errors.RefNotFoundException;
+import org.eclipse.jgit.errors.InvalidPatternException;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.kohsuke.args4j.Argument;
@@ -67,11 +70,12 @@ class Describe extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		try (Git git = new Git(db)) {
 			DescribeCommand cmd = git.describe();
-			if (tree != null)
+			if (tree != null) {
 				cmd.setTarget(tree);
+			}
 			cmd.setLong(longDesc);
 			cmd.setMatch(patterns.toArray(new String[0]));
 			String result = null;
@@ -80,10 +84,13 @@ protected void run() throws Exception {
 			} catch (RefNotFoundException e) {
 				throw die(CLIText.get().noNamesFound, e);
 			}
-			if (result == null)
+			if (result == null) {
 				throw die(CLIText.get().noNamesFound);
+			}
 
 			outw.println(result);
+		} catch (IOException | InvalidPatternException | GitAPIException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 }
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 97e3df3..7747dc7 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
@@ -62,6 +62,7 @@
 import org.eclipse.jgit.diff.RawTextComparator;
 import org.eclipse.jgit.diff.RenameDetector;
 import org.eclipse.jgit.dircache.DirCacheIterator;
+import org.eclipse.jgit.errors.RevisionSyntaxException;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.Repository;
@@ -150,12 +151,12 @@ void abbrev(@SuppressWarnings("unused") boolean on) {
 		diffFmt.setAbbreviationLength(OBJECT_ID_STRING_LENGTH);
 	}
 
-	@Option(name = "--src-prefix", usage = "usage_srcPrefix")
+	@Option(name = "--src-prefix", metaVar = "metaVar_prefix", usage = "usage_srcPrefix")
 	void sourcePrefix(String path) {
 		diffFmt.setOldPrefix(path);
 	}
 
-	@Option(name = "--dst-prefix", usage = "usage_dstPrefix")
+	@Option(name = "--dst-prefix", metaVar = "metaVar_prefix", usage = "usage_dstPrefix")
 	void dstPrefix(String path) {
 		diffFmt.setNewPrefix(path);
 	}
@@ -177,14 +178,15 @@ protected void init(Repository repository, String gitDir) {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		diffFmt.setRepository(db);
 		try {
 			if (cached) {
 				if (oldTree == null) {
 					ObjectId head = db.resolve(HEAD + "^{tree}"); //$NON-NLS-1$
-					if (head == null)
+					if (head == null) {
 						die(MessageFormat.format(CLIText.get().notATree, HEAD));
+					}
 					CanonicalTreeParser p = new CanonicalTreeParser();
 					try (ObjectReader reader = db.newObjectReader()) {
 						p.reset(reader, head);
@@ -195,15 +197,17 @@ protected void run() throws Exception {
 			} else if (oldTree == null) {
 				oldTree = new DirCacheIterator(db.readDirCache());
 				newTree = new FileTreeIterator(db);
-			} else if (newTree == null)
+			} else if (newTree == null) {
 				newTree = new FileTreeIterator(db);
+			}
 
 			TextProgressMonitor pm = new TextProgressMonitor(errw);
 			pm.setDelayStart(2, TimeUnit.SECONDS);
 			diffFmt.setProgressMonitor(pm);
 			diffFmt.setPathFilter(pathFilter);
-			if (detectRenames != null)
+			if (detectRenames != null) {
 				diffFmt.setDetectRenames(detectRenames.booleanValue());
+			}
 			if (renameLimit != null && diffFmt.isDetectRenames()) {
 				RenameDetector rd = diffFmt.getRenameDetector();
 				rd.setRenameLimit(renameLimit.intValue());
@@ -212,11 +216,12 @@ protected void run() throws Exception {
 			if (showNameAndStatusOnly) {
 				nameStatus(outw, diffFmt.scan(oldTree, newTree));
 				outw.flush();
-
 			} else {
 				diffFmt.format(oldTree, newTree);
 				diffFmt.flush();
 			}
+		} catch (RevisionSyntaxException | IOException e) {
+			throw die(e.getMessage(), e);
 		} finally {
 			diffFmt.close();
 		}
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 42aabc2..371395b 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
@@ -44,6 +44,7 @@
 
 package org.eclipse.jgit.pgm;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -74,7 +75,7 @@ void tree_0(final AbstractTreeIterator c) {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		try (TreeWalk walk = new TreeWalk(db)) {
 			walk.setRecursive(recursive);
 			for (AbstractTreeIterator i : trees)
@@ -83,13 +84,15 @@ protected void run() throws Exception {
 
 			final int nTree = walk.getTreeCount();
 			while (walk.next()) {
-				for (int i = 1; i < nTree; i++)
+				for (int i = 1; i < nTree; i++) {
 					outw.print(':');
+				}
 				for (int i = 0; i < nTree; i++) {
 					final FileMode m = walk.getFileMode(i);
 					final String s = m.toString();
-					for (int pad = 6 - s.length(); pad > 0; pad--)
+					for (int pad = 6 - s.length(); pad > 0; pad--) {
 						outw.print('0');
+					}
 					outw.print(s);
 					outw.print(' ');
 				}
@@ -103,12 +106,13 @@ protected void run() throws Exception {
 				if (nTree == 2) {
 					final int m0 = walk.getRawMode(0);
 					final int m1 = walk.getRawMode(1);
-					if (m0 == 0 && m1 != 0)
+					if (m0 == 0 && m1 != 0) {
 						chg = 'A';
-					else if (m0 != 0 && m1 == 0)
+					} else if (m0 != 0 && m1 == 0) {
 						chg = 'D';
-					else if (m0 != m1 && walk.idEqual(0, 1))
+					} else if (m0 != m1 && walk.idEqual(0, 1)) {
 						chg = 'T';
+					}
 				}
 				outw.print(chg);
 
@@ -116,6 +120,8 @@ else if (m0 != m1 && walk.idEqual(0, 1))
 				outw.print(walk.getPathString());
 				outw.println();
 			}
+		} catch (IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 }
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 61fd521..da3c498 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
@@ -51,6 +51,7 @@
 
 import org.eclipse.jgit.api.FetchCommand;
 import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.SubmoduleConfig.FetchRecurseSubmodulesMode;
 import org.eclipse.jgit.lib.TextProgressMonitor;
@@ -136,27 +137,33 @@ void noRecurseSubmodules(@SuppressWarnings("unused")
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		try (Git git = new Git(db)) {
 			FetchCommand fetch = git.fetch();
-			if (fsck != null)
+			if (fsck != null) {
 				fetch.setCheckFetchedObjects(fsck.booleanValue());
-			if (prune != null)
+			}
+			if (prune != null) {
 				fetch.setRemoveDeletedRefs(prune.booleanValue());
-			if (toget != null)
+			}
+			if (toget != null) {
 				fetch.setRefSpecs(toget);
+			}
 			if (tags != null) {
 				fetch.setTagOpt(tags.booleanValue() ? TagOpt.FETCH_TAGS
 						: TagOpt.NO_TAGS);
 			}
-			if (0 <= timeout)
+			if (0 <= timeout) {
 				fetch.setTimeout(timeout);
+			}
 			fetch.setDryRun(dryRun);
 			fetch.setRemote(remote);
-			if (thin != null)
+			if (thin != null) {
 				fetch.setThin(thin.booleanValue());
-			if (quiet == null || !quiet.booleanValue())
+			}
+			if (quiet == null || !quiet.booleanValue()) {
 				fetch.setProgressMonitor(new TextProgressMonitor(errw));
+			}
 			fetch.setRecurseSubmodules(recurseSubmodules).setCallback(this);
 			if (force != null) {
 				fetch.setForceUpdate(force.booleanValue());
@@ -164,10 +171,12 @@ protected void run() throws Exception {
 
 			FetchResult result = fetch.call();
 			if (result.getTrackingRefUpdates().isEmpty()
-					&& result.submoduleResults().isEmpty())
+					&& result.submoduleResults().isEmpty()) {
 				return;
-
+			}
 			showFetchResult(result);
+		} catch (GitAPIException | IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Gc.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Gc.java
index 56172f5..e65f0ec 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Gc.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Gc.java
@@ -44,6 +44,7 @@
 package org.eclipse.jgit.pgm;
 
 import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.lib.TextProgressMonitor;
 import org.kohsuke.args4j.Option;
 
@@ -60,11 +61,15 @@ class Gc extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		Git git = Git.wrap(db);
-		git.gc().setAggressive(aggressive)
-				.setPreserveOldPacks(preserveOldPacks)
-				.setPrunePreserved(prunePreserved)
-				.setProgressMonitor(new TextProgressMonitor(errw)).call();
+		try {
+			git.gc().setAggressive(aggressive)
+					.setPreserveOldPacks(preserveOldPacks)
+					.setPrunePreserved(prunePreserved)
+					.setProgressMonitor(new TextProgressMonitor(errw)).call();
+		} catch (GitAPIException e) {
+			throw die(e.getMessage(), e);
+		}
 	}
 }
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/IndexPack.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/IndexPack.java
index 2627671..394083c 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/IndexPack.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/IndexPack.java
@@ -45,6 +45,7 @@
 package org.eclipse.jgit.pgm;
 
 import java.io.BufferedInputStream;
+import java.io.IOException;
 
 import org.eclipse.jgit.internal.storage.file.ObjectDirectoryPackParser;
 import org.eclipse.jgit.lib.ObjectInserter;
@@ -62,7 +63,7 @@ class IndexPack extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		BufferedInputStream in = new BufferedInputStream(ins);
 		try (ObjectInserter inserter = db.newObjectInserter()) {
 			PackParser p = inserter.newPackParser(in);
@@ -73,6 +74,8 @@ protected void run() throws Exception {
 			}
 			p.parse(new TextProgressMonitor(errw));
 			inserter.flush();
+		} catch (IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 }
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java
index f880fc2..d24733d 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java
@@ -49,10 +49,12 @@
 package org.eclipse.jgit.pgm;
 
 import java.io.File;
+import java.io.IOException;
 import java.text.MessageFormat;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.InitCommand;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.kohsuke.args4j.Argument;
@@ -74,7 +76,7 @@ protected final boolean requiresRepository() {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		InitCommand command = Git.init();
 		command.setBare(bare);
 		if (gitdir != null) {
@@ -83,9 +85,14 @@ protected void run() throws Exception {
 		if (directory != null) {
 			command.setDirectory(new File(directory));
 		}
-		Repository repository = command.call().getRepository();
-		outw.println(MessageFormat.format(
-				CLIText.get().initializedEmptyGitRepositoryIn, repository
-						.getDirectory().getAbsolutePath()));
+		Repository repository;
+		try {
+			repository = command.call().getRepository();
+			outw.println(MessageFormat.format(
+					CLIText.get().initializedEmptyGitRepositoryIn,
+					repository.getDirectory().getAbsolutePath()));
+		} catch (GitAPIException | IOException e) {
+			throw die(e.getMessage(), e);
+		}
 	}
 }
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Log.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Log.java
index ad92a78..05b7980 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Log.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Log.java
@@ -193,12 +193,13 @@ protected void init(Repository repository, String gitDir) {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		diffFmt.setRepository(db);
 		try {
 			diffFmt.setPathFilter(pathFilter);
-			if (detectRenames != null)
+			if (detectRenames != null) {
 				diffFmt.setDetectRenames(detectRenames.booleanValue());
+			}
 			if (renameLimit != null && diffFmt.isDetectRenames()) {
 				RenameDetector rd = diffFmt.getRenameDetector();
 				rd.setRenameLimit(renameLimit.intValue());
@@ -220,11 +221,13 @@ protected void run() throws Exception {
 				}
 			}
 
-			if (decorate)
+			if (decorate) {
 				allRefsByPeeledObjectId = getRepository()
 						.getAllRefsByPeeledObjectId();
-
+			}
 			super.run();
+		} catch (Exception e) {
+			throw die(e.getMessage(), e);
 		} finally {
 			diffFmt.close();
 		}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsFiles.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsFiles.java
index dc13000..ef25844 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsFiles.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsFiles.java
@@ -48,11 +48,13 @@
 import static org.eclipse.jgit.lib.FileMode.REGULAR_FILE;
 import static org.eclipse.jgit.lib.FileMode.SYMLINK;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
 import org.eclipse.jgit.dircache.DirCacheIterator;
+import org.eclipse.jgit.errors.RevisionSyntaxException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
@@ -72,7 +74,7 @@ class LsFiles extends TextBuiltin {
 	private List<String> paths = new ArrayList<>();
 
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		try (RevWalk rw = new RevWalk(db);
 				TreeWalk tw = new TreeWalk(db)) {
 			final ObjectId head = db.resolve(Constants.HEAD);
@@ -96,6 +98,8 @@ protected void run() throws Exception {
 							QuotedString.GIT_PATH.quote(tw.getPathString()));
 				}
 			}
+		} catch (RevisionSyntaxException | IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsRemote.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsRemote.java
index 2711c15..1c2564d 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsRemote.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsRemote.java
@@ -51,6 +51,7 @@
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.LsRemoteCommand;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Ref;
 import org.kohsuke.args4j.Argument;
@@ -72,7 +73,7 @@ class LsRemote extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		LsRemoteCommand command = Git.lsRemoteRepository().setRemote(remote)
 				.setTimeout(timeout).setHeads(heads).setTags(tags);
 		TreeSet<Ref> refs = new TreeSet<>(new Comparator<Ref>() {
@@ -82,11 +83,16 @@ public int compare(Ref r1, Ref r2) {
 				return r1.getName().compareTo(r2.getName());
 			}
 		});
-		refs.addAll(command.call());
-		for (Ref r : refs) {
-			show(r.getObjectId(), r.getName());
-			if (r.getPeeledObjectId() != null)
-				show(r.getPeeledObjectId(), r.getName() + "^{}"); //$NON-NLS-1$
+		try {
+			refs.addAll(command.call());
+			for (Ref r : refs) {
+				show(r.getObjectId(), r.getName());
+				if (r.getPeeledObjectId() != null) {
+					show(r.getPeeledObjectId(), r.getName() + "^{}"); //$NON-NLS-1$
+				}
+			}
+		} catch (GitAPIException | IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 
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 01fa7ee..2a2bb7c 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
@@ -45,6 +45,7 @@
 
 package org.eclipse.jgit.pgm;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -72,18 +73,20 @@ class LsTree extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		try (TreeWalk walk = new TreeWalk(db)) {
 			walk.reset(); // drop the first empty tree, which we do not need here
-			if (paths.size() > 0)
+			if (paths.size() > 0) {
 				walk.setFilter(PathFilterGroup.createFromStrings(paths));
+			}
 			walk.setRecursive(recursive);
 			walk.addTree(tree);
 
 			while (walk.next()) {
 				final FileMode mode = walk.getFileMode(0);
-				if (mode == FileMode.TREE)
+				if (mode == FileMode.TREE) {
 					outw.print('0');
+				}
 				outw.print(mode);
 				outw.print(' ');
 				outw.print(Constants.typeString(mode.getObjectType()));
@@ -95,6 +98,8 @@ protected void run() throws Exception {
 				outw.print(QuotedString.GIT_PATH.quote(walk.getPathString()));
 				outw.println();
 			}
+		} catch (IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 }
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Merge.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Merge.java
index de059e9..0b362a4 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Merge.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Merge.java
@@ -52,6 +52,7 @@
 import org.eclipse.jgit.api.MergeCommand.FastForwardMode;
 import org.eclipse.jgit.api.MergeResult;
 import org.eclipse.jgit.api.errors.CheckoutConflictException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
@@ -103,110 +104,124 @@ void ffonly(@SuppressWarnings("unused") final boolean ignored) {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
-		if (squash && ff == FastForwardMode.NO_FF)
+	protected void run() {
+		if (squash && ff == FastForwardMode.NO_FF) {
 			throw die(CLIText.get().cannotCombineSquashWithNoff);
+		}
 		// determine the merge strategy
 		if (strategyName != null) {
 			mergeStrategy = MergeStrategy.get(strategyName);
-			if (mergeStrategy == null)
+			if (mergeStrategy == null) {
 				throw die(MessageFormat.format(
 						CLIText.get().unknownMergeStrategy, strategyName));
-		}
-
-		// determine the other revision we want to merge with HEAD
-		final Ref srcRef = db.findRef(ref);
-		final ObjectId src = db.resolve(ref + "^{commit}"); //$NON-NLS-1$
-		if (src == null)
-			throw die(MessageFormat.format(
-					CLIText.get().refDoesNotExistOrNoCommit, ref));
-
-		Ref oldHead = getOldHead();
-		MergeResult result;
-		try (Git git = new Git(db)) {
-			MergeCommand mergeCmd = git.merge().setStrategy(mergeStrategy)
-					.setSquash(squash).setFastForward(ff).setCommit(!noCommit);
-			if (srcRef != null)
-				mergeCmd.include(srcRef);
-			else
-				mergeCmd.include(src);
-
-			if (message != null)
-				mergeCmd.setMessage(message);
-
-			try {
-				result = mergeCmd.call();
-			} catch (CheckoutConflictException e) {
-				result = new MergeResult(e.getConflictingPaths()); // CHECKOUT_CONFLICT
 			}
 		}
 
-		switch (result.getMergeStatus()) {
-		case ALREADY_UP_TO_DATE:
-			if (squash)
-				outw.print(CLIText.get().nothingToSquash);
-			outw.println(CLIText.get().alreadyUpToDate);
-			break;
-		case FAST_FORWARD:
-			ObjectId oldHeadId = oldHead.getObjectId();
-			if (oldHeadId != null) {
-				String oldId = oldHeadId.abbreviate(7).name();
-				String newId = result.getNewHead().abbreviate(7).name();
-				outw.println(MessageFormat.format(CLIText.get().updating, oldId,
-						newId));
+		try {
+			// determine the other revision we want to merge with HEAD
+			final Ref srcRef = db.findRef(ref);
+			final ObjectId src = db.resolve(ref + "^{commit}"); //$NON-NLS-1$
+			if (src == null) {
+				throw die(MessageFormat
+						.format(CLIText.get().refDoesNotExistOrNoCommit, ref));
 			}
-			outw.println(result.getMergeStatus().toString());
-			break;
-		case CHECKOUT_CONFLICT:
-			outw.println(CLIText.get().mergeCheckoutConflict);
-			for (String collidingPath : result.getCheckoutConflicts())
-				outw.println("\t" + collidingPath); //$NON-NLS-1$
-			outw.println(CLIText.get().mergeCheckoutFailed);
-			break;
-		case CONFLICTING:
-			for (String collidingPath : result.getConflicts().keySet())
-				outw.println(MessageFormat.format(CLIText.get().mergeConflict,
-						collidingPath));
-			outw.println(CLIText.get().mergeFailed);
-			break;
-		case FAILED:
-			for (Map.Entry<String, MergeFailureReason> entry : result
-					.getFailingPaths().entrySet())
-				switch (entry.getValue()) {
-				case DIRTY_WORKTREE:
-				case DIRTY_INDEX:
-					outw.println(CLIText.get().dontOverwriteLocalChanges);
-					outw.println("        " + entry.getKey()); //$NON-NLS-1$
-					break;
-				case COULD_NOT_DELETE:
-					outw.println(CLIText.get().cannotDeleteFile);
-					outw.println("        " + entry.getKey()); //$NON-NLS-1$
-					break;
+
+			Ref oldHead = getOldHead();
+			MergeResult result;
+			try (Git git = new Git(db)) {
+				MergeCommand mergeCmd = git.merge().setStrategy(mergeStrategy)
+						.setSquash(squash).setFastForward(ff)
+						.setCommit(!noCommit);
+				if (srcRef != null) {
+					mergeCmd.include(srcRef);
+				} else {
+					mergeCmd.include(src);
 				}
-			break;
-		case MERGED:
-			String name;
-			if (!isMergedInto(oldHead, src))
-				name = mergeStrategy.getName();
-			else
-				name = "recursive"; //$NON-NLS-1$
-			outw.println(MessageFormat.format(CLIText.get().mergeMadeBy, name));
-			break;
-		case MERGED_NOT_COMMITTED:
-			outw.println(CLIText.get().mergeWentWellStoppedBeforeCommitting);
-			break;
-		case MERGED_SQUASHED:
-		case FAST_FORWARD_SQUASHED:
-		case MERGED_SQUASHED_NOT_COMMITTED:
-			outw.println(CLIText.get().mergedSquashed);
-			outw.println(CLIText.get().mergeWentWellStoppedBeforeCommitting);
-			break;
-		case ABORTED:
-			throw die(CLIText.get().ffNotPossibleAborting);
-		case NOT_SUPPORTED:
-			outw.println(MessageFormat.format(
-					CLIText.get().unsupportedOperation, result.toString()));
+
+				if (message != null) {
+					mergeCmd.setMessage(message);
+				}
+
+				try {
+					result = mergeCmd.call();
+				} catch (CheckoutConflictException e) {
+					result = new MergeResult(e.getConflictingPaths()); // CHECKOUT_CONFLICT
+				}
+			}
+
+			switch (result.getMergeStatus()) {
+			case ALREADY_UP_TO_DATE:
+				if (squash) {
+					outw.print(CLIText.get().nothingToSquash);
+				}
+				outw.println(CLIText.get().alreadyUpToDate);
+				break;
+			case FAST_FORWARD:
+				ObjectId oldHeadId = oldHead.getObjectId();
+				if (oldHeadId != null) {
+					String oldId = oldHeadId.abbreviate(7).name();
+					String newId = result.getNewHead().abbreviate(7).name();
+					outw.println(MessageFormat.format(CLIText.get().updating,
+							oldId, newId));
+				}
+				outw.println(result.getMergeStatus().toString());
+				break;
+			case CHECKOUT_CONFLICT:
+				outw.println(CLIText.get().mergeCheckoutConflict);
+				for (String collidingPath : result.getCheckoutConflicts()) {
+					outw.println("\t" + collidingPath); //$NON-NLS-1$
+				}
+				outw.println(CLIText.get().mergeCheckoutFailed);
+				break;
+			case CONFLICTING:
+				for (String collidingPath : result.getConflicts().keySet())
+					outw.println(MessageFormat.format(
+							CLIText.get().mergeConflict, collidingPath));
+				outw.println(CLIText.get().mergeFailed);
+				break;
+			case FAILED:
+				for (Map.Entry<String, MergeFailureReason> entry : result
+						.getFailingPaths().entrySet())
+					switch (entry.getValue()) {
+					case DIRTY_WORKTREE:
+					case DIRTY_INDEX:
+						outw.println(CLIText.get().dontOverwriteLocalChanges);
+						outw.println("        " + entry.getKey()); //$NON-NLS-1$
+						break;
+					case COULD_NOT_DELETE:
+						outw.println(CLIText.get().cannotDeleteFile);
+						outw.println("        " + entry.getKey()); //$NON-NLS-1$
+						break;
+					}
+				break;
+			case MERGED:
+				MergeStrategy strategy = isMergedInto(oldHead, src)
+						? MergeStrategy.RECURSIVE
+						: mergeStrategy;
+				outw.println(MessageFormat.format(CLIText.get().mergeMadeBy,
+						strategy.getName()));
+				break;
+			case MERGED_NOT_COMMITTED:
+				outw.println(
+						CLIText.get().mergeWentWellStoppedBeforeCommitting);
+				break;
+			case MERGED_SQUASHED:
+			case FAST_FORWARD_SQUASHED:
+			case MERGED_SQUASHED_NOT_COMMITTED:
+				outw.println(CLIText.get().mergedSquashed);
+				outw.println(
+						CLIText.get().mergeWentWellStoppedBeforeCommitting);
+				break;
+			case ABORTED:
+				throw die(CLIText.get().ffNotPossibleAborting);
+			case NOT_SUPPORTED:
+				outw.println(MessageFormat.format(
+						CLIText.get().unsupportedOperation, result.toString()));
+			}
+		} catch (GitAPIException | IOException e) {
+			throw die(e.getMessage(), e);
 		}
+
 	}
 
 	private Ref getOldHead() throws IOException {
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 6842d8d..60b1743 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
@@ -44,6 +44,7 @@
 
 package org.eclipse.jgit.pgm;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -67,16 +68,22 @@ void commit_0(final RevCommit c) {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
-		for (RevCommit c : commits)
-			argWalk.markStart(c);
-		argWalk.setRevFilter(RevFilter.MERGE_BASE);
-		int max = all ? Integer.MAX_VALUE : 1;
-		while (max-- > 0) {
-			final RevCommit b = argWalk.next();
-			if (b == null)
-				break;
-			outw.println(b.getId().name());
+	protected void run() {
+		try {
+			for (RevCommit c : commits) {
+				argWalk.markStart(c);
+			}
+			argWalk.setRevFilter(RevFilter.MERGE_BASE);
+			int max = all ? Integer.MAX_VALUE : 1;
+			while (max-- > 0) {
+				final RevCommit b = argWalk.next();
+				if (b == null) {
+					break;
+				}
+				outw.println(b.getId().name());
+			}
+		} catch (IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 }
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 be8ad37..e65e5d1 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
@@ -53,6 +53,7 @@
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.PushCommand;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectReader;
@@ -115,7 +116,7 @@ void nothin(@SuppressWarnings("unused") final boolean ignored) {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		try (Git git = new Git(db)) {
 			PushCommand push = git.push();
 			push.setDryRun(dryRun);
@@ -123,10 +124,12 @@ protected void run() throws Exception {
 			push.setProgressMonitor(new TextProgressMonitor(errw));
 			push.setReceivePack(receivePack);
 			push.setRefSpecs(refSpecs);
-			if (all)
+			if (all) {
 				push.setPushAll();
-			if (tags)
+			}
+			if (tags) {
 				push.setPushTags();
+			}
 			push.setRemote(remote);
 			push.setThin(thin);
 			push.setAtomic(atomic);
@@ -140,6 +143,8 @@ protected void run() throws Exception {
 					printPushResult(reader, result.getURI(), result);
 				}
 			}
+		} catch (GitAPIException | IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ReceivePack.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ReceivePack.java
index f3baafb..b601d80 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ReceivePack.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ReceivePack.java
@@ -45,6 +45,7 @@
 package org.eclipse.jgit.pgm;
 
 import java.io.File;
+import java.io.IOException;
 import java.text.MessageFormat;
 
 import org.eclipse.jgit.errors.RepositoryNotFoundException;
@@ -66,7 +67,7 @@ protected final boolean requiresRepository() {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		final org.eclipse.jgit.transport.ReceivePack rp;
 
 		try {
@@ -75,9 +76,15 @@ protected void run() throws Exception {
 		} catch (RepositoryNotFoundException notFound) {
 			throw die(MessageFormat.format(CLIText.get().notAGitRepository,
 					dstGitdir.getPath()));
+		} catch (IOException e) {
+			throw die(e.getMessage(), e);
 		}
 
 		rp = new org.eclipse.jgit.transport.ReceivePack(db);
-		rp.receive(ins, outs, errs);
+		try {
+			rp.receive(ins, outs, errs);
+		} catch (IOException e) {
+			throw die(e.getMessage(), e);
+		}
 	}
 }
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reflog.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reflog.java
index 6f4fcc2..410e88f 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reflog.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reflog.java
@@ -42,10 +42,12 @@
  */
 package org.eclipse.jgit.pgm;
 
+import java.io.IOException;
 import java.util.Collection;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.ReflogCommand;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ReflogEntry;
 import org.eclipse.jgit.lib.Repository;
@@ -59,7 +61,7 @@ class Reflog extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		try (Git git = new Git(db)) {
 			ReflogCommand cmd = git.reflog();
 			if (ref != null)
@@ -69,6 +71,8 @@ protected void run() throws Exception {
 			for (ReflogEntry entry : entries) {
 				outw.println(toString(entry, i++));
 			}
+		} catch (GitAPIException | IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Remote.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Remote.java
index 63eba15..58138fa 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Remote.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Remote.java
@@ -53,6 +53,7 @@
 import org.eclipse.jgit.api.RemoteListCommand;
 import org.eclipse.jgit.api.RemoteRemoveCommand;
 import org.eclipse.jgit.api.RemoteSetUrlCommand;
+import org.eclipse.jgit.api.RemoteSetUrlCommand.UriType;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.pgm.opt.CmdLineParser;
@@ -86,7 +87,7 @@ class Remote extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		try (Git git = new Git(db)) {
 			if (command == null) {
 				RemoteListCommand cmd = git.remoteList();
@@ -99,13 +100,13 @@ protected void run() throws Exception {
 				cmd.call();
 			} else if ("remove".equals(command) || "rm".equals(command)) { //$NON-NLS-1$ //$NON-NLS-2$
 				RemoteRemoveCommand cmd = git.remoteRemove();
-				cmd.setName(name);
+				cmd.setRemoteName(name);
 				cmd.call();
 			} else if ("set-url".equals(command)) { //$NON-NLS-1$
 				RemoteSetUrlCommand cmd = git.remoteSetUrl();
-				cmd.setName(name);
-				cmd.setUri(new URIish(uri));
-				cmd.setPush(push);
+				cmd.setRemoteName(name);
+				cmd.setRemoteUri(new URIish(uri));
+				cmd.setUriType(push ? UriType.PUSH : UriType.FETCH);
 				cmd.call();
 			} else if ("update".equals(command)) { //$NON-NLS-1$
 				// reuse fetch command for basic implementation of remote update
@@ -141,6 +142,8 @@ protected void run() throws Exception {
 				throw new JGitInternalException(MessageFormat
 						.format(CLIText.get().unknownSubcommand, command));
 			}
+		} catch (Exception e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Repo.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Repo.java
index f557211..eec562d 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Repo.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Repo.java
@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.pgm;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.gitrepo.RepoCommand;
 import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.Option;
@@ -60,11 +61,15 @@ class Repo extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
-		new RepoCommand(db)
-			.setURI(uri)
-			.setPath(path)
-			.setGroups(groups)
-			.call();
+	protected void run() {
+		try {
+			new RepoCommand(db)
+				.setURI(uri)
+				.setPath(path)
+				.setGroups(groups)
+				.call();
+		} catch (GitAPIException e) {
+			throw die(e.getMessage(), e);
+		}
 	}
 }
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 f84c848..b3e81c6 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
@@ -49,6 +49,8 @@
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.ResetCommand;
 import org.eclipse.jgit.api.ResetCommand.ResetType;
+import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.pgm.internal.CLIText;
 import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.Option;
 import org.kohsuke.args4j.spi.RestOfArgumentsHandler;
@@ -74,26 +76,33 @@ class Reset extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		try (Git git = new Git(db)) {
 			ResetCommand command = git.reset();
 			command.setRef(commit);
 			if (paths.size() > 0) {
-				for (String path : paths)
+				for (String path : paths) {
 					command.addPath(path);
+				}
 			} else {
 				ResetType mode = null;
-				if (soft)
+				if (soft) {
 					mode = selectMode(mode, ResetType.SOFT);
-				if (mixed)
+				}
+				if (mixed) {
 					mode = selectMode(mode, ResetType.MIXED);
-				if (hard)
+				}
+				if (hard) {
 					mode = selectMode(mode, ResetType.HARD);
-				if (mode == null)
-					throw die("no reset mode set"); //$NON-NLS-1$
+				}
+				if (mode == null) {
+					throw die(CLIText.get().resetNoMode);
+				}
 				command.setMode(mode);
 			}
 			command.call();
+		} catch (GitAPIException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 
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 ac08cd6..9ff12d8 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
@@ -45,6 +45,7 @@
 
 package org.eclipse.jgit.pgm;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -69,27 +70,31 @@ class RevParse extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
-		if (all) {
-			for (Ref r : db.getRefDatabase().getRefs()) {
-				ObjectId objectId = r.getObjectId();
-				// getRefs skips dangling symrefs, so objectId should never be
-				// null.
-				if (objectId == null) {
-					throw new NullPointerException();
+	protected void run() {
+		try {
+			if (all) {
+				for (Ref r : db.getRefDatabase().getRefs()) {
+					ObjectId objectId = r.getObjectId();
+					// getRefs skips dangling symrefs, so objectId should never
+					// be null.
+					if (objectId == null) {
+						throw new NullPointerException();
+					}
+					outw.println(objectId.name());
 				}
-				outw.println(objectId.name());
-			}
-		} else {
-			if (verify && commits.size() > 1) {
-				final CmdLineParser clp = new CmdLineParser(this);
-				throw new CmdLineException(clp,
-						CLIText.format(CLIText.get().needSingleRevision));
-			}
+			} else {
+				if (verify && commits.size() > 1) {
+					final CmdLineParser clp = new CmdLineParser(this);
+					throw new CmdLineException(clp,
+							CLIText.format(CLIText.get().needSingleRevision));
+				}
 
-			for (ObjectId o : commits) {
-				outw.println(o.name());
+				for (ObjectId o : commits) {
+					outw.println(o.name());
+				}
 			}
+		} catch (IOException | CmdLineException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 }
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 f591610..4b66462 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
@@ -49,6 +49,7 @@
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.RmCommand;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.Option;
 import org.kohsuke.args4j.spi.StopOptionHandler;
@@ -61,12 +62,15 @@ class Rm extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		try (Git git = new Git(db)) {
 			RmCommand command = git.rm();
-			for (String p : paths)
+			for (String p : paths) {
 				command.addFilepattern(p);
+			}
 			command.call();
+		} catch (GitAPIException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 }
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 89a15fe..ff3d003 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
@@ -59,6 +59,7 @@
 import org.eclipse.jgit.errors.CorruptObjectException;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.MissingObjectException;
+import org.eclipse.jgit.errors.RevisionSyntaxException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
@@ -175,22 +176,24 @@ protected void init(Repository repository, String gitDir) {
 	/** {@inheritDoc} */
 	@SuppressWarnings("boxing")
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		diffFmt.setRepository(db);
 		try {
 			diffFmt.setPathFilter(pathFilter);
-			if (detectRenames != null)
+			if (detectRenames != null) {
 				diffFmt.setDetectRenames(detectRenames.booleanValue());
+			}
 			if (renameLimit != null && diffFmt.isDetectRenames()) {
 				RenameDetector rd = diffFmt.getRenameDetector();
 				rd.setRenameLimit(renameLimit.intValue());
 			}
 
 			ObjectId objectId;
-			if (objectName == null)
+			if (objectName == null) {
 				objectId = db.resolve(Constants.HEAD);
-			else
+			} else {
 				objectId = db.resolve(objectName);
+			}
 
 			try (RevWalk rw = new RevWalk(db)) {
 				RevObject obj = rw.parseAny(objectId);
@@ -224,6 +227,8 @@ protected void run() throws Exception {
 							obj.getType()));
 				}
 			}
+		} catch (RevisionSyntaxException | IOException e) {
+			throw die(e.getMessage(), e);
 		} finally {
 			diffFmt.close();
 		}
@@ -273,7 +278,7 @@ private void show(RevTree obj) throws MissingObjectException,
 		}
 	}
 
-	private void show(RevWalk rw, RevCommit c) throws Exception {
+	private void show(RevWalk rw, RevCommit c) throws IOException {
 		char[] outbuffer = new char[Constants.OBJECT_ID_LENGTH * 2];
 
 		outw.print(CLIText.get().commitLabel);
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ShowRef.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ShowRef.java
index 6318a63..b8442c5 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ShowRef.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ShowRef.java
@@ -56,15 +56,20 @@
 class ShowRef extends TextBuiltin {
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
-		for (Ref r : getSortedRefs()) {
-			show(r.getObjectId(), r.getName());
-			if (r.getPeeledObjectId() != null)
-				show(r.getPeeledObjectId(), r.getName() + "^{}"); //$NON-NLS-1$
+	protected void run() {
+		try {
+			for (Ref r : getSortedRefs()) {
+				show(r.getObjectId(), r.getName());
+				if (r.getPeeledObjectId() != null) {
+					show(r.getPeeledObjectId(), r.getName() + "^{}"); //$NON-NLS-1$
+				}
+			}
+		} catch (IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 
-	private Iterable<Ref> getSortedRefs() throws Exception {
+	private Iterable<Ref> getSortedRefs() throws IOException {
 		List<Ref> all = db.getRefDatabase().getRefs();
 		// TODO(jrn) check if we can reintroduce fast-path by e.g. implementing
 		// SortedList
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 fb2fd7e..dfc8a94 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
@@ -54,6 +54,8 @@
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.StatusCommand;
+import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.errors.NoWorkTreeException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.IndexDiff.StageState;
 import org.eclipse.jgit.lib.Ref;
@@ -88,14 +90,18 @@ class Status extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		try (Git git = new Git(db)) {
 			StatusCommand statusCommand = git.status();
-			if (filterPaths != null && filterPaths.size() > 0)
-				for (String path : filterPaths)
+			if (filterPaths != null && filterPaths.size() > 0) {
+				for (String path : filterPaths) {
 					statusCommand.addPath(path);
+				}
+			}
 			org.eclipse.jgit.api.Status status = statusCommand.call();
 			printStatus(status);
+		} catch (GitAPIException | NoWorkTreeException | IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Tag.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Tag.java
index 43c1f54..1da4b1d 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Tag.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Tag.java
@@ -48,12 +48,14 @@
 
 package org.eclipse.jgit.pgm;
 
+import java.io.IOException;
 import java.text.MessageFormat;
 import java.util.List;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.ListTagCommand;
 import org.eclipse.jgit.api.TagCommand;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.RefAlreadyExistsException;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
@@ -82,7 +84,7 @@ class Tag extends TextBuiltin {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		try (Git git = new Git(db)) {
 			if (tagName != null) {
 				if (delete) {
@@ -115,6 +117,8 @@ protected void run() throws Exception {
 					outw.println(Repository.shortenRefName(ref.getName()));
 				}
 			}
+		} catch (GitAPIException | IOException e) {
+			throw die(e.getMessage(), e);
 		}
 	}
 }
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 c4b4018..05f2378 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
@@ -196,7 +196,7 @@ private Charset getLogOutputEncodingCharset(Repository repository) {
 				try {
 					return Charset.forName(logOutputEncoding);
 				} catch (IllegalArgumentException e) {
-					throw die(CLIText.get().cannotCreateOutputStream);
+					throw die(CLIText.get().cannotCreateOutputStream, e);
 				}
 			}
 		}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/UploadPack.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/UploadPack.java
index 5d032d2..c138302 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/UploadPack.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/UploadPack.java
@@ -45,6 +45,7 @@
 package org.eclipse.jgit.pgm;
 
 import java.io.File;
+import java.io.IOException;
 import java.text.MessageFormat;
 
 import org.eclipse.jgit.errors.RepositoryNotFoundException;
@@ -70,20 +71,21 @@ protected final boolean requiresRepository() {
 
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
-		final org.eclipse.jgit.transport.UploadPack up;
-
+	protected void run() {
 		try {
 			FileKey key = FileKey.lenient(srcGitdir, FS.DETECTED);
 			db = key.open(true /* must exist */);
+			org.eclipse.jgit.transport.UploadPack up = new org.eclipse.jgit.transport.UploadPack(
+					db);
+			if (0 <= timeout) {
+				up.setTimeout(timeout);
+			}
+			up.upload(ins, outs, errs);
 		} catch (RepositoryNotFoundException notFound) {
 			throw die(MessageFormat.format(CLIText.get().notAGitRepository,
 					srcGitdir.getPath()));
+		} catch (IOException e) {
+			throw die(e.getMessage(), e);
 		}
-
-		up = new org.eclipse.jgit.transport.UploadPack(db);
-		if (0 <= timeout)
-			up.setTimeout(timeout);
-		up.upload(ins, outs, errs);
 	}
 }
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Version.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Version.java
index 58acc5c..cb447e4 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Version.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Version.java
@@ -57,21 +57,28 @@
 class Version extends TextBuiltin {
 	/** {@inheritDoc} */
 	@Override
-	protected void run() throws Exception {
+	protected void run() {
 		// read the Implementation-Version from Manifest
 		String version = getImplementationVersion();
 
 		// if Implementation-Version is not available then try reading
 		// Bundle-Version
-		if (version == null)
+		if (version == null) {
 			version = getBundleVersion();
+		}
 
 		// if both Implementation-Version and Bundle-Version are not available
 		// then throw an exception
-		if (version == null)
+		if (version == null) {
 			throw die(CLIText.get().cannotReadPackageInformation);
+		}
 
-		outw.println(MessageFormat.format(CLIText.get().jgitVersion, version));
+		try {
+			outw.println(
+					MessageFormat.format(CLIText.get().jgitVersion, version));
+		} catch (IOException e) {
+			throw die(e.getMessage(), e);
+		}
 	}
 
 	/** {@inheritDoc} */
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 013ee1c..8a3e43e 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
@@ -163,6 +163,7 @@ public static String fatalError(String message) {
 	/***/ public String clonedEmptyRepository;
 	/***/ public String cloningInto;
 	/***/ public String commitLabel;
+	/***/ public String configOnlyListOptionSupported;
 	/***/ public String conflictingUsageOf_git_dir_andArguments;
 	/***/ public String couldNotCreateBranch;
 	/***/ public String dateInfo;
@@ -274,7 +275,7 @@ public static String fatalError(String message) {
 	/***/ public String onBranchToBeBorn;
 	/***/ public String onBranch;
 	/***/ public String onlyOneMetaVarExpectedIn;
-	/***/ public String onlyOneOfIncludeOnlyAllInteractiveCanBeUsed;
+	/***/ public String onlyOneCommitOptionAllowed;
 	/***/ public String password;
 	/***/ public String pathspecDidNotMatch;
 	/***/ public String pushTo;
@@ -285,6 +286,7 @@ public static String fatalError(String message) {
 	/***/ public String remoteSideDoesNotSupportDeletingRefs;
 	/***/ public String removing;
 	/***/ public String repaint;
+	/***/ public String resetNoMode;
 	/***/ public String s3InvalidBucket;
 	/***/ public String serviceNotSupported;
 	/***/ public String skippingObject;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/GpgSignHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/GpgSignHandler.java
new file mode 100644
index 0000000..e50301a
--- /dev/null
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/GpgSignHandler.java
@@ -0,0 +1,114 @@
+/*
+ * Copyright (C) 2018, Salesforce.
+ * 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.opt;
+
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.OptionDef;
+import org.kohsuke.args4j.spi.Parameters;
+import org.kohsuke.args4j.spi.Setter;
+import org.kohsuke.args4j.spi.StringOptionHandler;
+
+/**
+ * Special handler for the <code>--gpg-sign</code> option of the
+ * <code>commit</code> command.
+ *
+ * The following rules apply:
+ * <ul>
+ * <li>If no key is given, i.e. just <code>--gpg-sign</code> is passed, then it
+ * is the same as <code>--gpg-sign=default</code></li>
+ * </ul>
+ *
+ * @since 5.3
+ */
+public class GpgSignHandler extends StringOptionHandler {
+
+	/**
+	 * The value "default" which will be used when just the option is specified
+	 * without any argument
+	 */
+	public static final String DEFAULT = "default"; //$NON-NLS-1$
+
+	/**
+	 * <p>
+	 * Constructor for GpgSignHandler.
+	 * </p>
+	 *
+	 * @param parser
+	 *            The parser to which this handler belongs.
+	 * @param option
+	 *            The annotation.
+	 * @param setter
+	 *            Object to be used for setting value.
+	 */
+	public GpgSignHandler(CmdLineParser parser, OptionDef option,
+			Setter<? super String> setter) {
+		super(parser, option, setter);
+	}
+
+	/** {@inheritDoc} */
+	@Override
+	public int parseArguments(Parameters params) throws CmdLineException {
+		String alias = params.getParameter(-1);
+		if ("--gpg-sign".equals(alias) || "-S".equals(alias)) { //$NON-NLS-1$ //$NON-NLS-2$
+			try {
+				String key = params.getParameter(0);
+				if (key == null || key.startsWith("-")) { //$NON-NLS-1$
+					// ignore invalid values and assume default
+					setter.addValue(DEFAULT);
+					return 0;
+				}
+
+				// use what we have
+				setter.addValue(key);
+				return 1;
+			} catch (CmdLineException e) {
+				// no additional value, assume default
+				setter.addValue(DEFAULT);
+				return 0;
+			}
+		}
+		return 0;
+	}
+
+}
diff --git a/org.eclipse.jgit.ssh.apache.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.ssh.apache.test/META-INF/MANIFEST.MF
index 5456949..ca244d2 100644
--- a/org.eclipse.jgit.ssh.apache.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.ssh.apache.test/META-INF/MANIFEST.MF
@@ -3,17 +3,17 @@
 Bundle-Name: %Bundle-Name
 Automatic-Module-Name: org.eclipse.jgit.ssh.apache.test
 Bundle-SymbolicName: org.eclipse.jgit.ssh.apache.test
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Vendor: %Provider-Name
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Import-Package: org.eclipse.jgit.internal.transport.sshd.proxy;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.junit;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.junit.ssh;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.ssh;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.sshd;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)",
+Import-Package: org.eclipse.jgit.internal.transport.sshd.proxy;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.junit;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.junit.ssh;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.ssh;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.sshd;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)",
  org.junit;version="[4.12,5.0.0)",
  org.junit.experimental.theories;version="[4.12,5.0.0)",
  org.junit.runner;version="[4.12,5.0.0)"
diff --git a/org.eclipse.jgit.ssh.apache.test/pom.xml b/org.eclipse.jgit.ssh.apache.test/pom.xml
index a03f4ec..e2c8f7a 100644
--- a/org.eclipse.jgit.ssh.apache.test/pom.xml
+++ b/org.eclipse.jgit.ssh.apache.test/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.ssh.apache.test</artifactId>
@@ -106,7 +106,7 @@
             <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-surefire-plugin</artifactId>
             <configuration>
-              <argLine>-Djgit.test.long=true</argLine>
+              <argLine>@{argLine} -Djgit.test.long=true</argLine>
             </configuration>
           </plugin>
         </plugins>
@@ -133,7 +133,7 @@
       <plugin>
         <artifactId>maven-surefire-plugin</artifactId>
         <configuration>
-          <argLine>-Xmx1024m -Dfile.encoding=UTF-8 -Djava.io.tmpdir=${project.build.directory}</argLine>
+          <argLine>@{argLine} -Xmx1024m -Dfile.encoding=UTF-8 -Djava.io.tmpdir=${project.build.directory}</argLine>
           <includes>
             <include>**/*Test.java</include>
             <include>**/*Tests.java</include>
diff --git a/org.eclipse.jgit.ssh.apache/META-INF/MANIFEST.MF b/org.eclipse.jgit.ssh.apache/META-INF/MANIFEST.MF
index 29a12bb..6f724d8 100644
--- a/org.eclipse.jgit.ssh.apache/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.ssh.apache/META-INF/MANIFEST.MF
@@ -5,9 +5,9 @@
 Bundle-SymbolicName: org.eclipse.jgit.ssh.apache
 Bundle-Vendor: %Provider-Name
 Bundle-ActivationPolicy: lazy
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Export-Package: org.eclipse.jgit.internal.transport.sshd;version="5.2.3";x-internal:=true;
+Export-Package: org.eclipse.jgit.internal.transport.sshd;version="5.3.6";x-internal:=true;
   uses:="org.apache.sshd.client,
    org.apache.sshd.client.auth,
    org.apache.sshd.client.auth.keyboard,
@@ -22,9 +22,9 @@
    org.apache.sshd.common.signature,
    org.apache.sshd.common.util.buffer,
    org.eclipse.jgit.transport",
- org.eclipse.jgit.internal.transport.sshd.auth;version="5.2.3";x-internal:=true,
- org.eclipse.jgit.internal.transport.sshd.proxy;version="5.2.3";x-friends:="org.eclipse.jgit.ssh.apache.test",
- org.eclipse.jgit.transport.sshd;version="5.2.3";
+ org.eclipse.jgit.internal.transport.sshd.auth;version="5.3.6";x-internal:=true,
+ org.eclipse.jgit.internal.transport.sshd.proxy;version="5.3.6";x-friends:="org.eclipse.jgit.ssh.apache.test",
+ org.eclipse.jgit.transport.sshd;version="5.3.6";
   uses:="org.eclipse.jgit.transport,
    org.apache.sshd.client.config.hosts,
    org.apache.sshd.common.keyprovider,
@@ -72,12 +72,12 @@
  org.apache.sshd.common.util.net;version="[2.0.0,2.1.0)",
  org.apache.sshd.common.util.security;version="[2.0.0,2.1.0)",
  org.apache.sshd.server.auth;version="[2.0.0,2.1.0)",
- org.eclipse.jgit.annotations;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.fnmatch;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.transport.ssh;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.nls;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)",
+ org.eclipse.jgit.annotations;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.fnmatch;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.transport.ssh;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.nls;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)",
  org.slf4j;version="[1.7.0,2.0.0)"
diff --git a/org.eclipse.jgit.ssh.apache/META-INF/SOURCE-MANIFEST.MF b/org.eclipse.jgit.ssh.apache/META-INF/SOURCE-MANIFEST.MF
index a16ebd3..72ab0d6 100644
--- a/org.eclipse.jgit.ssh.apache/META-INF/SOURCE-MANIFEST.MF
+++ b/org.eclipse.jgit.ssh.apache/META-INF/SOURCE-MANIFEST.MF
@@ -3,5 +3,5 @@
 Bundle-Name: org.eclipse.jgit.ssh.apache - Sources
 Bundle-SymbolicName: org.eclipse.jgit.ssh.apache.source
 Bundle-Vendor: Eclipse.org - JGit
-Bundle-Version: 5.2.3.qualifier
-Eclipse-SourceBundle: org.eclipse.jgit.ssh.apache;version="5.2.3.qualifier";roots="."
+Bundle-Version: 5.3.6.qualifier
+Eclipse-SourceBundle: org.eclipse.jgit.ssh.apache;version="5.3.6.qualifier";roots="."
diff --git a/org.eclipse.jgit.ssh.apache/pom.xml b/org.eclipse.jgit.ssh.apache/pom.xml
index 2254133..16f5775 100644
--- a/org.eclipse.jgit.ssh.apache/pom.xml
+++ b/org.eclipse.jgit.ssh.apache/pom.xml
@@ -50,7 +50,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.ssh.apache</artifactId>
@@ -195,7 +195,7 @@
                   <ignoreMissingClasses>false</ignoreMissingClasses>
                   <skipPomModules>true</skipPomModules>
               </parameter>
-              <skip>true</skip><!-- TODO: Enable after the first release -->
+              <skip>false</skip>
           </configuration>
           <executions>
             <execution>
@@ -248,7 +248,7 @@
                   <ignoreMissingClasses>false</ignoreMissingClasses>
                   <skipPomModules>true</skipPomModules>
               </parameter>
-              <skip>true</skip><!-- TODO: Enable after the first release -->
+              <skip>false</skip>
           </configuration>
       </plugin>
     </plugins>
diff --git a/org.eclipse.jgit.ssh.apache/resources/org/eclipse/jgit/internal/transport/sshd/SshdText.properties b/org.eclipse.jgit.ssh.apache/resources/org/eclipse/jgit/internal/transport/sshd/SshdText.properties
index aa4e4cc..bdb4a7d 100644
--- a/org.eclipse.jgit.ssh.apache/resources/org/eclipse/jgit/internal/transport/sshd/SshdText.properties
+++ b/org.eclipse.jgit.ssh.apache/resources/org/eclipse/jgit/internal/transport/sshd/SshdText.properties
@@ -13,6 +13,7 @@
 identityFileCannotDecrypt=Given passphrase cannot decrypt identity {0}
 identityFileNoKey=No keys found in identity {0}
 identityFileMultipleKeys=Multiple key pairs found in identity {0}
+identityFileNotFound=Skipping identity ''{0}'': file not found
 identityFileUnsupportedFormat=Unsupported format in identity {0}
 kexServerKeyInvalid=Server key did not validate
 keyEncryptedMsg=Key ''{0}'' is encrypted. Enter the passphrase to decrypt it.
diff --git a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/CachingKeyPairProvider.java b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/CachingKeyPairProvider.java
index ad2ff52..1072f32 100644
--- a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/CachingKeyPairProvider.java
+++ b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/CachingKeyPairProvider.java
@@ -45,6 +45,7 @@
 import static java.text.MessageFormat.format;
 
 import java.io.IOException;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.security.GeneralSecurityException;
 import java.security.KeyPair;
@@ -62,7 +63,8 @@
  * A {@link EncryptedFileKeyPairProvider} that uses an external
  * {@link KeyCache}.
  */
-public class CachingKeyPairProvider extends EncryptedFileKeyPairProvider {
+public class CachingKeyPairProvider extends EncryptedFileKeyPairProvider
+		implements Iterable<KeyPair> {
 
 	private final KeyCache cache;
 
@@ -82,16 +84,26 @@ public CachingKeyPairProvider(List<Path> paths, KeyCache cache) {
 	}
 
 	@Override
-	protected Iterable<KeyPair> loadKeys(Collection<? extends Path> resources) {
+	public Iterator<KeyPair> iterator() {
+		Collection<? extends Path> resources = getPaths();
 		if (resources.isEmpty()) {
-			return Collections.emptyList();
+			return Collections.emptyListIterator();
 		}
-		return () -> new CancellingKeyPairIterator(resources);
+		return new CancellingKeyPairIterator(resources);
+	}
+
+	@Override
+	public Iterable<KeyPair> loadKeys() {
+		return this;
 	}
 
 	@Override
 	protected KeyPair doLoadKey(Path resource)
 			throws IOException, GeneralSecurityException {
+		if (!Files.exists(resource)) {
+			log.warn(format(SshdText.get().identityFileNotFound, resource));
+			return null;
+		}
 		// By calling doLoadKey(String, Path, FilePasswordProvider) instead of
 		// super.doLoadKey(Path) we can bypass the key caching in
 		// AbstractResourceKeyPairProvider, over which we have no real control.
diff --git a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/EncryptedFileKeyPairProvider.java b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/EncryptedFileKeyPairProvider.java
index ff81989..ef8e611 100644
--- a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/EncryptedFileKeyPairProvider.java
+++ b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/EncryptedFileKeyPairProvider.java
@@ -70,7 +70,7 @@
  * encrypted private key if the {@link FilePasswordProvider} is a
  * {@link RepeatingFilePasswordProvider}.
  */
-public class EncryptedFileKeyPairProvider extends FileKeyPairProvider {
+public abstract class EncryptedFileKeyPairProvider extends FileKeyPairProvider {
 
 	// TODO: remove this class once we're based on sshd > 2.1.0. See upstream
 	// issue SSHD-850 https://issues.apache.org/jira/browse/SSHD-850 and commit
diff --git a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitHostConfigEntry.java b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitHostConfigEntry.java
index a0705f2..7b22b88 100644
--- a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitHostConfigEntry.java
+++ b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitHostConfigEntry.java
@@ -54,7 +54,6 @@
  * lists of strings. The super class treats them as single strings containing
  * comma-separated lists.
  *
- * @since 5.2
  */
 public class JGitHostConfigEntry extends HostConfigEntry {
 
diff --git a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitSshClient.java b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitSshClient.java
index 212b67f..b9ff5e5 100644
--- a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitSshClient.java
+++ b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitSshClient.java
@@ -70,7 +70,7 @@
 import org.apache.sshd.common.future.SshFutureListener;
 import org.apache.sshd.common.io.IoConnectFuture;
 import org.apache.sshd.common.io.IoSession;
-import org.apache.sshd.common.keyprovider.FileKeyPairProvider;
+import org.apache.sshd.common.keyprovider.AbstractResourceKeyPairProvider;
 import org.apache.sshd.common.keyprovider.KeyPairProvider;
 import org.apache.sshd.common.session.helpers.AbstractSession;
 import org.apache.sshd.common.util.ValidateUtils;
@@ -243,12 +243,11 @@ private JGitClientSession createSession(IoSession ioSession,
 		int numberOfPasswordPrompts = getNumberOfPasswordPrompts(hostConfig);
 		session.getProperties().put(PASSWORD_PROMPTS,
 				Integer.valueOf(numberOfPasswordPrompts));
-		FilePasswordProvider provider = getFilePasswordProvider();
-		if (provider instanceof RepeatingFilePasswordProvider) {
-			((RepeatingFilePasswordProvider) provider)
+		FilePasswordProvider passwordProvider = getFilePasswordProvider();
+		if (passwordProvider instanceof RepeatingFilePasswordProvider) {
+			((RepeatingFilePasswordProvider) passwordProvider)
 					.setAttempts(numberOfPasswordPrompts);
 		}
-		FileKeyPairProvider ourConfiguredKeysProvider = null;
 		List<Path> identities = hostConfig.getIdentities().stream()
 				.map(s -> {
 					try {
@@ -260,16 +259,16 @@ private JGitClientSession createSession(IoSession ioSession,
 					}
 				}).filter(p -> p != null && Files.exists(p))
 				.collect(Collectors.toList());
-		ourConfiguredKeysProvider = new CachingKeyPairProvider(identities,
-				keyCache);
-		ourConfiguredKeysProvider.setPasswordFinder(getFilePasswordProvider());
+		CachingKeyPairProvider ourConfiguredKeysProvider = new CachingKeyPairProvider(
+				identities, keyCache);
+		ourConfiguredKeysProvider.setPasswordFinder(passwordProvider);
 		if (hostConfig.isIdentitiesOnly()) {
 			session.setKeyPairProvider(ourConfiguredKeysProvider);
 		} else {
 			KeyPairProvider defaultKeysProvider = getKeyPairProvider();
-			if (defaultKeysProvider instanceof FileKeyPairProvider) {
-				((FileKeyPairProvider) defaultKeysProvider)
-						.setPasswordFinder(getFilePasswordProvider());
+			if (defaultKeysProvider instanceof AbstractResourceKeyPairProvider<?>) {
+				((AbstractResourceKeyPairProvider<?>) defaultKeysProvider)
+						.setPasswordFinder(passwordProvider);
 			}
 			KeyPairProvider combinedProvider = new CombinedKeyPairProvider(
 					ourConfiguredKeysProvider, defaultKeysProvider);
diff --git a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitSshConfig.java b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitSshConfig.java
index 9eced0f..9846439 100644
--- a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitSshConfig.java
+++ b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitSshConfig.java
@@ -78,7 +78,6 @@
  * Therefore, this re-uses the parsing and caching from
  * {@link OpenSshConfigFile}.
  *
- * @since 5.2
  */
 public class JGitSshConfig implements HostConfigEntryResolver {
 
diff --git a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/KnownHostEntryReader.java b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/KnownHostEntryReader.java
index 4db24a1..659ffae 100644
--- a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/KnownHostEntryReader.java
+++ b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/KnownHostEntryReader.java
@@ -42,13 +42,13 @@
  */
 package org.eclipse.jgit.internal.transport.sshd;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static java.text.MessageFormat.format;
 import static org.apache.sshd.client.config.hosts.HostPatternsHolder.NON_STANDARD_PORT_PATTERN_ENCLOSURE_END_DELIM;
 import static org.apache.sshd.client.config.hosts.HostPatternsHolder.NON_STANDARD_PORT_PATTERN_ENCLOSURE_START_DELIM;
 
 import java.io.BufferedReader;
 import java.io.IOException;
-import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Arrays;
@@ -99,8 +99,7 @@ private KnownHostEntryReader() {
 	public static List<KnownHostEntry> readFromFile(Path path)
 			throws IOException {
 		List<KnownHostEntry> result = new LinkedList<>();
-		try (BufferedReader r = Files.newBufferedReader(path,
-				StandardCharsets.UTF_8)) {
+		try (BufferedReader r = Files.newBufferedReader(path, UTF_8)) {
 			r.lines().forEachOrdered(l -> {
 				if (l == null) {
 					return;
diff --git a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/OpenSshServerKeyVerifier.java b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/OpenSshServerKeyVerifier.java
index 540b586..7d8f3fd 100644
--- a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/OpenSshServerKeyVerifier.java
+++ b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/OpenSshServerKeyVerifier.java
@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.internal.transport.sshd;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static java.text.MessageFormat.format;
 
 import java.io.BufferedReader;
@@ -52,7 +53,6 @@
 import java.io.OutputStreamWriter;
 import java.net.InetSocketAddress;
 import java.net.SocketAddress;
-import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.InvalidPathException;
 import java.nio.file.Path;
@@ -134,7 +134,7 @@
  * <p>
  * Note that adding a key to the known hosts file may create the file. You can
  * specify in the constructor whether the user shall be asked about that, too.
- * If the the user declines updating the file, but the key was otherwise
+ * If the user declines updating the file, but the key was otherwise
  * accepted (user confirmed for "<b>ask</b>", or "no" or "accept-new" are
  * active), the key is accepted for this session only.
  * </p>
@@ -386,7 +386,7 @@ private void updateKnownHostsFile(ClientSession clientSession,
 			try {
 				try (BufferedWriter writer = new BufferedWriter(
 						new OutputStreamWriter(lock.getOutputStream(),
-								StandardCharsets.UTF_8))) {
+								UTF_8))) {
 					writer.newLine();
 					writer.write(entry.getConfigLine());
 					writer.newLine();
@@ -422,10 +422,9 @@ private void updateModifiedServerKey(ClientSession clientSession,
 		if (lock.lock()) {
 			try {
 				try (BufferedWriter writer = new BufferedWriter(
-						new OutputStreamWriter(lock.getOutputStream(),
-								StandardCharsets.UTF_8));
+						new OutputStreamWriter(lock.getOutputStream(), UTF_8));
 						BufferedReader reader = Files.newBufferedReader(path,
-								StandardCharsets.UTF_8)) {
+								UTF_8)) {
 					boolean done = false;
 					String line;
 					while ((line = reader.readLine()) != null) {
diff --git a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/RepeatingFilePasswordProvider.java b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/RepeatingFilePasswordProvider.java
index 5d58bd6..e491cae 100644
--- a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/RepeatingFilePasswordProvider.java
+++ b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/RepeatingFilePasswordProvider.java
@@ -51,7 +51,6 @@
  * A {@link FilePasswordProvider} augmented to support repeatedly asking for
  * passwords.
  *
- * @since 5.2
  */
 public interface RepeatingFilePasswordProvider extends FilePasswordProvider {
 
diff --git a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/SshdText.java b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/SshdText.java
index 5c79f2d..bf432be 100644
--- a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/SshdText.java
+++ b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/SshdText.java
@@ -33,6 +33,7 @@ public static SshdText get() {
 	/***/ public String identityFileCannotDecrypt;
 	/***/ public String identityFileNoKey;
 	/***/ public String identityFileMultipleKeys;
+	/***/ public String identityFileNotFound;
 	/***/ public String identityFileUnsupportedFormat;
 	/***/ public String kexServerKeyInvalid;
 	/***/ public String keyEncryptedMsg;
diff --git a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/auth/BasicAuthentication.java b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/auth/BasicAuthentication.java
index efb1f55..a257a5e 100644
--- a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/auth/BasicAuthentication.java
+++ b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/auth/BasicAuthentication.java
@@ -42,13 +42,14 @@
  */
 package org.eclipse.jgit.internal.transport.sshd.auth;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
+
 import java.net.Authenticator;
 import java.net.Authenticator.RequestorType;
 import java.net.InetSocketAddress;
 import java.net.PasswordAuthentication;
 import java.nio.ByteBuffer;
 import java.nio.CharBuffer;
-import java.nio.charset.StandardCharsets;
 import java.security.AccessController;
 import java.security.PrivilegedAction;
 import java.util.Arrays;
@@ -99,7 +100,7 @@ public BasicAuthentication(InetSocketAddress proxy, String initialUser,
 		if (pass == null) {
 			return new byte[0];
 		}
-		ByteBuffer bytes = StandardCharsets.UTF_8.encode(CharBuffer.wrap(pass));
+		ByteBuffer bytes = UTF_8.encode(CharBuffer.wrap(pass));
 		byte[] pwd = new byte[bytes.remaining()];
 		bytes.get(pwd);
 		if (bytes.hasArray()) {
diff --git a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/proxy/HttpClientConnector.java b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/proxy/HttpClientConnector.java
index 46cdd52..c66ee38 100644
--- a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/proxy/HttpClientConnector.java
+++ b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/proxy/HttpClientConnector.java
@@ -42,12 +42,13 @@
  */
 package org.eclipse.jgit.internal.transport.sshd.proxy;
 
+import static java.nio.charset.StandardCharsets.US_ASCII;
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static java.text.MessageFormat.format;
 
 import java.io.IOException;
 import java.net.HttpURLConnection;
 import java.net.InetSocketAddress;
-import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;
@@ -164,7 +165,7 @@ public void sendClientProxyMetadata(ClientSession sshSession)
 	}
 
 	private void send(StringBuilder msg, IoSession session) throws Exception {
-		byte[] data = eol(msg).toString().getBytes(StandardCharsets.US_ASCII);
+		byte[] data = eol(msg).toString().getBytes(US_ASCII);
 		Buffer buffer = new ByteArrayBuffer(data.length, false);
 		buffer.putRawBytes(data);
 		session.writePacket(buffer).verify(getTimeout());
@@ -196,7 +197,7 @@ public void messageReceived(IoSession session, Readable buffer)
 			int length = buffer.available();
 			byte[] data = new byte[length];
 			buffer.getRawBytes(data, 0, length);
-			String[] reply = new String(data, StandardCharsets.US_ASCII)
+			String[] reply = new String(data, US_ASCII)
 					.split("\r\n"); //$NON-NLS-1$
 			handleMessage(session, Arrays.asList(reply));
 		} catch (Exception e) {
@@ -348,7 +349,7 @@ public String getToken() throws Exception {
 				throw new IOException(format(
 						SshdText.get().proxyHttpInvalidUserName, proxy, user));
 			}
-			byte[] rawUser = user.getBytes(StandardCharsets.UTF_8);
+			byte[] rawUser = user.getBytes(UTF_8);
 			byte[] toEncode = new byte[rawUser.length + 1 + password.length];
 			System.arraycopy(rawUser, 0, toEncode, 0, rawUser.length);
 			toEncode[rawUser.length] = ':';
diff --git a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/proxy/Socks5ClientConnector.java b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/proxy/Socks5ClientConnector.java
index 1844fdc..27d6f41 100644
--- a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/proxy/Socks5ClientConnector.java
+++ b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/proxy/Socks5ClientConnector.java
@@ -42,12 +42,13 @@
  */
 package org.eclipse.jgit.internal.transport.sshd.proxy;
 
+import static java.nio.charset.StandardCharsets.US_ASCII;
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static java.text.MessageFormat.format;
 
 import java.io.IOException;
 import java.net.InetAddress;
 import java.net.InetSocketAddress;
-import java.nio.charset.StandardCharsets;
 
 import org.apache.sshd.client.session.ClientSession;
 import org.apache.sshd.common.io.IoSession;
@@ -295,8 +296,7 @@ private void sendConnectInfo(IoSession session) throws Exception {
 		byte type;
 		int length = 0;
 		if (rawAddress == null) {
-			remoteName = remoteAddress.getHostString()
-					.getBytes(StandardCharsets.US_ASCII);
+			remoteName = remoteAddress.getHostString().getBytes(US_ASCII);
 			if (remoteName == null || remoteName.length == 0) {
 				throw new IOException(
 						format(SshdText.get().proxySocksNoRemoteHostName,
@@ -542,7 +542,7 @@ public Buffer getToken() throws IOException {
 				return null;
 			}
 			try {
-				byte[] rawUser = user.getBytes(StandardCharsets.UTF_8);
+				byte[] rawUser = user.getBytes(UTF_8);
 				if (rawUser.length > 255) {
 					throw new IOException(format(
 							SshdText.get().proxySocksUsernameTooLong, proxy,
diff --git a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/transport/sshd/SshdSessionFactory.java b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/transport/sshd/SshdSessionFactory.java
index 4ec6f22..cdd47bf 100644
--- a/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/transport/sshd/SshdSessionFactory.java
+++ b/org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/transport/sshd/SshdSessionFactory.java
@@ -47,6 +47,7 @@
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.security.KeyPair;
 import java.time.Duration;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -68,7 +69,6 @@
 import org.apache.sshd.common.NamedFactory;
 import org.apache.sshd.common.compression.BuiltinCompressions;
 import org.apache.sshd.common.config.keys.FilePasswordProvider;
-import org.apache.sshd.common.keyprovider.FileKeyPairProvider;
 import org.apache.sshd.common.keyprovider.KeyPairProvider;
 import org.eclipse.jgit.annotations.NonNull;
 import org.eclipse.jgit.errors.TransportException;
@@ -89,7 +89,9 @@
 import org.eclipse.jgit.util.FS;
 
 /**
- * A {@link SshSessionFactory} that uses Apache MINA sshd.
+ * A {@link SshSessionFactory} that uses Apache MINA sshd. Classes from Apache
+ * MINA sshd are kept private to avoid API evolution problems when Apache MINA
+ * sshd interfaces change.
  *
  * @since 5.2
  */
@@ -103,7 +105,7 @@ public class SshdSessionFactory extends SshSessionFactory implements Closeable {
 
 	private final Map<Tuple, ServerKeyVerifier> defaultServerKeyVerifier = new ConcurrentHashMap<>();
 
-	private final Map<Tuple, FileKeyPairProvider> defaultKeys = new ConcurrentHashMap<>();
+	private final Map<Tuple, Iterable<KeyPair>> defaultKeys = new ConcurrentHashMap<>();
 
 	private final KeyCache keyCache;
 
@@ -161,7 +163,7 @@ public SshdSessionFactory(KeyCache keyCache, ProxyDataFactory proxies) {
 	private static final class Tuple {
 		private Object[] objects;
 
-		public Tuple(Object... objects) {
+		public Tuple(Object[] objects) {
 			this.objects = objects;
 		}
 
@@ -209,8 +211,8 @@ public SshdSession getSession(URIish uri,
 				}
 				HostConfigEntryResolver configFile = getHostConfigEntryResolver(
 						home, sshDir);
-				KeyPairProvider defaultKeysProvider = getDefaultKeysProvider(
-						sshDir);
+				KeyPairProvider defaultKeysProvider = toKeyPairProvider(
+						getDefaultKeys(sshDir));
 				KeyPasswordProvider passphrases = createKeyPasswordProvider(
 						credentialsProvider);
 				SshClient client = ClientBuilder.builder()
@@ -351,7 +353,7 @@ public File getSshDirectory() {
 	private HostConfigEntryResolver getHostConfigEntryResolver(
 			@NonNull File homeDir, @NonNull File sshDir) {
 		return defaultHostConfigEntryResolver.computeIfAbsent(
-				new Tuple(homeDir, sshDir),
+				new Tuple(new Object[] { homeDir, sshDir }),
 				t -> new JGitSshConfig(homeDir,
 						new File(sshDir, SshConstants.CONFIG),
 						getLocalUserName()));
@@ -375,7 +377,7 @@ private HostConfigEntryResolver getHostConfigEntryResolver(
 	private ServerKeyVerifier getServerKeyVerifier(@NonNull File homeDir,
 			@NonNull File sshDir) {
 		return defaultServerKeyVerifier.computeIfAbsent(
-				new Tuple(homeDir, sshDir),
+				new Tuple(new Object[] { homeDir, sshDir }),
 				t -> new OpenSshServerKeyVerifier(true,
 						getDefaultKnownHostsFiles(sshDir)));
 	}
@@ -395,20 +397,61 @@ protected List<Path> getDefaultKnownHostsFiles(@NonNull File sshDir) {
 	}
 
 	/**
-	 * Determines a {@link KeyPairProvider} to use to load the default keys.
+	 * Determines the default keys. The default implementation will lazy load
+	 * the {@link #getDefaultIdentities(File) default identity files}.
+	 * <p>
+	 * Subclasses may override and return an {@link Iterable} of whatever keys
+	 * are appropriate. If the returned iterable lazily loads keys, it should be
+	 * an instance of
+	 * {@link org.apache.sshd.common.keyprovider.AbstractResourceKeyPairProvider
+	 * AbstractResourceKeyPairProvider} so that the session can later pass it
+	 * the {@link #createKeyPasswordProvider(CredentialsProvider) password
+	 * provider} wrapped as a {@link FilePasswordProvider} via
+	 * {@link org.apache.sshd.common.keyprovider.AbstractResourceKeyPairProvider#setPasswordFinder(FilePasswordProvider)
+	 * AbstractResourceKeyPairProvider#setPasswordFinder(FilePasswordProvider)}
+	 * so that encrypted, password-protected keys can be loaded.
+	 * </p>
+	 * <p>
+	 * The default implementation uses exactly this mechanism; class
+	 * {@link CachingKeyPairProvider} may serve as a model for a customized
+	 * lazy-loading {@link Iterable} implementation
+	 * </p>
+	 * <p>
+	 * If the {@link Iterable} returned has the keys already pre-loaded or
+	 * otherwise doesn't need to decrypt encrypted keys, it can be any
+	 * {@link Iterable}, for instance a simple {@link java.util.List List}.
+	 * </p>
 	 *
 	 * @param sshDir
 	 *            to look in for keys
-	 * @return the {@link KeyPairProvider}
+	 * @return an {@link Iterable} over the default keys
+	 * @since 5.3
 	 */
 	@NonNull
-	private KeyPairProvider getDefaultKeysProvider(@NonNull File sshDir) {
-		return defaultKeys.computeIfAbsent(new Tuple(sshDir),
-				t -> new CachingKeyPairProvider(getDefaultIdentities(sshDir),
+	protected Iterable<KeyPair> getDefaultKeys(@NonNull File sshDir) {
+		List<Path> defaultIdentities = getDefaultIdentities(sshDir);
+		return defaultKeys.computeIfAbsent(
+				new Tuple(defaultIdentities.toArray(new Path[0])),
+				t -> new CachingKeyPairProvider(defaultIdentities,
 						getKeyCache()));
 	}
 
 	/**
+	 * Converts an {@link Iterable} of {link KeyPair}s into a
+	 * {@link KeyPairProvider}.
+	 *
+	 * @param keys
+	 *            to provide via the returned {@link KeyPairProvider}
+	 * @return a {@link KeyPairProvider} that provides the given {@code keys}
+	 */
+	private KeyPairProvider toKeyPairProvider(Iterable<KeyPair> keys) {
+		if (keys instanceof KeyPairProvider) {
+			return (KeyPairProvider) keys;
+		}
+		return () -> keys;
+	}
+
+	/**
 	 * Gets a list of default identities, i.e., private key files that shall
 	 * always be tried for public key authentication. Typically those are
 	 * ~/.ssh/id_dsa, ~/.ssh/id_rsa, and so on. The default implementation
diff --git a/org.eclipse.jgit.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
index 8bd041c..770cdcf 100644
--- a/org.eclipse.jgit.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
@@ -3,7 +3,7 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.test
 Bundle-SymbolicName: org.eclipse.jgit.test
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
@@ -17,56 +17,57 @@
  org.apache.commons.compress.compressors.bzip2;version="[1.15.0,2.0)",
  org.apache.commons.compress.compressors.gzip;version="[1.15.0,2.0)",
  org.apache.commons.compress.compressors.xz;version="[1.15.0,2.0)",
- org.eclipse.jgit.annotations;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.api;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.api.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.archive;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.attributes;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.awtui;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.blame;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.diff;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.dircache;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.events;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.fnmatch;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.gitrepo;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.hooks;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.ignore;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.ignore.internal;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.fsck;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.dfs;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.io;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.pack;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.reftable;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.storage.reftree;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.internal.transport.parser;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.junit;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.junit.ssh;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.junit.time;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lfs;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.merge;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.nls;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.notes;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.patch;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.pgm;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.pgm.internal;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revplot;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk.filter;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.storage.file;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.storage.pack;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.submodule;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.http;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport.resolver;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.treewalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.treewalk.filter;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util.io;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util.sha1;version="[5.2.3,5.3.0)",
+ org.bouncycastle.util.encoders;version="[1.60.0,2.0.0)",
+ org.eclipse.jgit.annotations;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.api;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.api.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.archive;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.attributes;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.awtui;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.blame;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.diff;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.dircache;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.events;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.fnmatch;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.gitrepo;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.hooks;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.ignore;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.ignore.internal;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.fsck;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.dfs;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.io;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.pack;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.reftable;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.storage.reftree;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.internal.transport.parser;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.junit;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.junit.ssh;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.junit.time;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lfs;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.merge;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.nls;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.notes;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.patch;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.pgm;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.pgm.internal;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revplot;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk.filter;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.storage.file;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.storage.pack;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.submodule;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.http;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport.resolver;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.treewalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.treewalk.filter;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util.io;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util.sha1;version="[5.3.6,5.4.0)",
  org.junit;version="[4.12,5.0.0)",
  org.junit.experimental.theories;version="[4.12,5.0.0)",
  org.junit.rules;version="[4.12,5.0.0)",
@@ -81,4 +82,4 @@
  org.tukaani.xz;version="[1.6.0,2.0)"
 Require-Bundle: org.hamcrest.core;bundle-version="[1.1.0,2.0.0)",
  org.hamcrest.library;bundle-version="[1.1.0,2.0.0)"
-Export-Package: org.eclipse.jgit.transport.ssh;version="5.2.3";x-friends:="org.eclipse.jgit.ssh.apache.test"
+Export-Package: org.eclipse.jgit.transport.ssh;version="5.3.6";x-friends:="org.eclipse.jgit.ssh.apache.test"
diff --git a/org.eclipse.jgit.test/pom.xml b/org.eclipse.jgit.test/pom.xml
index e6a99b2..6203cb3 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.test</artifactId>
@@ -76,11 +76,22 @@
     <dependency>
       <groupId>org.bouncycastle</groupId>
       <artifactId>bcprov-jdk15on</artifactId>
-      <version>1.59</version>
       <scope>test</scope>
      </dependency>
 
     <dependency>
+      <groupId>org.bouncycastle</groupId>
+      <artifactId>bcpg-jdk15on</artifactId>
+      <scope>test</scope>
+    </dependency>
+
+    <dependency>
+      <groupId>org.bouncycastle</groupId>
+      <artifactId>bcpkix-jdk15on</artifactId>
+      <scope>test</scope>
+    </dependency>
+
+    <dependency>
       <groupId>org.hamcrest</groupId>
       <artifactId>hamcrest-library</artifactId>
       <scope>test</scope>
@@ -141,7 +152,7 @@
             <artifactId>maven-surefire-plugin</artifactId>
             <version>${maven-surefire-plugin-version}</version>
             <configuration>
-              <argLine>-Djgit.test.long=true</argLine>
+              <argLine>@{argLine} -Djgit.test.long=true</argLine>
             </configuration>
           </plugin>
         </plugins>
@@ -186,7 +197,7 @@
       <plugin>
         <artifactId>maven-surefire-plugin</artifactId>
         <configuration>
-          <argLine>-Xmx1024m -Dfile.encoding=UTF-8 -Djava.io.tmpdir=${project.build.directory}</argLine>
+          <argLine>@{argLine} -Xmx1024m -Dfile.encoding=UTF-8 -Djava.io.tmpdir=${project.build.directory}</argLine>
           <includes>
             <include>**/*Test.java</include>
             <include>**/*Tests.java</include>
diff --git a/org.eclipse.jgit.test/src/org/eclipse/jgit/transport/ssh/SshTestBase.java b/org.eclipse.jgit.test/src/org/eclipse/jgit/transport/ssh/SshTestBase.java
index dde55b6..2f367ba 100644
--- a/org.eclipse.jgit.test/src/org/eclipse/jgit/transport/ssh/SshTestBase.java
+++ b/org.eclipse.jgit.test/src/org/eclipse/jgit/transport/ssh/SshTestBase.java
@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.transport.ssh;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
@@ -51,7 +52,6 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.util.List;
 import java.util.Locale;
@@ -409,8 +409,7 @@ public void testSshModifiedHostKeyWithProviderDeny() throws Exception {
 
 	private void checkKnownHostsModifiedHostKey(File backup, File newFile,
 			String wrongKey) throws IOException {
-		List<String> oldLines = Files.readAllLines(backup.toPath(),
-				StandardCharsets.UTF_8);
+		List<String> oldLines = Files.readAllLines(backup.toPath(), UTF_8);
 		// Find the original entry. We should have that again in known_hosts.
 		String oldKeyPart = null;
 		for (String oldLine : oldLines) {
@@ -424,8 +423,7 @@ private void checkKnownHostsModifiedHostKey(File backup, File newFile,
 			}
 		}
 		assertNotNull("Old key not found", oldKeyPart);
-		List<String> newLines = Files.readAllLines(newFile.toPath(),
-				StandardCharsets.UTF_8);
+		List<String> newLines = Files.readAllLines(newFile.toPath(), UTF_8);
 		assertFalse("Old host key still found in known_hosts file" + newFile,
 				hasHostKey("localhost", testPort, wrongKey, newLines));
 		assertTrue("New host key not found in known_hosts file" + newFile,
@@ -448,10 +446,10 @@ public void testSshModifiedHostKeyAllow() throws Exception {
 				"IdentityFile " + privateKey1.getAbsolutePath());
 		// File should not have been updated!
 		String[] oldLines = Files
-				.readAllLines(backup.toPath(), StandardCharsets.UTF_8)
+				.readAllLines(backup.toPath(), UTF_8)
 				.toArray(new String[0]);
 		String[] newLines = Files
-				.readAllLines(knownHosts.toPath(), StandardCharsets.UTF_8)
+				.readAllLines(knownHosts.toPath(), UTF_8)
 				.toArray(new String[0]);
 		assertArrayEquals("Known hosts file should not be modified", oldLines,
 				newLines);
diff --git a/org.eclipse.jgit.test/src/org/eclipse/jgit/transport/ssh/SshTestHarness.java b/org.eclipse.jgit.test/src/org/eclipse/jgit/transport/ssh/SshTestHarness.java
index 59925a5..ada16b7 100644
--- a/org.eclipse.jgit.test/src/org/eclipse/jgit/transport/ssh/SshTestHarness.java
+++ b/org.eclipse.jgit.test/src/org/eclipse/jgit/transport/ssh/SshTestHarness.java
@@ -42,6 +42,8 @@
  */
 package org.eclipse.jgit.transport.ssh;
 
+import static java.nio.charset.StandardCharsets.US_ASCII;
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotEquals;
@@ -54,7 +56,6 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
-import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -150,7 +151,7 @@ public void setUp() throws Exception {
 		knownHosts = new File(sshDir, "known_hosts");
 		Files.write(knownHosts.toPath(), Collections.singleton("[localhost]:"
 				+ testPort + ' '
-				+ publicHostKey.toString(StandardCharsets.US_ASCII.name())));
+				+ publicHostKey.toString(US_ASCII.name())));
 		factory = createSessionFactory();
 		SshSessionFactory.setInstance(factory);
 	}
@@ -200,8 +201,7 @@ private static File createKeyPair(File privateKeyFile) throws Exception {
 	 */
 	protected static String createKnownHostsFile(File file, String host,
 			int port, File publicKey) throws IOException {
-		List<String> lines = Files.readAllLines(publicKey.toPath(),
-				StandardCharsets.UTF_8);
+		List<String> lines = Files.readAllLines(publicKey.toPath(), UTF_8);
 		assertEquals("Public key has too many lines", 1, lines.size());
 		String pubKey = lines.get(0);
 		// Strip off the comment.
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 687926b..b28e26a 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
@@ -501,11 +501,11 @@ public void testAddExistingSingleSmallFileWithNewLine() throws IOException,
 					indexState(CONTENT));
 			db.getConfig().setString("core", null, "autocrlf", "true");
 			git.add().addFilepattern("a.txt").call();
-			assertEquals("[a.txt, mode:100644, content:row1\nrow2]",
+			assertEquals("[a.txt, mode:100644, content:row1\r\nrow2]",
 					indexState(CONTENT));
 			db.getConfig().setString("core", null, "autocrlf", "input");
 			git.add().addFilepattern("a.txt").call();
-			assertEquals("[a.txt, mode:100644, content:row1\nrow2]",
+			assertEquals("[a.txt, mode:100644, content:row1\r\nrow2]",
 					indexState(CONTENT));
 		}
 	}
@@ -523,19 +523,18 @@ public void testAddExistingSingleMediumSizeFileWithNewLine()
 		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print(crData);
 		}
-		String lfData = data.toString().replaceAll("\r", "");
 		try (Git git = new Git(db)) {
 			db.getConfig().setString("core", null, "autocrlf", "false");
 			git.add().addFilepattern("a.txt").call();
-			assertEquals("[a.txt, mode:100644, content:" + data + "]",
+			assertEquals("[a.txt, mode:100644, content:" + crData + "]",
 					indexState(CONTENT));
 			db.getConfig().setString("core", null, "autocrlf", "true");
 			git.add().addFilepattern("a.txt").call();
-			assertEquals("[a.txt, mode:100644, content:" + lfData + "]",
+			assertEquals("[a.txt, mode:100644, content:" + crData + "]",
 					indexState(CONTENT));
 			db.getConfig().setString("core", null, "autocrlf", "input");
 			git.add().addFilepattern("a.txt").call();
-			assertEquals("[a.txt, mode:100644, content:" + lfData + "]",
+			assertEquals("[a.txt, mode:100644, content:" + crData + "]",
 					indexState(CONTENT));
 		}
 	}
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 65c20aa..1f3527f 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
@@ -67,6 +67,7 @@
 
 import org.eclipse.jgit.api.CheckoutResult.Status;
 import org.eclipse.jgit.api.CreateBranchCommand.SetupUpstreamMode;
+import org.eclipse.jgit.api.errors.CheckoutConflictException;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRefNameException;
 import org.eclipse.jgit.api.errors.InvalidRemoteException;
@@ -115,7 +116,7 @@ public void setUp() throws Exception {
 		git.add().addFilepattern("Test.txt").call();
 		initialCommit = git.commit().setMessage("Initial commit").call();
 
-		// create a master branch and switch to it
+		// create a test branch and switch to it
 		git.branchCreate().setName("test").call();
 		RefUpdate rup = db.updateRef(Constants.HEAD);
 		rup.link("refs/heads/test");
@@ -144,6 +145,19 @@ public void testCheckout() throws Exception {
 	}
 
 	@Test
+	public void testCheckoutForced() throws Exception {
+		writeTrashFile("Test.txt", "Garbage");
+		try {
+			git.checkout().setName("master").call().getObjectId();
+			fail("Expected CheckoutConflictException didn't occur");
+		} catch (CheckoutConflictException e) {
+			// Expected
+		}
+		assertEquals(initialCommit.getId(), git.checkout().setName("master")
+				.setForced(true).call().getObjectId());
+	}
+
+	@Test
 	public void testCreateBranchOnCheckout() throws Exception {
 		git.checkout().setCreateBranch(true).setName("test2").call();
 		assertNotNull(db.exactRef("refs/heads/test2"));
@@ -171,7 +185,7 @@ public void testCheckoutWithConflict() throws Exception {
 			assertEquals(Status.CONFLICTS, co.getResult().getStatus());
 			assertTrue(co.getResult().getConflictList().contains("Test.txt"));
 		}
-		git.checkout().setName("master").setForce(true).call();
+		git.checkout().setName("master").setForced(true).call();
 		assertThat(read("Test.txt"), is("Hello world"));
 	}
 
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 f5f6529..383436c 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
@@ -424,6 +424,32 @@ public void testBareCloneRepositoryOnlyOneBranch() throws Exception {
 				specs.get(0));
 	}
 
+	@Test
+	public void testCloneRepositoryOnlyOneTag() throws Exception {
+		File directory = createTempDirectory("testCloneRepositoryWithBranch");
+		CloneCommand command = Git.cloneRepository();
+		command.setBranch("tag-initial");
+		command.setBranchesToClone(
+				Collections.singletonList("refs/tags/tag-initial"));
+		command.setDirectory(directory);
+		command.setURI(fileUri());
+		Git git2 = command.call();
+		addRepoToClose(git2.getRepository());
+		assertNotNull(git2);
+		assertNull(git2.getRepository().resolve("tag-for-blob"));
+		assertNull(git2.getRepository().resolve("refs/heads/master"));
+		assertNotNull(git2.getRepository().resolve("tag-initial"));
+		ObjectId taggedCommit = db.resolve("tag-initial^{commit}");
+		assertEquals(taggedCommit.name(), git2.getRepository().getFullBranch());
+		RemoteConfig cfg = new RemoteConfig(git2.getRepository().getConfig(),
+				Constants.DEFAULT_REMOTE_NAME);
+		List<RefSpec> specs = cfg.getFetchRefSpecs();
+		assertEquals(1, specs.size());
+		assertEquals(
+				new RefSpec("+refs/tags/tag-initial:refs/tags/tag-initial"),
+				specs.get(0));
+	}
+
 	public static String allRefNames(List<Ref> refs) {
 		StringBuilder sb = new StringBuilder();
 		for (Ref f : refs) {
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 a6072a0..e4b7ed7 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
@@ -46,6 +46,7 @@
 import static org.junit.Assert.assertNotEquals;
 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;
 
@@ -53,7 +54,10 @@
 import java.util.Date;
 import java.util.List;
 import java.util.TimeZone;
+import java.util.concurrent.atomic.AtomicInteger;
 
+import org.eclipse.jgit.api.CherryPickResult.CherryPickStatus;
+import org.eclipse.jgit.api.errors.CanceledException;
 import org.eclipse.jgit.api.errors.EmptyCommitException;
 import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
 import org.eclipse.jgit.diff.DiffEntry;
@@ -62,9 +66,11 @@
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.junit.time.TimeUtil;
+import org.eclipse.jgit.lib.CommitBuilder;
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
+import org.eclipse.jgit.lib.GpgSigner;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.RefUpdate;
@@ -73,7 +79,9 @@
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.submodule.SubmoduleWalk;
+import org.eclipse.jgit.transport.CredentialsProvider;
 import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.jgit.treewalk.filter.TreeFilter;
 import org.eclipse.jgit.util.FS;
@@ -616,9 +624,100 @@ public void commitOnlyShouldHandleIgnored() throws Exception {
 			writeTrashFile(".gitignore", "bar");
 			git.add().addFilepattern("subdir").call();
 			git.commit().setOnly("subdir").setMessage("first commit").call();
+			assertEquals("[subdir/foo, mode:100644, content:Hello World]",
+					indexState(CONTENT));
 		}
 	}
 
+	@Test
+	public void commitWithAutoCrlfAndNonNormalizedIndex() throws Exception {
+		try (Git git = new Git(db)) {
+			// Commit a file with CR/LF into the index
+			FileBasedConfig config = db.getConfig();
+			config.setString("core", null, "autocrlf", "false");
+			config.save();
+			writeTrashFile("file.txt", "line 1\r\nline 2\r\n");
+			git.add().addFilepattern("file.txt").call();
+			git.commit().setMessage("Initial").call();
+			assertEquals(
+					"[file.txt, mode:100644, content:line 1\r\nline 2\r\n]",
+					indexState(CONTENT));
+			config.setString("core", null, "autocrlf", "true");
+			config.save();
+			writeTrashFile("file.txt", "line 1\r\nline 1.5\r\nline 2\r\n");
+			writeTrashFile("file2.txt", "new\r\nfile\r\n");
+			git.add().addFilepattern("file.txt").addFilepattern("file2.txt")
+					.call();
+			git.commit().setMessage("Second").call();
+			assertEquals(
+					"[file.txt, mode:100644, content:line 1\r\nline 1.5\r\nline 2\r\n]"
+							+ "[file2.txt, mode:100644, content:new\nfile\n]",
+					indexState(CONTENT));
+			writeTrashFile("file2.txt", "new\r\nfile\r\ncontent\r\n");
+			git.add().addFilepattern("file2.txt").call();
+			git.commit().setMessage("Third").call();
+			assertEquals(
+					"[file.txt, mode:100644, content:line 1\r\nline 1.5\r\nline 2\r\n]"
+							+ "[file2.txt, mode:100644, content:new\nfile\ncontent\n]",
+					indexState(CONTENT));
+		}
+	}
+
+	private void testConflictWithAutoCrlf(String baseLf, String lf)
+			throws Exception {
+		try (Git git = new Git(db)) {
+			// Commit a file with CR/LF into the index
+			FileBasedConfig config = db.getConfig();
+			config.setString("core", null, "autocrlf", "false");
+			config.save();
+			writeTrashFile("file.txt", "foo" + baseLf);
+			git.add().addFilepattern("file.txt").call();
+			git.commit().setMessage("Initial").call();
+			// Switch to side branch
+			git.checkout().setCreateBranch(true).setName("side").call();
+			writeTrashFile("file.txt", "bar\r\n");
+			git.add().addFilepattern("file.txt").call();
+			RevCommit side = git.commit().setMessage("Side").call();
+			// Switch back to master and commit a conflict with the given lf
+			git.checkout().setName("master");
+			writeTrashFile("file.txt", "foob" + lf);
+			git.add().addFilepattern("file.txt").call();
+			git.commit().setMessage("Second").call();
+			// Switch on autocrlf=true
+			config.setString("core", null, "autocrlf", "true");
+			config.save();
+			// Cherry pick side: conflict. Resolve with CR-LF and commit.
+			CherryPickResult pick = git.cherryPick().include(side).call();
+			assertEquals("Expected a cherry-pick conflict",
+					CherryPickStatus.CONFLICTING, pick.getStatus());
+			writeTrashFile("file.txt", "foobar\r\n");
+			git.add().addFilepattern("file.txt").call();
+			git.commit().setMessage("Second").call();
+			assertEquals("[file.txt, mode:100644, content:foobar" + lf + "]",
+					indexState(CONTENT));
+		}
+	}
+
+	@Test
+	public void commitConflictWithAutoCrlfBaseCrLfOursLf() throws Exception {
+		testConflictWithAutoCrlf("\r\n", "\n");
+	}
+
+	@Test
+	public void commitConflictWithAutoCrlfBaseLfOursLf() throws Exception {
+		testConflictWithAutoCrlf("\n", "\n");
+	}
+
+	@Test
+	public void commitConflictWithAutoCrlfBasCrLfOursCrLf() throws Exception {
+		testConflictWithAutoCrlf("\r\n", "\r\n");
+	}
+
+	@Test
+	public void commitConflictWithAutoCrlfBaseLfOursCrLf() throws Exception {
+		testConflictWithAutoCrlf("\n", "\r\n");
+	}
+
 	private static void addUnmergedEntry(String file, DirCacheBuilder builder) {
 		DirCacheEntry stage1 = new DirCacheEntry(file, DirCacheEntry.STAGE_1);
 		DirCacheEntry stage2 = new DirCacheEntry(file, DirCacheEntry.STAGE_2);
@@ -630,4 +729,126 @@ private static void addUnmergedEntry(String file, DirCacheBuilder builder) {
 		builder.add(stage2);
 		builder.add(stage3);
 	}
+
+	@Test
+	public void callSignerWithProperSigningKey() throws Exception {
+		try (Git git = new Git(db)) {
+			writeTrashFile("file1", "file1");
+			git.add().addFilepattern("file1").call();
+
+			String[] signingKey = new String[1];
+			PersonIdent[] signingCommitters = new PersonIdent[1];
+			AtomicInteger callCount = new AtomicInteger();
+			GpgSigner.setDefault(new GpgSigner() {
+				@Override
+				public void sign(CommitBuilder commit, String gpgSigningKey,
+						PersonIdent signingCommitter, CredentialsProvider credentialsProvider) {
+					signingKey[0] = gpgSigningKey;
+					signingCommitters[0] = signingCommitter;
+					callCount.incrementAndGet();
+				}
+
+				@Override
+				public boolean canLocateSigningKey(String gpgSigningKey,
+						PersonIdent signingCommitter,
+						CredentialsProvider credentialsProvider)
+						throws CanceledException {
+					return false;
+				}
+			});
+
+			// first call should use config, which is expected to be null at
+			// this time
+			git.commit().setCommitter(committer).setSign(Boolean.TRUE)
+					.setMessage("initial commit")
+					.call();
+			assertNull(signingKey[0]);
+			assertEquals(1, callCount.get());
+			assertSame(committer, signingCommitters[0]);
+
+			writeTrashFile("file2", "file2");
+			git.add().addFilepattern("file2").call();
+
+			// second commit applies config value
+			String expectedConfigSigningKey = "config-" + System.nanoTime();
+			StoredConfig config = git.getRepository().getConfig();
+			config.setString("user", null, "signingKey",
+					expectedConfigSigningKey);
+			config.save();
+
+			git.commit().setCommitter(committer).setSign(Boolean.TRUE)
+					.setMessage("initial commit")
+					.call();
+			assertEquals(expectedConfigSigningKey, signingKey[0]);
+			assertEquals(2, callCount.get());
+			assertSame(committer, signingCommitters[0]);
+
+			writeTrashFile("file3", "file3");
+			git.add().addFilepattern("file3").call();
+
+			// now use specific on api
+			String expectedSigningKey = "my-" + System.nanoTime();
+			git.commit().setCommitter(committer).setSign(Boolean.TRUE)
+					.setSigningKey(expectedSigningKey)
+					.setMessage("initial commit").call();
+			assertEquals(expectedSigningKey, signingKey[0]);
+			assertEquals(3, callCount.get());
+			assertSame(committer, signingCommitters[0]);
+		}
+	}
+
+	@Test
+	public void callSignerOnlyWhenSigning() throws Exception {
+		try (Git git = new Git(db)) {
+			writeTrashFile("file1", "file1");
+			git.add().addFilepattern("file1").call();
+
+			AtomicInteger callCount = new AtomicInteger();
+			GpgSigner.setDefault(new GpgSigner() {
+				@Override
+				public void sign(CommitBuilder commit, String gpgSigningKey,
+						PersonIdent signingCommitter, CredentialsProvider credentialsProvider) {
+					callCount.incrementAndGet();
+				}
+
+				@Override
+				public boolean canLocateSigningKey(String gpgSigningKey,
+						PersonIdent signingCommitter,
+						CredentialsProvider credentialsProvider)
+						throws CanceledException {
+					return false;
+				}
+			});
+
+			// first call should use config, which is expected to be null at
+			// this time
+			git.commit().setMessage("initial commit").call();
+			assertEquals(0, callCount.get());
+
+			writeTrashFile("file2", "file2");
+			git.add().addFilepattern("file2").call();
+
+			// now force signing
+			git.commit().setSign(Boolean.TRUE).setMessage("commit").call();
+			assertEquals(1, callCount.get());
+
+			writeTrashFile("file3", "file3");
+			git.add().addFilepattern("file3").call();
+
+			// now rely on config
+			StoredConfig config = git.getRepository().getConfig();
+			config.setBoolean("commit", null, "gpgSign", true);
+			config.save();
+
+			git.commit().setMessage("commit").call();
+			assertEquals(2, callCount.get());
+
+			writeTrashFile("file4", "file4");
+			git.add().addFilepattern("file4").call();
+
+			// now force "no-sign" (even though config is true)
+			git.commit().setSign(Boolean.FALSE).setMessage("commit").call();
+			assertEquals(2, callCount.get());
+		}
+	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/MergeCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/MergeCommandTest.java
index 9af003d..5a15838 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/MergeCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/MergeCommandTest.java
@@ -1557,32 +1557,37 @@ public void testFastForwardOnlyNotPossible() throws Exception {
 
 	@Test
 	public void testRecursiveMergeWithConflict() throws Exception {
-		TestRepository<Repository> db_t = new TestRepository<>(db);
-		BranchBuilder master = db_t.branch("master");
-		RevCommit m0 = master.commit().add("f", "1\n2\n3\n4\n5\n6\n7\n8\n9\n")
-				.message("m0").create();
-		RevCommit m1 = master.commit()
-				.add("f", "1-master\n2\n3\n4\n5\n6\n7\n8\n9\n").message("m1")
-				.create();
-		db_t.getRevWalk().parseCommit(m1);
+		try (TestRepository<Repository> db_t = new TestRepository<>(db)) {
+			BranchBuilder master = db_t.branch("master");
+			RevCommit m0 = master.commit()
+					.add("f", "1\n2\n3\n4\n5\n6\n7\n8\n9\n").message("m0")
+					.create();
+			RevCommit m1 = master.commit()
+					.add("f", "1-master\n2\n3\n4\n5\n6\n7\n8\n9\n")
+					.message("m1").create();
+			db_t.getRevWalk().parseCommit(m1);
 
-		BranchBuilder side = db_t.branch("side");
-		RevCommit s1 = side.commit().parent(m0)
-				.add("f", "1\n2\n3\n4\n5\n6\n7\n8\n9-side\n").message("s1")
-				.create();
-		RevCommit s2 = side.commit().parent(m1)
-				.add("f", "1-master\n2\n3\n4\n5\n6\n7-res(side)\n8\n9-side\n")
-				.message("s2(merge)").create();
-		master.commit().parent(s1)
-				.add("f", "1-master\n2\n3\n4\n5\n6\n7-conflict\n8\n9-side\n")
-				.message("m2(merge)").create();
+			BranchBuilder side = db_t.branch("side");
+			RevCommit s1 = side.commit().parent(m0)
+					.add("f", "1\n2\n3\n4\n5\n6\n7\n8\n9-side\n").message("s1")
+					.create();
+			RevCommit s2 = side.commit().parent(m1)
+					.add("f",
+							"1-master\n2\n3\n4\n5\n6\n7-res(side)\n8\n9-side\n")
+					.message("s2(merge)").create();
+			master.commit().parent(s1)
+					.add("f",
+							"1-master\n2\n3\n4\n5\n6\n7-conflict\n8\n9-side\n")
+					.message("m2(merge)").create();
 
-		Git git = Git.wrap(db);
-		git.checkout().setName("master").call();
+			Git git = Git.wrap(db);
+			git.checkout().setName("master").call();
 
-		MergeResult result = git.merge().setStrategy(MergeStrategy.RECURSIVE)
-				.include("side", s2).call();
-		assertEquals(MergeStatus.CONFLICTING, result.getMergeStatus());
+			MergeResult result = git.merge()
+					.setStrategy(MergeStrategy.RECURSIVE).include("side", s2)
+					.call();
+			assertEquals(MergeStatus.CONFLICTING, result.getMergeStatus());
+		}
 	}
 
 	private Ref prepareSuccessfulMerge(Git git) throws Exception {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RemoteDeleteCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RemoteDeleteCommandTest.java
index 7055daf..50e7095 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RemoteDeleteCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RemoteDeleteCommandTest.java
@@ -56,7 +56,7 @@ public void testDelete() throws Exception {
 
 		// execute the command to remove the remote
 		RemoteRemoveCommand cmd = Git.wrap(db).remoteRemove();
-		cmd.setName(REMOTE_NAME);
+		cmd.setRemoteName(REMOTE_NAME);
 		RemoteConfig remote = cmd.call();
 
 		// assert that the removed remote is the initial remote
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RemoteSetUrlCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RemoteSetUrlCommandTest.java
index 6969c3d..d3265fe 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RemoteSetUrlCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RemoteSetUrlCommandTest.java
@@ -45,6 +45,7 @@
 import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
 
+import org.eclipse.jgit.api.RemoteSetUrlCommand.UriType;
 import org.eclipse.jgit.transport.RemoteConfig;
 import org.eclipse.jgit.transport.URIish;
 import org.junit.Test;
@@ -58,9 +59,9 @@ public void testSetUrl() throws Exception {
 
 		// execute the command to change the fetch url
 		RemoteSetUrlCommand cmd = Git.wrap(db).remoteSetUrl();
-		cmd.setName(REMOTE_NAME);
+		cmd.setRemoteName(REMOTE_NAME);
 		URIish newUri = new URIish("git://test.com/test");
-		cmd.setUri(newUri);
+		cmd.setRemoteUri(newUri);
 		RemoteConfig remote = cmd.call();
 
 		// assert that the changed remote has the new fetch url
@@ -79,10 +80,10 @@ public void testSetPushUrl() throws Exception {
 
 		// execute the command to change the push url
 		RemoteSetUrlCommand cmd = Git.wrap(db).remoteSetUrl();
-		cmd.setName(REMOTE_NAME);
+		cmd.setRemoteName(REMOTE_NAME);
 		URIish newUri = new URIish("git://test.com/test");
-		cmd.setUri(newUri);
-		cmd.setPush(true);
+		cmd.setRemoteUri(newUri);
+		cmd.setUriType(UriType.PUSH);
 		RemoteConfig remote = cmd.call();
 
 		// assert that the changed remote has the old fetch url and the new push
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RenameBranchCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RenameBranchCommandTest.java
index 5c437ac..9facce9 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RenameBranchCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RenameBranchCommandTest.java
@@ -49,14 +49,18 @@
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 
+import org.eclipse.jgit.api.errors.RefAlreadyExistsException;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.BranchConfig.BranchRebaseMode;
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.junit.Before;
+import org.junit.Rule;
 import org.junit.Test;
+import org.junit.rules.ExpectedException;
 
 /**
  * Unit tests of {@link RenameBranchCommand}
@@ -69,6 +73,9 @@ public class RenameBranchCommandTest extends RepositoryTestCase {
 
 	private Git git;
 
+	@Rule
+	public ExpectedException thrown = ExpectedException.none();
+
 	@Override
 	@Before
 	public void setUp() throws Exception {
@@ -81,6 +88,45 @@ public void setUp() throws Exception {
 	}
 
 	@Test
+	public void renameToExisting() throws Exception {
+		assertNotNull(git.branchCreate().setName("foo").call());
+		thrown.expect(RefAlreadyExistsException.class);
+		git.branchRename().setOldName("master").setNewName("foo").call();
+	}
+
+	@Test
+	public void renameToTag() throws Exception {
+		Ref ref = git.tag().setName("foo").call();
+		assertNotNull(ref);
+		assertEquals("Unexpected tag name", Constants.R_TAGS + "foo",
+				ref.getName());
+		ref = git.branchRename().setNewName("foo").call();
+		assertNotNull(ref);
+		assertEquals("Unexpected ref name", Constants.R_HEADS + "foo",
+				ref.getName());
+		// Check that we can rename it back
+		ref = git.branchRename().setOldName("foo").setNewName(Constants.MASTER)
+				.call();
+		assertNotNull(ref);
+		assertEquals("Unexpected ref name",
+				Constants.R_HEADS + Constants.MASTER, ref.getName());
+	}
+
+	@Test
+	public void renameToStupidName() throws Exception {
+		Ref ref = git.branchRename().setNewName(Constants.R_HEADS + "foo")
+				.call();
+		assertEquals("Unexpected ref name",
+				Constants.R_HEADS + Constants.R_HEADS + "foo",
+				ref.getName());
+		// And check that we can rename it back to a sane name
+		ref = git.branchRename().setNewName("foo").call();
+		assertNotNull(ref);
+		assertEquals("Unexpected ref name", Constants.R_HEADS + "foo",
+				ref.getName());
+	}
+
+	@Test
 	public void renameBranchNoConfigValues() throws Exception {
 		StoredConfig config = git.getRepository().getConfig();
 		config.unsetSection(ConfigConstants.CONFIG_BRANCH_SECTION,
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesNodeDirCacheIteratorTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesNodeDirCacheIteratorTest.java
index 7421e90..837de74 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesNodeDirCacheIteratorTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesNodeDirCacheIteratorTest.java
@@ -64,7 +64,7 @@
 import org.junit.Test;
 
 /**
- * Tests attributes node behavior on the the index.
+ * Tests attributes node behavior on the index.
  */
 public class AttributesNodeDirCacheIteratorTest extends RepositoryTestCase {
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/diff/RawTextTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/diff/RawTextTest.java
index 178d620..5333451 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/diff/RawTextTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/diff/RawTextTest.java
@@ -79,6 +79,36 @@ public void testNul() {
 	}
 
 	@Test
+	public void testCrLfTextYes() {
+		assertTrue(RawText
+				.isCrLfText(Constants.encodeASCII("line 1\r\nline 2\r\n")));
+	}
+
+	@Test
+	public void testCrLfTextNo() {
+		assertFalse(
+				RawText.isCrLfText(Constants.encodeASCII("line 1\nline 2\n")));
+	}
+
+	@Test
+	public void testCrLfTextBinary() {
+		assertFalse(RawText
+				.isCrLfText(Constants.encodeASCII("line 1\r\nline\0 2\r\n")));
+	}
+
+	@Test
+	public void testCrLfTextMixed() {
+		assertTrue(RawText
+				.isCrLfText(Constants.encodeASCII("line 1\nline 2\r\n")));
+	}
+
+	@Test
+	public void testCrLfTextCutShort() {
+		assertFalse(
+				RawText.isCrLfText(Constants.encodeASCII("line 1\nline 2\r")));
+	}
+
+	@Test
 	public void testEquals() {
 		final RawText a = new RawText(Constants.encodeASCII("foo-a\nfoo-b\n"));
 		final RawText b = new RawText(Constants.encodeASCII("foo-b\nfoo-c\n"));
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsPackFileTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsPackFileTest.java
new file mode 100644
index 0000000..dd41b6f
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsPackFileTest.java
@@ -0,0 +1,165 @@
+/*
+ * Copyright (C) 2019, Google LLC.
+ * 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.junit.Assert.assertEquals;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.util.zip.Deflater;
+
+import org.eclipse.jgit.internal.storage.pack.PackExt;
+import org.eclipse.jgit.internal.storage.pack.PackOutputStream;
+import org.eclipse.jgit.internal.storage.pack.PackWriter;
+import org.eclipse.jgit.junit.JGitTestUtil;
+import org.eclipse.jgit.junit.TestRng;
+import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.NullProgressMonitor;
+import org.junit.Before;
+import org.junit.Test;
+
+public class DfsPackFileTest {
+	InMemoryRepository db;
+	boolean bypassCache;
+	boolean clearCache;
+
+	@Before
+	public void setUp() {
+		db = new InMemoryRepository(new DfsRepositoryDescription("test"));
+	}
+
+	@Test
+	public void testCopyPackBypassCachesSmallCached() throws IOException {
+		bypassCache = true;
+		clearCache = false;
+		setupPack(512, 256);
+		assertPackSize();
+	}
+
+	@Test
+	public void testCopyPackBypassCacheSmallNoCache() throws IOException {
+		bypassCache = true;
+		clearCache = true;
+		setupPack(512, 256);
+		assertPackSize();
+	}
+
+	@Test
+	public void testCopyPackBypassCacheLargeCached() throws IOException {
+		bypassCache = true;
+		clearCache = false;
+		setupPack(512, 8000);
+		assertPackSize();
+	}
+
+	@Test
+	public void testCopyPackBypassCacheLargeNoCache() throws IOException {
+		bypassCache = true;
+		clearCache = true;
+		setupPack(512, 8000);
+		assertPackSize();
+	}
+
+	@Test
+	public void testCopyPackThroughCacheSmallCached() throws IOException {
+		bypassCache = false;
+		clearCache = false;
+		setupPack(512, 256);
+		assertPackSize();
+	}
+
+	@Test
+	public void testCopyPackThroughCacheSmallNoCache() throws IOException {
+		bypassCache = false;
+		clearCache = true;
+		setupPack(512, 256);
+		assertPackSize();
+	}
+
+	@Test
+	public void testCopyPackThroughCacheLargeCached() throws IOException {
+		bypassCache = false;
+		clearCache = false;
+		setupPack(512, 8000);
+		assertPackSize();
+	}
+
+	@Test
+	public void testCopyPackThroughCacheLargeNoCache() throws IOException {
+		bypassCache = false;
+		clearCache = true;
+		setupPack(512, 8000);
+		assertPackSize();
+	}
+
+	private void setupPack(int bs, int ps) throws IOException {
+		DfsBlockCacheConfig cfg = new DfsBlockCacheConfig().setBlockSize(bs)
+				.setBlockLimit(bs * 100).setStreamRatio(bypassCache ? 0F : 1F);
+		DfsBlockCache.reconfigure(cfg);
+
+		byte[] data = new TestRng(JGitTestUtil.getName()).nextBytes(ps);
+		DfsInserter ins = (DfsInserter) db.newObjectInserter();
+		ins.setCompressionLevel(Deflater.NO_COMPRESSION);
+		ins.insert(Constants.OBJ_BLOB, data);
+		ins.flush();
+
+		if (clearCache) {
+			DfsBlockCache.reconfigure(cfg);
+			db.getObjectDatabase().clearCache();
+		}
+	}
+
+	private void assertPackSize() throws IOException {
+		try (DfsReader ctx = db.getObjectDatabase().newReader();
+				PackWriter pw = new PackWriter(ctx);
+				ByteArrayOutputStream os = new ByteArrayOutputStream();
+				PackOutputStream out = new PackOutputStream(
+						NullProgressMonitor.INSTANCE, os, pw)) {
+			DfsPackFile pack = db.getObjectDatabase().getPacks()[0];
+			long packSize = pack.getPackDescription().getFileSize(PackExt.PACK);
+			pack.copyPackAsIs(out, ctx);
+			assertEquals(packSize - (12 + 20), os.size());
+		}
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcBranchPrunedTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcBranchPrunedTest.java
index c7ee925..8f29b3b 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcBranchPrunedTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcBranchPrunedTest.java
@@ -66,11 +66,11 @@ public void branch_historyNotPruned() throws Exception {
 		fsTick();
 		gc.prune(Collections.<ObjectId> emptySet());
 		do {
-			assertTrue(repo.hasObject(tip));
+			assertTrue(repo.getObjectDatabase().has(tip));
 			tr.parseBody(tip);
 			RevTree t = tip.getTree();
-			assertTrue(repo.hasObject(t));
-			assertTrue(repo.hasObject(tr.get(t, "a")));
+			assertTrue(repo.getObjectDatabase().has(t));
+			assertTrue(repo.getObjectDatabase().has(tr.get(t, "a")));
 			tip = tip.getParentCount() > 0 ? tip.getParent(0) : null;
 		} while (tip != null);
 	}
@@ -114,6 +114,6 @@ public void deleteMergedBranch_historyNotPruned() throws Exception {
 		gc.setExpireAgeMillis(0);
 		fsTick();
 		gc.prune(Collections.<ObjectId> emptySet());
-		assertTrue(repo.hasObject(b2Tip));
+		assertTrue(repo.getObjectDatabase().has(b2Tip));
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcConcurrentTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcConcurrentTest.java
index c60c357..05f7c65 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcConcurrentTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcConcurrentTest.java
@@ -177,7 +177,7 @@ public void repackAndUploadPack() throws Exception {
 		gc2.gc();
 
 		// Simulate parts of an UploadPack. This is the situation on
-		// server side (e.g. gerrit) when when clients are
+		// server side (e.g. gerrit) when clients are
 		// cloning/fetching while the server side repo's
 		// are gc'ed by an external process (e.g. scheduled
 		// native git gc)
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcDeleteEmptyRefsFoldersTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcDeleteEmptyRefsFoldersTest.java
index 3caae72..d450f94 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcDeleteEmptyRefsFoldersTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcDeleteEmptyRefsFoldersTest.java
@@ -91,6 +91,20 @@ public void emptyRefFoldersAreDeleted() throws Exception {
 		assertFalse(refDir02.getParent().getParent().toFile().exists());
 	}
 
+	@Test
+	public void emptyRefFoldersSkipFiles() throws Exception {
+		FileTime fileTime = FileTime.from(Instant.now().minusSeconds(31));
+		Path refFile = Files.createFile(refsDir.resolve(".DS_Store"));
+		Path refDir01 = Files.createDirectories(heads.resolve(REF_FOLDER_01));
+		Path refDir02 = Files.createDirectories(heads.resolve(REF_FOLDER_02));
+		setLastModifiedTime(fileTime, heads, REF_FOLDER_01);
+		setLastModifiedTime(fileTime, heads, REF_FOLDER_02);
+		assertTrue(refDir01.toFile().exists());
+		assertTrue(refDir02.toFile().exists());
+		gc.gc();
+		assertTrue(Files.exists(refFile));
+	}
+
 	private void setLastModifiedTime(FileTime fileTime, Path path, String folder) throws IOException {
 		long numParents = folder.chars().filter(c -> c == '/').count();
 		Path folderPath = path.resolve(folder);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPruneNonReferencedTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPruneNonReferencedTest.java
index 3452070..878dc86 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPruneNonReferencedTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPruneNonReferencedTest.java
@@ -64,7 +64,7 @@ public void nonReferencedNonExpiredObject_notPruned() throws Exception {
 		RevBlob a = tr.blob("a");
 		gc.setExpire(new Date(lastModified(a)));
 		gc.prune(Collections.<ObjectId> emptySet());
-		assertTrue(repo.hasObject(a));
+		assertTrue(repo.getObjectDatabase().has(a));
 	}
 
 	@Test
@@ -73,7 +73,7 @@ public void nonReferencedExpiredObject_pruned() throws Exception {
 		gc.setExpireAgeMillis(0);
 		fsTick();
 		gc.prune(Collections.<ObjectId> emptySet());
-		assertFalse(repo.hasObject(a));
+		assertFalse(repo.getObjectDatabase().has(a));
 	}
 
 	@Test
@@ -83,8 +83,8 @@ public void nonReferencedExpiredObjectTree_pruned() throws Exception {
 		gc.setExpireAgeMillis(0);
 		fsTick();
 		gc.prune(Collections.<ObjectId> emptySet());
-		assertFalse(repo.hasObject(t));
-		assertFalse(repo.hasObject(a));
+		assertFalse(repo.getObjectDatabase().has(t));
+		assertFalse(repo.getObjectDatabase().has(a));
 	}
 
 	@Test
@@ -96,8 +96,8 @@ public void nonReferencedObjects_onlyExpiredPruned() throws Exception {
 		RevBlob b = tr.blob("b");
 
 		gc.prune(Collections.<ObjectId> emptySet());
-		assertFalse(repo.hasObject(a));
-		assertTrue(repo.hasObject(b));
+		assertFalse(repo.getObjectDatabase().has(a));
+		assertTrue(repo.getObjectDatabase().has(b));
 	}
 
 	@Test
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcTagTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcTagTest.java
index 4afbeff..cf7a431 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcTagTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcTagTest.java
@@ -60,7 +60,7 @@ public void lightweightTag_objectNotPruned() throws Exception {
 		gc.setExpireAgeMillis(0);
 		fsTick();
 		gc.prune(Collections.<ObjectId> emptySet());
-		assertTrue(repo.hasObject(a));
+		assertTrue(repo.getObjectDatabase().has(a));
 	}
 
 	@Test
@@ -72,7 +72,7 @@ public void annotatedTag_objectNotPruned() throws Exception {
 		gc.setExpireAgeMillis(0);
 		fsTick();
 		gc.prune(Collections.<ObjectId> emptySet());
-		assertTrue(repo.hasObject(t));
-		assertTrue(repo.hasObject(a));
+		assertTrue(repo.getObjectDatabase().has(t));
+		assertTrue(repo.getObjectDatabase().has(a));
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ObjectDirectoryTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ObjectDirectoryTest.java
index 1d3ca03..9d47c7e 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ObjectDirectoryTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ObjectDirectoryTest.java
@@ -127,7 +127,7 @@ public void testScanningForPackfiles() throws Exception {
 			// scanning of the packs directory
 			ObjectId id = commitFile("file.txt", "test", "master").getId();
 			gc.gc();
-			assertFalse(receivingDB.hasObject(unknownID));
+			assertFalse(receivingDB.getObjectDatabase().has(unknownID));
 			assertTrue(receivingDB.getObjectDatabase().hasPackedObject(id));
 
 			// preparations
@@ -151,7 +151,7 @@ public void testScanningForPackfiles() throws Exception {
 			// JGit will not rescan the packs folder later on and fails to see
 			// the pack file created during gc.
 			assertTrue(tmpFile.createNewFile());
-			assertFalse(receivingDB.hasObject(unknownID));
+			assertFalse(receivingDB.getObjectDatabase().has(unknownID));
 
 			// trigger a gc. This will create packfiles which have likely the
 			// same mtime than the packfolder
@@ -181,8 +181,8 @@ public boolean accept(File dir, String name) {
 					.equals(fs.lastModifiedInstant(ret[0])));
 
 			// all objects are in a new packfile but we will not detect it
-			assertFalse(receivingDB.hasObject(unknownID));
-			assertTrue(receivingDB.hasObject(id2));
+			assertFalse(receivingDB.getObjectDatabase().has(unknownID));
+			assertTrue(receivingDB.getObjectDatabase().has(id2));
 		}
 	}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackWriterTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackWriterTest.java
index 04bed09..ca44862 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackWriterTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackWriterTest.java
@@ -469,10 +469,12 @@ public void testWritePack4SizeThinVsNoThin() throws Exception {
 	public void testDeltaStatistics() throws Exception {
 		config.setDeltaCompress(true);
 		FileRepository repo = createBareRepository();
-		TestRepository<FileRepository> testRepo = new TestRepository<>(repo);
 		ArrayList<RevObject> blobs = new ArrayList<>();
-		blobs.add(testRepo.blob(genDeltableData(1000)));
-		blobs.add(testRepo.blob(genDeltableData(1005)));
+		try (TestRepository<FileRepository> testRepo = new TestRepository<>(
+				repo)) {
+			blobs.add(testRepo.blob(genDeltableData(1000)));
+			blobs.add(testRepo.blob(genDeltableData(1005)));
+		}
 
 		try (PackWriter pw = new PackWriter(repo)) {
 			NullProgressMonitor m = NullProgressMonitor.INSTANCE;
@@ -535,25 +537,23 @@ public void testWriteIndex() throws Exception {
 	public void testExclude() throws Exception {
 		FileRepository repo = createBareRepository();
 
-		TestRepository<FileRepository> testRepo = new TestRepository<>(
-				repo);
-		BranchBuilder bb = testRepo.branch("refs/heads/master");
-		contentA = testRepo.blob("A");
-		c1 = bb.commit().add("f", contentA).create();
-		testRepo.getRevWalk().parseHeaders(c1);
-		PackIndex pf1 = writePack(repo, wants(c1), EMPTY_ID_SET);
-		assertContent(
-				pf1,
-				Arrays.asList(c1.getId(), c1.getTree().getId(),
-						contentA.getId()));
-		contentB = testRepo.blob("B");
-		c2 = bb.commit().add("f", contentB).create();
-		testRepo.getRevWalk().parseHeaders(c2);
-		PackIndex pf2 = writePack(repo, wants(c2), Sets.of((ObjectIdSet) pf1));
-		assertContent(
-				pf2,
-				Arrays.asList(c2.getId(), c2.getTree().getId(),
-						contentB.getId()));
+		try (TestRepository<FileRepository> testRepo = new TestRepository<>(
+				repo)) {
+			BranchBuilder bb = testRepo.branch("refs/heads/master");
+			contentA = testRepo.blob("A");
+			c1 = bb.commit().add("f", contentA).create();
+			testRepo.getRevWalk().parseHeaders(c1);
+			PackIndex pf1 = writePack(repo, wants(c1), EMPTY_ID_SET);
+			assertContent(pf1, Arrays.asList(c1.getId(), c1.getTree().getId(),
+					contentA.getId()));
+			contentB = testRepo.blob("B");
+			c2 = bb.commit().add("f", contentB).create();
+			testRepo.getRevWalk().parseHeaders(c2);
+			PackIndex pf2 = writePack(repo, wants(c2),
+					Sets.of((ObjectIdSet) pf1));
+			assertContent(pf2, Arrays.asList(c2.getId(), c2.getTree().getId(),
+					contentB.getId()));
+		}
 	}
 
 	private static void assertContent(PackIndex pi, List<ObjectId> expected) {
@@ -660,20 +660,21 @@ public void testShallowFetchShallowAncestorDepth2() throws Exception {
 
 	private FileRepository setupRepoForShallowFetch() throws Exception {
 		FileRepository repo = createBareRepository();
-		TestRepository<Repository> r = new TestRepository<>(repo);
-		BranchBuilder bb = r.branch("refs/heads/master");
-		contentA = r.blob("A");
-		contentB = r.blob("B");
-		contentC = r.blob("C");
-		contentD = r.blob("D");
-		contentE = r.blob("E");
-		c1 = bb.commit().add("a", contentA).create();
-		c2 = bb.commit().add("b", contentB).create();
-		c3 = bb.commit().add("c", contentC).create();
-		c4 = bb.commit().add("d", contentD).create();
-		c5 = bb.commit().add("e", contentE).create();
-		r.getRevWalk().parseHeaders(c5); // fully initialize the tip RevCommit
-		return repo;
+		try (TestRepository<Repository> r = new TestRepository<>(repo)) {
+			BranchBuilder bb = r.branch("refs/heads/master");
+			contentA = r.blob("A");
+			contentB = r.blob("B");
+			contentC = r.blob("C");
+			contentD = r.blob("D");
+			contentE = r.blob("E");
+			c1 = bb.commit().add("a", contentA).create();
+			c2 = bb.commit().add("b", contentB).create();
+			c3 = bb.commit().add("c", contentC).create();
+			c4 = bb.commit().add("d", contentD).create();
+			c5 = bb.commit().add("e", contentE).create();
+			r.getRevWalk().parseHeaders(c5); // fully initialize the tip RevCommit
+			return repo;
+		}
 	}
 
 	private static PackIndex writePack(FileRepository repo,
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 24e3bc0..2357edf 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
@@ -48,6 +48,7 @@
 import static org.eclipse.jgit.lib.Constants.R_TAGS;
 import static org.eclipse.jgit.lib.Ref.Storage.LOOSE;
 import static org.eclipse.jgit.lib.Ref.Storage.NEW;
+import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
@@ -62,6 +63,7 @@
 import java.time.Instant;
 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;
@@ -137,6 +139,33 @@ public void testCreate() throws IOException {
 		assertEquals("ref: refs/heads/master\n", read(new File(d, HEAD)));
 	}
 
+	@Test(expected = UnsupportedOperationException.class)
+	public void testVersioningNotImplemented_exactRef() throws IOException {
+		assertFalse(refdir.hasVersioning());
+
+		Ref ref = refdir.exactRef(HEAD);
+		assertNotNull(ref);
+		ref.getUpdateIndex(); // Not implemented on FS
+	}
+
+	@Test
+	public void testVersioningNotImplemented_getRefs() throws Exception {
+		assertFalse(refdir.hasVersioning());
+
+		RevCommit C = repo.commit().parent(B).create();
+		repo.update("master", C);
+		List<Ref> refs = refdir.getRefs();
+
+		for (Ref ref : refs) {
+			try {
+				ref.getUpdateIndex();
+				fail("FS doesn't implement ref versioning");
+			} catch (UnsupportedOperationException e) {
+				// ok
+			}
+		}
+	}
+
 	@Test
 	public void testGetRefs_EmptyDatabase() throws IOException {
 		Map<String, Ref> all;
@@ -395,15 +424,15 @@ public void testGetRefs_InvalidName() throws IOException {
 
 	@Test
 	public void testReadNotExistingBranchConfig() throws IOException {
-		assertNull("find branch config", refdir.getRef("config"));
-		assertNull("find branch config", refdir.getRef("refs/heads/config"));
+		assertNull("find branch config", refdir.findRef("config"));
+		assertNull("find branch config", refdir.findRef("refs/heads/config"));
 	}
 
 	@Test
 	public void testReadBranchConfig() throws IOException {
 		writeLooseRef("refs/heads/config", A);
 
-		assertNotNull("find branch config", refdir.getRef("config"));
+		assertNotNull("find branch config", refdir.findRef("config"));
 	}
 
 	@Test
@@ -647,7 +676,7 @@ public void testGetRefs_DiscoversModifiedLoose() throws IOException {
 
 	@Repeat(n = 100, abortOnFailure = false)
 	@Test
-	public void testGetRef_DiscoversModifiedLoose() throws IOException {
+	public void testFindRef_DiscoversModifiedLoose() throws IOException {
 		Map<String, Ref> all;
 
 		writeLooseRef("refs/heads/master", A);
@@ -656,7 +685,7 @@ public void testGetRef_DiscoversModifiedLoose() throws IOException {
 
 		writeLooseRef("refs/heads/master", B);
 
-		Ref master = refdir.getRef("refs/heads/master");
+		Ref master = refdir.findRef("refs/heads/master");
 		assertEquals(B, master.getObjectId());
 	}
 
@@ -691,7 +720,7 @@ public void testGetRefs_DiscoversDeletedLoose1() throws IOException {
 	}
 
 	@Test
-	public void testGetRef_DiscoversDeletedLoose() throws IOException {
+	public void testFindRef_DiscoversDeletedLoose() throws IOException {
 		Map<String, Ref> all;
 
 		writeLooseRef("refs/heads/master", A);
@@ -699,7 +728,7 @@ public void testGetRef_DiscoversDeletedLoose() throws IOException {
 		assertEquals(A, all.get(HEAD).getObjectId());
 
 		deleteLooseRef("refs/heads/master");
-		assertNull(refdir.getRef("refs/heads/master"));
+		assertNull(refdir.findRef("refs/heads/master"));
 		assertTrue(refdir.getRefs(RefDatabase.ALL).isEmpty());
 	}
 
@@ -859,7 +888,7 @@ public void testGetRefs_CycleInSymbolicRef() throws IOException {
 	}
 
 	@Test
-	public void testGetRef_CycleInSymbolicRef() throws IOException {
+	public void testFindRef_CycleInSymbolicRef() throws IOException {
 		Ref r;
 
 		writeLooseRef("refs/1", "ref: refs/2\n");
@@ -869,7 +898,7 @@ public void testGetRef_CycleInSymbolicRef() throws IOException {
 		writeLooseRef("refs/5", "ref: refs/end\n");
 		writeLooseRef("refs/end", A);
 
-		r = refdir.getRef("1");
+		r = refdir.findRef("1");
 		assertEquals("refs/1", r.getName());
 		assertEquals(A, r.getObjectId());
 		assertTrue(r.isSymbolic());
@@ -877,12 +906,12 @@ public void testGetRef_CycleInSymbolicRef() throws IOException {
 		writeLooseRef("refs/5", "ref: refs/6\n");
 		writeLooseRef("refs/6", "ref: refs/end\n");
 
-		r = refdir.getRef("1");
+		r = refdir.findRef("1");
 		assertNull("missing 1 due to cycle", r);
 
 		writeLooseRef("refs/heads/1", B);
 
-		r = refdir.getRef("1");
+		r = refdir.findRef("1");
 		assertEquals("refs/heads/1", r.getName());
 		assertEquals(B, r.getObjectId());
 		assertFalse(r.isSymbolic());
@@ -923,16 +952,16 @@ public void testGetRefs_PackedNotPeeled_Sorted() throws IOException {
 	}
 
 	@Test
-	public void testGetRef_PackedNotPeeled_WrongSort() throws IOException {
+	public void testFindRef_PackedNotPeeled_WrongSort() throws IOException {
 		writePackedRefs("" + //
 				v1_0.name() + " refs/tags/v1.0\n" + //
 				B.name() + " refs/heads/other\n" + //
 				A.name() + " refs/heads/master\n");
 
-		final Ref head = refdir.getRef(HEAD);
-		final Ref master = refdir.getRef("refs/heads/master");
-		final Ref other = refdir.getRef("refs/heads/other");
-		final Ref tag = refdir.getRef("refs/tags/v1.0");
+		final Ref head = refdir.findRef(HEAD);
+		final Ref master = refdir.findRef("refs/heads/master");
+		final Ref other = refdir.findRef("refs/heads/other");
+		final Ref tag = refdir.findRef("refs/tags/v1.0");
 
 		assertEquals(A, master.getObjectId());
 		assertFalse(master.isPeeled());
@@ -1037,22 +1066,22 @@ public void test_repack() throws Exception {
 	}
 
 	@Test
-	public void testGetRef_EmptyDatabase() throws IOException {
+	public void testFindRef_EmptyDatabase() throws IOException {
 		Ref r;
 
-		r = refdir.getRef(HEAD);
+		r = refdir.findRef(HEAD);
 		assertTrue(r.isSymbolic());
 		assertSame(LOOSE, r.getStorage());
 		assertEquals("refs/heads/master", r.getTarget().getName());
 		assertSame(NEW, r.getTarget().getStorage());
 		assertNull(r.getTarget().getObjectId());
 
-		assertNull(refdir.getRef("refs/heads/master"));
-		assertNull(refdir.getRef("refs/tags/v1.0"));
-		assertNull(refdir.getRef("FETCH_HEAD"));
-		assertNull(refdir.getRef("NOT.A.REF.NAME"));
-		assertNull(refdir.getRef("master"));
-		assertNull(refdir.getRef("v1.0"));
+		assertNull(refdir.findRef("refs/heads/master"));
+		assertNull(refdir.findRef("refs/tags/v1.0"));
+		assertNull(refdir.findRef("FETCH_HEAD"));
+		assertNull(refdir.findRef("NOT.A.REF.NAME"));
+		assertNull(refdir.findRef("master"));
+		assertNull(refdir.findRef("v1.0"));
 	}
 
 	@Test
@@ -1075,7 +1104,29 @@ public void testExactRef_EmptyDatabase() throws IOException {
 	}
 
 	@Test
-	public void testGetRef_FetchHead() throws IOException {
+	public void testGetAdditionalRefs_OrigHead() throws IOException {
+		writeLooseRef("ORIG_HEAD", A);
+
+		List<Ref> refs = refdir.getAdditionalRefs();
+		assertEquals(1, refs.size());
+
+		Ref r = refs.get(0);
+		assertFalse(r.isSymbolic());
+		assertEquals(A, r.getObjectId());
+		assertEquals("ORIG_HEAD", r.getName());
+		assertFalse(r.isPeeled());
+		assertNull(r.getPeeledObjectId());
+	}
+
+	@Test
+	public void testGetAdditionalRefs_OrigHeadBranch() throws IOException {
+		writeLooseRef("refs/heads/ORIG_HEAD", A);
+		List<Ref> refs = refdir.getAdditionalRefs();
+		assertArrayEquals(new Ref[0], refs.toArray());
+	}
+
+	@Test
+	public void testFindRef_FetchHead() throws IOException {
 		// This is an odd special case where we need to make sure we read
 		// exactly the first 40 bytes of the file and nothing further on
 		// that line, or the remainder of the file.
@@ -1083,7 +1134,7 @@ public void testGetRef_FetchHead() throws IOException {
 				+ "\tnot-for-merge"
 				+ "\tbranch 'master' of git://egit.eclipse.org/jgit\n");
 
-		Ref r = refdir.getRef("FETCH_HEAD");
+		Ref r = refdir.findRef("FETCH_HEAD");
 		assertFalse(r.isSymbolic());
 		assertEquals(A, r.getObjectId());
 		assertEquals("FETCH_HEAD", r.getName());
@@ -1109,12 +1160,12 @@ public void testExactRef_FetchHead() throws IOException {
 	}
 
 	@Test
-	public void testGetRef_AnyHeadWithGarbage() throws IOException {
+	public void testFindRef_AnyHeadWithGarbage() throws IOException {
 		write(new File(diskRepo.getDirectory(), "refs/heads/A"), A.name()
 				+ "012345 . this is not a standard reference\n"
 				+ "#and even more junk\n");
 
-		Ref r = refdir.getRef("refs/heads/A");
+		Ref r = refdir.findRef("refs/heads/A");
 		assertFalse(r.isSymbolic());
 		assertEquals(A, r.getObjectId());
 		assertEquals("refs/heads/A", r.getName());
@@ -1130,11 +1181,11 @@ public void testGetRefs_CorruptSymbolicReference() throws IOException {
 	}
 
 	@Test
-	public void testGetRef_CorruptSymbolicReference() throws IOException {
+	public void testFindRef_CorruptSymbolicReference() throws IOException {
 		String name = "refs/heads/A";
 		writeLooseRef(name, "ref: \n");
 		try {
-			refdir.getRef(name);
+			refdir.findRef(name);
 			fail("read an invalid reference");
 		} catch (IOException err) {
 			String msg = err.getMessage();
@@ -1151,12 +1202,12 @@ public void testGetRefs_CorruptObjectIdReference() throws IOException {
 	}
 
 	@Test
-	public void testGetRef_CorruptObjectIdReference() throws IOException {
+	public void testFindRef_CorruptObjectIdReference() throws IOException {
 		String name = "refs/heads/A";
 		String content = "zoo" + A.name();
 		writeLooseRef(name, content + "\n");
 		try {
-			refdir.getRef(name);
+			refdir.findRef(name);
 			fail("read an invalid reference");
 		} catch (IOException err) {
 			String msg = err.getMessage();
@@ -1191,8 +1242,8 @@ public void testPeelLooseTag() throws IOException {
 		writeLooseRef("refs/tags/v1_0", v1_0);
 		writeLooseRef("refs/tags/current", "ref: refs/tags/v1_0\n");
 
-		final Ref tag = refdir.getRef("refs/tags/v1_0");
-		final Ref cur = refdir.getRef("refs/tags/current");
+		final Ref tag = refdir.findRef("refs/tags/v1_0");
+		final Ref cur = refdir.findRef("refs/tags/current");
 
 		assertEquals(v1_0, tag.getObjectId());
 		assertFalse(tag.isSymbolic());
@@ -1224,14 +1275,14 @@ public void testPeelLooseTag() throws IOException {
 
 		// reuses cached peeling later, but not immediately due to
 		// the implementation so we have to fetch it once.
-		final Ref tag_p2 = refdir.getRef("refs/tags/v1_0");
+		final Ref tag_p2 = refdir.findRef("refs/tags/v1_0");
 		assertFalse(tag_p2.isSymbolic());
 		assertTrue(tag_p2.isPeeled());
 		assertEquals(v1_0, tag_p2.getObjectId());
 		assertEquals(v1_0.getObject(), tag_p2.getPeeledObjectId());
 
-		assertSame(tag_p2, refdir.getRef("refs/tags/v1_0"));
-		assertSame(tag_p2, refdir.getRef("refs/tags/current").getTarget());
+		assertSame(tag_p2, refdir.findRef("refs/tags/v1_0"));
+		assertSame(tag_p2, refdir.findRef("refs/tags/current").getTarget());
 		assertSame(tag_p2, refdir.peel(tag_p2));
 	}
 
@@ -1239,7 +1290,7 @@ public void testPeelLooseTag() throws IOException {
 	public void testPeelCommit() throws IOException {
 		writeLooseRef("refs/heads/master", A);
 
-		Ref master = refdir.getRef("refs/heads/master");
+		Ref master = refdir.findRef("refs/heads/master");
 		assertEquals(A, master.getObjectId());
 		assertFalse(master.isPeeled());
 		assertNull(master.getPeeledObjectId());
@@ -1252,7 +1303,7 @@ public void testPeelCommit() throws IOException {
 
 		// reuses cached peeling later, but not immediately due to
 		// the implementation so we have to fetch it once.
-		Ref master_p2 = refdir.getRef("refs/heads/master");
+		Ref master_p2 = refdir.findRef("refs/heads/master");
 		assertNotSame(master, master_p2);
 		assertEquals(A, master_p2.getObjectId());
 		assertTrue(master_p2.isPeeled());
@@ -1304,7 +1355,7 @@ public void testPackedRefsLockFailure() throws Exception {
 		} finally {
 			myLock.unlock();
 		}
-		Ref ref = refdir.getRef("refs/heads/master");
+		Ref ref = refdir.findRef("refs/heads/master");
 		assertEquals(Storage.LOOSE, ref.getStorage());
 	}
 
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 9eb1816..e2887d9 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
@@ -540,7 +540,7 @@ public void test024_createCommitNonAscii() throws IOException {
 				4294967295000L, 60));
 		commit.setCommitter(new PersonIdent("Joe Hacker", "joe2@example.com",
 				4294967295000L, 60));
-		commit.setEncoding("ISO-8859-1");
+		commit.setEncoding(ISO_8859_1);
 		commit.setMessage("\u00dcbergeeks");
 		ObjectId cid = insertCommit(commit);
 		assertEquals("2979b39d385014b33287054b87f77bcb3ecb5ebf", cid.name());
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
index 1d11573..11d6439 100644
--- 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
@@ -44,6 +44,7 @@
 package org.eclipse.jgit.internal.storage.reftable;
 
 import static org.eclipse.jgit.lib.Constants.HEAD;
+import static org.eclipse.jgit.lib.Constants.MASTER;
 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;
@@ -68,6 +69,7 @@
 import org.eclipse.jgit.lib.ObjectIdRef;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.RefComparator;
+import org.eclipse.jgit.lib.SymbolicRef;
 import org.junit.Test;
 
 public class MergedReftableTest {
@@ -128,6 +130,7 @@ public void oneTableScan() throws IOException {
 				Ref act = rc.getRef();
 				assertEquals(exp.getName(), act.getName());
 				assertEquals(exp.getObjectId(), act.getObjectId());
+				assertEquals(1, act.getUpdateIndex());
 			}
 			assertFalse(rc.next());
 		}
@@ -145,6 +148,7 @@ public void deleteIsHidden() throws IOException {
 			assertTrue(rc.next());
 			assertEquals("refs/heads/master", rc.getRef().getName());
 			assertEquals(id(2), rc.getRef().getObjectId());
+			assertEquals(1, rc.getRef().getUpdateIndex());
 			assertFalse(rc.next());
 		}
 	}
@@ -162,6 +166,7 @@ public void twoTableSeek() throws IOException {
 			assertEquals("refs/heads/master", rc.getRef().getName());
 			assertEquals(id(2), rc.getRef().getObjectId());
 			assertFalse(rc.next());
+			assertEquals(1, rc.getRef().getUpdateIndex());
 		}
 	}
 
@@ -177,6 +182,7 @@ public void twoTableById() throws IOException {
 			assertTrue(rc.next());
 			assertEquals("refs/heads/master", rc.getRef().getName());
 			assertEquals(id(2), rc.getRef().getObjectId());
+			assertEquals(1, rc.getRef().getUpdateIndex());
 			assertFalse(rc.next());
 		}
 	}
@@ -212,6 +218,7 @@ public void fourTableScan() throws IOException {
 				Ref act = rc.getRef();
 				assertEquals(exp.getName(), act.getName());
 				assertEquals(exp.getObjectId(), act.getObjectId());
+				assertEquals(1, rc.getRef().getUpdateIndex());
 			}
 			assertFalse(rc.next());
 		}
@@ -231,9 +238,11 @@ public void scanDuplicates() throws IOException {
 			assertTrue(rc.next());
 			assertEquals("refs/heads/apple", rc.getRef().getName());
 			assertEquals(id(3), rc.getRef().getObjectId());
+			assertEquals(2000, rc.getRef().getUpdateIndex());
 			assertTrue(rc.next());
 			assertEquals("refs/heads/banana", rc.getRef().getName());
 			assertEquals(id(2), rc.getRef().getObjectId());
+			assertEquals(1000, rc.getRef().getUpdateIndex());
 			assertFalse(rc.next());
 		}
 	}
@@ -251,12 +260,14 @@ public void scanIncludeDeletes() throws IOException {
 			Ref r = rc.getRef();
 			assertEquals("refs/heads/master", r.getName());
 			assertEquals(id(8), r.getObjectId());
+			assertEquals(1, rc.getRef().getUpdateIndex());
 
 			assertTrue(rc.next());
 			r = rc.getRef();
 			assertEquals("refs/heads/next", r.getName());
 			assertEquals(NEW, r.getStorage());
 			assertNull(r.getObjectId());
+			assertEquals(1, rc.getRef().getUpdateIndex());
 
 			assertFalse(rc.next());
 		}
@@ -277,6 +288,7 @@ public void oneTableSeek() throws IOException {
 				Ref act = rc.getRef();
 				assertEquals(exp.getName(), act.getName());
 				assertEquals(exp.getObjectId(), act.getObjectId());
+				assertEquals(1, act.getUpdateIndex());
 				assertFalse(rc.next());
 			}
 		}
@@ -303,17 +315,17 @@ public void missedUpdate() throws IOException {
 			assertTrue(rc.next());
 			assertEquals("refs/heads/a", rc.getRef().getName());
 			assertEquals(id(1), rc.getRef().getObjectId());
-			assertEquals(1, rc.getUpdateIndex());
+			assertEquals(1, rc.getRef().getUpdateIndex());
 
 			assertTrue(rc.next());
 			assertEquals("refs/heads/b", rc.getRef().getName());
 			assertEquals(id(2), rc.getRef().getObjectId());
-			assertEquals(2, rc.getUpdateIndex());
+			assertEquals(2, rc.getRef().getUpdateIndex());
 
 			assertTrue(rc.next());
 			assertEquals("refs/heads/c", rc.getRef().getName());
 			assertEquals(id(3), rc.getRef().getObjectId());
-			assertEquals(3, rc.getUpdateIndex());
+			assertEquals(3, rc.getRef().getUpdateIndex());
 		}
 	}
 
@@ -344,6 +356,63 @@ public void compaction() throws IOException {
 		}
 	}
 
+	@Test
+	public void versioningSymbolicReftargetMoves() throws IOException {
+		Ref master = ref(MASTER, 100);
+
+		List<Ref> delta1 = Arrays.asList(master, sym(HEAD, MASTER));
+		List<Ref> delta2 = Arrays.asList(ref(MASTER, 200));
+
+		MergedReftable mr = merge(write(delta1, 1), write(delta2, 2));
+		Ref head = mr.exactRef(HEAD);
+		assertEquals(head.getUpdateIndex(), 1);
+
+		Ref masterRef = mr.exactRef(MASTER);
+		assertEquals(masterRef.getUpdateIndex(), 2);
+	}
+
+	@Test
+	public void versioningSymbolicRefMoves() throws IOException {
+		Ref branchX = ref("refs/heads/branchX", 200);
+
+		List<Ref> delta1 = Arrays.asList(ref(MASTER, 100), branchX,
+				sym(HEAD, MASTER));
+		List<Ref> delta2 = Arrays.asList(sym(HEAD, "refs/heads/branchX"));
+		List<Ref> delta3 = Arrays.asList(sym(HEAD, MASTER));
+
+		MergedReftable mr = merge(write(delta1, 1), write(delta2, 2),
+				write(delta3, 3));
+		Ref head = mr.exactRef(HEAD);
+		assertEquals(head.getUpdateIndex(), 3);
+
+		Ref masterRef = mr.exactRef(MASTER);
+		assertEquals(masterRef.getUpdateIndex(), 1);
+
+		Ref branchRef = mr.exactRef(MASTER);
+		assertEquals(branchRef.getUpdateIndex(), 1);
+	}
+
+	@Test
+	public void versioningResolveRef() throws IOException {
+		List<Ref> delta1 = Arrays.asList(sym(HEAD, "refs/heads/tmp"),
+				sym("refs/heads/tmp", MASTER), ref(MASTER, 100));
+		List<Ref> delta2 = Arrays.asList(ref(MASTER, 200));
+		List<Ref> delta3 = Arrays.asList(ref(MASTER, 300));
+
+		MergedReftable mr = merge(write(delta1, 1), write(delta2, 2),
+				write(delta3, 3));
+		Ref head = mr.exactRef(HEAD);
+		Ref resolvedHead = mr.resolve(head);
+		assertEquals(resolvedHead.getObjectId(), id(300));
+		assertEquals("HEAD has not moved", resolvedHead.getUpdateIndex(), 1);
+
+		Ref master = mr.exactRef(MASTER);
+		Ref resolvedMaster = mr.resolve(master);
+		assertEquals(resolvedMaster.getObjectId(), id(300));
+		assertEquals("master also has update index",
+				resolvedMaster.getUpdateIndex(), 3);
+	}
+
 	private static MergedReftable merge(byte[]... table) {
 		List<Reftable> stack = new ArrayList<>(table.length);
 		for (byte[] b : table) {
@@ -360,6 +429,14 @@ private static Ref ref(String name, int id) {
 		return new ObjectIdRef.PeeledNonTag(PACKED, name, id(id));
 	}
 
+	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 Ref delete(String name) {
 		return new ObjectIdRef.Unpeeled(NEW, name, null);
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/ReftableCompactorTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/ReftableCompactorTest.java
index 46a37ff..1ea7309 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/ReftableCompactorTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/ReftableCompactorTest.java
@@ -108,7 +108,7 @@ public void oneTable() throws IOException {
 			assertTrue(rc.next());
 			assertEquals(MASTER, rc.getRef().getName());
 			assertEquals(id(1), rc.getRef().getObjectId());
-			assertEquals(0, rc.getUpdateIndex());
+			assertEquals(0, rc.getRef().getUpdateIndex());
 		}
 	}
 
@@ -155,7 +155,7 @@ public void twoTablesOneRef() throws IOException {
 			assertTrue(rc.next());
 			assertEquals(MASTER, rc.getRef().getName());
 			assertEquals(id(2), rc.getRef().getObjectId());
-			assertEquals(1, rc.getUpdateIndex());
+			assertEquals(1, rc.getRef().getUpdateIndex());
 		}
 	}
 
@@ -203,12 +203,12 @@ public void twoTablesTwoRefs() throws IOException {
 			assertTrue(rc.next());
 			assertEquals(MASTER, rc.getRef().getName());
 			assertEquals(id(3), rc.getRef().getObjectId());
-			assertEquals(1, rc.getUpdateIndex());
+			assertEquals(1, rc.getRef().getUpdateIndex());
 
 			assertTrue(rc.next());
 			assertEquals(NEXT, rc.getRef().getName());
 			assertEquals(id(2), rc.getRef().getObjectId());
-			assertEquals(0, rc.getUpdateIndex());
+			assertEquals(0, rc.getRef().getUpdateIndex());
 		}
 	}
 
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
index 0ee785c..a142166 100644
--- 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
@@ -186,6 +186,7 @@ public void oneIdRef() throws IOException {
 			assertFalse(act.isSymbolic());
 			assertEquals(exp.getName(), act.getName());
 			assertEquals(exp.getObjectId(), act.getObjectId());
+			assertEquals(0, act.getUpdateIndex());
 			assertNull(act.getPeeledObjectId());
 			assertFalse(rc.wasDeleted());
 			assertFalse(rc.next());
@@ -195,6 +196,7 @@ public void oneIdRef() throws IOException {
 			Ref act = rc.getRef();
 			assertNotNull(act);
 			assertEquals(exp.getName(), act.getName());
+			assertEquals(0, act.getUpdateIndex());
 			assertFalse(rc.next());
 		}
 	}
@@ -216,6 +218,7 @@ public void oneTagRef() throws IOException {
 			assertEquals(exp.getName(), act.getName());
 			assertEquals(exp.getObjectId(), act.getObjectId());
 			assertEquals(exp.getPeeledObjectId(), act.getPeeledObjectId());
+			assertEquals(0, act.getUpdateIndex());
 		}
 	}
 
@@ -237,6 +240,7 @@ public void oneSymbolicRef() throws IOException {
 			assertNotNull(act.getLeaf());
 			assertEquals(MASTER, act.getTarget().getName());
 			assertNull(act.getObjectId());
+			assertEquals(0, act.getUpdateIndex());
 		}
 	}
 
@@ -250,14 +254,17 @@ public void resolveSymbolicRef() throws IOException {
 		Ref head = t.exactRef(HEAD);
 		assertNull(head.getObjectId());
 		assertEquals("refs/heads/tmp", head.getTarget().getName());
+		assertEquals(0, head.getUpdateIndex());
 
 		head = t.resolve(head);
 		assertNotNull(head);
 		assertEquals(id(1), head.getObjectId());
+		assertEquals(0, head.getUpdateIndex());
 
 		Ref master = t.exactRef(MASTER);
 		assertNotNull(master);
 		assertSame(master, t.resolve(master));
+		assertEquals(0, master.getUpdateIndex());
 	}
 
 	@Test
@@ -335,14 +342,17 @@ public void namespaceHeads() throws IOException {
 		try (RefCursor rc = t.seekRefsWithPrefix("refs/tags/")) {
 			assertTrue(rc.next());
 			assertEquals(V1_0, rc.getRef().getName());
+			assertEquals(0, rc.getRef().getUpdateIndex());
 			assertFalse(rc.next());
 		}
 		try (RefCursor rc = t.seekRefsWithPrefix("refs/heads/")) {
 			assertTrue(rc.next());
 			assertEquals(MASTER, rc.getRef().getName());
+			assertEquals(0, rc.getRef().getUpdateIndex());
 
 			assertTrue(rc.next());
 			assertEquals(NEXT, rc.getRef().getName());
+			assertEquals(0, rc.getRef().getUpdateIndex());
 
 			assertFalse(rc.next());
 		}
@@ -432,11 +442,12 @@ public void withReflog() throws IOException {
 			assertTrue(rc.next());
 			assertEquals(MASTER, rc.getRef().getName());
 			assertEquals(id(1), rc.getRef().getObjectId());
-			assertEquals(1, rc.getUpdateIndex());
+			assertEquals(1, rc.getRef().getUpdateIndex());
 
 			assertTrue(rc.next());
 			assertEquals(NEXT, rc.getRef().getName());
 			assertEquals(id(2), rc.getRef().getObjectId());
+			assertEquals(1, rc.getRef().getUpdateIndex());
 			assertFalse(rc.next());
 		}
 		try (LogCursor lc = t.allLogs()) {
@@ -569,6 +580,7 @@ public void byObjectIdOneRefNoIndex() throws IOException {
 			assertTrue("has 42", rc.next());
 			assertEquals("refs/heads/42", rc.getRef().getName());
 			assertEquals(id(42), rc.getRef().getObjectId());
+			assertEquals(0, rc.getRef().getUpdateIndex());
 			assertFalse(rc.next());
 		}
 		try (RefCursor rc = t.byObjectId(id(100))) {
@@ -579,6 +591,7 @@ public void byObjectIdOneRefNoIndex() throws IOException {
 			assertTrue("has master", rc.next());
 			assertEquals("refs/heads/master", rc.getRef().getName());
 			assertEquals(id(100), rc.getRef().getObjectId());
+			assertEquals(0, rc.getRef().getUpdateIndex());
 
 			assertFalse(rc.next());
 		}
@@ -600,6 +613,7 @@ public void byObjectIdOneRefWithIndex() throws IOException {
 			assertTrue("has 42", rc.next());
 			assertEquals("refs/heads/42", rc.getRef().getName());
 			assertEquals(id(42), rc.getRef().getObjectId());
+			assertEquals(0, rc.getRef().getUpdateIndex());
 			assertFalse(rc.next());
 		}
 		try (RefCursor rc = t.byObjectId(id(100))) {
@@ -610,6 +624,7 @@ public void byObjectIdOneRefWithIndex() throws IOException {
 			assertTrue("has master", rc.next());
 			assertEquals("refs/heads/master", rc.getRef().getName());
 			assertEquals(id(100), rc.getRef().getObjectId());
+			assertEquals(0, rc.getRef().getUpdateIndex());
 
 			assertFalse(rc.next());
 		}
@@ -654,7 +669,6 @@ public void badCrc32() throws IOException {
 		}
 	}
 
-
 	private static void assertScan(List<Ref> refs, Reftable t)
 			throws IOException {
 		try (RefCursor rc = t.allRefs()) {
@@ -663,6 +677,7 @@ private static void assertScan(List<Ref> refs, Reftable t)
 				Ref act = rc.getRef();
 				assertEquals(exp.getName(), act.getName());
 				assertEquals(exp.getObjectId(), act.getObjectId());
+				assertEquals(0, rc.getRef().getUpdateIndex());
 			}
 			assertFalse(rc.next());
 		}
@@ -676,6 +691,7 @@ private static void assertSeek(List<Ref> refs, Reftable t)
 				Ref act = rc.getRef();
 				assertEquals(exp.getName(), act.getName());
 				assertEquals(exp.getObjectId(), act.getObjectId());
+				assertEquals(0, rc.getRef().getUpdateIndex());
 				assertFalse(rc.next());
 			}
 		}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/RefTreeDatabaseTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/RefTreeDatabaseTest.java
index ae52ad5..8ef21e6 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/RefTreeDatabaseTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/RefTreeDatabaseTest.java
@@ -362,8 +362,8 @@ public void testGetRefs_CycleInSymbolicRef() throws IOException {
 
 	@Test
 	public void testGetRef_NonExistingBranchConfig() throws IOException {
-		assertNull("find branch config", refdb.getRef("config"));
-		assertNull("find branch config", refdb.getRef("refs/heads/config"));
+		assertNull("find branch config", refdb.findRef("config"));
+		assertNull("find branch config", refdb.findRef("refs/heads/config"));
 	}
 
 	@Test
@@ -371,7 +371,7 @@ public void testGetRef_FindBranchConfig() throws IOException {
 		update("refs/heads/config", A);
 
 		for (String t : new String[] { "config", "refs/heads/config" }) {
-			Ref r = refdb.getRef(t);
+			Ref r = refdb.findRef(t);
 			assertNotNull("find branch config (" + t + ")", r);
 			assertEquals("for " + t, "refs/heads/config", r.getName());
 			assertEquals("for " + t, A, r.getObjectId());
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/CommitBuilderTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/CommitBuilderTest.java
new file mode 100644
index 0000000..27ea505
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/CommitBuilderTest.java
@@ -0,0 +1,201 @@
+/*
+ * Copyright (C) 2018, Salesforce.
+ * 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 java.nio.charset.StandardCharsets.US_ASCII;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertSame;
+import static org.junit.Assert.fail;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.text.MessageFormat;
+
+import org.eclipse.jgit.internal.JGitText;
+import org.junit.Test;
+
+public class CommitBuilderTest {
+
+	private void assertGpgSignatureStringOutcome(String signature,
+			String expectedOutcome) throws IOException {
+		ByteArrayOutputStream out = new ByteArrayOutputStream();
+		CommitBuilder.writeGpgSignatureString(signature, out);
+		String formatted_signature = new String(out.toByteArray(), US_ASCII);
+		assertEquals(expectedOutcome, formatted_signature);
+	}
+
+	@Test
+	public void writeGpgSignatureString_1() throws Exception {
+		// @formatter:off
+		String signature = "-----BEGIN PGP SIGNATURE-----\n" +
+				"Version: BCPG v1.60\n" +
+				"\n" +
+				"iQEcBAABCAAGBQJb9cVhAAoJEKX+6Axg/6TZeFsH/0CY0WX/z7U8+7S5giFX4wH4\n" +
+				"opvBwqyt6OX8lgNwTwBGHFNt8LdmDCCmKoq/XwkNi3ARVjLhe3gBcKXNoavvPk2Z\n" +
+				"gIg5ChevGkU4afWCOMLVEYnkCBGw2+86XhrK1P7gTHEk1Rd+Yv1ZRDJBY+fFO7yz\n" +
+				"uSBuF5RpEY2sJiIvp27Gub/rY3B5NTR/feO/z+b9oiP/fMUhpRwG5KuWUsn9NPjw\n" +
+				"3tvbgawYpU/2UnS+xnavMY4t2fjRYjsoxndPLb2MUX8X7vC7FgWLBlmI/rquLZVM\n" +
+				"IQEKkjnA+lhejjK1rv+ulq4kGZJFKGYWYYhRDwFg5PTkzhudhN2SGUq5Wxq1Eg4=\n" +
+				"=b9OI\n" +
+				"-----END PGP SIGNATURE-----";
+		String expectedOutcome = "-----BEGIN PGP SIGNATURE-----\n" +
+				" Version: BCPG v1.60\n" +
+				" \n" +
+				" iQEcBAABCAAGBQJb9cVhAAoJEKX+6Axg/6TZeFsH/0CY0WX/z7U8+7S5giFX4wH4\n" +
+				" opvBwqyt6OX8lgNwTwBGHFNt8LdmDCCmKoq/XwkNi3ARVjLhe3gBcKXNoavvPk2Z\n" +
+				" gIg5ChevGkU4afWCOMLVEYnkCBGw2+86XhrK1P7gTHEk1Rd+Yv1ZRDJBY+fFO7yz\n" +
+				" uSBuF5RpEY2sJiIvp27Gub/rY3B5NTR/feO/z+b9oiP/fMUhpRwG5KuWUsn9NPjw\n" +
+				" 3tvbgawYpU/2UnS+xnavMY4t2fjRYjsoxndPLb2MUX8X7vC7FgWLBlmI/rquLZVM\n" +
+				" IQEKkjnA+lhejjK1rv+ulq4kGZJFKGYWYYhRDwFg5PTkzhudhN2SGUq5Wxq1Eg4=\n" +
+				" =b9OI\n" +
+				" -----END PGP SIGNATURE-----";
+		// @formatter:on
+		assertGpgSignatureStringOutcome(signature, expectedOutcome);
+	}
+
+	@Test
+	public void writeGpgSignatureString_failsForNonAscii() throws Exception {
+		String signature = "Ü Ä";
+		try {
+			CommitBuilder.writeGpgSignatureString(signature,
+					new ByteArrayOutputStream());
+			fail("Exception expected");
+		} catch (IllegalArgumentException e) {
+			// good
+			String message = MessageFormat.format(JGitText.get().notASCIIString,
+					signature);
+			assertEquals(message, e.getMessage());
+		}
+	}
+
+	@Test
+	public void writeGpgSignatureString_oneLineNotModified() throws Exception {
+		String signature = "    A string   ";
+		String expectedOutcome = signature;
+		assertGpgSignatureStringOutcome(signature, expectedOutcome);
+	}
+
+	@Test
+	public void writeGpgSignatureString_preservesRandomWhitespace()
+			throws Exception {
+		// @formatter:off
+		String signature = "    String with    \n"
+				+ "Line 2\n"
+				+ " Line 3\n"
+				+ "Line 4   \n"
+				+ "  Line 5  ";
+		String expectedOutcome = "    String with    \n"
+				+ " Line 2\n"
+				+ "  Line 3\n"
+				+ " Line 4   \n"
+				+ "   Line 5  ";
+		// @formatter:on
+		assertGpgSignatureStringOutcome(signature, expectedOutcome);
+	}
+
+	@Test
+	public void writeGpgSignatureString_replaceCR() throws Exception {
+		// @formatter:off
+		String signature = "String with \r"
+				+ "Line 2\r"
+				+ "Line 3\r"
+				+ "Line 4\r"
+				+ "Line 5";
+		String expectedOutcome = "String with \n"
+				+ " Line 2\n"
+				+ " Line 3\n"
+				+ " Line 4\n"
+				+ " Line 5";
+		// @formatter:on
+		assertGpgSignatureStringOutcome(signature, expectedOutcome);
+	}
+
+	@Test
+	public void writeGpgSignatureString_replaceCRLF() throws Exception {
+		// @formatter:off
+		String signature = "String with \r\n"
+				+ "Line 2\r\n"
+				+ "Line 3\r\n"
+				+ "Line 4\r\n"
+				+ "Line 5";
+		String expectedOutcome = "String with \n"
+				+ " Line 2\n"
+				+ " Line 3\n"
+				+ " Line 4\n"
+				+ " Line 5";
+		// @formatter:on
+		assertGpgSignatureStringOutcome(signature, expectedOutcome);
+	}
+
+	@Test
+	public void writeGpgSignatureString_replaceCRLFMixed() throws Exception {
+		// @formatter:off
+		String signature = "String with \r"
+				+ "Line 2\r\n"
+				+ "Line 3\r"
+				+ "Line 4\r\n"
+				+ "Line 5";
+		String expectedOutcome = "String with \n"
+				+ " Line 2\n"
+				+ " Line 3\n"
+				+ " Line 4\n"
+				+ " Line 5";
+		// @formatter:on
+		assertGpgSignatureStringOutcome(signature, expectedOutcome);
+	}
+
+	@Test
+	public void setGpgSignature() throws Exception {
+		GpgSignature dummy = new GpgSignature(new byte[0]);
+
+		CommitBuilder builder = new CommitBuilder();
+		assertNull(builder.getGpgSignature());
+
+		builder.setGpgSignature(dummy);
+		assertSame(dummy, builder.getGpgSignature());
+
+		builder.setGpgSignature(null);
+		assertNull(builder.getGpgSignature());
+	}
+}
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 534b323..483051c 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
@@ -267,10 +267,10 @@ public void testResetHardFromIndexEntryWithoutFileToTreeWithoutFile()
 	public void testInitialCheckout() throws Exception {
 		ChangeRecorder recorder = new ChangeRecorder();
 		ListenerHandle handle = null;
-		try (Git git = new Git(db)) {
+		try (Git git = new Git(db);
+				TestRepository<Repository> db_t = new TestRepository<>(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());
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ObjectIdRefTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ObjectIdRefTest.java
index fb16c6b..6553bfa 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ObjectIdRefTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ObjectIdRefTest.java
@@ -48,6 +48,10 @@
 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.util.Arrays;
+import java.util.List;
 
 import org.junit.Test;
 
@@ -115,10 +119,43 @@ public void testConstructor_Peeled() {
 	}
 
 	@Test
+	public void testUpdateIndex() {
+		ObjectIdRef r;
+
+		r = new ObjectIdRef.Unpeeled(Ref.Storage.LOOSE, name, ID_A, 3);
+		assertTrue(r.getUpdateIndex() == 3);
+
+		r = new ObjectIdRef.PeeledTag(Ref.Storage.LOOSE, name, ID_A, ID_B, 4);
+		assertTrue(r.getUpdateIndex() == 4);
+
+		r = new ObjectIdRef.PeeledNonTag(Ref.Storage.LOOSE, name, ID_A, 5);
+		assertTrue(r.getUpdateIndex() == 5);
+	}
+
+	@Test
+	public void testUpdateIndexNotSet() {
+		List<ObjectIdRef> r = Arrays.asList(
+				new ObjectIdRef.Unpeeled(Ref.Storage.LOOSE, name, ID_A),
+				new ObjectIdRef.PeeledTag(Ref.Storage.LOOSE, name, ID_A, ID_B),
+				new ObjectIdRef.PeeledNonTag(Ref.Storage.LOOSE, name, ID_A));
+
+		for (ObjectIdRef ref : r) {
+			try {
+				ref.getUpdateIndex();
+				fail("Update index wasn't set. It must throw");
+			} catch (UnsupportedOperationException u) {
+				// Ok
+			}
+		}
+	}
+
+
+	@Test
 	public void testToString() {
 		ObjectIdRef r;
 
 		r = new ObjectIdRef.Unpeeled(Ref.Storage.LOOSE, name, ID_A);
-		assertEquals("Ref[" + name + "=" + ID_A.name() + "]", r.toString());
+		assertEquals("Ref[" + name + "=" + ID_A.name() + "(-1)]",
+				r.toString());
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RefDatabaseConflictingNamesTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RefDatabaseConflictingNamesTest.java
index 1c21194..cbb47fa 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RefDatabaseConflictingNamesTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RefDatabaseConflictingNamesTest.java
@@ -95,7 +95,7 @@ public boolean isNameConflicting(String name) throws IOException {
 		}
 
 		@Override
-		public Ref getRef(String name) throws IOException {
+		public Ref exactRef(String name) throws IOException {
 			return null;
 		}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RepositoryCacheTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RepositoryCacheTest.java
index 58b005c..15c4e4a 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RepositoryCacheTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RepositoryCacheTest.java
@@ -110,7 +110,7 @@ public void testFileKeyOpenExisting() throws IOException {
 	@Test
 	public void testFileKeyOpenNew() throws IOException {
 		File gitdir;
-		try (Repository n = createRepository(true, false)) {
+		try (Repository n = createRepository(true)) {
 			gitdir = n.getDirectory();
 		}
 		recursiveDelete(gitdir);
@@ -192,7 +192,7 @@ public void testRepositoryUsageCount() throws Exception {
 	@Test
 	public void testRepositoryUsageCountWithRegisteredRepository()
 			throws IOException {
-		@SuppressWarnings("resource") // We are testing the close() method
+		@SuppressWarnings({"resource", "deprecation"}) // We are testing the close() method
 		Repository repo = createRepository(false, false);
 		assertEquals(1, repo.useCnt.get());
 		RepositoryCache.register(repo);
@@ -240,9 +240,9 @@ public void testRepositoryUnregisteringWhenExpiredAndUsageCountNegative()
 
 	@Test
 	public void testRepositoryUnregisteringWhenExpired() throws Exception {
-		@SuppressWarnings("resource") // We are testing the close() method
+		@SuppressWarnings({"resource", "deprecation"}) // We are testing the close() method
 		Repository repoA = createRepository(true, false);
-		@SuppressWarnings("resource") // We are testing the close() method
+		@SuppressWarnings({"resource", "deprecation"}) // We are testing the close() method
 		Repository repoB = createRepository(true, false);
 		Repository repoC = createBareRepository();
 		RepositoryCache.register(repoA);
@@ -276,7 +276,7 @@ public void testRepositoryUnregisteringWhenExpired() throws Exception {
 
 	@Test
 	public void testReconfigure() throws InterruptedException, IOException {
-		@SuppressWarnings("resource") // We are testing the close() method
+		@SuppressWarnings({"resource", "deprecation"}) // We are testing the close() method
 		Repository repo = createRepository(false, false);
 		RepositoryCache.register(repo);
 		assertTrue(RepositoryCache.isCached(repo));
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/SymbolicRefTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/SymbolicRefTest.java
index 1342253..99b2211 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/SymbolicRefTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/SymbolicRefTest.java
@@ -68,7 +68,7 @@ public void testConstructor() {
 		SymbolicRef r;
 
 		t = new ObjectIdRef.Unpeeled(Ref.Storage.NEW, targetName, null);
-		r = new SymbolicRef(name, t);
+		r = new SymbolicRef(name, t, 1);
 		assertSame(Ref.Storage.LOOSE, r.getStorage());
 		assertSame(name, r.getName());
 		assertNull("no id on new ref", r.getObjectId());
@@ -77,9 +77,10 @@ public void testConstructor() {
 		assertSame("leaf is t", t, r.getLeaf());
 		assertSame("target is t", t, r.getTarget());
 		assertTrue("is symbolic", r.isSymbolic());
+		assertTrue("holds update index", r.getUpdateIndex() == 1);
 
 		t = new ObjectIdRef.Unpeeled(Ref.Storage.PACKED, targetName, ID_A);
-		r = new SymbolicRef(name, t);
+		r = new SymbolicRef(name, t, 2);
 		assertSame(Ref.Storage.LOOSE, r.getStorage());
 		assertSame(name, r.getName());
 		assertSame(ID_A, r.getObjectId());
@@ -88,6 +89,7 @@ public void testConstructor() {
 		assertSame("leaf is t", t, r.getLeaf());
 		assertSame("target is t", t, r.getTarget());
 		assertTrue("is symbolic", r.isSymbolic());
+		assertTrue("holds update index", r.getUpdateIndex() == 2);
 	}
 
 	@Test
@@ -133,6 +135,6 @@ public void testToString() {
 		d = new SymbolicRef("D", c);
 
 		assertEquals("SymbolicRef[D -> C -> B -> " + targetName + "="
-				+ ID_A.name() + "]", d.toString());
+				+ ID_A.name() + "(-1)]", d.toString());
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergerTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergerTest.java
index fa02227..2ae9c11 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergerTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergerTest.java
@@ -1071,7 +1071,7 @@ public void checkLockedFilesToBeDeleted(MergeStrategy strategy)
 		git.add().addFilepattern("c.txt").call();
 		git.commit().setMessage("added c.txt").call();
 
-		// Get a handle to the the file so on windows it can't be deleted.
+		// Get a handle to the file so on windows it can't be deleted.
 		try (FileInputStream fis = new FileInputStream(
 				new File(db.getWorkTree(), "b.txt"))) {
 			MergeResult mergeRes = git.merge().setStrategy(strategy)
@@ -1365,14 +1365,15 @@ private void checkModificationTimeStampOrder(String... pathes) {
 	}
 
 	private String readBlob(ObjectId treeish, String path) throws Exception {
-		TestRepository<?> tr = new TestRepository<>(db);
-		RevWalk rw = tr.getRevWalk();
-		RevTree tree = rw.parseTree(treeish);
-		RevObject obj = tr.get(tree, path);
-		if (obj == null) {
-			return null;
+		try (TestRepository<?> tr = new TestRepository<>(db)) {
+			RevWalk rw = tr.getRevWalk();
+			RevTree tree = rw.parseTree(treeish);
+			RevObject obj = tr.get(tree, path);
+			if (obj == null) {
+				return null;
+			}
+			return new String(
+					rw.getObjectReader().open(obj, OBJ_BLOB).getBytes(), UTF_8);
 		}
-		return new String(rw.getObjectReader().open(obj, OBJ_BLOB).getBytes(),
-				UTF_8);
 	}
 }
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 5832518..9151b04 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
@@ -263,8 +263,10 @@ public void repositoryWithInitializedSubmodule() throws Exception {
 				.getRepository();
 		assertNotNull(subRepo);
 
-		TestRepository<?> subTr = new TestRepository<>(subRepo);
-		ObjectId id = subTr.branch(Constants.HEAD).commit().create().copy();
+		ObjectId id;
+		try (TestRepository<?> subTr = new TestRepository<>(subRepo)) {
+			id = subTr.branch(Constants.HEAD).commit().create().copy();
+		}
 
 		DirCache cache = db.lockDirCache();
 		DirCacheEditor editor = cache.editor();
@@ -315,50 +317,52 @@ public void repositoryWithDifferentRevCheckedOutSubmodule() throws Exception {
 				.getRepository();
 		assertNotNull(subRepo);
 
-		TestRepository<?> subTr = new TestRepository<>(subRepo);
-		ObjectId id = subTr.branch(Constants.HEAD).commit().create().copy();
+		try (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) {
 
-		DirCache cache = db.lockDirCache();
-		DirCacheEditor editor = cache.editor();
-		editor.add(new PathEdit(path) {
+				@Override
+				public void apply(DirCacheEntry ent) {
+					ent.setFileMode(FileMode.GITLINK);
+					ent.setObjectId(id);
+				}
+			});
+			editor.commit();
 
-			@Override
-			public void apply(DirCacheEntry ent) {
-				ent.setFileMode(FileMode.GITLINK);
-				ent.setObjectId(id);
-			}
-		});
-		editor.commit();
+			String url = "git://server/repo.git";
+			StoredConfig config = db.getConfig();
+			config.setString(ConfigConstants.CONFIG_SUBMODULE_SECTION, path,
+					ConfigConstants.CONFIG_KEY_URL, url);
+			config.save();
 
-		String url = "git://server/repo.git";
-		StoredConfig config = db.getConfig();
-		config.setString(ConfigConstants.CONFIG_SUBMODULE_SECTION, path,
-				ConfigConstants.CONFIG_KEY_URL, url);
-		config.save();
+			FileBasedConfig modulesConfig = new FileBasedConfig(
+					new File(db.getWorkTree(), Constants.DOT_GIT_MODULES),
+					db.getFS());
+			modulesConfig.setString(ConfigConstants.CONFIG_SUBMODULE_SECTION,
+					path, ConfigConstants.CONFIG_KEY_PATH, path);
+			modulesConfig.setString(ConfigConstants.CONFIG_SUBMODULE_SECTION,
+					path, ConfigConstants.CONFIG_KEY_URL, url);
+			modulesConfig.save();
 
-		FileBasedConfig modulesConfig = new FileBasedConfig(new File(
-				db.getWorkTree(), Constants.DOT_GIT_MODULES), db.getFS());
-		modulesConfig.setString(ConfigConstants.CONFIG_SUBMODULE_SECTION, path,
-				ConfigConstants.CONFIG_KEY_PATH, path);
-		modulesConfig.setString(ConfigConstants.CONFIG_SUBMODULE_SECTION, path,
-				ConfigConstants.CONFIG_KEY_URL, url);
-		modulesConfig.save();
+			ObjectId newId = subTr.branch(Constants.HEAD).commit().create()
+					.copy();
 
-		ObjectId newId = subTr.branch(Constants.HEAD).commit().create().copy();
-
-		SubmoduleStatusCommand command = new SubmoduleStatusCommand(db);
-		Map<String, SubmoduleStatus> statuses = command.call();
-		assertNotNull(statuses);
-		assertEquals(1, statuses.size());
-		Entry<String, SubmoduleStatus> module = statuses.entrySet().iterator()
-				.next();
-		assertNotNull(module);
-		assertEquals(path, module.getKey());
-		SubmoduleStatus status = module.getValue();
-		assertNotNull(status);
-		assertEquals(path, status.getPath());
-		assertEquals(id, status.getIndexId());
-		assertEquals(newId, status.getHeadId());
-		assertEquals(SubmoduleStatusType.REV_CHECKED_OUT, status.getType());
+			SubmoduleStatusCommand command = new SubmoduleStatusCommand(db);
+			Map<String, SubmoduleStatus> statuses = command.call();
+			assertNotNull(statuses);
+			assertEquals(1, statuses.size());
+			Entry<String, SubmoduleStatus> module = statuses.entrySet()
+					.iterator().next();
+			assertNotNull(module);
+			assertEquals(path, module.getKey());
+			SubmoduleStatus status = module.getValue();
+			assertNotNull(status);
+			assertEquals(path, status.getPath());
+			assertEquals(id, status.getIndexId());
+			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 a0cd37e..ea1ace3 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
@@ -145,7 +145,6 @@ public void apply(DirCacheEntry ent) {
 		assertFalse(gen.next());
 	}
 
-	@SuppressWarnings("resource" /* java 7 */)
 	@Test
 	public void repositoryWithRootLevelSubmoduleAbsoluteRef()
 			throws IOException, ConfigInvalidException {
@@ -189,17 +188,16 @@ public void apply(DirCacheEntry ent) {
 		assertNull(gen.getModulesPath());
 		assertNull(gen.getModulesUpdate());
 		assertNull(gen.getModulesUrl());
-		Repository subRepo = gen.getRepository();
-		assertNotNull(subRepo);
-		assertEquals(modulesGitDir.getAbsolutePath(),
-				subRepo.getDirectory().getAbsolutePath());
-		assertEquals(new File(db.getWorkTree(), path).getAbsolutePath(),
-				subRepo.getWorkTree().getAbsolutePath());
-		subRepo.close();
+		try (Repository subRepo = gen.getRepository()) {
+			assertNotNull(subRepo);
+			assertEquals(modulesGitDir.getAbsolutePath(),
+					subRepo.getDirectory().getAbsolutePath());
+			assertEquals(new File(db.getWorkTree(), path).getAbsolutePath(),
+					subRepo.getWorkTree().getAbsolutePath());
+		}
 		assertFalse(gen.next());
 	}
 
-	@SuppressWarnings("resource" /* java 7 */)
 	@Test
 	public void repositoryWithRootLevelSubmoduleRelativeRef()
 			throws IOException, ConfigInvalidException {
@@ -244,13 +242,14 @@ public void apply(DirCacheEntry ent) {
 		assertNull(gen.getModulesPath());
 		assertNull(gen.getModulesUpdate());
 		assertNull(gen.getModulesUrl());
-		Repository subRepo = gen.getRepository();
-		assertNotNull(subRepo);
-		assertEqualsFile(modulesGitDir, subRepo.getDirectory());
-		assertEqualsFile(new File(db.getWorkTree(), path),
-				subRepo.getWorkTree());
-		subRepo.close();
-		assertFalse(gen.next());
+		try (Repository subRepo = gen.getRepository()) {
+			assertNotNull(subRepo);
+			assertEqualsFile(modulesGitDir, subRepo.getDirectory());
+			assertEqualsFile(new File(db.getWorkTree(), path),
+					subRepo.getWorkTree());
+			subRepo.close();
+			assertFalse(gen.next());
+		}
 	}
 
 	@Test
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/BundleWriterTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/BundleWriterTest.java
index 7b31bfa..dce9db5 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/BundleWriterTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/BundleWriterTest.java
@@ -77,10 +77,38 @@
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.test.resources.SampleDataRepositoryTestCase;
+import org.junit.Rule;
 import org.junit.Test;
+import org.junit.rules.ExpectedException;
 
 public class BundleWriterTest extends SampleDataRepositoryTestCase {
 
+	@Rule
+	public ExpectedException thrown = ExpectedException.none();
+
+	@Test
+	public void testEmptyBundleFails() throws Exception {
+		Repository newRepo = createBareRepository();
+		thrown.expect(TransportException.class);
+		fetchFromBundle(newRepo, new byte[0]);
+	}
+
+	@Test
+	public void testNonBundleFails() throws Exception {
+		Repository newRepo = createBareRepository();
+		thrown.expect(TransportException.class);
+		fetchFromBundle(newRepo, "Not a bundle file".getBytes(UTF_8));
+	}
+
+	@Test
+	public void testGarbageBundleFails() throws Exception {
+		Repository newRepo = createBareRepository();
+		thrown.expect(TransportException.class);
+		fetchFromBundle(newRepo,
+				(TransportBundle.V2_BUNDLE_SIGNATURE + '\n' + "Garbage")
+						.getBytes(UTF_8));
+	}
+
 	@Test
 	public void testWriteSingleRef() throws Exception {
 		// Create a tiny bundle, (well one of) the first commits only
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
index 1e65a20..3de4210 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/JschConfigSessionFactoryTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/JschConfigSessionFactoryTest.java
@@ -49,8 +49,11 @@
 import java.util.Arrays;
 import java.util.concurrent.TimeUnit;
 
+import org.eclipse.jgit.junit.MockSystemReader;
 import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.util.SystemReader;
 import org.junit.After;
+import org.junit.Before;
 import org.junit.Test;
 
 import com.jcraft.jsch.Session;
@@ -67,8 +70,14 @@ public class JschConfigSessionFactoryTest {
 
 	DefaultSshSessionFactory factory = new DefaultSshSessionFactory();
 
+	@Before
+	public void setup() {
+		SystemReader.setInstance(new MockSystemReader());
+	}
+
 	@After
 	public void removeTmpConfig() {
+		SystemReader.setInstance(null);
 		if (tmpConfigFile == null) {
 			return;
 		}
@@ -87,7 +96,8 @@ public void testNoConfigEntry() throws Exception {
 		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(SystemReader.getInstance().getProperty("user.name"),
+				session.getUserName());
 		assertEquals(22, session.getPort());
 	}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PackParserTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PackParserTest.java
index b6d0611..fd952f3 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PackParserTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PackParserTest.java
@@ -141,8 +141,10 @@ public void test2() throws  IOException {
 
 	@Test
 	public void testTinyThinPack() throws Exception {
-		TestRepository d = new TestRepository<Repository>(db);
-		RevBlob a = d.blob("a");
+		RevBlob a;
+		try (TestRepository d = new TestRepository<Repository>(db)) {
+			a = d.blob("a");
+		}
 
 		TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
 
@@ -162,8 +164,9 @@ public void testTinyThinPack() throws Exception {
 	@Test
 	public void testPackWithDuplicateBlob() throws Exception {
 		final byte[] data = Constants.encode("0123456789abcdefg");
-		TestRepository<Repository> d = new TestRepository<>(db);
-		assertTrue(db.hasObject(d.blob(data)));
+		try (TestRepository<Repository> d = new TestRepository<>(db)) {
+			assertTrue(db.getObjectDatabase().has(d.blob(data)));
+		}
 
 		TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
 		packHeader(pack, 1);
@@ -179,8 +182,10 @@ public void testPackWithDuplicateBlob() throws Exception {
 
 	@Test
 	public void testPackWithTrailingGarbage() throws Exception {
-		TestRepository d = new TestRepository<Repository>(db);
-		RevBlob a = d.blob("a");
+		RevBlob a;
+		try (TestRepository d = new TestRepository<Repository>(db)) {
+			a = d.blob("a");
+		}
 
 		TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
 		packHeader(pack, 1);
@@ -206,9 +211,10 @@ public void testPackWithTrailingGarbage() throws Exception {
 
 	@Test
 	public void testMaxObjectSizeFullBlob() throws Exception {
-		TestRepository d = new TestRepository<Repository>(db);
 		final byte[] data = Constants.encode("0123456789");
-		d.blob(data);
+		try (TestRepository d = new TestRepository<Repository>(db)) {
+			d.blob(data);
+		}
 
 		TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
 
@@ -238,8 +244,10 @@ public void testMaxObjectSizeFullBlob() throws Exception {
 
 	@Test
 	public void testMaxObjectSizeDeltaBlock() throws Exception {
-		TestRepository d = new TestRepository<Repository>(db);
-		RevBlob a = d.blob("a");
+		RevBlob a;
+		try (TestRepository d = new TestRepository<Repository>(db)) {
+			a = d.blob("a");
+		}
 
 		TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
 
@@ -269,8 +277,10 @@ public void testMaxObjectSizeDeltaBlock() throws Exception {
 
 	@Test
 	public void testMaxObjectSizeDeltaResultSize() throws Exception {
-		TestRepository d = new TestRepository<Repository>(db);
-		RevBlob a = d.blob("0123456789");
+		RevBlob a;
+		try (TestRepository d = new TestRepository<Repository>(db)) {
+			a = d.blob("0123456789");
+		}
 
 		TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
 
@@ -299,8 +309,10 @@ public void testMaxObjectSizeDeltaResultSize() throws Exception {
 
 	@Test
 	public void testNonMarkingInputStream() throws Exception {
-		TestRepository d = new TestRepository<Repository>(db);
-		RevBlob a = d.blob("a");
+		RevBlob a;
+		try (TestRepository d = new TestRepository<Repository>(db)) {
+			a = d.blob("a");
+		}
 
 		TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
 		packHeader(pack, 1);
@@ -337,8 +349,10 @@ public void mark(int maxlength) {
 
 	@Test
 	public void testDataAfterPackFooterSingleRead() throws Exception {
-		TestRepository d = new TestRepository<Repository>(db);
-		RevBlob a = d.blob("a");
+		RevBlob a;
+		try (TestRepository d = new TestRepository<Repository>(db)) {
+			a = d.blob("a");
+		}
 
 		TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(32*1024);
 		packHeader(pack, 1);
@@ -395,9 +409,11 @@ public void testDataAfterPackFooterSplitObjectRead() throws Exception {
 
 	@Test
 	public void testDataAfterPackFooterSplitHeaderRead() throws Exception {
-		TestRepository d = new TestRepository<Repository>(db);
 		final byte[] data = Constants.encode("a");
-		RevBlob b = d.blob(data);
+		RevBlob b;
+		try (TestRepository d = new TestRepository<Repository>(db)) {
+			b = d.blob(data);
+		}
 
 		int objects = 248;
 		TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(32 * 1024);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushConnectionTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushConnectionTest.java
index 63478f6..cea432e 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushConnectionTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushConnectionTest.java
@@ -216,15 +216,16 @@ public void limitCommandBytes() throws IOException {
 
 	@Test
 	public void commandOrder() throws Exception {
-		TestRepository<?> tr = new TestRepository<>(client);
 		List<RemoteRefUpdate> updates = new ArrayList<>();
-		// Arbitrary non-sorted order.
-		for (int i = 9; i >= 0; i--) {
-			String name = "refs/heads/b" + i;
-			tr.branch(name).commit().create();
-			RemoteRefUpdate rru = new RemoteRefUpdate(client, name, name, false, null,
-					ObjectId.zeroId());
-			updates.add(rru);
+		try (TestRepository<?> tr = new TestRepository<>(client)) {
+			// Arbitrary non-sorted order.
+			for (int i = 9; i >= 0; i--) {
+				String name = "refs/heads/b" + i;
+				tr.branch(name).commit().create();
+				RemoteRefUpdate rru = new RemoteRefUpdate(client, name, name,
+						false, null, ObjectId.zeroId());
+				updates.add(rru);
+			}
 		}
 
 		PushResult result;
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 dfa50b6..50c8a29 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
@@ -110,24 +110,26 @@ public void setUp() throws Exception {
 
 		// Fill dst with a some common history.
 		//
-		TestRepository<Repository> d = new TestRepository<>(dst);
-		a = d.blob("a");
-		A = d.commit(d.tree(d.file("a", a)));
-		B = d.commit().parent(A).create();
-		d.update(R_MASTER, B);
+		try (TestRepository<Repository> d = new TestRepository<>(dst)) {
+			a = d.blob("a");
+			A = d.commit(d.tree(d.file("a", a)));
+			B = d.commit().parent(A).create();
+			d.update(R_MASTER, B);
 
-		// Clone from dst into src
-		//
-		try (Transport t = Transport.open(src, uriOf(dst))) {
-			t.fetch(PM, Collections.singleton(new RefSpec("+refs/*:refs/*")));
-			assertEquals(B, src.resolve(R_MASTER));
+			// Clone from dst into src
+			//
+			try (Transport t = Transport.open(src, uriOf(dst))) {
+				t.fetch(PM,
+						Collections.singleton(new RefSpec("+refs/*:refs/*")));
+				assertEquals(B, src.resolve(R_MASTER));
+			}
+
+			// Now put private stuff into dst.
+			//
+			b = d.blob("b");
+			P = d.commit(d.tree(d.file("b", b)), A);
+			d.update(R_PRIVATE, P);
 		}
-
-		// Now put private stuff into dst.
-		//
-		b = d.blob("b");
-		P = d.commit(d.tree(d.file("b", b)), A);
-		d.update(R_PRIVATE, P);
 	}
 
 	@Test
@@ -236,36 +238,38 @@ public void testSuccess() throws Exception {
 		// Verify the only storage of b is our packed delta above.
 		//
 		ObjectDirectory od = (ObjectDirectory) src.getObjectDatabase();
-		assertTrue("has b", src.hasObject(b));
+		assertTrue("has b", od.has(b));
 		assertFalse("b not loose", od.fileFor(b).exists());
 
 		// Now use b but in a different commit than what is hidden.
 		//
-		TestRepository<Repository> s = new TestRepository<>(src);
-		RevCommit N = s.commit().parent(B).add("q", b).create();
-		s.update(R_MASTER, N);
+		try (TestRepository<Repository> s = new TestRepository<>(src)) {
+			RevCommit N = s.commit().parent(B).add("q", b).create();
+			s.update(R_MASTER, N);
 
-		// Push this new content to the remote, doing strict validation.
-		//
-		PushResult r;
-		RemoteRefUpdate u = new RemoteRefUpdate( //
-				src, //
-				R_MASTER, // src name
-				R_MASTER, // dst name
-				false, // do not force update
-				null, // local tracking branch
-				null // expected id
-		);
-		try (TransportLocal t = newTransportLocalWithStrictValidation()) {
-			t.setPushThin(true);
-			r = t.push(PM, Collections.singleton(u));
-			dst.close();
+			// Push this new content to the remote, doing strict validation.
+			//
+			PushResult r;
+			RemoteRefUpdate u = new RemoteRefUpdate( //
+					src, //
+					R_MASTER, // src name
+					R_MASTER, // dst name
+					false, // do not force update
+					null, // local tracking branch
+					null // expected id
+			);
+			try (TransportLocal t = newTransportLocalWithStrictValidation()) {
+				t.setPushThin(true);
+				r = t.push(PM, Collections.singleton(u));
+				dst.close();
+			}
+
+			assertNotNull("have result", r);
+			assertNull("private not advertised", r.getAdvertisedRef(R_PRIVATE));
+			assertSame("master updated", RemoteRefUpdate.Status.OK,
+					u.getStatus());
+			assertEquals(N, dst.resolve(R_MASTER));
 		}
-
-		assertNotNull("have result", r);
-		assertNull("private not advertised", r.getAdvertisedRef(R_PRIVATE));
-		assertSame("master updated", RemoteRefUpdate.Status.OK, u.getStatus());
-		assertEquals(N, dst.resolve(R_MASTER));
 	}
 
 	@Test
@@ -318,154 +322,165 @@ private static void receive(final ReceivePack rp,
 	@Test
 	public void testUsingHiddenDeltaBaseFails() throws Exception {
 		byte[] delta = { 0x1, 0x1, 0x1, 'c' };
-		TestRepository<Repository> s = new TestRepository<>(src);
-		RevCommit N = s.commit().parent(B).add("q",
-				s.blob(BinaryDelta.apply(dst.open(b).getCachedBytes(), delta)))
-				.create();
+		try (TestRepository<Repository> s = new TestRepository<>(src)) {
+			RevCommit N = s.commit().parent(B)
+					.add("q",
+							s.blob(BinaryDelta.apply(
+									dst.open(b).getCachedBytes(), delta)))
+					.create();
 
-		final TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
-		packHeader(pack, 3);
-		copy(pack, src.open(N));
-		copy(pack, src.open(s.parseBody(N).getTree()));
-		pack.write((Constants.OBJ_REF_DELTA) << 4 | 4);
-		b.copyRawTo(pack);
-		deflate(pack, delta);
-		digest(pack);
+			final TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
+			packHeader(pack, 3);
+			copy(pack, src.open(N));
+			copy(pack, src.open(s.parseBody(N).getTree()));
+			pack.write((Constants.OBJ_REF_DELTA) << 4 | 4);
+			b.copyRawTo(pack);
+			deflate(pack, delta);
+			digest(pack);
 
-		final TemporaryBuffer.Heap inBuf = new TemporaryBuffer.Heap(1024);
-		final PacketLineOut inPckLine = new PacketLineOut(inBuf);
-		inPckLine.writeString(ObjectId.zeroId().name() + ' ' + N.name() + ' '
-				+ "refs/heads/s" + '\0'
-				+ BasePackPushConnection.CAPABILITY_REPORT_STATUS);
-		inPckLine.end();
-		pack.writeTo(inBuf, PM);
+			final TemporaryBuffer.Heap inBuf = new TemporaryBuffer.Heap(1024);
+			final PacketLineOut inPckLine = new PacketLineOut(inBuf);
+			inPckLine.writeString(ObjectId.zeroId().name() + ' ' + N.name()
+					+ ' ' + "refs/heads/s" + '\0'
+					+ BasePackPushConnection.CAPABILITY_REPORT_STATUS);
+			inPckLine.end();
+			pack.writeTo(inBuf, PM);
 
-		final TemporaryBuffer.Heap outBuf = new TemporaryBuffer.Heap(1024);
-		final ReceivePack rp = new ReceivePack(dst);
-		rp.setCheckReceivedObjects(true);
-		rp.setCheckReferencedObjectsAreReachable(true);
-		rp.setAdvertiseRefsHook(new HidePrivateHook());
-		try {
-			receive(rp, inBuf, outBuf);
-			fail("Expected UnpackException");
-		} catch (UnpackException failed) {
-			Throwable err = failed.getCause();
-			assertTrue(err instanceof MissingObjectException);
-			MissingObjectException moe = (MissingObjectException) err;
-			assertEquals(b, moe.getObjectId());
+			final TemporaryBuffer.Heap outBuf = new TemporaryBuffer.Heap(1024);
+			final ReceivePack rp = new ReceivePack(dst);
+			rp.setCheckReceivedObjects(true);
+			rp.setCheckReferencedObjectsAreReachable(true);
+			rp.setAdvertiseRefsHook(new HidePrivateHook());
+			try {
+				receive(rp, inBuf, outBuf);
+				fail("Expected UnpackException");
+			} catch (UnpackException failed) {
+				Throwable err = failed.getCause();
+				assertTrue(err instanceof MissingObjectException);
+				MissingObjectException moe = (MissingObjectException) err;
+				assertEquals(b, moe.getObjectId());
+			}
+
+			final PacketLineIn r = asPacketLineIn(outBuf);
+			String master = r.readString();
+			int nul = master.indexOf('\0');
+			assertTrue("has capability list", nul > 0);
+			assertEquals(B.name() + ' ' + R_MASTER, master.substring(0, nul));
+			assertSame(PacketLineIn.END, r.readString());
+
+			assertEquals("unpack error Missing blob " + b.name(),
+					r.readString());
+			assertEquals("ng refs/heads/s n/a (unpacker error)",
+					r.readString());
+			assertSame(PacketLineIn.END, r.readString());
 		}
-
-		final PacketLineIn r = asPacketLineIn(outBuf);
-		String master = r.readString();
-		int nul = master.indexOf('\0');
-		assertTrue("has capability list", nul > 0);
-		assertEquals(B.name() + ' ' + R_MASTER, master.substring(0, nul));
-		assertSame(PacketLineIn.END, r.readString());
-
-		assertEquals("unpack error Missing blob " + b.name(), r.readString());
-		assertEquals("ng refs/heads/s n/a (unpacker error)", r.readString());
-		assertSame(PacketLineIn.END, r.readString());
 	}
 
 	@Test
 	public void testUsingHiddenCommonBlobFails() throws Exception {
 		// Try to use the 'b' blob that is hidden.
 		//
-		TestRepository<Repository> s = new TestRepository<>(src);
-		RevCommit N = s.commit().parent(B).add("q", s.blob("b")).create();
+		try (TestRepository<Repository> s = new TestRepository<>(src)) {
+			RevCommit N = s.commit().parent(B).add("q", s.blob("b")).create();
 
-		// But don't include it in the pack.
-		//
-		final TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
-		packHeader(pack, 2);
-		copy(pack, src.open(N));
-		copy(pack,src.open(s.parseBody(N).getTree()));
-		digest(pack);
+			// But don't include it in the pack.
+			//
+			final TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
+			packHeader(pack, 2);
+			copy(pack, src.open(N));
+			copy(pack, src.open(s.parseBody(N).getTree()));
+			digest(pack);
 
-		final TemporaryBuffer.Heap inBuf = new TemporaryBuffer.Heap(1024);
-		final PacketLineOut inPckLine = new PacketLineOut(inBuf);
-		inPckLine.writeString(ObjectId.zeroId().name() + ' ' + N.name() + ' '
-				+ "refs/heads/s" + '\0'
-				+ BasePackPushConnection.CAPABILITY_REPORT_STATUS);
-		inPckLine.end();
-		pack.writeTo(inBuf, PM);
+			final TemporaryBuffer.Heap inBuf = new TemporaryBuffer.Heap(1024);
+			final PacketLineOut inPckLine = new PacketLineOut(inBuf);
+			inPckLine.writeString(ObjectId.zeroId().name() + ' ' + N.name()
+					+ ' ' + "refs/heads/s" + '\0'
+					+ BasePackPushConnection.CAPABILITY_REPORT_STATUS);
+			inPckLine.end();
+			pack.writeTo(inBuf, PM);
 
-		final TemporaryBuffer.Heap outBuf = new TemporaryBuffer.Heap(1024);
-		final ReceivePack rp = new ReceivePack(dst);
-		rp.setCheckReceivedObjects(true);
-		rp.setCheckReferencedObjectsAreReachable(true);
-		rp.setAdvertiseRefsHook(new HidePrivateHook());
-		try {
-			receive(rp, inBuf, outBuf);
-			fail("Expected UnpackException");
-		} catch (UnpackException failed) {
-			Throwable err = failed.getCause();
-			assertTrue(err instanceof MissingObjectException);
-			MissingObjectException moe = (MissingObjectException) err;
-			assertEquals(b, moe.getObjectId());
+			final TemporaryBuffer.Heap outBuf = new TemporaryBuffer.Heap(1024);
+			final ReceivePack rp = new ReceivePack(dst);
+			rp.setCheckReceivedObjects(true);
+			rp.setCheckReferencedObjectsAreReachable(true);
+			rp.setAdvertiseRefsHook(new HidePrivateHook());
+			try {
+				receive(rp, inBuf, outBuf);
+				fail("Expected UnpackException");
+			} catch (UnpackException failed) {
+				Throwable err = failed.getCause();
+				assertTrue(err instanceof MissingObjectException);
+				MissingObjectException moe = (MissingObjectException) err;
+				assertEquals(b, moe.getObjectId());
+			}
+
+			final PacketLineIn r = asPacketLineIn(outBuf);
+			String master = r.readString();
+			int nul = master.indexOf('\0');
+			assertTrue("has capability list", nul > 0);
+			assertEquals(B.name() + ' ' + R_MASTER, master.substring(0, nul));
+			assertSame(PacketLineIn.END, r.readString());
+
+			assertEquals("unpack error Missing blob " + b.name(),
+					r.readString());
+			assertEquals("ng refs/heads/s n/a (unpacker error)",
+					r.readString());
+			assertSame(PacketLineIn.END, r.readString());
 		}
-
-		final PacketLineIn r = asPacketLineIn(outBuf);
-		String master = r.readString();
-		int nul = master.indexOf('\0');
-		assertTrue("has capability list", nul > 0);
-		assertEquals(B.name() + ' ' + R_MASTER, master.substring(0, nul));
-		assertSame(PacketLineIn.END, r.readString());
-
-		assertEquals("unpack error Missing blob " + b.name(), r.readString());
-		assertEquals("ng refs/heads/s n/a (unpacker error)", r.readString());
-		assertSame(PacketLineIn.END, r.readString());
 	}
 
 	@Test
 	public void testUsingUnknownBlobFails() throws Exception {
 		// Try to use the 'n' blob that is not on the server.
 		//
-		TestRepository<Repository> s = new TestRepository<>(src);
-		RevBlob n = s.blob("n");
-		RevCommit N = s.commit().parent(B).add("q", n).create();
+		try (TestRepository<Repository> s = new TestRepository<>(src)) {
+			RevBlob n = s.blob("n");
+			RevCommit N = s.commit().parent(B).add("q", n).create();
 
-		// But don't include it in the pack.
-		//
-		final TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
-		packHeader(pack, 2);
-		copy(pack, src.open(N));
-		copy(pack,src.open(s.parseBody(N).getTree()));
-		digest(pack);
+			// But don't include it in the pack.
+			//
+			final TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
+			packHeader(pack, 2);
+			copy(pack, src.open(N));
+			copy(pack, src.open(s.parseBody(N).getTree()));
+			digest(pack);
 
-		final TemporaryBuffer.Heap inBuf = new TemporaryBuffer.Heap(1024);
-		final PacketLineOut inPckLine = new PacketLineOut(inBuf);
-		inPckLine.writeString(ObjectId.zeroId().name() + ' ' + N.name() + ' '
-				+ "refs/heads/s" + '\0'
-				+ BasePackPushConnection.CAPABILITY_REPORT_STATUS);
-		inPckLine.end();
-		pack.writeTo(inBuf, PM);
+			final TemporaryBuffer.Heap inBuf = new TemporaryBuffer.Heap(1024);
+			final PacketLineOut inPckLine = new PacketLineOut(inBuf);
+			inPckLine.writeString(ObjectId.zeroId().name() + ' ' + N.name()
+					+ ' ' + "refs/heads/s" + '\0'
+					+ BasePackPushConnection.CAPABILITY_REPORT_STATUS);
+			inPckLine.end();
+			pack.writeTo(inBuf, PM);
 
-		final TemporaryBuffer.Heap outBuf = new TemporaryBuffer.Heap(1024);
-		final ReceivePack rp = new ReceivePack(dst);
-		rp.setCheckReceivedObjects(true);
-		rp.setCheckReferencedObjectsAreReachable(true);
-		rp.setAdvertiseRefsHook(new HidePrivateHook());
-		try {
-			receive(rp, inBuf, outBuf);
-			fail("Expected UnpackException");
-		} catch (UnpackException failed) {
-			Throwable err = failed.getCause();
-			assertTrue(err instanceof MissingObjectException);
-			MissingObjectException moe = (MissingObjectException) err;
-			assertEquals(n, moe.getObjectId());
+			final TemporaryBuffer.Heap outBuf = new TemporaryBuffer.Heap(1024);
+			final ReceivePack rp = new ReceivePack(dst);
+			rp.setCheckReceivedObjects(true);
+			rp.setCheckReferencedObjectsAreReachable(true);
+			rp.setAdvertiseRefsHook(new HidePrivateHook());
+			try {
+				receive(rp, inBuf, outBuf);
+				fail("Expected UnpackException");
+			} catch (UnpackException failed) {
+				Throwable err = failed.getCause();
+				assertTrue(err instanceof MissingObjectException);
+				MissingObjectException moe = (MissingObjectException) err;
+				assertEquals(n, moe.getObjectId());
+			}
+
+			final PacketLineIn r = asPacketLineIn(outBuf);
+			String master = r.readString();
+			int nul = master.indexOf('\0');
+			assertTrue("has capability list", nul > 0);
+			assertEquals(B.name() + ' ' + R_MASTER, master.substring(0, nul));
+			assertSame(PacketLineIn.END, r.readString());
+
+			assertEquals("unpack error Missing blob " + n.name(),
+					r.readString());
+			assertEquals("ng refs/heads/s n/a (unpacker error)",
+					r.readString());
+			assertSame(PacketLineIn.END, r.readString());
 		}
-
-		final PacketLineIn r = asPacketLineIn(outBuf);
-		String master = r.readString();
-		int nul = master.indexOf('\0');
-		assertTrue("has capability list", nul > 0);
-		assertEquals(B.name() + ' ' + R_MASTER, master.substring(0, nul));
-		assertSame(PacketLineIn.END, r.readString());
-
-		assertEquals("unpack error Missing blob " + n.name(), r.readString());
-		assertEquals("ng refs/heads/s n/a (unpacker error)", r.readString());
-		assertSame(PacketLineIn.END, r.readString());
 	}
 
 	@Test
@@ -509,75 +524,79 @@ private TemporaryBuffer.Heap setupSourceRepoInvalidGitmodules()
 				.append("    url = -upayload.sh\n")
 				.toString();
 
-		TestRepository<Repository> s = new TestRepository<>(src);
-		RevBlob blob = s.blob(fakeGitmodules);
-		RevCommit N = s.commit().parent(B)
-				.add(".gitmodules", blob).create();
-		RevTree t = s.parseBody(N).getTree();
+		try (TestRepository<Repository> s = new TestRepository<>(src)) {
+			RevBlob blob = s.blob(fakeGitmodules);
+			RevCommit N = s.commit().parent(B).add(".gitmodules", blob)
+					.create();
+			RevTree t = s.parseBody(N).getTree();
 
-		final TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
-		packHeader(pack, 3);
-		copy(pack, src.open(N));
-		copy(pack, src.open(t));
-		copy(pack, src.open(blob));
-		digest(pack);
+			final TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
+			packHeader(pack, 3);
+			copy(pack, src.open(N));
+			copy(pack, src.open(t));
+			copy(pack, src.open(blob));
+			digest(pack);
 
-		final TemporaryBuffer.Heap inBuf = new TemporaryBuffer.Heap(1024);
-		final PacketLineOut inPckLine = new PacketLineOut(inBuf);
-		inPckLine.writeString(ObjectId.zeroId().name() + ' ' + N.name() + ' '
-				+ "refs/heads/s" + '\0'
-				+ BasePackPushConnection.CAPABILITY_REPORT_STATUS);
-		inPckLine.end();
-		pack.writeTo(inBuf, PM);
-		return inBuf;
+			final TemporaryBuffer.Heap inBuf = new TemporaryBuffer.Heap(1024);
+			final PacketLineOut inPckLine = new PacketLineOut(inBuf);
+			inPckLine.writeString(ObjectId.zeroId().name() + ' ' + N.name()
+					+ ' ' + "refs/heads/s" + '\0'
+					+ BasePackPushConnection.CAPABILITY_REPORT_STATUS);
+			inPckLine.end();
+			pack.writeTo(inBuf, PM);
+			return inBuf;
+		}
 	}
 
 	@Test
 	public void testUsingUnknownTreeFails() throws Exception {
-		TestRepository<Repository> s = new TestRepository<>(src);
-		RevCommit N = s.commit().parent(B).add("q", s.blob("a")).create();
-		RevTree t = s.parseBody(N).getTree();
+		try (TestRepository<Repository> s = new TestRepository<>(src)) {
+			RevCommit N = s.commit().parent(B).add("q", s.blob("a")).create();
+			RevTree t = s.parseBody(N).getTree();
 
-		// Don't include the tree in the pack.
-		//
-		final TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
-		packHeader(pack, 1);
-		copy(pack, src.open(N));
-		digest(pack);
+			// Don't include the tree in the pack.
+			//
+			final TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(1024);
+			packHeader(pack, 1);
+			copy(pack, src.open(N));
+			digest(pack);
 
-		final TemporaryBuffer.Heap inBuf = new TemporaryBuffer.Heap(1024);
-		final PacketLineOut inPckLine = new PacketLineOut(inBuf);
-		inPckLine.writeString(ObjectId.zeroId().name() + ' ' + N.name() + ' '
-				+ "refs/heads/s" + '\0'
-				+ BasePackPushConnection.CAPABILITY_REPORT_STATUS);
-		inPckLine.end();
-		pack.writeTo(inBuf, PM);
+			final TemporaryBuffer.Heap inBuf = new TemporaryBuffer.Heap(1024);
+			final PacketLineOut inPckLine = new PacketLineOut(inBuf);
+			inPckLine.writeString(ObjectId.zeroId().name() + ' ' + N.name()
+					+ ' ' + "refs/heads/s" + '\0'
+					+ BasePackPushConnection.CAPABILITY_REPORT_STATUS);
+			inPckLine.end();
+			pack.writeTo(inBuf, PM);
 
-		final TemporaryBuffer.Heap outBuf = new TemporaryBuffer.Heap(1024);
-		final ReceivePack rp = new ReceivePack(dst);
-		rp.setCheckReceivedObjects(true);
-		rp.setCheckReferencedObjectsAreReachable(true);
-		rp.setAdvertiseRefsHook(new HidePrivateHook());
-		try {
-			receive(rp, inBuf, outBuf);
-			fail("Expected UnpackException");
-		} catch (UnpackException failed) {
-			Throwable err = failed.getCause();
-			assertTrue(err instanceof MissingObjectException);
-			MissingObjectException moe = (MissingObjectException) err;
-			assertEquals(t, moe.getObjectId());
+			final TemporaryBuffer.Heap outBuf = new TemporaryBuffer.Heap(1024);
+			final ReceivePack rp = new ReceivePack(dst);
+			rp.setCheckReceivedObjects(true);
+			rp.setCheckReferencedObjectsAreReachable(true);
+			rp.setAdvertiseRefsHook(new HidePrivateHook());
+			try {
+				receive(rp, inBuf, outBuf);
+				fail("Expected UnpackException");
+			} catch (UnpackException failed) {
+				Throwable err = failed.getCause();
+				assertTrue(err instanceof MissingObjectException);
+				MissingObjectException moe = (MissingObjectException) err;
+				assertEquals(t, moe.getObjectId());
+			}
+
+			final PacketLineIn r = asPacketLineIn(outBuf);
+			String master = r.readString();
+			int nul = master.indexOf('\0');
+			assertTrue("has capability list", nul > 0);
+			assertEquals(B.name() + ' ' + R_MASTER, master.substring(0, nul));
+			assertSame(PacketLineIn.END, r.readString());
+
+			assertEquals("unpack error Missing tree " + t.name(),
+					r.readString());
+			assertEquals("ng refs/heads/s n/a (unpacker error)",
+					r.readString());
+			assertSame(PacketLineIn.END, r.readString());
 		}
-
-		final PacketLineIn r = asPacketLineIn(outBuf);
-		String master = r.readString();
-		int nul = master.indexOf('\0');
-		assertTrue("has capability list", nul > 0);
-		assertEquals(B.name() + ' ' + R_MASTER, master.substring(0, nul));
-		assertSame(PacketLineIn.END, r.readString());
-
-		assertEquals("unpack error Missing tree " + t.name(), r.readString());
-		assertEquals("ng refs/heads/s n/a (unpacker error)", r.readString());
-		assertSame(PacketLineIn.END, r.readString());
 	}
 
 	private static void packHeader(TemporaryBuffer.Heap tinyPack, int cnt)
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/SideBandOutputStreamTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/SideBandOutputStreamTest.java
index b6cf356..0bf9a80 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/SideBandOutputStreamTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/SideBandOutputStreamTest.java
@@ -77,76 +77,76 @@ public void setUp() throws Exception {
 
 	@Test
 	public void testWrite_CH_DATA() throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		final SideBandOutputStream out = new SideBandOutputStream(CH_DATA,
-				SMALL_BUF, rawOut);
-		out.write(new byte[] { 'a', 'b', 'c' });
-		out.flush();
+		try (SideBandOutputStream out = new SideBandOutputStream(CH_DATA,
+				SMALL_BUF, rawOut)) {
+			out.write(new byte[] { 'a', 'b', 'c' });
+			out.flush();
+		}
 		assertBuffer("0008\001abc");
 	}
 
 	@Test
 	public void testWrite_CH_PROGRESS() throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		final SideBandOutputStream out = new SideBandOutputStream(CH_PROGRESS,
-				SMALL_BUF, rawOut);
-		out.write(new byte[] { 'a', 'b', 'c' });
-		out.flush();
+		try (SideBandOutputStream out = new SideBandOutputStream(CH_PROGRESS,
+				SMALL_BUF, rawOut)) {
+			out.write(new byte[] { 'a', 'b', 'c' });
+			out.flush();
+		}
 		assertBuffer("0008\002abc");
 	}
 
 	@Test
 	public void testWrite_CH_ERROR() throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		final SideBandOutputStream out = new SideBandOutputStream(CH_ERROR,
-				SMALL_BUF, rawOut);
-		out.write(new byte[] { 'a', 'b', 'c' });
-		out.flush();
+		try (SideBandOutputStream out = new SideBandOutputStream(CH_ERROR,
+				SMALL_BUF, rawOut)) {
+			out.write(new byte[] { 'a', 'b', 'c' });
+			out.flush();
+		}
 		assertBuffer("0008\003abc");
 	}
 
 	@Test
 	public void testWrite_Small() throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		final SideBandOutputStream out = new SideBandOutputStream(CH_DATA,
-				SMALL_BUF, rawOut);
-		out.write('a');
-		out.write('b');
-		out.write('c');
-		out.flush();
+		try (SideBandOutputStream out = new SideBandOutputStream(CH_DATA,
+				SMALL_BUF, rawOut)) {
+			out.write('a');
+			out.write('b');
+			out.write('c');
+			out.flush();
+		}
 		assertBuffer("0008\001abc");
 	}
 
 	@Test
 	public void testWrite_SmallBlocks1() throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		final SideBandOutputStream out = new SideBandOutputStream(CH_DATA, 6,
-				rawOut);
-		out.write('a');
-		out.write('b');
-		out.write('c');
-		out.flush();
+		try (SideBandOutputStream out = new SideBandOutputStream(CH_DATA, 6,
+				rawOut)) {
+			out.write('a');
+			out.write('b');
+			out.write('c');
+			out.flush();
+		}
 		assertBuffer("0006\001a0006\001b0006\001c");
 	}
 
 	@Test
 	public void testWrite_SmallBlocks2() throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		final SideBandOutputStream out = new SideBandOutputStream(CH_DATA, 6,
-				rawOut);
-		out.write(new byte[] { 'a', 'b', 'c' });
-		out.flush();
+		try (SideBandOutputStream out = new SideBandOutputStream(CH_DATA, 6,
+				rawOut)) {
+			out.write(new byte[] { 'a', 'b', 'c' });
+			out.flush();
+		}
 		assertBuffer("0006\001a0006\001b0006\001c");
 	}
 
 	@Test
 	public void testWrite_SmallBlocks3() throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		final SideBandOutputStream out = new SideBandOutputStream(CH_DATA, 7,
-				rawOut);
-		out.write('a');
-		out.write(new byte[] { 'b', 'c' });
-		out.flush();
+		try (SideBandOutputStream out = new SideBandOutputStream(CH_DATA, 7,
+				rawOut)) {
+			out.write('a');
+			out.write(new byte[] { 'b', 'c' });
+			out.flush();
+		}
 		assertBuffer("0007\001ab0006\001c");
 	}
 
@@ -158,11 +158,11 @@ public void testWrite_Large() throws IOException {
 			buf[i] = (byte) i;
 		}
 
-		@SuppressWarnings("resource" /* java 7 */)
-		final SideBandOutputStream out = new SideBandOutputStream(CH_DATA,
-				MAX_BUF, rawOut);
-		out.write(buf);
-		out.flush();
+		try (SideBandOutputStream out = new SideBandOutputStream(CH_DATA,
+				MAX_BUF, rawOut)) {
+			out.write(buf);
+			out.flush();
+		}
 
 		final byte[] act = rawOut.toByteArray();
 		final String explen = Integer.toString(buf.length + HDR_SIZE, 16);
@@ -174,7 +174,6 @@ public void testWrite_Large() throws IOException {
 		}
 	}
 
-	@SuppressWarnings("resource" /* java 7 */)
 	@Test
 	public void testFlush() throws IOException {
 		final int[] flushCnt = new int[1];
@@ -190,7 +189,10 @@ public void flush() throws IOException {
 			}
 		};
 
-		new SideBandOutputStream(CH_DATA, SMALL_BUF, mockout).flush();
+		try (SideBandOutputStream out = new SideBandOutputStream(CH_DATA,
+				SMALL_BUF, mockout)) {
+			out.flush();
+		}
 		assertEquals(1, flushCnt[0]);
 	}
 
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
index 8acbcce..1cbe8a4 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/UploadPackTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/UploadPackTest.java
@@ -128,13 +128,13 @@ public UploadPack create(Object req, Repository db)
 				}, null);
 		uri = testProtocol.register(ctx, server);
 
-		assertFalse(client.hasObject(commit0.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(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()));
+			assertTrue(client.getObjectDatabase().has(commit0.toObjectId()));
 		}
 	}
 
@@ -147,7 +147,7 @@ public void testFetchUnreachableBlobWithBitmap() throws Exception {
 		testProtocol = generateReachableCommitUploadPackProtocol();
 		uri = testProtocol.register(ctx, server);
 
-		assertFalse(client.hasObject(blob.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(blob.toObjectId()));
 
 		try (Transport tn = testProtocol.open(uri, client, "server")) {
 			thrown.expect(TransportException.class);
@@ -168,12 +168,12 @@ public void testFetchReachableBlobWithBitmap() throws Exception {
 		testProtocol = generateReachableCommitUploadPackProtocol();
 		uri = testProtocol.register(ctx, server);
 
-		assertFalse(client.hasObject(blob.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(blob.toObjectId()));
 
 		try (Transport tn = testProtocol.open(uri, client, "server")) {
 			tn.fetch(NullProgressMonitor.INSTANCE,
 					Collections.singletonList(new RefSpec(blob.name())));
-			assertTrue(client.hasObject(blob.toObjectId()));
+			assertTrue(client.getObjectDatabase().has(blob.toObjectId()));
 		}
 	}
 
@@ -186,7 +186,7 @@ public void testFetchReachableBlobWithoutBitmap() throws Exception {
 		testProtocol = generateReachableCommitUploadPackProtocol();
 		uri = testProtocol.register(ctx, server);
 
-		assertFalse(client.hasObject(blob.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(blob.toObjectId()));
 
 		try (Transport tn = testProtocol.open(uri, client, "server")) {
 			thrown.expect(TransportException.class);
@@ -200,224 +200,233 @@ public void testFetchReachableBlobWithoutBitmap() throws Exception {
 	@Test
 	public void testFetchWithBlobNoneFilter() throws Exception {
 		InMemoryRepository server2 = newRepo("server2");
-		TestRepository<InMemoryRepository> remote2 =
-				new TestRepository<>(server2);
-		RevBlob blob1 = remote2.blob("foobar");
-		RevBlob blob2 = remote2.blob("fooba");
-		RevTree tree = remote2.tree(remote2.file("1", blob1),
-				remote2.file("2", blob2));
-		RevCommit commit = remote2.commit(tree);
-		remote2.update("master", commit);
+		try (TestRepository<InMemoryRepository> remote2 = new TestRepository<>(
+				server2)) {
+			RevBlob blob1 = remote2.blob("foobar");
+			RevBlob blob2 = remote2.blob("fooba");
+			RevTree tree = remote2.tree(remote2.file("1", blob1),
+					remote2.file("2", blob2));
+			RevCommit commit = remote2.commit(tree);
+			remote2.update("master", commit);
 
-		server2.getConfig().setBoolean("uploadpack", null, "allowfilter", true);
+			server2.getConfig().setBoolean("uploadpack", null, "allowfilter",
+					true);
 
-		testProtocol = new TestProtocol<>(
-				new UploadPackFactory<Object>() {
-					@Override
-					public UploadPack create(Object req, Repository db)
-							throws ServiceNotEnabledException,
-							ServiceNotAuthorizedException {
-						UploadPack up = new UploadPack(db);
-						return up;
-					}
-				}, null);
-		uri = testProtocol.register(ctx, server2);
+			testProtocol = new TestProtocol<>(new UploadPackFactory<Object>() {
+				@Override
+				public UploadPack create(Object req, Repository db)
+						throws ServiceNotEnabledException,
+						ServiceNotAuthorizedException {
+					UploadPack up = new UploadPack(db);
+					return up;
+				}
+			}, null);
+			uri = testProtocol.register(ctx, server2);
 
-		try (Transport tn = testProtocol.open(uri, client, "server2")) {
-			tn.setFilterBlobLimit(0);
-			tn.fetch(NullProgressMonitor.INSTANCE,
-					Collections.singletonList(new RefSpec(commit.name())));
-			assertTrue(client.hasObject(tree.toObjectId()));
-			assertFalse(client.hasObject(blob1.toObjectId()));
-			assertFalse(client.hasObject(blob2.toObjectId()));
+			try (Transport tn = testProtocol.open(uri, client, "server2")) {
+				tn.setFilterBlobLimit(0);
+				tn.fetch(NullProgressMonitor.INSTANCE,
+						Collections.singletonList(new RefSpec(commit.name())));
+				assertTrue(client.getObjectDatabase().has(tree.toObjectId()));
+				assertFalse(client.getObjectDatabase().has(blob1.toObjectId()));
+				assertFalse(client.getObjectDatabase().has(blob2.toObjectId()));
+			}
 		}
 	}
 
 	@Test
 	public void testFetchExplicitBlobWithFilter() throws Exception {
 		InMemoryRepository server2 = newRepo("server2");
-		TestRepository<InMemoryRepository> remote2 =
-				new TestRepository<>(server2);
-		RevBlob blob1 = remote2.blob("foobar");
-		RevBlob blob2 = remote2.blob("fooba");
-		RevTree tree = remote2.tree(remote2.file("1", blob1),
-				remote2.file("2", blob2));
-		RevCommit commit = remote2.commit(tree);
-		remote2.update("master", commit);
-		remote2.update("a_blob", blob1);
+		try (TestRepository<InMemoryRepository> remote2 = new TestRepository<>(
+				server2)) {
+			RevBlob blob1 = remote2.blob("foobar");
+			RevBlob blob2 = remote2.blob("fooba");
+			RevTree tree = remote2.tree(remote2.file("1", blob1),
+					remote2.file("2", blob2));
+			RevCommit commit = remote2.commit(tree);
+			remote2.update("master", commit);
+			remote2.update("a_blob", blob1);
 
-		server2.getConfig().setBoolean("uploadpack", null, "allowfilter", true);
+			server2.getConfig().setBoolean("uploadpack", null, "allowfilter",
+					true);
 
-		testProtocol = new TestProtocol<>(
-				new UploadPackFactory<Object>() {
-					@Override
-					public UploadPack create(Object req, Repository db)
-							throws ServiceNotEnabledException,
-							ServiceNotAuthorizedException {
-						UploadPack up = new UploadPack(db);
-						return up;
-					}
-				}, null);
-		uri = testProtocol.register(ctx, server2);
+			testProtocol = new TestProtocol<>(new UploadPackFactory<Object>() {
+				@Override
+				public UploadPack create(Object req, Repository db)
+						throws ServiceNotEnabledException,
+						ServiceNotAuthorizedException {
+					UploadPack up = new UploadPack(db);
+					return up;
+				}
+			}, null);
+			uri = testProtocol.register(ctx, server2);
 
-		try (Transport tn = testProtocol.open(uri, client, "server2")) {
-			tn.setFilterBlobLimit(0);
-			tn.fetch(NullProgressMonitor.INSTANCE, Arrays.asList(
-						new RefSpec(commit.name()),
-						new RefSpec(blob1.name())));
-			assertTrue(client.hasObject(tree.toObjectId()));
-			assertTrue(client.hasObject(blob1.toObjectId()));
-			assertFalse(client.hasObject(blob2.toObjectId()));
+			try (Transport tn = testProtocol.open(uri, client, "server2")) {
+				tn.setFilterBlobLimit(0);
+				tn.fetch(NullProgressMonitor.INSTANCE, Arrays.asList(
+						new RefSpec(commit.name()), new RefSpec(blob1.name())));
+				assertTrue(client.getObjectDatabase().has(tree.toObjectId()));
+				assertTrue(client.getObjectDatabase().has(blob1.toObjectId()));
+				assertFalse(client.getObjectDatabase().has(blob2.toObjectId()));
+			}
 		}
 	}
 
 	@Test
 	public void testFetchWithBlobLimitFilter() throws Exception {
 		InMemoryRepository server2 = newRepo("server2");
-		TestRepository<InMemoryRepository> remote2 =
-				new TestRepository<>(server2);
-		RevBlob longBlob = remote2.blob("foobar");
-		RevBlob shortBlob = remote2.blob("fooba");
-		RevTree tree = remote2.tree(remote2.file("1", longBlob),
-				remote2.file("2", shortBlob));
-		RevCommit commit = remote2.commit(tree);
-		remote2.update("master", commit);
+		try (TestRepository<InMemoryRepository> remote2 = new TestRepository<>(
+				server2)) {
+			RevBlob longBlob = remote2.blob("foobar");
+			RevBlob shortBlob = remote2.blob("fooba");
+			RevTree tree = remote2.tree(remote2.file("1", longBlob),
+					remote2.file("2", shortBlob));
+			RevCommit commit = remote2.commit(tree);
+			remote2.update("master", commit);
 
-		server2.getConfig().setBoolean("uploadpack", null, "allowfilter", true);
+			server2.getConfig().setBoolean("uploadpack", null, "allowfilter",
+					true);
 
-		testProtocol = new TestProtocol<>(
-				new UploadPackFactory<Object>() {
-					@Override
-					public UploadPack create(Object req, Repository db)
-							throws ServiceNotEnabledException,
-							ServiceNotAuthorizedException {
-						UploadPack up = new UploadPack(db);
-						return up;
-					}
-				}, null);
-		uri = testProtocol.register(ctx, server2);
+			testProtocol = new TestProtocol<>(new UploadPackFactory<Object>() {
+				@Override
+				public UploadPack create(Object req, Repository db)
+						throws ServiceNotEnabledException,
+						ServiceNotAuthorizedException {
+					UploadPack up = new UploadPack(db);
+					return up;
+				}
+			}, null);
+			uri = testProtocol.register(ctx, server2);
 
-		try (Transport tn = testProtocol.open(uri, client, "server2")) {
-			tn.setFilterBlobLimit(5);
-			tn.fetch(NullProgressMonitor.INSTANCE,
-					Collections.singletonList(new RefSpec(commit.name())));
-			assertFalse(client.hasObject(longBlob.toObjectId()));
-			assertTrue(client.hasObject(shortBlob.toObjectId()));
+			try (Transport tn = testProtocol.open(uri, client, "server2")) {
+				tn.setFilterBlobLimit(5);
+				tn.fetch(NullProgressMonitor.INSTANCE,
+						Collections.singletonList(new RefSpec(commit.name())));
+				assertFalse(
+						client.getObjectDatabase().has(longBlob.toObjectId()));
+				assertTrue(
+						client.getObjectDatabase().has(shortBlob.toObjectId()));
+			}
 		}
 	}
 
 	@Test
 	public void testFetchExplicitBlobWithFilterAndBitmaps() throws Exception {
 		InMemoryRepository server2 = newRepo("server2");
-		TestRepository<InMemoryRepository> remote2 =
-				new TestRepository<>(server2);
-		RevBlob blob1 = remote2.blob("foobar");
-		RevBlob blob2 = remote2.blob("fooba");
-		RevTree tree = remote2.tree(remote2.file("1", blob1),
-				remote2.file("2", blob2));
-		RevCommit commit = remote2.commit(tree);
-		remote2.update("master", commit);
-		remote2.update("a_blob", blob1);
+		try (TestRepository<InMemoryRepository> remote2 = new TestRepository<>(
+				server2)) {
+			RevBlob blob1 = remote2.blob("foobar");
+			RevBlob blob2 = remote2.blob("fooba");
+			RevTree tree = remote2.tree(remote2.file("1", blob1),
+					remote2.file("2", blob2));
+			RevCommit commit = remote2.commit(tree);
+			remote2.update("master", commit);
+			remote2.update("a_blob", blob1);
 
-		server2.getConfig().setBoolean("uploadpack", null, "allowfilter", true);
+			server2.getConfig().setBoolean("uploadpack", null, "allowfilter",
+					true);
 
-		// generate bitmaps
-		new DfsGarbageCollector(server2).pack(null);
-		server2.scanForRepoChanges();
+			// generate bitmaps
+			new DfsGarbageCollector(server2).pack(null);
+			server2.scanForRepoChanges();
 
-		testProtocol = new TestProtocol<>(
-				new UploadPackFactory<Object>() {
-					@Override
-					public UploadPack create(Object req, Repository db)
-							throws ServiceNotEnabledException,
-							ServiceNotAuthorizedException {
-						UploadPack up = new UploadPack(db);
-						return up;
-					}
-				}, null);
-		uri = testProtocol.register(ctx, server2);
+			testProtocol = new TestProtocol<>(new UploadPackFactory<Object>() {
+				@Override
+				public UploadPack create(Object req, Repository db)
+						throws ServiceNotEnabledException,
+						ServiceNotAuthorizedException {
+					UploadPack up = new UploadPack(db);
+					return up;
+				}
+			}, null);
+			uri = testProtocol.register(ctx, server2);
 
-		try (Transport tn = testProtocol.open(uri, client, "server2")) {
-			tn.setFilterBlobLimit(0);
-			tn.fetch(NullProgressMonitor.INSTANCE, Arrays.asList(
-						new RefSpec(commit.name()),
-						new RefSpec(blob1.name())));
-			assertTrue(client.hasObject(blob1.toObjectId()));
-			assertFalse(client.hasObject(blob2.toObjectId()));
+			try (Transport tn = testProtocol.open(uri, client, "server2")) {
+				tn.setFilterBlobLimit(0);
+				tn.fetch(NullProgressMonitor.INSTANCE, Arrays.asList(
+						new RefSpec(commit.name()), new RefSpec(blob1.name())));
+				assertTrue(client.getObjectDatabase().has(blob1.toObjectId()));
+				assertFalse(client.getObjectDatabase().has(blob2.toObjectId()));
+			}
 		}
 	}
 
 	@Test
 	public void testFetchWithBlobLimitFilterAndBitmaps() throws Exception {
 		InMemoryRepository server2 = newRepo("server2");
-		TestRepository<InMemoryRepository> remote2 =
-				new TestRepository<>(server2);
-		RevBlob longBlob = remote2.blob("foobar");
-		RevBlob shortBlob = remote2.blob("fooba");
-		RevTree tree = remote2.tree(remote2.file("1", longBlob),
-				remote2.file("2", shortBlob));
-		RevCommit commit = remote2.commit(tree);
-		remote2.update("master", commit);
+		try (TestRepository<InMemoryRepository> remote2 = new TestRepository<>(
+				server2)) {
+			RevBlob longBlob = remote2.blob("foobar");
+			RevBlob shortBlob = remote2.blob("fooba");
+			RevTree tree = remote2.tree(remote2.file("1", longBlob),
+					remote2.file("2", shortBlob));
+			RevCommit commit = remote2.commit(tree);
+			remote2.update("master", commit);
 
-		server2.getConfig().setBoolean("uploadpack", null, "allowfilter", true);
+			server2.getConfig().setBoolean("uploadpack", null, "allowfilter",
+					true);
 
-		// generate bitmaps
-		new DfsGarbageCollector(server2).pack(null);
-		server2.scanForRepoChanges();
+			// generate bitmaps
+			new DfsGarbageCollector(server2).pack(null);
+			server2.scanForRepoChanges();
 
-		testProtocol = new TestProtocol<>(
-				new UploadPackFactory<Object>() {
-					@Override
-					public UploadPack create(Object req, Repository db)
-							throws ServiceNotEnabledException,
-							ServiceNotAuthorizedException {
-						UploadPack up = new UploadPack(db);
-						return up;
-					}
-				}, null);
-		uri = testProtocol.register(ctx, server2);
+			testProtocol = new TestProtocol<>(new UploadPackFactory<Object>() {
+				@Override
+				public UploadPack create(Object req, Repository db)
+						throws ServiceNotEnabledException,
+						ServiceNotAuthorizedException {
+					UploadPack up = new UploadPack(db);
+					return up;
+				}
+			}, null);
+			uri = testProtocol.register(ctx, server2);
 
-		try (Transport tn = testProtocol.open(uri, client, "server2")) {
-			tn.setFilterBlobLimit(5);
-			tn.fetch(NullProgressMonitor.INSTANCE,
-					Collections.singletonList(new RefSpec(commit.name())));
-			assertFalse(client.hasObject(longBlob.toObjectId()));
-			assertTrue(client.hasObject(shortBlob.toObjectId()));
+			try (Transport tn = testProtocol.open(uri, client, "server2")) {
+				tn.setFilterBlobLimit(5);
+				tn.fetch(NullProgressMonitor.INSTANCE,
+						Collections.singletonList(new RefSpec(commit.name())));
+				assertFalse(
+						client.getObjectDatabase().has(longBlob.toObjectId()));
+				assertTrue(
+						client.getObjectDatabase().has(shortBlob.toObjectId()));
+			}
 		}
 	}
 
 	@Test
 	public void testFetchWithNonSupportingServer() throws Exception {
 		InMemoryRepository server2 = newRepo("server2");
-		TestRepository<InMemoryRepository> remote2 =
-				new TestRepository<>(server2);
-		RevBlob blob = remote2.blob("foo");
-		RevTree tree = remote2.tree(remote2.file("1", blob));
-		RevCommit commit = remote2.commit(tree);
-		remote2.update("master", commit);
+		try (TestRepository<InMemoryRepository> remote2 = new TestRepository<>(
+				server2)) {
+			RevBlob blob = remote2.blob("foo");
+			RevTree tree = remote2.tree(remote2.file("1", blob));
+			RevCommit commit = remote2.commit(tree);
+			remote2.update("master", commit);
 
-		server2.getConfig().setBoolean("uploadpack", null, "allowfilter", false);
+			server2.getConfig().setBoolean("uploadpack", null, "allowfilter",
+					false);
 
-		testProtocol = new TestProtocol<>(
-				new UploadPackFactory<Object>() {
-					@Override
-					public UploadPack create(Object req, Repository db)
-							throws ServiceNotEnabledException,
-							ServiceNotAuthorizedException {
-						UploadPack up = new UploadPack(db);
-						return up;
-					}
-				}, null);
-		uri = testProtocol.register(ctx, server2);
+			testProtocol = new TestProtocol<>(new UploadPackFactory<Object>() {
+				@Override
+				public UploadPack create(Object req, Repository db)
+						throws ServiceNotEnabledException,
+						ServiceNotAuthorizedException {
+					UploadPack up = new UploadPack(db);
+					return up;
+				}
+			}, null);
+			uri = testProtocol.register(ctx, server2);
 
-		try (Transport tn = testProtocol.open(uri, client, "server2")) {
-			tn.setFilterBlobLimit(0);
+			try (Transport tn = testProtocol.open(uri, client, "server2")) {
+				tn.setFilterBlobLimit(0);
 
-			thrown.expect(TransportException.class);
-			thrown.expectMessage("filter requires server to advertise that capability");
+				thrown.expect(TransportException.class);
+				thrown.expectMessage(
+						"filter requires server to advertise that capability");
 
-			tn.fetch(NullProgressMonitor.INSTANCE,
-					Collections.singletonList(new RefSpec(commit.name())));
+				tn.fetch(NullProgressMonitor.INSTANCE,
+						Collections.singletonList(new RefSpec(commit.name())));
+			}
 		}
 	}
 
@@ -965,10 +974,10 @@ public void testV2FetchServerStopsNegotiation() throws Exception {
 		assertThat(pckIn.readString(), theInstance(PacketLineIn.DELIM));
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
-		assertFalse(client.hasObject(fooParent.toObjectId()));
-		assertTrue(client.hasObject(fooChild.toObjectId()));
-		assertFalse(client.hasObject(barParent.toObjectId()));
-		assertTrue(client.hasObject(barChild.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(fooParent.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(fooChild.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(barParent.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(barChild.toObjectId()));
 	}
 
 	@Test
@@ -992,10 +1001,10 @@ public void testV2FetchClientStopsNegotiation() throws Exception {
 
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
-		assertFalse(client.hasObject(fooParent.toObjectId()));
-		assertTrue(client.hasObject(fooChild.toObjectId()));
-		assertTrue(client.hasObject(barParent.toObjectId()));
-		assertTrue(client.hasObject(barChild.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(fooParent.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(fooChild.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(barParent.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(barChild.toObjectId()));
 	}
 
 	@Test
@@ -1078,7 +1087,7 @@ public void testV2FetchIncludeTag() throws Exception {
 		PacketLineIn pckIn = new PacketLineIn(recvStream);
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
-		assertFalse(client.hasObject(tag.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(tag.toObjectId()));
 
 		// With tag.
 		recvStream = uploadPackV2(
@@ -1091,7 +1100,7 @@ public void testV2FetchIncludeTag() throws Exception {
 		pckIn = new PacketLineIn(recvStream);
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
-		assertTrue(client.hasObject(tag.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(tag.toObjectId()));
 	}
 
 	@Test
@@ -1149,8 +1158,8 @@ public void testV2FetchShallow() throws Exception {
 		PacketLineIn pckIn = new PacketLineIn(recvStream);
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
-		assertTrue(client.hasObject(barChild.toObjectId()));
-		assertFalse(client.hasObject(commonParent.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(barChild.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(commonParent.toObjectId()));
 
 		// With shallow, the server knows that we don't have
 		// commonParent, so it sends it.
@@ -1165,7 +1174,7 @@ public void testV2FetchShallow() throws Exception {
 		pckIn = new PacketLineIn(recvStream);
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
-		assertTrue(client.hasObject(commonParent.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(commonParent.toObjectId()));
 	}
 
 	@Test
@@ -1188,8 +1197,8 @@ public void testV2FetchDeepenAndDone() throws Exception {
 		assertThat(pckIn.readString(), theInstance(PacketLineIn.DELIM));
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
-		assertTrue(client.hasObject(child.toObjectId()));
-		assertFalse(client.hasObject(parent.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(child.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(parent.toObjectId()));
 
 		// Without that, the parent is sent too.
 		recvStream = uploadPackV2(
@@ -1201,7 +1210,7 @@ public void testV2FetchDeepenAndDone() throws Exception {
 		pckIn = new PacketLineIn(recvStream);
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
-		assertTrue(client.hasObject(parent.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(parent.toObjectId()));
 	}
 
 	@Test
@@ -1268,15 +1277,15 @@ public void testV2FetchShallowSince() throws Exception {
 
 		// The server does not send this because it is committed
 		// earlier than the given deepen-since time.
-		assertFalse(client.hasObject(tooOld.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(tooOld.toObjectId()));
 
 		// The server does not send this because the client claims to
 		// have it.
-		assertFalse(client.hasObject(boundary.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(boundary.toObjectId()));
 
 		// The server sends both these commits.
-		assertTrue(client.hasObject(beyondBoundary.toObjectId()));
-		assertTrue(client.hasObject(merge.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(beyondBoundary.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(merge.toObjectId()));
 	}
 
 	@Test
@@ -1316,9 +1325,9 @@ public void testV2FetchShallowSince_excludedParentWithMultipleChildren() throws
 		parsePack(recvStream);
 
 		// Only the children are sent.
-		assertFalse(client.hasObject(base.toObjectId()));
-		assertTrue(client.hasObject(child1.toObjectId()));
-		assertTrue(client.hasObject(child2.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(base.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(child1.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(child2.toObjectId()));
 	}
 
 	@Test
@@ -1384,16 +1393,16 @@ public void testV2FetchDeepenNot() throws Exception {
 
 		// The server does not send these because they are excluded by
 		// deepen-not.
-		assertFalse(client.hasObject(side.toObjectId()));
-		assertFalse(client.hasObject(one.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(side.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(one.toObjectId()));
 
 		// The server does not send this because the client claims to
 		// have it.
-		assertFalse(client.hasObject(three.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(three.toObjectId()));
 
 		// The server sends both these commits.
-		assertTrue(client.hasObject(merge.toObjectId()));
-		assertTrue(client.hasObject(two.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(merge.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(two.toObjectId()));
 	}
 
 	@Test
@@ -1441,10 +1450,10 @@ public void testV2FetchDeepenNot_supportAnnotatedTags() throws Exception {
 		assertThat(pckIn.readString(), theInstance(PacketLineIn.DELIM));
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
-		assertFalse(client.hasObject(one.toObjectId()));
-		assertFalse(client.hasObject(two.toObjectId()));
-		assertTrue(client.hasObject(three.toObjectId()));
-		assertTrue(client.hasObject(four.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(one.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(two.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(three.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(four.toObjectId()));
 	}
 
 	@Test
@@ -1485,9 +1494,9 @@ public void testV2FetchDeepenNot_excludedParentWithMultipleChildren() throws Exc
 		parsePack(recvStream);
 
 		// Only the children are sent.
-		assertFalse(client.hasObject(base.toObjectId()));
-		assertTrue(client.hasObject(child1.toObjectId()));
-		assertTrue(client.hasObject(child2.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(base.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(child1.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(child2.toObjectId()));
 	}
 
 	@Test
@@ -1538,8 +1547,8 @@ public void testV2FetchFilter() throws Exception {
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
 
-		assertFalse(client.hasObject(big.toObjectId()));
-		assertTrue(client.hasObject(small.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(big.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(small.toObjectId()));
 	}
 
 	@Test
@@ -1610,9 +1619,9 @@ public void testV2FetchWantRef() throws Exception {
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
 
-		assertTrue(client.hasObject(one.toObjectId()));
-		assertTrue(client.hasObject(two.toObjectId()));
-		assertFalse(client.hasObject(three.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(one.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(two.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(three.toObjectId()));
 	}
 
 	@Test
@@ -1666,9 +1675,9 @@ public void testV2FetchMixedWantRef() throws Exception {
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
 
-		assertTrue(client.hasObject(one.toObjectId()));
-		assertTrue(client.hasObject(two.toObjectId()));
-		assertFalse(client.hasObject(three.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(one.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(two.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(three.toObjectId()));
 	}
 
 	@Test
@@ -1699,7 +1708,7 @@ public void testV2FetchWantRefWeAlreadyHave() throws Exception {
 		// ... but the client does not need the object itself.
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
-		assertFalse(client.hasObject(one.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(one.toObjectId()));
 	}
 
 	@Test
@@ -1728,8 +1737,8 @@ public void testV2FetchWantRefAndDeepen() throws Exception {
 		assertThat(pckIn.readString(), theInstance(PacketLineIn.DELIM));
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
-		assertTrue(client.hasObject(child.toObjectId()));
-		assertFalse(client.hasObject(parent.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(child.toObjectId()));
+		assertFalse(client.getObjectDatabase().has(parent.toObjectId()));
 	}
 
 	@Test
@@ -1765,9 +1774,9 @@ public void testV2FetchMissingShallow() throws Exception {
 		assertThat(pckIn.readString(), is("packfile"));
 		parsePack(recvStream);
 
-		assertTrue(client.hasObject(one.toObjectId()));
-		assertTrue(client.hasObject(two.toObjectId()));
-		assertTrue(client.hasObject(three.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(one.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(two.toObjectId()));
+		assertTrue(client.getObjectDatabase().has(three.toObjectId()));
 	}
 
 	@Test
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorTest.java
index 9a0e7d2..754341d 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorTest.java
@@ -48,9 +48,11 @@
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
+import static org.junit.Assume.assumeNoException;
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.InvalidPathException;
 import java.security.MessageDigest;
 import java.time.Instant;
 
@@ -668,9 +670,23 @@ public void testCustomFileModeStrategyFromParentIterator() throws Exception {
 	public void testFileModeSymLinkIsNotATree() throws IOException {
 		org.junit.Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
 		FS fs = db.getFS();
-		// mål = target in swedish, just to get som unicode in here
+		// mål = target in swedish, just to get some unicode in here
 		writeTrashFile("mål/data", "targetdata");
-		fs.createSymLink(new File(trash, "länk"), "mål");
+		File file = new File(trash, "länk");
+
+		try {
+			file.toPath();
+		} catch (InvalidPathException e) {
+			// When executing a test with LANG environment variable set to non
+			// UTF-8 encoding, it seems that JRE cannot handle Unicode file
+			// paths. This happens when this test is executed in Bazel as it
+			// unsets LANG
+			// (https://docs.bazel.build/versions/master/test-encyclopedia.html#initial-conditions).
+			// Skip the test if the runtime cannot handle Unicode characters.
+			assumeNoException(e);
+		}
+
+		fs.createSymLink(file, "mål");
 		FileTreeIterator fti = new FileTreeIterator(db);
 		assertFalse(fti.eof());
 		while (!fti.getEntryPathString().equals("länk")) {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java
index 3e1202c..89a2fc4 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java
@@ -47,12 +47,14 @@
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
+import static org.junit.Assume.assumeNoException;
 import static org.junit.Assume.assumeTrue;
 
 import java.io.File;
 import java.io.IOException;
 import java.nio.charset.Charset;
 import java.nio.file.Files;
+import java.nio.file.InvalidPathException;
 import java.nio.file.Path;
 import java.nio.file.attribute.FileTime;
 import java.nio.file.attribute.PosixFileAttributeView;
@@ -103,16 +105,17 @@ public void tearDown() throws Exception {
 	public void testSymlinkAttributes() throws IOException, InterruptedException {
 		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
 		FS fs = FS.DETECTED;
-		File link = new File(trash, "ä");
-		File target = new File(trash, "å");
-		fs.createSymLink(link, "å");
+		File link = new File(trash, "a");
+		File target = new File(trash, "b");
+		fs.createSymLink(link, "b");
 		assertTrue(fs.exists(link));
 		String targetName = fs.readSymLink(link);
-		assertEquals("å", targetName);
+		assertEquals("b", targetName);
 		assertTrue(fs.lastModifiedInstant(link).compareTo(EPOCH) > 0);
 		assertTrue(fs.exists(link));
 		assertFalse(fs.canExecute(link));
-		assertEquals(2, fs.length(link));
+		// The length of a symbolic link is a length of the target file path.
+		assertEquals(1, fs.length(link));
 		assertFalse(fs.exists(target));
 		assertFalse(fs.isFile(target));
 		assertFalse(fs.isDirectory(target));
@@ -133,6 +136,32 @@ public void testSymlinkAttributes() throws IOException, InterruptedException {
 	}
 
 	@Test
+	public void testUnicodeFilePath() throws IOException {
+		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
+		FS fs = FS.DETECTED;
+		File link = new File(trash, "ä");
+		File target = new File(trash, "å");
+
+		try {
+			// Check if the runtime can support Unicode file paths.
+			link.toPath();
+			target.toPath();
+		} catch (InvalidPathException e) {
+			// When executing a test with LANG environment variable set to non
+			// UTF-8 encoding, it seems that JRE cannot handle Unicode file
+			// paths. This happens when this test is executed in Bazel as it
+			// unsets LANG
+			// (https://docs.bazel.build/versions/master/test-encyclopedia.html#initial-conditions).
+			// Skip the test if the runtime cannot handle Unicode characters.
+			assumeNoException(e);
+		}
+
+		fs.createSymLink(link, "å");
+		assertTrue(fs.exists(link));
+		assertEquals("å", fs.readSymLink(link));
+	}
+
+	@Test
 	public void testExecutableAttributes() throws Exception {
 		FS fs = FS.DETECTED.newInstance();
 		// If this assumption fails the test is halted and ignored.
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/TemporaryBufferTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/TemporaryBufferTest.java
index edcce12..9f1395b 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/TemporaryBufferTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/TemporaryBufferTest.java
@@ -404,16 +404,16 @@ public void testRandomWrites() throws IOException {
 
 	@Test
 	public void testHeap() throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		final TemporaryBuffer b = new TemporaryBuffer.Heap(2 * 8 * 1024);
-		final byte[] r = new byte[8 * 1024];
-		b.write(r);
-		b.write(r);
-		try {
-			b.write(1);
-			fail("accepted too many bytes of data");
-		} catch (IOException e) {
-			assertEquals("In-memory buffer limit exceeded", e.getMessage());
+		try (TemporaryBuffer b = new TemporaryBuffer.Heap(2 * 8 * 1024)) {
+			final byte[] r = new byte[8 * 1024];
+			b.write(r);
+			b.write(r);
+			try {
+				b.write(1);
+				fail("accepted too many bytes of data");
+			} catch (IOException e) {
+				assertEquals("In-memory buffer limit exceeded", e.getMessage());
+			}
 		}
 	}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/UnionInputStreamTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/UnionInputStreamTest.java
index a6e0eed..e38bbfe 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/UnionInputStreamTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/UnionInputStreamTest.java
@@ -69,53 +69,52 @@ public void testEmptyStream() throws IOException {
 
 	@Test
 	public void testReadSingleBytes() throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		final UnionInputStream u = new UnionInputStream();
+		try (UnionInputStream u = new UnionInputStream()) {
+			assertTrue(u.isEmpty());
+			u.add(new ByteArrayInputStream(new byte[] { 1, 0, 2 }));
+			u.add(new ByteArrayInputStream(new byte[] { 3 }));
+			u.add(new ByteArrayInputStream(new byte[] { 4, 5 }));
 
-		assertTrue(u.isEmpty());
-		u.add(new ByteArrayInputStream(new byte[] { 1, 0, 2 }));
-		u.add(new ByteArrayInputStream(new byte[] { 3 }));
-		u.add(new ByteArrayInputStream(new byte[] { 4, 5 }));
+			assertFalse(u.isEmpty());
+			assertEquals(3, u.available());
+			assertEquals(1, u.read());
+			assertEquals(0, u.read());
+			assertEquals(2, u.read());
+			assertEquals(0, u.available());
 
-		assertFalse(u.isEmpty());
-		assertEquals(3, u.available());
-		assertEquals(1, u.read());
-		assertEquals(0, u.read());
-		assertEquals(2, u.read());
-		assertEquals(0, u.available());
+			assertEquals(3, u.read());
+			assertEquals(0, u.available());
 
-		assertEquals(3, u.read());
-		assertEquals(0, u.available());
+			assertEquals(4, u.read());
+			assertEquals(1, u.available());
+			assertEquals(5, u.read());
+			assertEquals(0, u.available());
+			assertEquals(-1, u.read());
 
-		assertEquals(4, u.read());
-		assertEquals(1, u.available());
-		assertEquals(5, u.read());
-		assertEquals(0, u.available());
-		assertEquals(-1, u.read());
-
-		assertTrue(u.isEmpty());
-		u.add(new ByteArrayInputStream(new byte[] { (byte) 255 }));
-		assertEquals(255, u.read());
-		assertEquals(-1, u.read());
-		assertTrue(u.isEmpty());
+			assertTrue(u.isEmpty());
+			u.add(new ByteArrayInputStream(new byte[] { (byte) 255 }));
+			assertEquals(255, u.read());
+			assertEquals(-1, u.read());
+			assertTrue(u.isEmpty());
+		}
 	}
 
 	@Test
 	public void testReadByteBlocks() throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		final UnionInputStream u = new UnionInputStream();
-		u.add(new ByteArrayInputStream(new byte[] { 1, 0, 2 }));
-		u.add(new ByteArrayInputStream(new byte[] { 3 }));
-		u.add(new ByteArrayInputStream(new byte[] { 4, 5 }));
+		try (UnionInputStream u = new UnionInputStream()) {
+			u.add(new ByteArrayInputStream(new byte[] { 1, 0, 2 }));
+			u.add(new ByteArrayInputStream(new byte[] { 3 }));
+			u.add(new ByteArrayInputStream(new byte[] { 4, 5 }));
 
-		final byte[] r = new byte[5];
-		assertEquals(3, u.read(r, 0, 5));
-		assertTrue(Arrays.equals(new byte[] { 1, 0, 2, }, slice(r, 3)));
-		assertEquals(1, u.read(r, 0, 5));
-		assertEquals(3, r[0]);
-		assertEquals(2, u.read(r, 0, 5));
-		assertTrue(Arrays.equals(new byte[] { 4, 5, }, slice(r, 2)));
-		assertEquals(-1, u.read(r, 0, 5));
+			final byte[] r = new byte[5];
+			assertEquals(3, u.read(r, 0, 5));
+			assertTrue(Arrays.equals(new byte[] { 1, 0, 2, }, slice(r, 3)));
+			assertEquals(1, u.read(r, 0, 5));
+			assertEquals(3, r[0]);
+			assertEquals(2, u.read(r, 0, 5));
+			assertTrue(Arrays.equals(new byte[] { 4, 5, }, slice(r, 2)));
+			assertEquals(-1, u.read(r, 0, 5));
+		}
 	}
 
 	private static byte[] slice(byte[] in, int len) {
@@ -126,89 +125,88 @@ public void testReadByteBlocks() throws IOException {
 
 	@Test
 	public void testArrayConstructor() throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		final UnionInputStream u = new UnionInputStream(
+		try (UnionInputStream u = new UnionInputStream(
 				new ByteArrayInputStream(new byte[] { 1, 0, 2 }),
 				new ByteArrayInputStream(new byte[] { 3 }),
-				new ByteArrayInputStream(new byte[] { 4, 5 }));
-
-		final byte[] r = new byte[5];
-		assertEquals(3, u.read(r, 0, 5));
-		assertTrue(Arrays.equals(new byte[] { 1, 0, 2, }, slice(r, 3)));
-		assertEquals(1, u.read(r, 0, 5));
-		assertEquals(3, r[0]);
-		assertEquals(2, u.read(r, 0, 5));
-		assertTrue(Arrays.equals(new byte[] { 4, 5, }, slice(r, 2)));
-		assertEquals(-1, u.read(r, 0, 5));
+				new ByteArrayInputStream(new byte[] { 4, 5 }))) {
+			final byte[] r = new byte[5];
+			assertEquals(3, u.read(r, 0, 5));
+			assertTrue(Arrays.equals(new byte[] { 1, 0, 2, }, slice(r, 3)));
+			assertEquals(1, u.read(r, 0, 5));
+			assertEquals(3, r[0]);
+			assertEquals(2, u.read(r, 0, 5));
+			assertTrue(Arrays.equals(new byte[] { 4, 5, }, slice(r, 2)));
+			assertEquals(-1, u.read(r, 0, 5));
+		}
 	}
 
 	@Test
-	public void testMarkSupported() {
-		@SuppressWarnings("resource" /* java 7 */)
-		final UnionInputStream u = new UnionInputStream();
-		assertFalse(u.markSupported());
-		u.add(new ByteArrayInputStream(new byte[] { 1, 0, 2 }));
-		assertFalse(u.markSupported());
+	public void testMarkSupported() throws IOException {
+		try (UnionInputStream u = new UnionInputStream()) {
+			assertFalse(u.markSupported());
+			u.add(new ByteArrayInputStream(new byte[] { 1, 0, 2 }));
+			assertFalse(u.markSupported());
+		}
 	}
 
 	@Test
 	public void testSkip() throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		final UnionInputStream u = new UnionInputStream();
-		u.add(new ByteArrayInputStream(new byte[] { 1, 0, 2 }));
-		u.add(new ByteArrayInputStream(new byte[] { 3 }));
-		u.add(new ByteArrayInputStream(new byte[] { 4, 5 }));
-		assertEquals(0, u.skip(0));
-		assertEquals(3, u.skip(3));
-		assertEquals(3, u.read());
-		assertEquals(2, u.skip(5));
-		assertEquals(0, u.skip(5));
-		assertEquals(-1, u.read());
+		try (UnionInputStream u = new UnionInputStream()) {
+			u.add(new ByteArrayInputStream(new byte[] { 1, 0, 2 }));
+			u.add(new ByteArrayInputStream(new byte[] { 3 }));
+			u.add(new ByteArrayInputStream(new byte[] { 4, 5 }));
+			assertEquals(0, u.skip(0));
+			assertEquals(3, u.skip(3));
+			assertEquals(3, u.read());
+			assertEquals(2, u.skip(5));
+			assertEquals(0, u.skip(5));
+			assertEquals(-1, u.read());
 
-		u.add(new ByteArrayInputStream(new byte[] { 20, 30 }) {
-			@Override
-			@SuppressWarnings("UnsynchronizedOverridesSynchronized")
-			// This is only used in tests and is thread-safe
-			public long skip(long n) {
-				return 0;
-			}
-		});
-		assertEquals(2, u.skip(8));
-		assertEquals(-1, u.read());
+			u.add(new ByteArrayInputStream(new byte[] { 20, 30 }) {
+				@Override
+				@SuppressWarnings("UnsynchronizedOverridesSynchronized")
+				// This is only used in tests and is thread-safe
+				public long skip(long n) {
+					return 0;
+				}
+			});
+			assertEquals(2, u.skip(8));
+			assertEquals(-1, u.read());
+		}
 	}
 
 	@Test
 	public void testAutoCloseDuringRead() throws IOException {
-		@SuppressWarnings("resource" /* java 7 */)
-		final UnionInputStream u = new UnionInputStream();
-		final boolean closed[] = new boolean[2];
-		u.add(new ByteArrayInputStream(new byte[] { 1 }) {
-			@Override
-			public void close() {
-				closed[0] = true;
-			}
-		});
-		u.add(new ByteArrayInputStream(new byte[] { 2 }) {
-			@Override
-			public void close() {
-				closed[1] = true;
-			}
-		});
+		try (UnionInputStream u = new UnionInputStream()) {
+			final boolean closed[] = new boolean[2];
+			u.add(new ByteArrayInputStream(new byte[] { 1 }) {
+				@Override
+				public void close() {
+					closed[0] = true;
+				}
+			});
+			u.add(new ByteArrayInputStream(new byte[] { 2 }) {
+				@Override
+				public void close() {
+					closed[1] = true;
+				}
+			});
 
-		assertFalse(closed[0]);
-		assertFalse(closed[1]);
+			assertFalse(closed[0]);
+			assertFalse(closed[1]);
 
-		assertEquals(1, u.read());
-		assertFalse(closed[0]);
-		assertFalse(closed[1]);
+			assertEquals(1, u.read());
+			assertFalse(closed[0]);
+			assertFalse(closed[1]);
 
-		assertEquals(2, u.read());
-		assertTrue(closed[0]);
-		assertFalse(closed[1]);
+			assertEquals(2, u.read());
+			assertTrue(closed[0]);
+			assertFalse(closed[1]);
 
-		assertEquals(-1, u.read());
-		assertTrue(closed[0]);
-		assertTrue(closed[1]);
+			assertEquals(-1, u.read());
+			assertTrue(closed[0]);
+			assertTrue(closed[1]);
+		}
 	}
 
 	@Test
@@ -267,18 +265,18 @@ public int read(byte b[], int off, int len) throws IOException {
 				throw new IOException("Expected");
 			}
 		};
-		@SuppressWarnings("resource" /* java 7 */)
-		final UnionInputStream u = new UnionInputStream(
-				new ByteArrayInputStream(new byte[]{1,2,3}),
-				errorReadStream);
-		byte buf[] = new byte[10];
-		assertEquals(3, u.read(buf, 0, 10));
-		assertTrue(Arrays.equals(new byte[] {1,2,3}, slice(buf, 3)));
-		try {
-			u.read(buf, 0, 1);
-			fail("Expected exception from errorReadStream");
-		} catch (IOException e) {
-			assertEquals("Expected", e.getMessage());
+		try (UnionInputStream u = new UnionInputStream(
+				new ByteArrayInputStream(new byte[] { 1, 2, 3 }),
+				errorReadStream)) {
+			byte buf[] = new byte[10];
+			assertEquals(3, u.read(buf, 0, 10));
+			assertTrue(Arrays.equals(new byte[] { 1, 2, 3 }, slice(buf, 3)));
+			try {
+				u.read(buf, 0, 1);
+				fail("Expected exception from errorReadStream");
+			} catch (IOException e) {
+				assertEquals("Expected", e.getMessage());
+			}
 		}
 	}
 }
diff --git a/org.eclipse.jgit.ui/META-INF/MANIFEST.MF b/org.eclipse.jgit.ui/META-INF/MANIFEST.MF
index 380de32..7e0d1b8 100644
--- a/org.eclipse.jgit.ui/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.ui/META-INF/MANIFEST.MF
@@ -4,14 +4,14 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.ui
 Bundle-SymbolicName: org.eclipse.jgit.ui
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Vendor: %provider_name
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Export-Package: org.eclipse.jgit.awtui;version="5.2.3"
-Import-Package: org.eclipse.jgit.errors;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.lib;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.nls;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revplot;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.revwalk;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.transport;version="[5.2.3,5.3.0)",
- org.eclipse.jgit.util;version="[5.2.3,5.3.0)"
+Export-Package: org.eclipse.jgit.awtui;version="5.3.6"
+Import-Package: org.eclipse.jgit.errors;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.lib;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.nls;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revplot;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.revwalk;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.transport;version="[5.3.6,5.4.0)",
+ org.eclipse.jgit.util;version="[5.3.6,5.4.0)"
diff --git a/org.eclipse.jgit.ui/pom.xml b/org.eclipse.jgit.ui/pom.xml
index 0cb3d65..934149d 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-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 857fcac..14856a2 100644
--- a/org.eclipse.jgit/.settings/.api_filters
+++ b/org.eclipse.jgit/.settings/.api_filters
@@ -34,28 +34,6 @@
             </message_arguments>
         </filter>
     </resource>
-    <resource path="src/org/eclipse/jgit/gitrepo/RepoCommand.java" type="org.eclipse.jgit.gitrepo.RepoCommand$DefaultRemoteReader">
-        <filter id="338792546">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.gitrepo.RepoCommand.DefaultRemoteReader"/>
-                <message_argument value="readFile(String, String, String)"/>
-            </message_arguments>
-        </filter>
-        <filter id="338792546">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.gitrepo.RepoCommand.DefaultRemoteReader"/>
-                <message_argument value="readFileFromRepo(Repository, String, String)"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/gitrepo/RepoCommand.java" type="org.eclipse.jgit.gitrepo.RepoCommand$RemoteReader">
-        <filter id="403804204">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.gitrepo.RepoCommand.RemoteReader"/>
-                <message_argument value="readFileWithMode(String, String, String)"/>
-            </message_arguments>
-        </filter>
-    </resource>
     <resource path="src/org/eclipse/jgit/lib/ConfigConstants.java" type="org.eclipse.jgit.lib.ConfigConstants">
         <filter id="1142947843">
             <message_arguments>
@@ -76,39 +54,33 @@
             </message_arguments>
         </filter>
     </resource>
-    <resource path="src/org/eclipse/jgit/lib/GitmoduleEntry.java" type="org.eclipse.jgit.lib.GitmoduleEntry">
-        <filter id="1109393411">
+    <resource path="src/org/eclipse/jgit/lib/ObjectIdRef.java" type="org.eclipse.jgit.lib.ObjectIdRef">
+        <filter id="338722907">
             <message_arguments>
-                <message_argument value="4.7.5"/>
-                <message_argument value="org.eclipse.jgit.lib.GitmoduleEntry"/>
+                <message_argument value="org.eclipse.jgit.lib.ObjectIdRef"/>
+                <message_argument value="ObjectIdRef(Ref.Storage, String, ObjectId)"/>
             </message_arguments>
         </filter>
     </resource>
-    <resource path="src/org/eclipse/jgit/lib/ObjectChecker.java" type="org.eclipse.jgit.lib.ObjectChecker">
-        <filter id="1142947843">
+    <resource path="src/org/eclipse/jgit/lib/Ref.java" type="org.eclipse.jgit.lib.Ref">
+        <filter id="404000815">
             <message_arguments>
-                <message_argument value="4.7.5"/>
-                <message_argument value="getGitsubmodules()"/>
+                <message_argument value="org.eclipse.jgit.lib.Ref"/>
+                <message_argument value="getUpdateIndex()"/>
             </message_arguments>
         </filter>
     </resource>
-    <resource path="src/org/eclipse/jgit/revwalk/DepthWalk.java" type="org.eclipse.jgit.revwalk.DepthWalk">
-        <filter id="403804204">
+    <resource path="src/org/eclipse/jgit/lib/RefDatabase.java" type="org.eclipse.jgit.lib.RefDatabase">
+        <filter id="421650549">
             <message_arguments>
-                <message_argument value="org.eclipse.jgit.revwalk.DepthWalk"/>
-                <message_argument value="getDeepenNotFlag()"/>
+                <message_argument value="org.eclipse.jgit.lib.RefDatabase"/>
+                <message_argument value="exactRef(String)"/>
             </message_arguments>
         </filter>
-        <filter id="404000815">
+        <filter id="421654647">
             <message_arguments>
-                <message_argument value="org.eclipse.jgit.revwalk.DepthWalk"/>
-                <message_argument value="getDeepenNots()"/>
-            </message_arguments>
-        </filter>
-        <filter id="404000815">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.revwalk.DepthWalk"/>
-                <message_argument value="getDeepenSince()"/>
+                <message_argument value="org.eclipse.jgit.lib.RefDatabase"/>
+                <message_argument value="getRef(String)"/>
             </message_arguments>
         </filter>
     </resource>
@@ -168,11 +140,41 @@
             </message_arguments>
         </filter>
     </resource>
-    <resource path="src/org/eclipse/jgit/transport/RemoteSession.java" type="org.eclipse.jgit.transport.RemoteSession">
-        <filter id="404000815">
+    <resource path="src/org/eclipse/jgit/transport/BaseReceivePack.java" type="org.eclipse.jgit.transport.BaseReceivePack">
+        <filter id="421650549">
             <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.RemoteSession"/>
-                <message_argument value="getFtpChannel()"/>
+                <message_argument value="org.eclipse.jgit.transport.BaseReceivePack"/>
+                <message_argument value="getAdvertisedRefs()"/>
+            </message_arguments>
+        </filter>
+        <filter id="421650549">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.transport.BaseReceivePack"/>
+                <message_argument value="getPushCertificate()"/>
+            </message_arguments>
+        </filter>
+        <filter id="421650549">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.transport.BaseReceivePack"/>
+                <message_argument value="getRepository()"/>
+            </message_arguments>
+        </filter>
+        <filter id="421650549">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.transport.BaseReceivePack"/>
+                <message_argument value="getRevWalk()"/>
+            </message_arguments>
+        </filter>
+        <filter id="421650549">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.transport.BaseReceivePack"/>
+                <message_argument value="setAdvertisedRefs(Map&lt;String,Ref&gt;, Set&lt;ObjectId&gt;)"/>
+            </message_arguments>
+        </filter>
+        <filter id="421650549">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.transport.BaseReceivePack"/>
+                <message_argument value="setPushCertificate(PushCertificate)"/>
             </message_arguments>
         </filter>
     </resource>
@@ -190,14 +192,6 @@
             </message_arguments>
         </filter>
     </resource>
-    <resource path="src/org/eclipse/jgit/transport/http/HttpConnection.java" type="org.eclipse.jgit.transport.http.HttpConnection">
-        <filter id="403804204">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.http.HttpConnection"/>
-                <message_argument value="getHeaderFields(String)"/>
-            </message_arguments>
-        </filter>
-    </resource>
     <resource path="src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java" type="org.eclipse.jgit.treewalk.WorkingTreeIterator">
         <filter id="1142947843">
             <message_arguments>
diff --git a/org.eclipse.jgit/BUILD b/org.eclipse.jgit/BUILD
index 0549b23..c7d9fde 100644
--- a/org.eclipse.jgit/BUILD
+++ b/org.eclipse.jgit/BUILD
@@ -24,6 +24,9 @@
     resources = RESOURCES,
     deps = [
         ":insecure_cipher_factory",
+        "//lib:bcpg",
+        "//lib:bcpkix",
+        "//lib:bcprov",
         "//lib:javaewah",
         "//lib:jsch",
         "//lib:jzlib",
diff --git a/org.eclipse.jgit/META-INF/MANIFEST.MF b/org.eclipse.jgit/META-INF/MANIFEST.MF
index 66701b0..aca44a7 100644
--- a/org.eclipse.jgit/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit/META-INF/MANIFEST.MF
@@ -3,12 +3,12 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit
 Bundle-SymbolicName: org.eclipse.jgit
-Bundle-Version: 5.2.3.qualifier
+Bundle-Version: 5.3.6.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
-Export-Package: org.eclipse.jgit.annotations;version="5.2.3",
- org.eclipse.jgit.api;version="5.2.3";
+Export-Package: org.eclipse.jgit.annotations;version="5.3.6",
+ org.eclipse.jgit.api;version="5.3.6";
   uses:="org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.diff,
@@ -22,53 +22,53 @@
    org.eclipse.jgit.submodule,
    org.eclipse.jgit.transport,
    org.eclipse.jgit.merge",
- org.eclipse.jgit.api.errors;version="5.2.3";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.errors",
- org.eclipse.jgit.attributes;version="5.2.3",
- org.eclipse.jgit.blame;version="5.2.3";
+ org.eclipse.jgit.api.errors;version="5.3.6";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.errors",
+ org.eclipse.jgit.attributes;version="5.3.6",
+ org.eclipse.jgit.blame;version="5.3.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.diff",
- org.eclipse.jgit.diff;version="5.2.3";
+ org.eclipse.jgit.diff;version="5.3.6";
   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="5.2.3";
+ org.eclipse.jgit.dircache;version="5.3.6";
   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="5.2.3";
+ org.eclipse.jgit.errors;version="5.3.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.internal.storage.pack,
    org.eclipse.jgit.transport,
    org.eclipse.jgit.dircache",
- org.eclipse.jgit.events;version="5.2.3";uses:="org.eclipse.jgit.lib",
- org.eclipse.jgit.fnmatch;version="5.2.3",
- org.eclipse.jgit.gitrepo;version="5.2.3";
+ org.eclipse.jgit.events;version="5.3.6";uses:="org.eclipse.jgit.lib",
+ org.eclipse.jgit.fnmatch;version="5.3.6",
+ org.eclipse.jgit.gitrepo;version="5.3.6";
   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="5.2.3";x-internal:=true,
- org.eclipse.jgit.hooks;version="5.2.3";uses:="org.eclipse.jgit.lib",
- org.eclipse.jgit.ignore;version="5.2.3",
- org.eclipse.jgit.ignore.internal;version="5.2.3";x-friends:="org.eclipse.jgit.test",
- org.eclipse.jgit.internal;version="5.2.3";x-friends:="org.eclipse.jgit.test,org.eclipse.jgit.http.test",
- org.eclipse.jgit.internal.fsck;version="5.2.3";x-friends:="org.eclipse.jgit.test",
- org.eclipse.jgit.internal.ketch;version="5.2.3";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.internal.revwalk;version="5.2.3";x-internal:=true,
- org.eclipse.jgit.internal.storage.dfs;version="5.2.3";
+ org.eclipse.jgit.gitrepo.internal;version="5.3.6";x-internal:=true,
+ org.eclipse.jgit.hooks;version="5.3.6";uses:="org.eclipse.jgit.lib",
+ org.eclipse.jgit.ignore;version="5.3.6",
+ org.eclipse.jgit.ignore.internal;version="5.3.6";x-friends:="org.eclipse.jgit.test",
+ org.eclipse.jgit.internal;version="5.3.6";x-friends:="org.eclipse.jgit.test,org.eclipse.jgit.http.test",
+ org.eclipse.jgit.internal.fsck;version="5.3.6";x-friends:="org.eclipse.jgit.test",
+ org.eclipse.jgit.internal.ketch;version="5.3.6";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.revwalk;version="5.3.6";x-internal:=true,
+ org.eclipse.jgit.internal.storage.dfs;version="5.3.6";
   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="5.2.3";
+ org.eclipse.jgit.internal.storage.file;version="5.3.6";
   x-friends:="org.eclipse.jgit.test,
    org.eclipse.jgit.junit,
    org.eclipse.jgit.junit.http,
@@ -77,18 +77,18 @@
    org.eclipse.jgit.pgm,
    org.eclipse.jgit.pgm.test,
    org.eclipse.jgit.ssh.apache",
- org.eclipse.jgit.internal.storage.io;version="5.2.3";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.internal.storage.pack;version="5.2.3";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.internal.storage.reftable;version="5.2.3";
+ org.eclipse.jgit.internal.storage.io;version="5.3.6";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.storage.pack;version="5.3.6";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.storage.reftable;version="5.3.6";
   x-friends:="org.eclipse.jgit.http.test,
    org.eclipse.jgit.junit,
    org.eclipse.jgit.test,
    org.eclipse.jgit.pgm",
- org.eclipse.jgit.internal.storage.reftree;version="5.2.3";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.internal.submodule;version="5.2.3";x-internal:=true,
- org.eclipse.jgit.internal.transport.parser;version="5.2.3";x-friends:="org.eclipse.jgit.test,org.eclipse.jgit.http.server",
- org.eclipse.jgit.internal.transport.ssh;version="5.2.3";x-friends:="org.eclipse.jgit.ssh.apache",
- org.eclipse.jgit.lib;version="5.2.3";
+ org.eclipse.jgit.internal.storage.reftree;version="5.3.6";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.submodule;version="5.3.6";x-internal:=true,
+ org.eclipse.jgit.internal.transport.parser;version="5.3.6";x-friends:="org.eclipse.jgit.http.server,org.eclipse.jgit.test",
+ org.eclipse.jgit.internal.transport.ssh;version="5.3.6";x-friends:="org.eclipse.jgit.ssh.apache",
+ org.eclipse.jgit.lib;version="5.3.6";
   uses:="org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.util,
@@ -98,33 +98,33 @@
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.transport,
    org.eclipse.jgit.submodule",
- org.eclipse.jgit.lib.internal;version="5.2.3";x-internal:=true,
- org.eclipse.jgit.merge;version="5.2.3";
+ org.eclipse.jgit.lib.internal;version="5.3.6";x-internal:=true,
+ org.eclipse.jgit.merge;version="5.3.6";
   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="5.2.3",
- org.eclipse.jgit.notes;version="5.2.3";
+ org.eclipse.jgit.nls;version="5.3.6",
+ org.eclipse.jgit.notes;version="5.3.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.merge",
- org.eclipse.jgit.patch;version="5.2.3";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.diff",
- org.eclipse.jgit.revplot;version="5.2.3";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.revwalk",
- org.eclipse.jgit.revwalk;version="5.2.3";
+ org.eclipse.jgit.patch;version="5.3.6";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.diff",
+ org.eclipse.jgit.revplot;version="5.3.6";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.revwalk",
+ org.eclipse.jgit.revwalk;version="5.3.6";
   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="5.2.3";uses:="org.eclipse.jgit.revwalk,org.eclipse.jgit.lib,org.eclipse.jgit.util",
- org.eclipse.jgit.storage.file;version="5.2.3";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.util",
- org.eclipse.jgit.storage.pack;version="5.2.3";uses:="org.eclipse.jgit.lib",
- org.eclipse.jgit.submodule;version="5.2.3";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.treewalk.filter,org.eclipse.jgit.treewalk",
- org.eclipse.jgit.transport;version="5.2.3";
+ org.eclipse.jgit.revwalk.filter;version="5.3.6";uses:="org.eclipse.jgit.revwalk,org.eclipse.jgit.lib,org.eclipse.jgit.util",
+ org.eclipse.jgit.storage.file;version="5.3.6";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.util",
+ org.eclipse.jgit.storage.pack;version="5.3.6";uses:="org.eclipse.jgit.lib",
+ org.eclipse.jgit.submodule;version="5.3.6";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.treewalk.filter,org.eclipse.jgit.treewalk",
+ org.eclipse.jgit.transport;version="5.3.6";
   uses:="org.eclipse.jgit.transport.resolver,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.internal.storage.pack,
@@ -132,33 +132,44 @@
    org.eclipse.jgit.util,
    org.eclipse.jgit.util.io,
    org.eclipse.jgit.internal.storage.file,
+   org.eclipse.jgit.internal.transport.parser,
    org.eclipse.jgit.lib,
    org.eclipse.jgit.transport.http,
    org.eclipse.jgit.errors,
    org.eclipse.jgit.storage.pack",
- org.eclipse.jgit.transport.http;version="5.2.3";uses:="javax.net.ssl",
- org.eclipse.jgit.transport.resolver;version="5.2.3";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.transport",
- org.eclipse.jgit.treewalk;version="5.2.3";
+ org.eclipse.jgit.transport.http;version="5.3.6";uses:="javax.net.ssl",
+ org.eclipse.jgit.transport.resolver;version="5.3.6";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.transport",
+ org.eclipse.jgit.treewalk;version="5.3.6";
   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="5.2.3";uses:="org.eclipse.jgit.treewalk",
- org.eclipse.jgit.util;version="5.2.3";
+ org.eclipse.jgit.treewalk.filter;version="5.3.6";uses:="org.eclipse.jgit.treewalk",
+ org.eclipse.jgit.util;version="5.3.6";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.transport.http,
    org.eclipse.jgit.storage.file,
    org.ietf.jgss",
- org.eclipse.jgit.util.io;version="5.2.3",
- org.eclipse.jgit.util.sha1;version="5.2.3",
- org.eclipse.jgit.util.time;version="5.2.3"
+ org.eclipse.jgit.util.io;version="5.3.6",
+ org.eclipse.jgit.util.sha1;version="5.3.6",
+ org.eclipse.jgit.util.time;version="5.3.6"
 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)",
  javax.crypto,
  javax.net.ssl,
+ org.bouncycastle;version="[1.60.0,2.0.0)",
+ org.bouncycastle.bcpg;version="[1.60.0,2.0.0)",
+ org.bouncycastle.gpg;version="[1.60.0,2.0.0)",
+ org.bouncycastle.gpg.keybox;version="[1.60.0,2.0.0)",
+ org.bouncycastle.jce.provider;version="[1.60.0,2.0.0)",
+ org.bouncycastle.openpgp;version="[1.60.0,2.0.0)",
+ org.bouncycastle.openpgp.jcajce;version="[1.60.0,2.0.0)",
+ org.bouncycastle.openpgp.operator;version="[1.60.0,2.0.0)",
+ org.bouncycastle.openpgp.operator.jcajce;version="[1.60.0,2.0.0)",
+ org.bouncycastle.util.encoders;version="[1.60.0,2.0.0)",
  org.slf4j;version="[1.7.0,2.0.0)",
  org.xml.sax,
  org.xml.sax.helpers
diff --git a/org.eclipse.jgit/META-INF/SOURCE-MANIFEST.MF b/org.eclipse.jgit/META-INF/SOURCE-MANIFEST.MF
index 8e22086..70b4c8f 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: 5.2.3.qualifier
-Eclipse-SourceBundle: org.eclipse.jgit;version="5.2.3.qualifier";roots="."
+Bundle-Version: 5.3.6.qualifier
+Eclipse-SourceBundle: org.eclipse.jgit;version="5.3.6.qualifier";roots="."
diff --git a/org.eclipse.jgit/pom.xml b/org.eclipse.jgit/pom.xml
index c30d648..8a14e6a 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>5.2.3-SNAPSHOT</version>
+    <version>5.3.6-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit</artifactId>
@@ -84,12 +84,26 @@
       <artifactId>JavaEWAH</artifactId>
     </dependency>
 
-
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>slf4j-api</artifactId>
     </dependency>
 
+    <dependency>
+      <groupId>org.bouncycastle</groupId>
+      <artifactId>bcpg-jdk15on</artifactId>
+    </dependency>
+
+    <dependency>
+      <groupId>org.bouncycastle</groupId>
+      <artifactId>bcprov-jdk15on</artifactId>
+    </dependency>
+
+    <dependency>
+      <groupId>org.bouncycastle</groupId>
+      <artifactId>bcpkix-jdk15on</artifactId>
+    </dependency>
+
   </dependencies>
 
   <build>
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 ebb0414..c41a565 100644
--- a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
+++ b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
@@ -196,6 +196,7 @@
 createNewFileFailed=Could not create new file {0}
 createRequiresZeroOldId=Create requires old ID to be zero
 credentialPassword=Password
+credentialPassphrase=Passphrase
 credentialUsername=Username
 daemonAlreadyRunning=Daemon already running
 daysAgo={0} days ago
@@ -289,6 +290,14 @@
 funnyRefname=funny refname
 gcFailed=Garbage collection failed.
 gcTooManyUnpruned=Too many loose, unpruneable objects after garbage collection.  Consider adjusting gc.auto or gc.pruneExpire.
+gpgFailedToParseSecretKey=Failed to parse secret key file in directory: {0}. Is the entered passphrase correct?
+gpgNoCredentialsProvider=missing credentials provider
+gpgNoKeyring=neither pubring.kbx nor secring.gpg files found
+gpgNoKeyInLegacySecring=no matching secret key found in legacy secring.gpg for key or user id: {0}
+gpgNoPublicKeyFound=Unable to find a public-key with key or user id: {0}
+gpgNoSecretKeyForPublicKey=unable to find associated secret key for public key: {0}
+gpgKeyInfo=GPG Key (fingerprint {0})
+gpgSigningCancelled=Signing was cancelled
 headRequiredToStash=HEAD required to stash local changes
 hoursAgo={0} hours ago
 httpConfigCannotNormalizeURL=Cannot normalize URL path {0}: too many .. segments
@@ -456,6 +465,7 @@
 oldIdMustNotBeNull=Expected old ID must not be null
 onlyOneFetchSupported=Only one fetch supported
 onlyOneOperationCallPerConnectionIsSupported=Only one operation call per connection is supported.
+onlyOpenPgpSupportedForSigning=OpenPGP is the only supported signing option with JGit at this time (gpg.format must be set to openpgp).
 openFilesMustBeAtLeast1=Open files must be >= 1
 openingConnection=Opening connection
 operationCanceled=Operation {0} was canceled
@@ -531,8 +541,9 @@
 remoteDoesNotHaveSpec=Remote does not have {0} available for fetch.
 remoteDoesNotSupportSmartHTTPPush=remote does not support smart HTTP push
 remoteHungUpUnexpectedly=remote hung up unexpectedly
-remoteNameCantBeNull=Remote name can't be null.
-renameBranchFailedBecauseTag=Can not rename as Ref {0} is a tag
+remoteNameCannotBeNull=Remote name cannot be null.
+renameBranchFailedAmbiguous=Cannot rename branch {0}; name is ambiguous: {1} or {2}
+renameBranchFailedNotABranch=Cannot rename {0}: this is not a branch
 renameBranchFailedUnknownReason=Rename failed with unknown reason
 renameBranchUnexpectedResult=Unexpected rename result {0}
 renameCancelled=Rename detection was cancelled
@@ -572,7 +583,7 @@
 sequenceTooLargeForDiffAlgorithm=Sequence too large for difference algorithm.
 serviceNotEnabledNoName=Service not enabled
 serviceNotPermitted={1} not permitted on ''{0}''
-sha1CollisionDetected1=SHA-1 collision detected on {0}
+sha1CollisionDetected=SHA-1 collision detected on {0}
 shallowCommitsAlreadyInitialized=Shallow commits have already been initialized
 shallowPacksRequireDepthWalk=Shallow packs require a DepthWalk
 shortCompressedStreamAt=Short compressed stream at {0}
@@ -663,6 +674,7 @@
 unableToReadPackfile=Unable to read packfile {0}
 unableToRemovePath=Unable to remove path ''{0}''
 unableToWrite=Unable to write {0}
+unableToSignCommitNoSecretKey=Unable to sign commit. Signing key not available.
 unauthorized=Unauthorized
 unencodeableFile=Unencodable file: {0}
 unexpectedCompareResult=Unexpected metadata comparison result: {0}
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 455a2e6..e05f6f1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
@@ -162,7 +162,9 @@ private Stage(int number) {
 
 	private String name;
 
-	private boolean force = false;
+	private boolean forceRefUpdate = false;
+
+	private boolean forced = false;
 
 	private boolean createBranch = false;
 
@@ -269,7 +271,11 @@ public Ref call() throws GitAPIException, RefAlreadyExistsException,
 			try {
 				dco = new DirCacheCheckout(repo, headTree, dc,
 						newCommit.getTree());
-				dco.setFailOnConflict(!force);
+				dco.setFailOnConflict(true);
+				dco.setForce(forced);
+				if (forced) {
+					dco.setFailOnConflict(false);
+				}
 				dco.setProgressMonitor(monitor);
 				try {
 					dco.checkout();
@@ -286,7 +292,7 @@ public Ref call() throws GitAPIException, RefAlreadyExistsException,
 				ref = null;
 			String toName = Repository.shortenRefName(name);
 			RefUpdate refUpdate = repo.updateRef(Constants.HEAD, ref == null);
-			refUpdate.setForceUpdate(force);
+			refUpdate.setForceUpdate(forceRefUpdate);
 			refUpdate.setRefLogMessage(refLogMessage + " to " + toName, false); //$NON-NLS-1$
 			Result updateResult;
 			if (ref != null)
@@ -666,10 +672,54 @@ public CheckoutCommand setOrphan(boolean orphan) {
 	 *            set to a new start-point; if false, the existing branch will
 	 *            not be changed
 	 * @return this instance
+	 * @deprecated this method was badly named comparing its semantics to native
+	 *             git's checkout --force option, use
+	 *             {@link #setForceRefUpdate(boolean)} instead
 	 */
+	@Deprecated
 	public CheckoutCommand setForce(boolean force) {
+		return setForceRefUpdate(force);
+	}
+
+	/**
+	 * Specify to force the ref update in case of a branch switch.
+	 *
+	 * In releases prior to 5.2 this method was called setForce() but this name
+	 * was misunderstood to implement native git's --force option, which is not
+	 * true.
+	 *
+	 * @param forceRefUpdate
+	 *            if <code>true</code> and the branch with the given name
+	 *            already exists, the start-point of an existing branch will be
+	 *            set to a new start-point; if false, the existing branch will
+	 *            not be changed
+	 * @return this instance
+	 * @since 5.3
+	 */
+	public CheckoutCommand setForceRefUpdate(boolean forceRefUpdate) {
 		checkCallable();
-		this.force = force;
+		this.forceRefUpdate = forceRefUpdate;
+		return this;
+	}
+
+	/**
+	 * Allow a checkout even if the workingtree or index differs from HEAD. This
+	 * matches native git's '--force' option.
+	 *
+	 * JGit releases before 5.2 had a method <code>setForce()</code> offering
+	 * semantics different from this new <code>setForced()</code>. This old
+	 * semantic can now be found in {@link #setForceRefUpdate(boolean)}
+	 *
+	 * @param forced
+	 *            if set to <code>true</code> then allow the checkout even if
+	 *            workingtree or index doesn't match HEAD. Overwrite workingtree
+	 *            files and index content with the new content in this case.
+	 * @return this instance
+	 * @since 5.3
+	 */
+	public CheckoutCommand setForced(boolean forced) {
+		checkCallable();
+		this.forced = forced;
 		return this;
 	}
 
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 10a54ee..9f63d0f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
@@ -303,18 +303,25 @@ private FetchResult fetch(Repository clonedRepo, URIish u)
 	}
 
 	private List<RefSpec> calculateRefSpecs(boolean fetchAll, String dst) {
-		RefSpec wcrs = new RefSpec();
-		wcrs = wcrs.setForceUpdate(true);
-		wcrs = wcrs.setSourceDestination(Constants.R_HEADS + '*', dst);
+		RefSpec heads = new RefSpec();
+		heads = heads.setForceUpdate(true);
+		heads = heads.setSourceDestination(Constants.R_HEADS + '*', dst);
 		List<RefSpec> specs = new ArrayList<>();
 		if (!fetchAll) {
+			RefSpec tags = new RefSpec();
+			tags = tags.setForceUpdate(true);
+			tags = tags.setSourceDestination(Constants.R_TAGS + '*',
+					Constants.R_TAGS + '*');
 			for (String selectedRef : branchesToClone) {
-				if (wcrs.matchSource(selectedRef)) {
-					specs.add(wcrs.expandFromSource(selectedRef));
+				if (heads.matchSource(selectedRef)) {
+					specs.add(heads.expandFromSource(selectedRef));
+				} else if (tags.matchSource(selectedRef)) {
+					specs.add(tags.expandFromSource(selectedRef));
 				}
 			}
 		} else {
-			specs.add(wcrs);
+			// We'll fetch the tags anyway.
+			specs.add(heads);
 		}
 		return specs;
 	}
@@ -590,11 +597,15 @@ public CloneCommand setProgressMonitor(ProgressMonitor monitor) {
 	}
 
 	/**
-	 * Set whether all branches have to be fetched
+	 * Set whether all branches have to be fetched.
+	 * <p>
+	 * If {@code false}, use {@link #setBranchesToClone(Collection)} to define
+	 * what will be cloned. If neither are set, all branches will be cloned.
+	 * </p>
 	 *
 	 * @param cloneAllBranches
-	 *            true when all branches have to be fetched (indicates wildcard
-	 *            in created fetch refspec), false otherwise.
+	 *            {@code true} when all branches have to be fetched (indicates
+	 *            wildcard in created fetch refspec), {@code false} otherwise.
 	 * @return {@code this}
 	 */
 	public CloneCommand setCloneAllBranches(boolean cloneAllBranches) {
@@ -616,12 +627,17 @@ public CloneCommand setCloneSubmodules(boolean cloneSubmodules) {
 	}
 
 	/**
-	 * Set branches to clone
+	 * Set the branches or tags to clone.
+	 * <p>
+	 * This is ignored if {@link #setCloneAllBranches(boolean)
+	 * setCloneAllBranches(true)} is used. If {@code branchesToClone} is
+	 * {@code null} or empty, it's also ignored and all branches will be cloned.
+	 * </p>
 	 *
 	 * @param branchesToClone
-	 *            collection of branches to clone. Ignored when allSelected is
-	 *            true. Must be specified as full ref names (e.g.
-	 *            <code>refs/heads/master</code>).
+	 *            collection of branches to clone. Must be specified as full ref
+	 *            names (e.g. {@code refs/heads/master} or
+	 *            {@code refs/tags/v1.0.0}).
 	 * @return {@code this}
 	 */
 	public CloneCommand setBranchesToClone(Collection<String> branchesToClone) {
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 cea28fa..61d51cc 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
@@ -61,6 +61,7 @@
 import org.eclipse.jgit.api.errors.NoHeadException;
 import org.eclipse.jgit.api.errors.NoMessageException;
 import org.eclipse.jgit.api.errors.UnmergedPathsException;
+import org.eclipse.jgit.api.errors.UnsupportedSigningFormatException;
 import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheBuildIterator;
@@ -76,6 +77,9 @@
 import org.eclipse.jgit.lib.CommitBuilder;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
+import org.eclipse.jgit.lib.GpgConfig;
+import org.eclipse.jgit.lib.GpgConfig.GpgFormat;
+import org.eclipse.jgit.lib.GpgSigner;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectInserter;
 import org.eclipse.jgit.lib.PersonIdent;
@@ -84,10 +88,12 @@
 import org.eclipse.jgit.lib.RefUpdate.Result;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.RepositoryState;
+import org.eclipse.jgit.lib.internal.BouncyCastleGpgSigner;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevObject;
 import org.eclipse.jgit.revwalk.RevTag;
 import org.eclipse.jgit.revwalk.RevWalk;
+import org.eclipse.jgit.transport.CredentialsProvider;
 import org.eclipse.jgit.treewalk.CanonicalTreeParser;
 import org.eclipse.jgit.treewalk.FileTreeIterator;
 import org.eclipse.jgit.treewalk.TreeWalk;
@@ -139,6 +145,14 @@ public class CommitCommand extends GitCommand<RevCommit> {
 
 	private Boolean allowEmpty;
 
+	private Boolean signCommit;
+
+	private String signingKey;
+
+	private GpgSigner gpgSigner;
+
+	private CredentialsProvider credentialsProvider;
+
 	/**
 	 * Constructor for CommitCommand
 	 *
@@ -147,6 +161,7 @@ public class CommitCommand extends GitCommand<RevCommit> {
 	 */
 	protected CommitCommand(Repository repo) {
 		super(repo);
+		this.credentialsProvider = CredentialsProvider.getDefault();
 	}
 
 	/**
@@ -251,6 +266,12 @@ public RevCommit call() throws GitAPIException, NoHeadException,
 
 				commit.setParentIds(parents);
 				commit.setTreeId(indexTreeId);
+
+				if (signCommit.booleanValue()) {
+					gpgSigner.sign(commit, signingKey, committer,
+							credentialsProvider);
+				}
+
 				ObjectId commitId = odi.insert(commit);
 				odi.flush();
 
@@ -517,9 +538,10 @@ private int lookupOnly(String pathString) {
 	 *
 	 * @throws NoMessageException
 	 *             if the commit message has not been specified
+	 * @throws UnsupportedSigningFormatException if the configured gpg.format is not supported
 	 */
 	private void processOptions(RepositoryState state, RevWalk rw)
-			throws NoMessageException {
+			throws NoMessageException, UnsupportedSigningFormatException {
 		if (committer == null)
 			committer = new PersonIdent(repo);
 		if (author == null && !amend)
@@ -572,6 +594,25 @@ private void processOptions(RepositoryState state, RevWalk rw)
 			// as long as we don't support -C option we have to have
 			// an explicit message
 			throw new NoMessageException(JGitText.get().commitMessageNotSpecified);
+
+		GpgConfig gpgConfig = new GpgConfig(repo.getConfig());
+		if (signCommit == null) {
+			signCommit = gpgConfig.isSignCommits() ? Boolean.TRUE
+					: Boolean.FALSE;
+		}
+		if (signingKey == null) {
+			signingKey = gpgConfig.getSigningKey();
+		}
+		if (gpgSigner == null) {
+			if (gpgConfig.getKeyFormat() != GpgFormat.OPENPGP) {
+				throw new UnsupportedSigningFormatException(
+						JGitText.get().onlyOpenPgpSupportedForSigning);
+			}
+			gpgSigner = GpgSigner.getDefault();
+			if (gpgSigner == null) {
+				gpgSigner = new BouncyCastleGpgSigner();
+			}
+		}
 	}
 
 	private boolean isMergeDuringRebase(RepositoryState state) {
@@ -873,4 +914,55 @@ public CommitCommand setHookOutputStream(String hookName,
 		hookOutRedirect.put(hookName, hookStdOut);
 		return this;
 	}
+
+	/**
+	 * Sets the signing key
+	 * <p>
+	 * Per spec of user.signingKey: this will be sent to the GPG program as is,
+	 * i.e. can be anything supported by the GPG program.
+	 * </p>
+	 * <p>
+	 * Note, if none was set or <code>null</code> is specified a default will be
+	 * obtained from the configuration.
+	 * </p>
+	 *
+	 * @param signingKey
+	 *            signing key (maybe <code>null</code>)
+	 * @return {@code this}
+	 * @since 5.3
+	 */
+	public CommitCommand setSigningKey(String signingKey) {
+		checkCallable();
+		this.signingKey = signingKey;
+		return this;
+	}
+
+	/**
+	 * Sets whether the commit should be signed.
+	 *
+	 * @param sign
+	 *            <code>true</code> to sign, <code>false</code> to not sign and
+	 *            <code>null</code> for default behavior (read from
+	 *            configuration)
+	 * @return {@code this}
+	 * @since 5.3
+	 */
+	public CommitCommand setSign(Boolean sign) {
+		checkCallable();
+		this.signCommit = sign;
+		return this;
+	}
+
+	/**
+	 * Sets a {@link CredentialsProvider}
+	 *
+	 * @param credentialsProvider
+	 *            the provider to use when querying for credentials (eg., during
+	 *            signing)
+	 * @since 5.3
+	 */
+	public void setCredentialsProvider(
+			CredentialsProvider credentialsProvider) {
+		this.credentialsProvider = credentialsProvider;
+	}
 }
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 73e93a1..2c9c5f2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
@@ -193,7 +193,8 @@ private void fetchSubmodules(FetchResult results)
 					// updated to an object that is not currently present in the
 					// submodule.
 					if ((recurseMode == FetchRecurseSubmodulesMode.ON_DEMAND
-							&& !submoduleRepo.hasObject(walk.getObjectId()))
+							&& !submoduleRepo.getObjectDatabase()
+									.has(walk.getObjectId()))
 							|| recurseMode == FetchRecurseSubmodulesMode.YES) {
 						FetchCommand f = new FetchCommand(submoduleRepo)
 								.setProgressMonitor(monitor)
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 9653c36..0e3d000 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
@@ -158,11 +158,14 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 
 	private static final String ONTO = "onto"; //$NON-NLS-1$
 
-	private static final String ONTO_NAME = "onto-name"; //$NON-NLS-1$
+	private static final String ONTO_NAME = "onto_name"; //$NON-NLS-1$
 
 	private static final String PATCH = "patch"; //$NON-NLS-1$
 
-	private static final String REBASE_HEAD = "head"; //$NON-NLS-1$
+	private static final String REBASE_HEAD = "orig-head"; //$NON-NLS-1$
+
+	/** Pre git 1.7.6 file name for {@link #REBASE_HEAD}. */
+	private static final String REBASE_HEAD_LEGACY = "head"; //$NON-NLS-1$
 
 	private static final String AMEND = "amend"; //$NON-NLS-1$
 
@@ -177,6 +180,10 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	/**
 	 * The folder containing the hashes of (potentially) rewritten commits when
 	 * --preserve-merges is used.
+	 * <p>
+	 * Native git rebase --merge uses a <em>file</em> of that name to record
+	 * commits to copy notes at the end of the whole rebase.
+	 * </p>
 	 */
 	private static final String REWRITTEN = "rewritten"; //$NON-NLS-1$
 
@@ -289,7 +296,7 @@ public RebaseResult call() throws GitAPIException, NoHeadException,
 				}
 				this.upstreamCommit = walk.parseCommit(repo
 						.resolve(upstreamCommitId));
-				preserveMerges = rebaseState.getRewrittenDir().exists();
+				preserveMerges = rebaseState.getRewrittenDir().isDirectory();
 				break;
 			case BEGIN:
 				autoStash();
@@ -1120,10 +1127,14 @@ else if (!isInteractive() && walk.isMergedInto(headCommit, upstream)) {
 
 		repo.writeOrigHead(headId);
 		rebaseState.createFile(REBASE_HEAD, headId.name());
+		rebaseState.createFile(REBASE_HEAD_LEGACY, headId.name());
 		rebaseState.createFile(HEAD_NAME, headName);
 		rebaseState.createFile(ONTO, upstreamCommit.name());
 		rebaseState.createFile(ONTO_NAME, upstreamCommitName);
-		if (isInteractive()) {
+		if (isInteractive() || preserveMerges) {
+			// --preserve-merges is an interactive mode for native git. Without
+			// this, native git rebase --continue after a conflict would fall
+			// into merge mode.
 			rebaseState.createFile(INTERACTIVE, ""); //$NON-NLS-1$
 		}
 		rebaseState.createFile(QUIET, ""); //$NON-NLS-1$
@@ -1333,8 +1344,8 @@ private void checkParameters() throws WrongRepositoryStateException {
 
 	private RebaseResult abort(RebaseResult result) throws IOException,
 			GitAPIException {
+		ObjectId origHead = getOriginalHead();
 		try {
-			ObjectId origHead = repo.readOrigHead();
 			String commitId = origHead != null ? origHead.name() : null;
 			monitor.beginTask(MessageFormat.format(
 					JGitText.get().abortingRebase, commitId),
@@ -1373,7 +1384,7 @@ private RebaseResult abort(RebaseResult result) throws IOException,
 				// update the HEAD
 				res = refUpdate.link(headName);
 			} else {
-				refUpdate.setNewObjectId(repo.readOrigHead());
+				refUpdate.setNewObjectId(origHead);
 				res = refUpdate.forceUpdate();
 
 			}
@@ -1400,6 +1411,19 @@ private RebaseResult abort(RebaseResult result) throws IOException,
 		}
 	}
 
+	private ObjectId getOriginalHead() throws IOException {
+		try {
+			return ObjectId.fromString(rebaseState.readFile(REBASE_HEAD));
+		} catch (FileNotFoundException e) {
+			try {
+				return ObjectId
+						.fromString(rebaseState.readFile(REBASE_HEAD_LEGACY));
+			} catch (FileNotFoundException ex) {
+				return repo.readOrigHead();
+			}
+		}
+	}
+
 	private boolean checkoutCommit(String headName, RevCommit commit)
 			throws IOException,
 			CheckoutConflictException {
@@ -1706,7 +1730,20 @@ public File getRewrittenDir() {
 		}
 
 		public String readFile(String name) throws IOException {
-			return readFile(getDir(), name);
+			try {
+				return readFile(getDir(), name);
+			} catch (FileNotFoundException e) {
+				if (ONTO_NAME.equals(name)) {
+					// Older JGit mistakenly wrote a file "onto-name" instead of
+					// "onto_name". Try that wrong name just in case somebody
+					// upgraded while a rebase started by JGit was in progress.
+					File oldFile = getFile(ONTO_NAME.replace('_', '-'));
+					if (oldFile.exists()) {
+						return readFile(oldFile);
+					}
+				}
+				throw e;
+			}
 		}
 
 		public void createFile(String name, String content) throws IOException {
@@ -1721,14 +1758,18 @@ public String getPath(String name) {
 			return (getDir().getName() + "/" + name); //$NON-NLS-1$
 		}
 
-		private static String readFile(File directory, String fileName)
-				throws IOException {
-			byte[] content = IO.readFully(new File(directory, fileName));
+		private static String readFile(File file) throws IOException {
+			byte[] content = IO.readFully(file);
 			// strip off the last LF
 			int end = RawParseUtils.prevLF(content, content.length);
 			return RawParseUtils.decode(content, 0, end + 1);
 		}
 
+		private static String readFile(File directory, String fileName)
+				throws IOException {
+			return readFile(new File(directory, fileName));
+		}
+
 		private static void createFile(File parentDir, String name,
 				String content)
 				throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RemoteRemoveCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RemoteRemoveCommand.java
index 7a5885c..016cb15 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RemoteRemoveCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RemoteRemoveCommand.java
@@ -65,7 +65,7 @@
  */
 public class RemoteRemoveCommand extends GitCommand<RemoteConfig> {
 
-	private String name;
+	private String remoteName;
 
 	/**
 	 * <p>
@@ -84,9 +84,24 @@ protected RemoteRemoveCommand(Repository repo) {
 	 *
 	 * @param name
 	 *            a remote name
+	 * @deprecated use {@link #setRemoteName} instead
 	 */
+	@Deprecated
 	public void setName(String name) {
-		this.name = name;
+		this.remoteName = name;
+	}
+
+	/**
+	 * The name of the remote to remove.
+	 *
+	 * @param remoteName
+	 *            a remote name
+	 * @return {@code this}
+	 * @since 5.3
+	 */
+	public RemoteRemoveCommand setRemoteName(String remoteName) {
+		this.remoteName = remoteName;
+		return this;
 	}
 
 	/**
@@ -101,8 +116,8 @@ public RemoteConfig call() throws GitAPIException {
 
 		try {
 			StoredConfig config = repo.getConfig();
-			RemoteConfig remote = new RemoteConfig(config, name);
-			config.unsetSection(ConfigConstants.CONFIG_KEY_REMOTE, name);
+			RemoteConfig remote = new RemoteConfig(config, remoteName);
+			config.unsetSection(ConfigConstants.CONFIG_KEY_REMOTE, remoteName);
 			config.save();
 			return remote;
 		} catch (IOException | URISyntaxException e) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RemoteSetUrlCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RemoteSetUrlCommand.java
index d7b7a31..21d4023 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RemoteSetUrlCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RemoteSetUrlCommand.java
@@ -54,7 +54,7 @@
 import org.eclipse.jgit.transport.URIish;
 
 /**
- * Used to to change the URL of a remote.
+ * Used to change the URL of a remote.
  *
  * This class has setters for all supported options and arguments of this
  * command and a {@link #call()} method to finally execute the command.
@@ -66,11 +66,28 @@
  */
 public class RemoteSetUrlCommand extends GitCommand<RemoteConfig> {
 
-	private String name;
+	/**
+	 * The available URI types for the remote.
+	 *
+	 * @since 5.3
+	 */
+	public enum UriType {
+		/**
+		 * Fetch URL for the remote.
+		 */
+		FETCH,
+		/**
+		 * Push URL for the remote.
+		 */
+		PUSH
+	}
 
-	private URIish uri;
 
-	private boolean push;
+	private String remoteName;
+
+	private URIish remoteUri;
+
+	private UriType type;
 
 	/**
 	 * <p>
@@ -89,9 +106,24 @@ protected RemoteSetUrlCommand(Repository repo) {
 	 *
 	 * @param name
 	 *            a remote name
+	 * @deprecated use {@link #setRemoteName} instead
 	 */
+	@Deprecated
 	public void setName(String name) {
-		this.name = name;
+		this.remoteName = name;
+	}
+
+	/**
+	 * The name of the remote to change the URL for.
+	 *
+	 * @param remoteName
+	 *            a remote remoteName
+	 * @return {@code this}
+	 * @since 5.3
+	 */
+	public RemoteSetUrlCommand setRemoteName(String remoteName) {
+		this.remoteName = remoteName;
+		return this;
 	}
 
 	/**
@@ -99,9 +131,24 @@ public void setName(String name) {
 	 *
 	 * @param uri
 	 *            an URL for the remote
+	 * @deprecated use {@link #setRemoteUri} instead
 	 */
+	@Deprecated
 	public void setUri(URIish uri) {
-		this.uri = uri;
+		this.remoteUri = uri;
+	}
+
+	/**
+	 * The new URL for the remote.
+	 *
+	 * @param remoteUri
+	 *            an URL for the remote
+	 * @return {@code this}
+	 * @since 5.3
+	 */
+	public RemoteSetUrlCommand setRemoteUri(URIish remoteUri) {
+		this.remoteUri = remoteUri;
+		return this;
 	}
 
 	/**
@@ -110,9 +157,28 @@ public void setUri(URIish uri) {
 	 * @param push
 	 *            <code>true</code> to set the push url, <code>false</code> to
 	 *            set the fetch url
+	 * @deprecated use {@link #setUriType} instead
 	 */
+	@Deprecated
 	public void setPush(boolean push) {
-		this.push = push;
+		if (push) {
+			setUriType(UriType.PUSH);
+		} else {
+			setUriType(UriType.FETCH);
+		}
+	}
+
+	/**
+	 * Whether to change the push URL of the remote instead of the fetch URL.
+	 *
+	 * @param type
+	 *            the <code>UriType</code> value to set
+	 * @return {@code this}
+	 * @since 5.3
+	 */
+	public RemoteSetUrlCommand setUriType(UriType type) {
+		this.type = type;
+		return this;
 	}
 
 	/**
@@ -127,8 +193,8 @@ public RemoteConfig call() throws GitAPIException {
 
 		try {
 			StoredConfig config = repo.getConfig();
-			RemoteConfig remote = new RemoteConfig(config, name);
-			if (push) {
+			RemoteConfig remote = new RemoteConfig(config, remoteName);
+			if (type == UriType.PUSH) {
 				List<URIish> uris = remote.getPushURIs();
 				if (uris.size() > 1) {
 					throw new JGitInternalException(
@@ -136,7 +202,7 @@ public RemoteConfig call() throws GitAPIException {
 				} else if (uris.size() == 1) {
 					remote.removePushURI(uris.get(0));
 				}
-				remote.addPushURI(uri);
+				remote.addPushURI(remoteUri);
 			} else {
 				List<URIish> uris = remote.getURIs();
 				if (uris.size() > 1) {
@@ -145,7 +211,7 @@ public RemoteConfig call() throws GitAPIException {
 				} else if (uris.size() == 1) {
 					remote.removeURI(uris.get(0));
 				}
-				remote.addURI(uri);
+				remote.addURI(remoteUri);
 			}
 
 			remote.update(config);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RenameBranchCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RenameBranchCommand.java
index 24d9dd4..7e8c33c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RenameBranchCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RenameBranchCommand.java
@@ -94,25 +94,38 @@ public Ref call() throws GitAPIException, RefNotFoundException, InvalidRefNameEx
 			RefAlreadyExistsException, DetachedHeadException {
 		checkCallable();
 
-		if (newName == null)
+		if (newName == null) {
 			throw new InvalidRefNameException(MessageFormat.format(JGitText
 					.get().branchNameInvalid, "<null>")); //$NON-NLS-1$
-
+		}
 		try {
 			String fullOldName;
 			String fullNewName;
-			if (repo.findRef(newName) != null)
-				throw new RefAlreadyExistsException(MessageFormat.format(
-						JGitText.get().refAlreadyExists1, newName));
 			if (oldName != null) {
-				Ref ref = repo.findRef(oldName);
-				if (ref == null)
-					throw new RefNotFoundException(MessageFormat.format(
-							JGitText.get().refNotResolved, oldName));
-				if (ref.getName().startsWith(Constants.R_TAGS))
-					throw new RefNotFoundException(MessageFormat.format(
-							JGitText.get().renameBranchFailedBecauseTag,
-							oldName));
+				// Don't just rely on findRef -- if there are local and remote
+				// branches with the same name, and oldName is a short name, it
+				// does not uniquely identify the ref and we might end up
+				// renaming the wrong branch or finding a tag instead even
+				// if a unique branch for the name exists!
+				//
+				// OldName may be a either a short or a full name.
+				Ref ref = repo.exactRef(oldName);
+				if (ref == null) {
+					ref = repo.exactRef(Constants.R_HEADS + oldName);
+					Ref ref2 = repo.exactRef(Constants.R_REMOTES + oldName);
+					if (ref != null && ref2 != null) {
+						throw new RefNotFoundException(MessageFormat.format(
+								JGitText.get().renameBranchFailedAmbiguous,
+								oldName, ref.getName(), ref2.getName()));
+					} else if (ref == null) {
+						if (ref2 != null) {
+							ref = ref2;
+						} else {
+							throw new RefNotFoundException(MessageFormat.format(
+									JGitText.get().refNotResolved, oldName));
+						}
+					}
+				}
 				fullOldName = ref.getName();
 			} else {
 				fullOldName = repo.getFullBranch();
@@ -124,26 +137,34 @@ public Ref call() throws GitAPIException, RefNotFoundException, InvalidRefNameEx
 					throw new DetachedHeadException();
 			}
 
-			if (fullOldName.startsWith(Constants.R_REMOTES))
+			if (fullOldName.startsWith(Constants.R_REMOTES)) {
 				fullNewName = Constants.R_REMOTES + newName;
-			else {
+			} else if (fullOldName.startsWith(Constants.R_HEADS)) {
 				fullNewName = Constants.R_HEADS + newName;
+			} else {
+				throw new RefNotFoundException(MessageFormat.format(
+						JGitText.get().renameBranchFailedNotABranch,
+						fullOldName));
 			}
 
-			if (!Repository.isValidRefName(fullNewName))
+			if (!Repository.isValidRefName(fullNewName)) {
 				throw new InvalidRefNameException(MessageFormat.format(JGitText
 						.get().branchNameInvalid, fullNewName));
-
+			}
+			if (repo.exactRef(fullNewName) != null) {
+				throw new RefAlreadyExistsException(MessageFormat
+						.format(JGitText.get().refAlreadyExists1, fullNewName));
+			}
 			RefRename rename = repo.renameRef(fullOldName, fullNewName);
 			Result renameResult = rename.rename();
 
 			setCallable(false);
 
-			if (Result.RENAMED != renameResult)
+			if (Result.RENAMED != renameResult) {
 				throw new JGitInternalException(MessageFormat.format(JGitText
 						.get().renameBranchUnexpectedResult, renameResult
 						.name()));
-
+			}
 			if (fullNewName.startsWith(Constants.R_HEADS)) {
 				String shortOldName = fullOldName.substring(Constants.R_HEADS
 						.length());
@@ -154,8 +175,9 @@ public Ref call() throws GitAPIException, RefNotFoundException, InvalidRefNameEx
 					String[] values = repoConfig.getStringList(
 							ConfigConstants.CONFIG_BRANCH_SECTION,
 							shortOldName, name);
-					if (values.length == 0)
+					if (values.length == 0) {
 						continue;
+					}
 					// Keep any existing values already configured for the
 					// new branch name
 					String[] existing = repoConfig.getStringList(
@@ -180,10 +202,11 @@ public Ref call() throws GitAPIException, RefNotFoundException, InvalidRefNameEx
 				repoConfig.save();
 			}
 
-			Ref resultRef = repo.findRef(newName);
-			if (resultRef == null)
+			Ref resultRef = repo.exactRef(fullNewName);
+			if (resultRef == null) {
 				throw new JGitInternalException(
 						JGitText.get().renameBranchFailedUnknownReason);
+			}
 			return resultRef;
 		} catch (IOException ioe) {
 			throw new JGitInternalException(ioe.getMessage(), ioe);
@@ -191,7 +214,13 @@ public Ref call() throws GitAPIException, RefNotFoundException, InvalidRefNameEx
 	}
 
 	/**
-	 * Set the new name of the branch
+	 * Sets the new short name of the branch.
+	 * <p>
+	 * The full name is constructed using the prefix of the branch to be renamed
+	 * defined by either {@link #setOldName(String)} or HEAD. If that old branch
+	 * is a local branch, the renamed branch also will be, and if the old branch
+	 * is a remote branch, so will be the renamed branch.
+	 * </p>
 	 *
 	 * @param newName
 	 *            the new name
@@ -204,7 +233,11 @@ public RenameBranchCommand setNewName(String newName) {
 	}
 
 	/**
-	 * Set the old name of the branch
+	 * Sets the old name of the branch.
+	 * <p>
+	 * {@code oldName} may be a short or a full name. Using a full name is
+	 * recommended to unambiguously identify the branch to be renamed.
+	 * </p>
 	 *
 	 * @param oldName
 	 *            the name of the branch to rename; if not set, the currently
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 ff7c4c6..aeb9395 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
@@ -96,9 +96,9 @@ public class StashApplyCommand extends GitCommand<ObjectId> {
 
 	private String stashRef;
 
-	private boolean applyIndex = true;
+	private boolean restoreIndex = true;
 
-	private boolean applyUntracked = true;
+	private boolean restoreUntracked = true;
 
 	private boolean ignoreRepositoryState;
 
@@ -196,7 +196,7 @@ public ObjectId call() throws GitAPIException,
 					.getParent(1));
 			ObjectId stashHeadCommit = stashCommit.getParent(0);
 			ObjectId untrackedCommit = null;
-			if (applyUntracked && stashCommit.getParentCount() == 3)
+			if (restoreUntracked && stashCommit.getParentCount() == 3)
 				untrackedCommit = revWalk.parseCommit(stashCommit.getParent(2));
 
 			ResolveMerger merger = (ResolveMerger) strategy.newMerger(repo);
@@ -216,7 +216,7 @@ public ObjectId call() throws GitAPIException,
 						dc, merger.getResultTreeId());
 				dco.setFailOnConflict(true);
 				dco.checkout(); // Ignoring failed deletes....
-				if (applyIndex) {
+				if (restoreIndex) {
 					ResolveMerger ixMerger = (ResolveMerger) strategy
 							.newMerger(repo, true);
 					ixMerger.setCommitNames(new String[] { "stashed HEAD", //$NON-NLS-1$
@@ -277,9 +277,24 @@ public ObjectId call() throws GitAPIException,
 	 *
 	 * @param applyIndex
 	 *            true (default) if the command should restore the index state
+	 * @deprecated use {@link #setRestoreIndex} instead
 	 */
+	@Deprecated
 	public void setApplyIndex(boolean applyIndex) {
-		this.applyIndex = applyIndex;
+		this.restoreIndex = applyIndex;
+	}
+
+	/**
+	 * Whether to restore the index state
+	 *
+	 * @param restoreIndex
+	 *            true (default) if the command should restore the index state
+	 * @return {@code this}
+	 * @since 5.3
+	 */
+	public StashApplyCommand setRestoreIndex(boolean restoreIndex) {
+		this.restoreIndex = restoreIndex;
+		return this;
 	}
 
 	/**
@@ -302,9 +317,24 @@ public StashApplyCommand setStrategy(MergeStrategy strategy) {
 	 * @param applyUntracked
 	 *            true (default) if the command should restore untracked files
 	 * @since 3.4
+	 * @deprecated use {@link #setRestoreUntracked} instead
 	 */
+	@Deprecated
 	public void setApplyUntracked(boolean applyUntracked) {
-		this.applyUntracked = applyUntracked;
+		this.restoreUntracked = applyUntracked;
+	}
+
+	/**
+	 * Whether the command should restore untracked files
+	 *
+	 * @param restoreUntracked
+	 *            true (default) if the command should restore untracked files
+	 * @return {@code this}
+	 * @since 5.3
+	 */
+	public StashApplyCommand setRestoreUntracked(boolean restoreUntracked) {
+		this.restoreUntracked = restoreUntracked;
+		return this;
 	}
 
 	private void resetIndex(RevTree tree) throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/JGitInternalException.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/JGitInternalException.java
index 57d8a13..c723da3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/JGitInternalException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/JGitInternalException.java
@@ -44,7 +44,7 @@
  * <p>
  * During command execution a lot of exceptions may be thrown. Some of them
  * represent error situations which can be handled specifically by the caller of
- * the command. But a lot of exceptions are so low-level that is is unlikely
+ * the command. But a lot of exceptions are so low-level that it is unlikely
  * that the caller of the command can handle them effectively. The huge number
  * of these low-level exceptions which are thrown by the commands lead to a
  * complicated and wide interface of the commands. Callers of the API have to
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/UnsupportedSigningFormatException.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/UnsupportedSigningFormatException.java
new file mode 100644
index 0000000..eb5db6a
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/UnsupportedSigningFormatException.java
@@ -0,0 +1,69 @@
+/*
+ * Copyright (C) 2018, Salesforce 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.api.errors;
+
+/**
+ * Exception thrown when the configured gpg.format is not supported.
+ *
+ * @since 5.3
+ */
+public class UnsupportedSigningFormatException extends GitAPIException {
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * Constructor for UnsupportedGpgFormatException
+	 *
+	 * @param message
+	 *            error message
+	 * @param cause
+	 *            a {@link java.lang.Throwable}
+	 */
+	public UnsupportedSigningFormatException(String message, Throwable cause) {
+		super(message, cause);
+	}
+
+	/**
+	 * Constructor for UnsupportedGpgFormatException
+	 *
+	 * @param message
+	 *            error message
+	 */
+	public UnsupportedSigningFormatException(String message) {
+		super(message);
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/RawText.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/RawText.java
index bd41d90..6c0d90e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/RawText.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/RawText.java
@@ -309,6 +309,74 @@ public static boolean isBinary(byte[] raw, int length) {
 	}
 
 	/**
+	 * Determine heuristically whether a byte array represents text content
+	 * using CR-LF as line separator.
+	 *
+	 * @param raw
+	 *            the raw file content.
+	 * @return {@code true} if raw is likely to be CR-LF delimited text,
+	 *         {@code false} otherwise
+	 * @since 5.3
+	 */
+	public static boolean isCrLfText(byte[] raw) {
+		return isCrLfText(raw, raw.length);
+	}
+
+	/**
+	 * Determine heuristically whether the bytes contained in a stream represent
+	 * text content using CR-LF as line separator.
+	 *
+	 * Note: Do not further use this stream after having called this method! The
+	 * stream may not be fully read and will be left at an unknown position
+	 * after consuming an unknown number of bytes. The caller is responsible for
+	 * closing the stream.
+	 *
+	 * @param raw
+	 *            input stream containing the raw file content.
+	 * @return {@code true} if raw is likely to be CR-LF delimited text,
+	 *         {@code false} otherwise
+	 * @throws java.io.IOException
+	 *             if input stream could not be read
+	 * @since 5.3
+	 */
+	public static boolean isCrLfText(InputStream raw) throws IOException {
+		byte[] buffer = new byte[FIRST_FEW_BYTES];
+		int cnt = 0;
+		while (cnt < buffer.length) {
+			int n = raw.read(buffer, cnt, buffer.length - cnt);
+			if (n == -1) {
+				break;
+			}
+			cnt += n;
+		}
+		return isCrLfText(buffer, cnt);
+	}
+
+	/**
+	 * Determine heuristically whether a byte array represents text content
+	 * using CR-LF as line separator.
+	 *
+	 * @param raw
+	 *            the raw file content.
+	 * @param length
+	 *            number of bytes in {@code raw} to evaluate.
+	 * @return {@code true} if raw is likely to be CR-LF delimited text,
+	 *         {@code false} otherwise
+	 * @since 5.3
+	 */
+	public static boolean isCrLfText(byte[] raw, int length) {
+		boolean has_crlf = false;
+		for (int ptr = 0; ptr < length - 1; ptr++) {
+			if (raw[ptr] == '\0') {
+				return false; // binary
+			} else if (raw[ptr] == '\r' && raw[ptr + 1] == '\n') {
+				has_crlf = true;
+			}
+		}
+		return has_crlf;
+	}
+
+	/**
 	 * Get the line delimiter for the first line.
 	 *
 	 * @since 2.0
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SequenceComparator.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SequenceComparator.java
index ccd0055..3bc95a2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SequenceComparator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SequenceComparator.java
@@ -84,7 +84,7 @@ public abstract class SequenceComparator<S extends Sequence> {
 	 * method must produce the same integer result for both items.
 	 *
 	 * It is not required for two items to have different hash values if they
-	 * are are unequal according to the {@code equals()} method.
+	 * are unequal according to the {@code equals()} method.
 	 *
 	 * @param seq
 	 *            the sequence.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java
index 5897ffb..539f237 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java
@@ -236,7 +236,7 @@ void sort() {
 	 * A region of a file is defined as a line in a text file or a fixed-size
 	 * block in a binary file. To prepare an index, each region in the file is
 	 * hashed; the values and counts of hashes are retained in a sorted table.
-	 * Define the similarity fraction F as the the count of matching regions
+	 * Define the similarity fraction F as the count of matching regions
 	 * between the two files divided between the maximum count of regions in
 	 * either file. The similarity score is F multiplied by the maxScore
 	 * constant, yielding a range [0, maxScore]. It is defined as maxScore for
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 8aa97df..2d62286 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
@@ -156,9 +156,11 @@ public CheckoutMetadata(EolStreamType eolStreamType,
 
 	private boolean failOnConflict = true;
 
+	private boolean force = false;
+
 	private ArrayList<String> toBeDeleted = new ArrayList<>();
 
-	private boolean emptyDirCache;
+	private boolean initialCheckout;
 
 	private boolean performingCheckout;
 
@@ -231,7 +233,7 @@ public DirCacheCheckout(Repository repo, ObjectId headCommitTree, DirCache dc,
 		this.headCommitTree = headCommitTree;
 		this.mergeCommitTree = mergeCommitTree;
 		this.workingTree = workingTree;
-		this.emptyDirCache = (dc == null) || (dc.getEntryCount() == 0);
+		this.initialCheckout = !repo.isBare() && !repo.getIndexFile().exists();
 	}
 
 	/**
@@ -430,11 +432,11 @@ void processEntry(CanonicalTreeParser m, DirCacheBuildIterator i,
 					if (mtime == null || mtime.equals(Instant.EPOCH)) {
 						entry.setLastModified(f.getEntryLastModifiedInstant());
 					}
-					keep(entry);
+					keep(entry, f);
 				}
 			} else
 				// The index contains a folder
-				keep(i.getDirCacheEntry());
+				keep(i.getDirCacheEntry(), f);
 		} else {
 			// There is no entry in the merge commit. Means: we want to delete
 			// what's currently in the index and working tree
@@ -824,14 +826,14 @@ void processEntry(CanonicalTreeParser h, CanonicalTreeParser m,
 
 				break;
 			case 0xDFD: // 3 4
-				keep(dce);
+				keep(dce, f);
 				break;
 			case 0xF0D: // 18
 				remove(name);
 				break;
 			case 0xDFF: // 5 5b 6 6b
 				if (equalIdAndMode(iId, iMode, mId, mMode))
-					keep(dce); // 5 6
+					keep(dce, f); // 5 6
 				else
 					conflict(name, dce, h, m); // 5b 6b
 				break;
@@ -861,7 +863,7 @@ void processEntry(CanonicalTreeParser h, CanonicalTreeParser m,
 					conflict(name, dce, h, m); // 9
 				break;
 			case 0xFD0: // keep without a rule
-				keep(dce);
+				keep(dce, f);
 				break;
 			case 0xFFD: // 12 13 14
 				if (equalIdAndMode(hId, hMode, iId, iMode))
@@ -881,7 +883,7 @@ void processEntry(CanonicalTreeParser h, CanonicalTreeParser m,
 					conflict(name, dce, h, m);
 				break;
 			default:
-				keep(dce);
+				keep(dce, f);
 			}
 			return;
 		}
@@ -964,10 +966,10 @@ else if (m == null)
 				// called before). Ignore the cached deletion and use what we
 				// find in Merge. Potentially updates the file.
 				if (equalIdAndMode(hId, hMode, mId, mMode)) {
-					if (emptyDirCache)
+					if (initialCheckout)
 						update(name, mId, mMode);
 					else
-						keep(dce);
+						keep(dce, f);
 				} else
 					conflict(name, dce, h, m);
 			}
@@ -1030,7 +1032,7 @@ else if (m == null)
 						// Nothing in Head
 						// Something in Index
 						// -> Merge contains nothing new. Keep the index.
-						keep(dce);
+						keep(dce, f);
 				} else
 					// Merge contains something and it is not the same as Index
 					// Nothing in Head
@@ -1179,7 +1181,7 @@ && isModified_IndexTree(name, iId, iMode, mId, mMode,
 					// to the other one.
 					// -> In all three cases we don't touch index and file.
 
-					keep(dce);
+					keep(dce, f);
 				}
 			}
 		}
@@ -1228,9 +1230,15 @@ private void conflict(String path, DirCacheEntry e, AbstractTreeIterator h, Abst
 		}
 	}
 
-	private void keep(DirCacheEntry e) {
+	private void keep(DirCacheEntry e, WorkingTreeIterator f)
+			throws IOException {
 		if (e != null && !FileMode.TREE.equals(e.getFileMode()))
 			builder.add(e);
+		if (force) {
+			if (f.isModified(e, true, this.walk.getObjectReader())) {
+				checkoutEntry(repo, e, this.walk.getObjectReader());
+			}
+		}
 	}
 
 	private void remove(String path) {
@@ -1265,6 +1273,20 @@ public void setFailOnConflict(boolean failOnConflict) {
 	}
 
 	/**
+	 * If <code>true</code>, dirty worktree files may be overridden. If
+	 * <code>false</code> dirty worktree files will not be overridden in order
+	 * not to delete unsaved content. This corresponds to native git's 'git
+	 * checkout -f' option. By default this option is set to false.
+	 *
+	 * @param force
+	 *            a boolean.
+	 * @since 5.3
+	 */
+	public void setForce(boolean force) {
+		this.force = force;
+	}
+
+	/**
 	 * This method implements how to handle conflicts when
 	 * {@link #failOnConflict} is false
 	 *
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 e9d86df..cb62925 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java
@@ -147,7 +147,7 @@ public interface RemoteReader {
 		 *            The URI of the remote repository
 		 * @param ref
 		 *            Name of the ref to lookup. May be a short-hand form, e.g.
-		 *            "master" which is is automatically expanded to
+		 *            "master" which is automatically expanded to
 		 *            "refs/heads/master" if "refs/heads/master" already exists.
 		 * @return the sha1 of the remote repository, or null if the ref does
 		 *         not exist.
@@ -187,7 +187,7 @@ public interface RemoteReader {
 		 *            The URI of the remote repository
 		 * @param ref
 		 *            Name of the ref to lookup. May be a short-hand form, e.g.
-		 *            "master" which is is automatically expanded to
+		 *            "master" which is automatically expanded to
 		 *            "refs/heads/master" if "refs/heads/master" already exists.
 		 * @param path
 		 *            The relative path (inside the repo) to the file to read
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 f65e374..d51e052 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
@@ -257,6 +257,7 @@ public static JGitText get() {
 	/***/ public String createNewFileFailed;
 	/***/ public String createRequiresZeroOldId;
 	/***/ public String credentialPassword;
+	/***/ public String credentialPassphrase;
 	/***/ public String credentialUsername;
 	/***/ public String daemonAlreadyRunning;
 	/***/ public String daysAgo;
@@ -350,6 +351,14 @@ public static JGitText get() {
 	/***/ public String funnyRefname;
 	/***/ public String gcFailed;
 	/***/ public String gcTooManyUnpruned;
+	/***/ public String gpgFailedToParseSecretKey;
+	/***/ public String gpgNoCredentialsProvider;
+	/***/ public String gpgNoKeyring;
+	/***/ public String gpgNoKeyInLegacySecring;
+	/***/ public String gpgNoPublicKeyFound;
+	/***/ public String gpgNoSecretKeyForPublicKey;
+	/***/ public String gpgKeyInfo;
+	/***/ public String gpgSigningCancelled;
 	/***/ public String headRequiredToStash;
 	/***/ public String hoursAgo;
 	/***/ public String httpConfigCannotNormalizeURL;
@@ -517,6 +526,7 @@ public static JGitText get() {
 	/***/ public String oldIdMustNotBeNull;
 	/***/ public String onlyOneFetchSupported;
 	/***/ public String onlyOneOperationCallPerConnectionIsSupported;
+	/***/ public String onlyOpenPgpSupportedForSigning;
 	/***/ public String openFilesMustBeAtLeast1;
 	/***/ public String openingConnection;
 	/***/ public String operationCanceled;
@@ -592,8 +602,9 @@ public static JGitText get() {
 	/***/ public String remoteDoesNotHaveSpec;
 	/***/ public String remoteDoesNotSupportSmartHTTPPush;
 	/***/ public String remoteHungUpUnexpectedly;
-	/***/ public String remoteNameCantBeNull;
-	/***/ public String renameBranchFailedBecauseTag;
+	/***/ public String remoteNameCannotBeNull;
+	/***/ public String renameBranchFailedAmbiguous;
+	/***/ public String renameBranchFailedNotABranch;
 	/***/ public String renameBranchFailedUnknownReason;
 	/***/ public String renameBranchUnexpectedResult;
 	/***/ public String renameCancelled;
@@ -633,7 +644,7 @@ public static JGitText get() {
 	/***/ public String sequenceTooLargeForDiffAlgorithm;
 	/***/ public String serviceNotEnabledNoName;
 	/***/ public String serviceNotPermitted;
-	/***/ public String sha1CollisionDetected1;
+	/***/ public String sha1CollisionDetected;
 	/***/ public String shallowCommitsAlreadyInitialized;
 	/***/ public String shallowPacksRequireDepthWalk;
 	/***/ public String shortCompressedStreamAt;
@@ -724,6 +735,7 @@ public static JGitText get() {
 	/***/ public String unableToReadPackfile;
 	/***/ public String unableToRemovePath;
 	/***/ public String unableToWrite;
+	/***/ public String unableToSignCommitNoSecretKey;
 	/***/ public String unauthorized;
 	/***/ public String unencodeableFile;
 	/***/ public String unexpectedCompareResult;
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
index 58d12ab..c7d6c58 100644
--- 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
@@ -48,7 +48,6 @@
 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;
 
@@ -133,19 +132,19 @@ else if (size < cache.getBlockSize())
 	}
 
 	DfsBlock getOrLoadBlock(long pos, DfsReader ctx) throws IOException {
-		return cache.getOrLoad(this, pos, ctx, null);
+		try (LazyChannel c = new LazyChannel(ctx, desc, ext)) {
+			return cache.getOrLoad(this, pos, ctx, c);
+		}
 	}
 
-	DfsBlock readOneBlock(long pos, DfsReader ctx,
-			@Nullable ReadableChannel fileChannel) throws IOException {
+	DfsBlock readOneBlock(long pos, DfsReader ctx, ReadableChannel rc)
+			throws IOException {
 		if (invalid) {
 			throw new PackInvalidException(getFileName(), invalidatingCause);
 		}
 
 		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;
@@ -193,9 +192,6 @@ DfsBlock readOneBlock(long pos, DfsReader ctx,
 
 			return new DfsBlock(key, pos, buf);
 		} finally {
-			if (rc != fileChannel) {
-				rc.close();
-			}
 			ctx.stats.readBlockMicros += elapsedMicros(start);
 		}
 	}
@@ -211,4 +207,37 @@ static int read(ReadableChannel rc, ByteBuffer buf) throws IOException {
 	static long elapsedMicros(long start) {
 		return (System.nanoTime() - start) / 1000L;
 	}
+
+	/**
+	 * A supplier of readable channel that opens the channel lazily.
+	 */
+	private static class LazyChannel
+			implements AutoCloseable, DfsBlockCache.ReadableChannelSupplier {
+		private final DfsReader ctx;
+		private final DfsPackDescription desc;
+		private final PackExt ext;
+
+		private ReadableChannel rc;
+
+		LazyChannel(DfsReader ctx, DfsPackDescription desc, PackExt ext) {
+			this.ctx = ctx;
+			this.desc = desc;
+			this.ext = ext;
+		}
+
+		@Override
+		public ReadableChannel get() throws IOException {
+			if (rc == null) {
+				rc = ctx.db.openFile(desc, ext);
+			}
+			return rc;
+		}
+
+		@Override
+		public void close() throws IOException {
+			if (rc != null) {
+				rc.close();
+			}
+		}
+	}
 }
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 4687952..c6e2fae 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
@@ -49,9 +49,9 @@
 import java.util.concurrent.atomic.AtomicReference;
 import java.util.concurrent.atomic.AtomicReferenceArray;
 import java.util.concurrent.locks.ReentrantLock;
+import java.util.function.Consumer;
 import java.util.stream.LongStream;
 
-import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.internal.storage.pack.PackExt;
 
@@ -128,9 +128,18 @@ public static DfsBlockCache getInstance() {
 	/** Hash bucket directory; entries are chained below. */
 	private final AtomicReferenceArray<HashEntry> table;
 
-	/** Locks to prevent concurrent loads for same (PackFile,position). */
+	/**
+	 * Locks to prevent concurrent loads for same (PackFile,position) block. The
+	 * number of locks is {@link DfsBlockCacheConfig#getConcurrencyLevel()} to
+	 * cap the overall concurrent block loads.
+	 */
 	private final ReentrantLock[] loadLocks;
 
+	/**
+	 * A separate pool of locks to prevent concurrent loads for same index or bitmap from PackFile.
+	 */
+	private final ReentrantLock[] refLocks;
+
 	/** Maximum number of bytes the cache should hold. */
 	private final long maxBytes;
 
@@ -177,19 +186,30 @@ public static DfsBlockCache getInstance() {
 	/** Protects the clock and its related data. */
 	private final ReentrantLock clockLock;
 
+	/**
+	 * A consumer of object reference lock wait time milliseconds.  May be used to build a metric.
+	 */
+	private final Consumer<Long> refLockWaitTime;
+
 	/** Current position of the clock. */
 	private Ref clockHand;
 
 	@SuppressWarnings("unchecked")
 	private DfsBlockCache(DfsBlockCacheConfig cfg) {
 		tableSize = tableSize(cfg);
-		if (tableSize < 1)
+		if (tableSize < 1) {
 			throw new IllegalArgumentException(JGitText.get().tSizeMustBeGreaterOrEqual1);
+		}
 
 		table = new AtomicReferenceArray<>(tableSize);
 		loadLocks = new ReentrantLock[cfg.getConcurrencyLevel()];
-		for (int i = 0; i < loadLocks.length; i++)
+		for (int i = 0; i < loadLocks.length; i++) {
 			loadLocks[i] = new ReentrantLock(true /* fair */);
+		}
+		refLocks = new ReentrantLock[cfg.getConcurrencyLevel()];
+		for (int i = 0; i < refLocks.length; i++) {
+			refLocks[i] = new ReentrantLock(true /* fair */);
+		}
 
 		maxBytes = cfg.getBlockLimit();
 		maxStreamThroughCache = (long) (maxBytes * cfg.getStreamRatio());
@@ -207,6 +227,8 @@ private DfsBlockCache(DfsBlockCacheConfig cfg) {
 		statMiss = new AtomicReference<>(newCounters());
 		statEvict = new AtomicReference<>(newCounters());
 		liveBytes = new AtomicReference<>(newCounters());
+
+		refLockWaitTime = cfg.getRefLockWaitTimeConsumer();
 	}
 
 	boolean shouldCopyThroughCache(long length) {
@@ -333,15 +355,17 @@ int getBlockSize() {
 	private static int tableSize(DfsBlockCacheConfig cfg) {
 		final int wsz = cfg.getBlockSize();
 		final long limit = cfg.getBlockLimit();
-		if (wsz <= 0)
+		if (wsz <= 0) {
 			throw new IllegalArgumentException(JGitText.get().invalidWindowSize);
-		if (limit < wsz)
+		}
+		if (limit < wsz) {
 			throw new IllegalArgumentException(JGitText.get().windowSizeMustBeLesserThanLimit);
+		}
 		return (int) Math.min(5 * (limit / wsz) / 2, Integer.MAX_VALUE);
 	}
 
 	/**
-	 * Lookup a cached object, creating and loading it if it doesn't exist.
+	 * Look up a cached object, creating and loading it if it doesn't exist.
 	 *
 	 * @param file
 	 *            the pack that "contains" the cached object.
@@ -350,13 +374,13 @@ private static int tableSize(DfsBlockCacheConfig cfg) {
 	 * @param ctx
 	 *            current thread's reader.
 	 * @param fileChannel
-	 *            optional channel to read {@code pack}.
+	 *            supplier for 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(BlockBasedFile file, long position, DfsReader ctx,
-			@Nullable ReadableChannel fileChannel) throws IOException {
+			ReadableChannelSupplier fileChannel) throws IOException {
 		final long requestedPosition = position;
 		position = file.alignToBlock(position);
 
@@ -388,11 +412,13 @@ DfsBlock getOrLoad(BlockBasedFile file, long position, DfsReader ctx,
 			getStat(statMiss, key).incrementAndGet();
 			boolean credit = true;
 			try {
-				v = file.readOneBlock(requestedPosition, ctx, fileChannel);
+				v = file.readOneBlock(requestedPosition, ctx,
+						fileChannel.get());
 				credit = false;
 			} finally {
-				if (credit)
+				if (credit) {
 					creditSpace(blockSize, key);
+				}
 			}
 			if (position != v.start) {
 				// The file discovered its blockSize and adjusted.
@@ -405,8 +431,9 @@ DfsBlock getOrLoad(BlockBasedFile file, long position, DfsReader ctx,
 			ref.hot = true;
 			for (;;) {
 				HashEntry n = new HashEntry(clean(e2), ref);
-				if (table.compareAndSet(slot, e2, n))
+				if (table.compareAndSet(slot, e2, n)) {
 					break;
+				}
 				e2 = table.get(slot);
 			}
 			addToClock(ref, blockSize - v.size());
@@ -416,8 +443,9 @@ DfsBlock getOrLoad(BlockBasedFile file, 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(file.key, requestedPosition))
+		if (v.contains(file.key, requestedPosition)) {
 			return v;
+		}
 		return getOrLoad(file, requestedPosition, ctx, fileChannel);
 	}
 
@@ -488,6 +516,63 @@ void put(DfsBlock v) {
 		put(v.stream, v.start, v.size(), v);
 	}
 
+	/**
+	 * Look up a cached object, creating and loading it if it doesn't exist.
+	 *
+	 * @param key
+	 *            the stream key of the pack.
+	 * @param loader
+	 *            the function to load the reference.
+	 * @return the object reference.
+	 * @throws IOException
+	 *             the reference was not in the cache and could not be loaded.
+	 */
+	<T> Ref<T> getOrLoadRef(DfsStreamKey key, RefLoader<T> loader)
+			throws IOException {
+		int slot = slot(key, 0);
+		HashEntry e1 = table.get(slot);
+		Ref<T> ref = scanRef(e1, key, 0);
+		if (ref != null) {
+			getStat(statHit, key).incrementAndGet();
+			return ref;
+		}
+
+		ReentrantLock regionLock = lockForRef(key);
+		long lockStart = System.currentTimeMillis();
+		regionLock.lock();
+		try {
+			HashEntry e2 = table.get(slot);
+			if (e2 != e1) {
+				ref = scanRef(e2, key, 0);
+				if (ref != null) {
+					getStat(statHit, key).incrementAndGet();
+					return ref;
+				}
+			}
+
+			if (refLockWaitTime != null) {
+				refLockWaitTime.accept(
+						Long.valueOf(System.currentTimeMillis() - lockStart));
+			}
+			getStat(statMiss, key).incrementAndGet();
+			ref = loader.load();
+			ref.hot = true;
+			// Reserve after loading to get the size of the object
+			reserveSpace(ref.size, key);
+			for (;;) {
+				HashEntry n = new HashEntry(clean(e2), ref);
+				if (table.compareAndSet(slot, e2, n)) {
+					break;
+				}
+				e2 = table.get(slot);
+			}
+			addToClock(ref, 0);
+		} finally {
+			regionLock.unlock();
+		}
+		return ref;
+	}
+
 	<T> Ref<T> putRef(DfsStreamKey key, long size, T v) {
 		return put(key, 0, (int) Math.min(size, Integer.MAX_VALUE), v);
 	}
@@ -496,8 +581,9 @@ <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);
-		if (ref != null)
+		if (ref != null) {
 			return ref;
+		}
 
 		reserveSpace(size, key);
 		ReentrantLock regionLock = lockFor(key, pos);
@@ -516,8 +602,9 @@ <T> Ref<T> put(DfsStreamKey key, long pos, int size, T v) {
 			ref.hot = true;
 			for (;;) {
 				HashEntry n = new HashEntry(clean(e2), ref);
-				if (table.compareAndSet(slot, e2, n))
+				if (table.compareAndSet(slot, e2, n)) {
 					break;
+				}
 				e2 = table.get(slot);
 			}
 			addToClock(ref, 0);
@@ -534,10 +621,11 @@ boolean contains(DfsStreamKey key, long position) {
 	@SuppressWarnings("unchecked")
 	<T> T get(DfsStreamKey key, long position) {
 		T val = (T) scan(table.get(slot(key, position)), key, position);
-		if (val == null)
+		if (val == null) {
 			getStat(statMiss, key).incrementAndGet();
-		else
+		} else {
 			getStat(statHit, key).incrementAndGet();
+		}
 		return val;
 	}
 
@@ -546,21 +634,13 @@ private <T> T scan(HashEntry n, DfsStreamKey key, long 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)
-			getStat(statHit, key).incrementAndGet();
-		else
-			getStat(statMiss, key).incrementAndGet();
-		return r;
-	}
-
 	@SuppressWarnings("unchecked")
 	private <T> Ref<T> scanRef(HashEntry n, DfsStreamKey key, long position) {
 		for (; n != null; n = n.next) {
 			Ref<T> r = n.ref;
-			if (r.position == position && r.key.equals(key))
+			if (r.position == position && r.key.equals(key)) {
 				return r.get() != null ? r : null;
+			}
 		}
 		return null;
 	}
@@ -573,6 +653,10 @@ private ReentrantLock lockFor(DfsStreamKey key, long position) {
 		return loadLocks[(hash(key.hash, position) >>> 1) % loadLocks.length];
 	}
 
+	private ReentrantLock lockForRef(DfsStreamKey key) {
+		return refLocks[(key.hash >>> 1) % refLocks.length];
+	}
+
 	private static AtomicLong[] newCounters() {
 		AtomicLong[] ret = new AtomicLong[PackExt.values().length];
 		for (int i = 0; i < ret.length; i++) {
@@ -613,8 +697,9 @@ private static AtomicLong getStat(AtomicReference<AtomicLong[]> stats,
 	private static HashEntry clean(HashEntry top) {
 		while (top != null && top.ref.next == null)
 			top = top.next;
-		if (top == null)
+		if (top == null) {
 			return null;
+		}
 		HashEntry n = clean(top.next);
 		return n == top.next ? top : new HashEntry(n, top.ref);
 	}
@@ -649,8 +734,9 @@ static final class Ref<T> {
 
 		T get() {
 			T v = value;
-			if (v != null)
+			if (v != null) {
 				hot = true;
+			}
 			return v;
 		}
 
@@ -658,4 +744,21 @@ boolean has() {
 			return value != null;
 		}
 	}
+
+	@FunctionalInterface
+	interface RefLoader<T> {
+		Ref<T> load() throws IOException;
+	}
+
+	/**
+	 * Supplier for readable channel
+	 */
+	@FunctionalInterface
+	interface ReadableChannelSupplier {
+		/**
+		 * @return ReadableChannel
+		 * @throws IOException
+		 */
+		ReadableChannel get() throws IOException;
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlockCacheConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlockCacheConfig.java
index dd7cb89..cd1fa5f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlockCacheConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBlockCacheConfig.java
@@ -51,6 +51,7 @@
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_STREAM_RATIO;
 
 import java.text.MessageFormat;
+import java.util.function.Consumer;
 
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Config;
@@ -71,6 +72,8 @@ public class DfsBlockCacheConfig {
 	private double streamRatio;
 	private int concurrencyLevel;
 
+	private Consumer<Long> refLock;
+
 	/**
 	 * Create a default configuration.
 	 */
@@ -194,6 +197,27 @@ public DfsBlockCacheConfig setStreamRatio(double ratio) {
 	}
 
 	/**
+	 * Get the consumer of the object reference lock wait time in milliseconds.
+	 *
+	 * @return consumer of wait time in milliseconds.
+	 */
+	public Consumer<Long> getRefLockWaitTimeConsumer() {
+		return refLock;
+	}
+
+	/**
+	 * Set the consumer for lock wait time.
+	 *
+	 * @param c
+	 *            consumer of wait time in milliseconds.
+	 * @return {@code this}
+	 */
+	public DfsBlockCacheConfig setRefLockWaitTimeConsumer(Consumer<Long> c) {
+		refLock = c;
+		return this;
+	}
+
+	/**
 	 * Update properties by setting fields from the configuration.
 	 * <p>
 	 * If a property is not defined in the configuration, then it is left
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 c131f94..be1387e 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
@@ -88,6 +88,8 @@
  * objects are similar.
  */
 public final class DfsPackFile extends BlockBasedFile {
+	private static final int REC_SIZE = Constants.OBJECT_ID_LENGTH + 8;
+
 	/**
 	 * Lock for initialization of {@link #index} and {@link #corruptObjects}.
 	 * <p>
@@ -96,13 +98,13 @@ public final class DfsPackFile extends BlockBasedFile {
 	private final Object initLock = new Object();
 
 	/** Index mapping {@link ObjectId} to position within the pack stream. */
-	private volatile DfsBlockCache.Ref<PackIndex> index;
+	private volatile PackIndex index;
 
 	/** Reverse version of {@link #index} mapping position to {@link ObjectId}. */
-	private volatile DfsBlockCache.Ref<PackReverseIndex> reverseIndex;
+	private volatile PackReverseIndex reverseIndex;
 
 	/** Index of compressed bitmap mapping entire object graph. */
-	private volatile DfsBlockCache.Ref<PackBitmapIndex> bitmapIndex;
+	private volatile PackBitmapIndex bitmapIndex;
 
 	/**
 	 * Objects we have tried to read, and discovered to be corrupt.
@@ -148,15 +150,15 @@ public DfsPackDescription getPackDescription() {
 	 * @return whether the pack index file is loaded and cached in memory.
 	 */
 	public boolean isIndexLoaded() {
-		DfsBlockCache.Ref<PackIndex> idxref = index;
-		return idxref != null && idxref.has();
+		return index != null;
 	}
 
 	void setPackIndex(PackIndex idx) {
 		long objCnt = idx.getObjectCount();
 		int recSize = Constants.OBJECT_ID_LENGTH + 8;
 		long sz = objCnt * recSize;
-		index = cache.putRef(desc.getStreamKey(INDEX), sz, idx);
+		cache.putRef(desc.getStreamKey(INDEX), sz, idx);
+		index = idx;
 	}
 
 	/**
@@ -174,11 +176,8 @@ public PackIndex getPackIndex(DfsReader ctx) throws IOException {
 	}
 
 	private PackIndex idx(DfsReader ctx) throws IOException {
-		DfsBlockCache.Ref<PackIndex> idxref = index;
-		if (idxref != null) {
-			PackIndex idx = idxref.get();
-			if (idx != null)
-				return idx;
+		if (index != null) {
+			return index;
 		}
 
 		if (invalid) {
@@ -189,56 +188,61 @@ private PackIndex idx(DfsReader ctx) throws IOException {
 				.dispatch(new BeforeDfsPackIndexLoadedEvent(this));
 
 		synchronized (initLock) {
-			idxref = index;
-			if (idxref != null) {
-				PackIndex idx = idxref.get();
-				if (idx != null)
-					return idx;
+			if (index != null) {
+				return index;
 			}
 
-			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();
-				try (ReadableChannel rc = ctx.db.openFile(desc, INDEX)) {
-					InputStream in = Channels.newInputStream(rc);
-					int wantSize = 8192;
-					int bs = rc.blockSize();
-					if (0 < bs && bs < wantSize)
-						bs = (wantSize / bs) * bs;
-					else if (bs <= 0)
-						bs = wantSize;
-					idx = PackIndex.read(new BufferedInputStream(in, bs));
-					ctx.stats.readIdxBytes += rc.position();
-				} finally {
-					ctx.stats.readIdxMicros += elapsedMicros(start);
+				DfsStreamKey idxKey = desc.getStreamKey(INDEX);
+				DfsBlockCache.Ref<PackIndex> idxref = cache.getOrLoadRef(idxKey,
+						() -> {
+							try {
+								ctx.stats.readIdx++;
+								long start = System.nanoTime();
+								try (ReadableChannel rc = ctx.db.openFile(desc,
+										INDEX)) {
+									InputStream in = Channels
+											.newInputStream(rc);
+									int wantSize = 8192;
+									int bs = rc.blockSize();
+									if (0 < bs && bs < wantSize) {
+										bs = (wantSize / bs) * bs;
+									} else if (bs <= 0) {
+										bs = wantSize;
+									}
+									PackIndex idx = PackIndex.read(
+											new BufferedInputStream(in, bs));
+									int sz = (int) Math.min(
+											idx.getObjectCount() * REC_SIZE,
+											Integer.MAX_VALUE);
+									ctx.stats.readIdxBytes += rc.position();
+									index = idx;
+									return new DfsBlockCache.Ref<>(idxKey, 0,
+											sz, idx);
+								} finally {
+									ctx.stats.readIdxMicros += elapsedMicros(
+											start);
+								}
+							} catch (EOFException e) {
+								throw new IOException(MessageFormat.format(
+										DfsText.get().shortReadOfIndex,
+										desc.getFileName(INDEX)), e);
+							} catch (IOException e) {
+								throw new IOException(MessageFormat.format(
+										DfsText.get().cannotReadIndex,
+										desc.getFileName(INDEX)), e);
+							}
+						});
+				PackIndex idx = idxref.get();
+				if (index == null && idx != null) {
+					index = idx;
 				}
-			} catch (EOFException e) {
-				invalid = true;
-				invalidatingCause = e;
-				throw new IOException(MessageFormat.format(
-						DfsText.get().shortReadOfIndex,
-						desc.getFileName(INDEX)), e);
+				return index;
 			} catch (IOException e) {
 				invalid = true;
 				invalidatingCause = e;
-				throw new IOException(MessageFormat.format(
-						DfsText.get().cannotReadIndex,
-						desc.getFileName(INDEX)), e);
+				throw e;
 			}
-
-			setPackIndex(idx);
-			return idx;
 		}
 	}
 
@@ -247,102 +251,94 @@ final boolean isGarbage() {
 	}
 
 	PackBitmapIndex getBitmapIndex(DfsReader ctx) throws IOException {
-		if (invalid || isGarbage() || !desc.hasFileExt(BITMAP_INDEX))
+		if (invalid || isGarbage() || !desc.hasFileExt(BITMAP_INDEX)) {
 			return null;
+		}
 
-		DfsBlockCache.Ref<PackBitmapIndex> idxref = bitmapIndex;
-		if (idxref != null) {
-			PackBitmapIndex idx = idxref.get();
-			if (idx != null)
-				return idx;
+		if (bitmapIndex != null) {
+			return bitmapIndex;
 		}
 
 		synchronized (initLock) {
-			idxref = bitmapIndex;
-			if (idxref != null) {
-				PackBitmapIndex idx = idxref.get();
-				if (idx != null)
-					return idx;
+			if (bitmapIndex != null) {
+				return bitmapIndex;
 			}
 
+			PackIndex idx = idx(ctx);
+			PackReverseIndex revidx = getReverseIdx(ctx);
 			DfsStreamKey bitmapKey = desc.getStreamKey(BITMAP_INDEX);
-			idxref = cache.getRef(bitmapKey);
-			if (idxref != null) {
-				PackBitmapIndex idx = idxref.get();
-				if (idx != null) {
-					bitmapIndex = idxref;
-					return idx;
-				}
+			DfsBlockCache.Ref<PackBitmapIndex> idxref = cache
+					.getOrLoadRef(bitmapKey, () -> {
+						ctx.stats.readBitmap++;
+						long start = System.nanoTime();
+						try (ReadableChannel rc = ctx.db.openFile(desc,
+								BITMAP_INDEX)) {
+							long size;
+							PackBitmapIndex bmidx;
+							try {
+								InputStream in = Channels.newInputStream(rc);
+								int wantSize = 8192;
+								int bs = rc.blockSize();
+								if (0 < bs && bs < wantSize) {
+									bs = (wantSize / bs) * bs;
+								} else if (bs <= 0) {
+									bs = wantSize;
+								}
+								in = new BufferedInputStream(in, bs);
+								bmidx = PackBitmapIndex.read(in, idx, revidx);
+							} finally {
+								size = rc.position();
+								ctx.stats.readIdxBytes += size;
+								ctx.stats.readIdxMicros += elapsedMicros(start);
+							}
+							int sz = (int) Math.min(size, Integer.MAX_VALUE);
+							bitmapIndex = bmidx;
+							return new DfsBlockCache.Ref<>(bitmapKey, 0, sz,
+									bmidx);
+						} catch (EOFException e) {
+							throw new IOException(MessageFormat.format(
+									DfsText.get().shortReadOfIndex,
+									desc.getFileName(BITMAP_INDEX)), e);
+						} catch (IOException e) {
+							throw new IOException(MessageFormat.format(
+									DfsText.get().cannotReadIndex,
+									desc.getFileName(BITMAP_INDEX)), e);
+						}
+					});
+			PackBitmapIndex bmidx = idxref.get();
+			if (bitmapIndex == null && bmidx != null) {
+				bitmapIndex = bmidx;
 			}
-
-			long size;
-			PackBitmapIndex idx;
-			ctx.stats.readBitmap++;
-			long start = System.nanoTime();
-			try (ReadableChannel rc = ctx.db.openFile(desc, BITMAP_INDEX)) {
-				try {
-					InputStream in = Channels.newInputStream(rc);
-					int wantSize = 8192;
-					int bs = rc.blockSize();
-					if (0 < bs && bs < wantSize)
-						bs = (wantSize / bs) * bs;
-					else if (bs <= 0)
-						bs = wantSize;
-					in = new BufferedInputStream(in, bs);
-					idx = PackBitmapIndex.read(
-							in, idx(ctx), getReverseIdx(ctx));
-				} finally {
-					size = rc.position();
-					ctx.stats.readIdxBytes += size;
-					ctx.stats.readIdxMicros += elapsedMicros(start);
-				}
-			} catch (EOFException e) {
-				throw new IOException(MessageFormat.format(
-						DfsText.get().shortReadOfIndex,
-						desc.getFileName(BITMAP_INDEX)), e);
-			} catch (IOException e) {
-				throw new IOException(MessageFormat.format(
-						DfsText.get().cannotReadIndex,
-						desc.getFileName(BITMAP_INDEX)), e);
-			}
-
-			bitmapIndex = cache.putRef(bitmapKey, size, idx);
-			return idx;
+			return bitmapIndex;
 		}
 	}
 
 	PackReverseIndex getReverseIdx(DfsReader ctx) throws IOException {
-		DfsBlockCache.Ref<PackReverseIndex> revref = reverseIndex;
-		if (revref != null) {
-			PackReverseIndex revidx = revref.get();
-			if (revidx != null)
-				return revidx;
+		if (reverseIndex != null) {
+			return reverseIndex;
 		}
 
 		synchronized (initLock) {
-			revref = reverseIndex;
-			if (revref != null) {
-				PackReverseIndex revidx = revref.get();
-				if (revidx != null)
-					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;
-				}
+			if (reverseIndex != null) {
+				return reverseIndex;
 			}
 
 			PackIndex idx = idx(ctx);
-			PackReverseIndex revidx = new PackReverseIndex(idx);
-			long cnt = idx.getObjectCount();
-			reverseIndex = cache.putRef(revKey, cnt * 8, revidx);
-			return revidx;
+			DfsStreamKey revKey = new DfsStreamKey.ForReverseIndex(
+					desc.getStreamKey(INDEX));
+			DfsBlockCache.Ref<PackReverseIndex> revref = cache
+					.getOrLoadRef(revKey, () -> {
+						PackReverseIndex revidx = new PackReverseIndex(idx);
+						int sz = (int) Math.min(idx.getObjectCount() * 8,
+								Integer.MAX_VALUE);
+						reverseIndex = revidx;
+						return new DfsBlockCache.Ref<>(revKey, 0, sz, revidx);
+					});
+			PackReverseIndex revidx = revref.get();
+			if (reverseIndex == null && revidx != null) {
+				reverseIndex = revidx;
+			}
+			return reverseIndex;
 		}
 	}
 
@@ -420,110 +416,94 @@ long getObjectCount(DfsReader ctx) throws IOException {
 			return null;
 		}
 
-		if (ctx.inflate(this, position, dstbuf, false) != sz)
+		if (ctx.inflate(this, position, dstbuf, false) != sz) {
 			throw new EOFException(MessageFormat.format(
 					JGitText.get().shortCompressedStreamAt,
 					Long.valueOf(position)));
+		}
 		return dstbuf;
 	}
 
-	void copyPackAsIs(PackOutputStream out, DfsReader ctx)
-			throws IOException {
+	void copyPackAsIs(PackOutputStream out, DfsReader ctx) throws IOException {
 		// If the length hasn't been determined yet, pin to set it.
 		if (length == -1) {
 			ctx.pin(this, 0);
 			ctx.unpin();
 		}
-		if (cache.shouldCopyThroughCache(length))
-			copyPackThroughCache(out, ctx);
-		else
-			copyPackBypassCache(out, ctx);
+		try (ReadableChannel rc = ctx.db.openFile(desc, PACK)) {
+			int sz = ctx.getOptions().getStreamPackBufferSize();
+			if (sz > 0) {
+				rc.setReadAheadBytes(sz);
+			}
+			if (cache.shouldCopyThroughCache(length)) {
+				copyPackThroughCache(out, ctx, rc);
+			} else {
+				copyPackBypassCache(out, rc);
+			}
+		}
 	}
 
-	private void copyPackThroughCache(PackOutputStream out, DfsReader ctx)
-			throws IOException {
-		@SuppressWarnings("resource") // Explicitly closed in finally block
-		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);
-					}
-				}
+	private void copyPackThroughCache(PackOutputStream out, DfsReader ctx,
+			ReadableChannel rc) throws IOException {
+		long position = 12;
+		long remaining = length - (12 + 20);
+		while (0 < remaining) {
+			DfsBlock b = cache.getOrLoad(this, position, ctx, () -> rc);
+			int ptr = (int) (position - b.start);
+			if (b.size() <= ptr) {
+				throw packfileIsTruncated();
+			}
+			int n = (int) Math.min(b.size() - ptr, remaining);
+			b.write(out, position, n);
+			position += n;
+			remaining -= n;
+		}
+	}
 
+	private long copyPackBypassCache(PackOutputStream out, ReadableChannel rc)
+			throws IOException {
+		ByteBuffer buf = newCopyBuffer(out, rc);
+		long position = 12;
+		long remaining = length - (12 + 20);
+		boolean packHeadSkipped = false;
+		while (0 < remaining) {
+			DfsBlock b = cache.get(key, alignToBlock(position));
+			if (b != null) {
 				int ptr = (int) (position - b.start);
+				if (b.size() <= ptr) {
+					throw packfileIsTruncated();
+				}
 				int n = (int) Math.min(b.size() - ptr, remaining);
 				b.write(out, position, n);
 				position += n;
 				remaining -= n;
+				rc.position(position);
+				packHeadSkipped = true;
+				continue;
 			}
-		} finally {
-			if (rc != null) {
-				rc.close();
+
+			// Need to skip the 'PACK' header for the first read
+			int ptr = packHeadSkipped ? 0 : 12;
+			buf.position(0);
+			int bufLen = read(rc, buf);
+			if (bufLen <= ptr) {
+				throw packfileIsTruncated();
 			}
+			int n = (int) Math.min(bufLen - ptr, remaining);
+			out.write(buf.array(), ptr, n);
+			position += n;
+			remaining -= n;
+			packHeadSkipped = true;
 		}
-	}
-
-	private long copyPackBypassCache(PackOutputStream out, DfsReader ctx)
-			throws IOException {
-		try (ReadableChannel rc = ctx.db.openFile(desc, PACK)) {
-			ByteBuffer buf = newCopyBuffer(out, rc);
-			if (ctx.getOptions().getStreamPackBufferSize() > 0)
-				rc.setReadAheadBytes(ctx.getOptions().getStreamPackBufferSize());
-			long position = 12;
-			long remaining = length - (12 + 20);
-			boolean packHeadSkipped = false;
-			while (0 < remaining) {
-				DfsBlock b = cache.get(key, alignToBlock(position));
-				if (b != null) {
-					int ptr = (int) (position - b.start);
-					int n = (int) Math.min(b.size() - ptr, remaining);
-					b.write(out, position, n);
-					position += n;
-					remaining -= n;
-					rc.position(position);
-					packHeadSkipped = true;
-					continue;
-				}
-
-				buf.position(0);
-				int n = read(rc, buf);
-				if (n <= 0)
-					throw packfileIsTruncated();
-				else if (n > remaining)
-					n = (int) remaining;
-
-				if (!packHeadSkipped) {
-					// Need skip the 'PACK' header for the first read
-					out.write(buf.array(), 12, n - 12);
-					packHeadSkipped = true;
-				} else {
-					out.write(buf.array(), 0, n);
-				}
-				position += n;
-				remaining -= n;
-			}
-			return position;
-		}
+		return position;
 	}
 
 	private ByteBuffer newCopyBuffer(PackOutputStream out, ReadableChannel rc) {
 		int bs = blockSize(rc);
 		byte[] copyBuf = out.getCopyBuffer();
-		if (bs > copyBuf.length)
+		if (bs > copyBuf.length) {
 			copyBuf = new byte[bs];
+		}
 		return ByteBuffer.wrap(copyBuf, 0, bs);
 	}
 
@@ -635,8 +615,9 @@ void copyAsIs(PackOutputStream out, DfsObjectToPack src,
 						readFully(pos, buf, 0, n, ctx);
 						crc1.update(buf, 0, n);
 						inf.setInput(buf, 0, n);
-						while (inf.inflate(tmp, 0, tmp.length) > 0)
+						while (inf.inflate(tmp, 0, tmp.length) > 0) {
 							continue;
+						}
 						pos += n;
 						cnt -= n;
 					}
@@ -770,8 +751,9 @@ ObjectLoader load(DfsReader ctx, long pos)
 
 					if (sz < ctx.getStreamFileThreshold()) {
 						data = decompress(pos + p, (int) sz, ctx);
-						if (data != null)
+						if (data != null) {
 							return new ObjectLoader.SmallObject(typeCode, data);
+						}
 					}
 					return new LargePackedWholeObject(typeCode, sz, pos, p, this, ctx.db);
 				}
@@ -787,8 +769,9 @@ ObjectLoader load(DfsReader ctx, long pos)
 					}
 					base = pos - base;
 					delta = new Delta(delta, pos, (int) sz, p, base);
-					if (sz != delta.deltaSize)
+					if (sz != delta.deltaSize) {
 						break SEARCH;
+					}
 
 					DeltaBaseCache.Entry e = ctx.getDeltaBaseCache().get(key, base);
 					if (e != null) {
@@ -805,8 +788,9 @@ ObjectLoader load(DfsReader ctx, long pos)
 					readFully(pos + p, ib, 0, 20, ctx);
 					long base = findDeltaBase(ctx, ObjectId.fromRaw(ib));
 					delta = new Delta(delta, pos, (int) sz, p + 20, base);
-					if (sz != delta.deltaSize)
+					if (sz != delta.deltaSize) {
 						break SEARCH;
+					}
 
 					DeltaBaseCache.Entry e = ctx.getDeltaBaseCache().get(key, base);
 					if (e != null) {
@@ -834,10 +818,11 @@ ObjectLoader load(DfsReader ctx, long pos)
 			assert(delta != null);
 			do {
 				// Cache only the base immediately before desired object.
-				if (cached)
+				if (cached) {
 					cached = false;
-				else if (delta.next == null)
+				} else if (delta.next == null) {
 					ctx.getDeltaBaseCache().put(key, delta.basePos, type, data);
+				}
 
 				pos = delta.deltaPos;
 
@@ -848,8 +833,9 @@ else if (delta.next == null)
 				}
 
 				final long sz = BinaryDelta.getResultSize(cmds);
-				if (Integer.MAX_VALUE <= sz)
+				if (Integer.MAX_VALUE <= sz) {
 					throw new LargeObjectException.ExceedsByteArrayLimit();
+				}
 
 				final byte[] result;
 				try {
@@ -879,9 +865,10 @@ else if (delta.next == null)
 	private long findDeltaBase(DfsReader ctx, ObjectId baseId)
 			throws IOException, MissingObjectException {
 		long ofs = idx(ctx).findOffset(baseId);
-		if (ofs < 0)
+		if (ofs < 0) {
 			throw new MissingObjectException(baseId,
 					JGitText.get().missingDeltaBase);
+		}
 		return ofs;
 	}
 
@@ -938,8 +925,9 @@ int getObjectType(DfsReader ctx, long pos) throws IOException {
 
 			case Constants.OBJ_OFS_DELTA: {
 				int p = 1;
-				while ((c & 0x80) != 0)
+				while ((c & 0x80) != 0) {
 					c = ib[p++] & 0xff;
+				}
 				c = ib[p++] & 0xff;
 				long ofs = c & 127;
 				while ((c & 128) != 0) {
@@ -954,8 +942,9 @@ int getObjectType(DfsReader ctx, long pos) throws IOException {
 
 			case Constants.OBJ_REF_DELTA: {
 				int p = 1;
-				while ((c & 0x80) != 0)
+				while ((c & 0x80) != 0) {
 					c = ib[p++] & 0xff;
+				}
 				readFully(pos + p, ib, 0, 20, ctx);
 				pos = findDeltaBase(ctx, ObjectId.fromRaw(ib));
 				continue;
@@ -998,8 +987,9 @@ long getObjectSize(DfsReader ctx, long pos)
 
 		case Constants.OBJ_OFS_DELTA:
 			c = ib[p++] & 0xff;
-			while ((c & 128) != 0)
+			while ((c & 128) != 0) {
 				c = ib[p++] & 0xff;
+			}
 			deltaAt = pos + p;
 			break;
 
@@ -1032,8 +1022,9 @@ void representation(DfsObjectRepresentation r, final long pos,
 		int c = ib[0] & 0xff;
 		int p = 1;
 		final int typeCode = (c >> 4) & 7;
-		while ((c & 0x80) != 0)
+		while ((c & 0x80) != 0) {
 			c = ib[p++] & 0xff;
+		}
 
 		long len = rev.findNextOffset(pos, length - 20) - pos;
 		switch (typeCode) {
@@ -1077,8 +1068,9 @@ void representation(DfsObjectRepresentation r, final long pos,
 
 	boolean isCorrupt(long offset) {
 		LongList list = corruptObjects;
-		if (list == null)
+		if (list == null) {
 			return false;
+		}
 		synchronized (list) {
 			return list.contains(offset);
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsRefDatabase.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsRefDatabase.java
index a884346..8b2a03d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsRefDatabase.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsRefDatabase.java
@@ -107,20 +107,6 @@ public Ref exactRef(String name) throws IOException {
 
 	/** {@inheritDoc} */
 	@Override
-	public Ref getRef(String needle) throws IOException {
-		RefCache curr = read();
-		for (String prefix : SEARCH_PATH) {
-			Ref ref = curr.ids.get(prefix + needle);
-			if (ref != null) {
-				ref = resolve(ref, 0, curr.ids);
-				return ref;
-			}
-		}
-		return null;
-	}
-
-	/** {@inheritDoc} */
-	@Override
 	public List<Ref> getAdditionalRefs() {
 		return Collections.emptyList();
 	}
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
index 7502471..4853298 100644
--- 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
@@ -128,7 +128,7 @@ public ByteBuffer read(long pos, int cnt) throws IOException {
 				open().setReadAheadBytes(readAhead);
 			}
 
-			DfsBlock block = cache.getOrLoad(file, pos, ctx, ch);
+			DfsBlock block = cache.getOrLoad(file, pos, ctx, () -> open());
 			if (block.start == pos && block.size() >= cnt) {
 				return block.zeroCopyByteBuffer(cnt);
 			}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsReftableDatabase.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsReftableDatabase.java
index 7081630..83394bb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsReftableDatabase.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsReftableDatabase.java
@@ -99,6 +99,12 @@ protected DfsReftableDatabase(DfsRepository repo) {
 
 	/** {@inheritDoc} */
 	@Override
+	public boolean hasVersioning() {
+		return true;
+	}
+
+	/** {@inheritDoc} */
+	@Override
 	public boolean performsAtomicTransactions() {
 		return true;
 	}
@@ -223,18 +229,6 @@ public Ref exactRef(String name) throws IOException {
 
 	/** {@inheritDoc} */
 	@Override
-	public Ref getRef(String needle) throws IOException {
-		for (String prefix : SEARCH_PATH) {
-			Ref ref = exactRef(prefix + needle);
-			if (ref != null) {
-				return ref;
-			}
-		}
-		return null;
-	}
-
-	/** {@inheritDoc} */
-	@Override
 	public Map<String, Ref> getRefs(String prefix) throws IOException {
 		RefList.Builder<Ref> all = new RefList.Builder<>();
 		lock.lock();
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 791a108..7400308 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
@@ -160,7 +160,6 @@ public class GC {
 	 *
 	 * @param e
 	 *            the executor to be used for running auto-gc
-	 * @since 4.8
 	 */
 	public static void setExecutor(ExecutorService e) {
 		executor = e;
@@ -918,7 +917,8 @@ private void deleteEmptyRefsFolders() throws IOException {
 		// Avoid deleting a folder that was created after the threshold so that concurrent
 		// operations trying to create a reference are not impacted
 		Instant threshold = Instant.now().minus(30, ChronoUnit.SECONDS);
-		try (Stream<Path> entries = Files.list(refs)) {
+		try (Stream<Path> entries = Files.list(refs)
+				.filter(Files::isDirectory)) {
 			Iterator<Path> iterator = entries.iterator();
 			while (iterator.hasNext()) {
 				try (Stream<Path> s = Files.list(iterator.next())) {
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 3552266..258ccee 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
@@ -198,7 +198,6 @@ public final File getDirectory() {
 	 * <p>Getter for the field <code>packDirectory</code>.</p>
 	 *
 	 * @return the location of the <code>pack</code> directory.
-	 * @since 4.10
 	 */
 	public final File getPackDirectory() {
 		return packDirectory;
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 de7e4b3..a4729bb 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
@@ -74,6 +74,7 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.HashMap;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
@@ -319,16 +320,14 @@ private RefList<LooseRef> getLooseRefs() {
 		return loose;
 	}
 
-	/** {@inheritDoc} */
-	@Override
-	public Ref exactRef(String name) throws IOException {
-		RefList<Ref> packed = getPackedRefs();
-		Ref ref;
+	@Nullable
+	private Ref readAndResolve(String name, RefList<Ref> packed) throws IOException {
 		try {
-			ref = readRef(name, packed);
+			Ref ref = readRef(name, packed);
 			if (ref != null) {
 				ref = resolve(ref, 0, null, null, packed);
 			}
+			return ref;
 		} catch (IOException e) {
 			if (name.contains("/") //$NON-NLS-1$
 					|| !(e.getCause() instanceof InvalidObjectIdException)) {
@@ -338,35 +337,55 @@ public Ref exactRef(String name) throws IOException {
 			// While looking for a ref outside of refs/ (e.g., 'config'), we
 			// found a non-ref file (e.g., a config file) instead.  Treat this
 			// as a ref-not-found condition.
-			ref = null;
+			return null;
 		}
-		fireRefsChanged();
-		return ref;
 	}
 
 	/** {@inheritDoc} */
 	@Override
-	public Ref getRef(String needle) throws IOException {
-		final RefList<Ref> packed = getPackedRefs();
-		Ref ref = null;
-		for (String prefix : SEARCH_PATH) {
-			try {
-				ref = readRef(prefix + needle, packed);
+	public Ref exactRef(String name) throws IOException {
+		try {
+			return readAndResolve(name, getPackedRefs());
+		} finally {
+			fireRefsChanged();
+		}
+	}
+
+	/** {@inheritDoc} */
+	@Override
+	@NonNull
+	public Map<String, Ref> exactRef(String... refs) throws IOException {
+		try {
+			RefList<Ref> packed = getPackedRefs();
+			Map<String, Ref> result = new HashMap<>(refs.length);
+			for (String name : refs) {
+				Ref ref = readAndResolve(name, packed);
 				if (ref != null) {
-					ref = resolve(ref, 0, null, null, packed);
-				}
-				if (ref != null) {
-					break;
-				}
-			} catch (IOException e) {
-				if (!(!needle.contains("/") && "".equals(prefix) && e //$NON-NLS-1$ //$NON-NLS-2$
-						.getCause() instanceof InvalidObjectIdException)) {
-					throw e;
+					result.put(name, ref);
 				}
 			}
+			return result;
+		} finally {
+			fireRefsChanged();
 		}
-		fireRefsChanged();
-		return ref;
+	}
+
+	/** {@inheritDoc} */
+	@Override
+	@Nullable
+	public Ref firstExactRef(String... refs) throws IOException {
+		try {
+			RefList<Ref> packed = getPackedRefs();
+			for (String name : refs) {
+				Ref ref = readAndResolve(name, packed);
+				if (ref != null) {
+					return ref;
+				}
+			}
+			return null;
+		} finally {
+			fireRefsChanged();
+		}
 	}
 
 	/** {@inheritDoc} */
@@ -414,7 +433,7 @@ public Map<String, Ref> getRefs(String prefix) throws IOException {
 	public List<Ref> getAdditionalRefs() throws IOException {
 		List<Ref> ret = new LinkedList<>();
 		for (String name : additionalRefsNames) {
-			Ref r = getRef(name);
+			Ref r = exactRef(name);
 			if (r != null)
 				ret.add(r);
 		}
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 45ce634..1a0d695 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
@@ -87,7 +87,7 @@ protected boolean tryLock(boolean deref) throws IOException {
 		String name = dst.getName();
 		lock = new LockFile(database.fileFor(name));
 		if (lock.lock()) {
-			dst = database.getRef(name);
+			dst = database.findRef(name);
 			setOldObjectId(dst != null ? dst.getObjectId() : null);
 			return true;
 		} else {
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 8cf1d4e..e8fac51 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
@@ -146,7 +146,7 @@ private static final int bits(int newSize) {
 	 * Modify the configuration of the window cache.
 	 * <p>
 	 * The new configuration is applied immediately. If the new limits are
-	 * smaller than what what is currently cached, older entries will be purged
+	 * smaller than what is currently cached, older entries will be purged
 	 * as soon as possible to allow the cache to meet the new limit.
 	 *
 	 * @deprecated use {@code cfg.install()} to avoid internal reference.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/DeltaEncoder.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/DeltaEncoder.java
index 343faf4..cfc1ccd 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/DeltaEncoder.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/DeltaEncoder.java
@@ -73,7 +73,7 @@ public class DeltaEncoder {
 	/** Maximum number of bytes used by a copy instruction. */
 	private static final int MAX_COPY_CMD_SIZE = 8;
 
-	/** Maximum length that an an insert command can encode at once. */
+	/** Maximum length that an insert command can encode at once. */
 	private static final int MAX_INSERT_DATA_SIZE = 127;
 
 	private final OutputStream out;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java
index 24af8a7..1e3d74a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java
@@ -642,7 +642,6 @@ public void setShallowPack(int depth,
 
 	/**
 	 * @param bytes exclude blobs of size greater than this
-	 * @since 5.0
 	 */
 	public void setFilterBlobLimit(long bytes) {
 		filterBlobLimit = bytes;
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
index ce2ba4a..44529bf 100644
--- 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
@@ -170,24 +170,27 @@ long readUpdateIndexDelta() {
 		return readVarint64();
 	}
 
-	Ref readRef() throws IOException {
+	Ref readRef(long minUpdateIndex) throws IOException {
+		long updateIndex = minUpdateIndex + readUpdateIndexDelta();
 		String name = RawParseUtils.decode(UTF_8, nameBuf, 0, nameLen);
 		switch (valueType & VALUE_TYPE_MASK) {
 		case VALUE_NONE: // delete
-			return newRef(name);
+			return newRef(name, updateIndex);
 
 		case VALUE_1ID:
-			return new ObjectIdRef.PeeledNonTag(PACKED, name, readValueId());
+			return new ObjectIdRef.PeeledNonTag(PACKED, name, readValueId(),
+					updateIndex);
 
 		case VALUE_2ID: { // annotated tag
 			ObjectId id1 = readValueId();
 			ObjectId id2 = readValueId();
-			return new ObjectIdRef.PeeledTag(PACKED, name, id1, id2);
+			return new ObjectIdRef.PeeledTag(PACKED, name, id1, id2,
+					updateIndex);
 		}
 
 		case VALUE_SYMREF: {
 			String val = readValueString();
-			return new SymbolicRef(name, newRef(val));
+			return new SymbolicRef(name, newRef(val, updateIndex), updateIndex);
 		}
 
 		default:
@@ -410,7 +413,7 @@ void verifyIndex() throws IOException {
 	 * <ul>
 	 * <li>{@link #name()}
 	 * <li>{@link #match(byte[], boolean)}
-	 * <li>{@link #readRef()}
+	 * <li>{@link #readRef(long)}
 	 * <li>{@link #readLogUpdateIndex()}
 	 * <li>{@link #readLogEntry()}
 	 * <li>{@link #readBlockPositionList()}
@@ -575,8 +578,8 @@ private long readVarint64() {
 		return val;
 	}
 
-	private static Ref newRef(String name) {
-		return new ObjectIdRef.Unpeeled(NEW, name, null);
+	private static Ref newRef(String name, long updateIndex) {
+		return new ObjectIdRef.Unpeeled(NEW, name, null, updateIndex);
 	}
 
 	private static IOException invalidBlock() {
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
index 17894b1..c740bf2 100644
--- 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
@@ -168,7 +168,6 @@ 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);
@@ -206,7 +205,6 @@ public boolean next() throws IOException {
 				}
 
 				ref = t.rc.getRef();
-				updateIndex = t.rc.getUpdateIndex();
 				boolean include = includeDeletes || !t.rc.wasDeleted();
 				add(t);
 				skipShadowedRefs(ref.getName());
@@ -242,11 +240,6 @@ public Ref getRef() {
 		}
 
 		@Override
-		public long getUpdateIndex() {
-			return updateIndex;
-		}
-
-		@Override
 		public void close() {
 			if (head != null) {
 				head.rc.close();
@@ -285,7 +278,7 @@ String name() {
 		}
 
 		long updateIndex() {
-			return rc.getUpdateIndex();
+			return rc.getRef().getUpdateIndex();
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/RefCursor.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/RefCursor.java
index 5d4af30..9749ffb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/RefCursor.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/RefCursor.java
@@ -69,13 +69,6 @@ public abstract class RefCursor implements AutoCloseable {
 	public abstract Ref getRef();
 
 	/**
-	 * Get updateIndex that last modified the current reference.
-	 *
-	 * @return updateIndex that last modified the current reference.
-	 */
-	public abstract long getUpdateIndex();
-
-	/**
 	 * Whether the current reference was deleted.
 	 *
 	 * @return {@code true} if the current reference was deleted.
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
index a1087e2..cb02628 100644
--- 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
@@ -280,7 +280,7 @@ private Ref resolve(Ref ref, int depth) throws IOException {
 		if (dst == null) {
 			return null; // claim it doesn't exist
 		}
-		return new SymbolicRef(ref.getName(), dst);
+		return new SymbolicRef(ref.getName(), dst, ref.getUpdateIndex());
 	}
 
 	/** {@inheritDoc} */
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
index ed73a9e..c4e8f69 100644
--- 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
@@ -256,7 +256,7 @@ public Stats getStats() {
 	private void mergeRefs(MergedReftable mr) throws IOException {
 		try (RefCursor rc = mr.allRefs()) {
 			while (rc.next()) {
-				writer.writeRef(rc.getRef(), rc.getUpdateIndex());
+				writer.writeRef(rc.getRef(), rc.getRef().getUpdateIndex());
 			}
 		}
 	}
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
index 81b30e4..bf3a9ae 100644
--- 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
@@ -479,7 +479,6 @@ private class RefCursorImpl extends RefCursor {
 		private final boolean prefix;
 
 		private Ref ref;
-		private long updateIndex;
 		BlockReader block;
 
 		RefCursorImpl(long scanEnd, byte[] match, boolean prefix) {
@@ -508,8 +507,7 @@ public boolean next() throws IOException {
 					return false;
 				}
 
-				updateIndex = minUpdateIndex + block.readUpdateIndexDelta();
-				ref = block.readRef();
+				ref = block.readRef(minUpdateIndex);
 				if (!includeDeletes && wasDeleted()) {
 					continue;
 				}
@@ -523,11 +521,6 @@ public Ref getRef() {
 		}
 
 		@Override
-		public long getUpdateIndex() {
-			return updateIndex;
-		}
-
-		@Override
 		public void close() {
 			// Do nothing.
 		}
@@ -605,7 +598,6 @@ private class ObjCursorImpl extends RefCursor {
 		private final ObjectId match;
 
 		private Ref ref;
-		private long updateIndex;
 		private int listIdx;
 
 		private LongList blockPos;
@@ -679,8 +671,7 @@ public boolean next() throws IOException {
 				}
 
 				block.parseKey();
-				updateIndex = minUpdateIndex + block.readUpdateIndexDelta();
-				ref = block.readRef();
+				ref = block.readRef(minUpdateIndex);
 				ObjectId id = ref.getObjectId();
 				if (id != null && match.equals(id)
 						&& (includeDeletes || !wasDeleted())) {
@@ -695,11 +686,6 @@ public Ref getRef() {
 		}
 
 		@Override
-		public long getUpdateIndex() {
-			return updateIndex;
-		}
-
-		@Override
 		public void close() {
 			// Do nothing.
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftree/RefTreeDatabase.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftree/RefTreeDatabase.java
index 27daaf0..ddd05b3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftree/RefTreeDatabase.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftree/RefTreeDatabase.java
@@ -206,16 +206,6 @@ public void close() {
 
 	/** {@inheritDoc} */
 	@Override
-	public Ref getRef(String name) throws IOException {
-		String[] needle = new String[SEARCH_PATH.length];
-		for (int i = 0; i < SEARCH_PATH.length; i++) {
-			needle[i] = SEARCH_PATH[i] + name;
-		}
-		return firstExactRef(needle);
-	}
-
-	/** {@inheritDoc} */
-	@Override
 	public Ref exactRef(String name) throws IOException {
 		if (!repo.isBare() && name.indexOf('/') < 0 && !HEAD.equals(name)) {
 			// Pass through names like MERGE_HEAD, ORIG_HEAD, FETCH_HEAD.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftree/Scanner.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftree/Scanner.java
index 2ef0f20..2fa59f3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftree/Scanner.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftree/Scanner.java
@@ -221,10 +221,11 @@ private static Ref resolve(Ref ref, int depth, RefList<Ref> refs)
 		return new SymbolicRef(ref.getName(), dst);
 	}
 
-	@SuppressWarnings("resource")
 	private static RevTree toTree(ObjectReader reader, AnyObjectId id)
 			throws IOException {
-		return new RevWalk(reader).parseTree(id);
+		try (RevWalk rw = new RevWalk(reader)) {
+			return rw.parseTree(id);
+		}
 	}
 
 	private static boolean curElementHasPeelSuffix(AbstractTreeIterator itr) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/submodule/SubmoduleValidator.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/submodule/SubmoduleValidator.java
index 7b872b1..cd6af6a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/submodule/SubmoduleValidator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/submodule/SubmoduleValidator.java
@@ -61,7 +61,7 @@
  * Validations for the git submodule fields (name, path, uri).
  *
  * Invalid values in these fields can cause security problems as reported in
- * CVE-2018-11235 and and CVE-2018-17456
+ * CVE-2018-11235 and CVE-2018-17456
  */
 public class SubmoduleValidator {
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/parser/FirstCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/parser/FirstCommand.java
new file mode 100644
index 0000000..0426b17
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/parser/FirstCommand.java
@@ -0,0 +1,108 @@
+/*
+ * Copyright (C) 2018, Google LLC.
+ * 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.transport.parser;
+
+import static java.util.Arrays.asList;
+import static java.util.Collections.emptySet;
+import static java.util.Collections.unmodifiableSet;
+import static java.util.stream.Collectors.toSet;
+
+import java.util.Set;
+
+import org.eclipse.jgit.annotations.NonNull;
+
+/**
+ * In a push, the client sends a list of commands. The first command
+ * is special, as it can include a list of capabilities at its end.
+ * <p>
+ * For example:
+ * "oid oid name\0cap1 cap cap3"
+ * <p>
+ * Not to be confused with {@link FirstWant}, nor with the first line
+ * of the reference advertisement parsed by
+ * {@code BasePackConnection.readAdvertisedRefs}.
+ * <p>
+ * This class parses the inputted command line and holds the results:
+ * the actual command line and the capabilities.
+ */
+public final class FirstCommand {
+	private final String line;
+	private final Set<String> capabilities;
+
+	/**
+	 * Parse the first line of a receive-pack request.
+	 *
+	 * @param line
+	 *            line from the client.
+	 * @return an instance of FirstCommand with capabilities parsed out
+	 */
+	@NonNull
+	public static FirstCommand fromLine(String line) {
+		int nul = line.indexOf('\0');
+		if (nul < 0) {
+			return new FirstCommand(line, emptySet());
+		}
+		Set<String> opts =
+				asList(line.substring(nul + 1).split(" ")) //$NON-NLS-1$
+					.stream()
+					.collect(toSet());
+		return new FirstCommand(line.substring(0, nul), unmodifiableSet(opts));
+	}
+
+	private FirstCommand(String line, Set<String> capabilities) {
+		this.line = line;
+		this.capabilities = capabilities;
+	}
+
+	/** @return non-capabilities part of the line. */
+	@NonNull
+	public String getLine() {
+		return line;
+	}
+
+	/** @return capabilities parsed from the line, as an immutable set. */
+	@NonNull
+	public Set<String> getCapabilities() {
+		return capabilities;
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/parser/FirstWant.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/parser/FirstWant.java
index 2dae021..401c507 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/parser/FirstWant.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/parser/FirstWant.java
@@ -67,7 +67,6 @@
  * This class parses the input want line and holds the results: the actual want
  * line and the capabilities.
  *
- * @since 5.2
  */
 public class FirstWant {
 	private final String line;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/CommitBuilder.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/CommitBuilder.java
index c30833d..6cbddec 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/CommitBuilder.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/CommitBuilder.java
@@ -49,11 +49,15 @@
 
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
+import java.io.OutputStream;
 import java.io.OutputStreamWriter;
 import java.io.UnsupportedEncodingException;
 import java.nio.charset.Charset;
+import java.text.MessageFormat;
 import java.util.List;
 
+import org.eclipse.jgit.internal.JGitText;
+
 /**
  * Mutable builder to construct a commit recording the state of a project.
  *
@@ -76,6 +80,8 @@ public class CommitBuilder {
 
 	private static final byte[] hcommitter = Constants.encodeASCII("committer"); //$NON-NLS-1$
 
+	private static final byte[] hgpgsig = Constants.encodeASCII("gpgsig"); //$NON-NLS-1$
+
 	private static final byte[] hencoding = Constants.encodeASCII("encoding"); //$NON-NLS-1$
 
 	private ObjectId treeId;
@@ -86,6 +92,8 @@ public class CommitBuilder {
 
 	private PersonIdent committer;
 
+	private GpgSignature gpgSignature;
+
 	private String message;
 
 	private Charset encoding;
@@ -108,7 +116,7 @@ public ObjectId getTreeId() {
 	}
 
 	/**
-	 * Set the tree id for this commit object
+	 * Set the tree id for this commit object.
 	 *
 	 * @param id
 	 *            the tree identity.
@@ -146,7 +154,7 @@ public PersonIdent getCommitter() {
 	}
 
 	/**
-	 * Set the committer and commit time for this object
+	 * Set the committer and commit time for this object.
 	 *
 	 * @param newCommitter
 	 *            the committer information. Should not be null.
@@ -156,6 +164,38 @@ public void setCommitter(PersonIdent newCommitter) {
 	}
 
 	/**
+	 * Set the GPG signature of this commit.
+	 * <p>
+	 * Note, the signature set here will change the payload of the commit, i.e.
+	 * the output of {@link #build()} will include the signature. Thus, the
+	 * typical flow will be:
+	 * <ol>
+	 * <li>call {@link #build()} without a signature set to obtain payload</li>
+	 * <li>create {@link GpgSignature} from payload</li>
+	 * <li>set {@link GpgSignature}</li>
+	 * </ol>
+	 * </p>
+	 *
+	 * @param newSignature
+	 *            the signature to set or <code>null</code> to unset
+	 * @since 5.3
+	 */
+	public void setGpgSignature(GpgSignature newSignature) {
+		gpgSignature = newSignature;
+	}
+
+	/**
+	 * Get the GPG signature of this commit.
+	 *
+	 * @return the GPG signature of this commit, maybe <code>null</code> if the
+	 *         commit is not to be signed
+	 * @since 5.3
+	 */
+	public GpgSignature getGpgSignature() {
+		return gpgSignature;
+	}
+
+	/**
 	 * Get the ancestors of this commit.
 	 *
 	 * @return the ancestors of this commit. Never null.
@@ -250,18 +290,20 @@ public void setMessage(String newMessage) {
 	}
 
 	/**
-	 * Set the encoding for the commit information
+	 * Set the encoding for the commit information.
 	 *
 	 * @param encodingName
 	 *            the encoding name. See
 	 *            {@link java.nio.charset.Charset#forName(String)}.
+	 * @deprecated use {@link #setEncoding(Charset)} instead.
 	 */
+	@Deprecated
 	public void setEncoding(String encodingName) {
 		encoding = Charset.forName(encodingName);
 	}
 
 	/**
-	 * Set the encoding for the commit information
+	 * Set the encoding for the commit information.
 	 *
 	 * @param enc
 	 *            the encoding to use.
@@ -316,6 +358,13 @@ public Charset getEncoding() {
 			w.flush();
 			os.write('\n');
 
+			if (getGpgSignature() != null) {
+				os.write(hgpgsig);
+				os.write(' ');
+				writeGpgSignatureString(getGpgSignature().toExternalString(), os);
+				os.write('\n');
+			}
+
 			if (getEncoding() != UTF_8) {
 				os.write(hencoding);
 				os.write(' ');
@@ -339,6 +388,50 @@ public Charset getEncoding() {
 	}
 
 	/**
+	 * Writes signature to output as per <a href=
+	 * "https://github.com/git/git/blob/master/Documentation/technical/signature-format.txt#L66,L89">gpgsig
+	 * header</a>.
+	 * <p>
+	 * CRLF and CR will be sanitized to LF and signature will have a hanging
+	 * indent of one space starting with line two.
+	 * </p>
+	 *
+	 * @param in
+	 *            signature string with line breaks
+	 * @param out
+	 *            output stream
+	 * @throws IOException
+	 *             thrown by the output stream
+	 * @throws IllegalArgumentException
+	 *             if the signature string contains non 7-bit ASCII chars
+	 */
+	static void writeGpgSignatureString(String in, OutputStream out)
+			throws IOException, IllegalArgumentException {
+		for (int i = 0; i < in.length(); ++i) {
+			char ch = in.charAt(i);
+			if (ch == '\r') {
+				if (i + 1 < in.length() && in.charAt(i + 1) == '\n') {
+					out.write('\n');
+					out.write(' ');
+					++i;
+				} else {
+					out.write('\n');
+					out.write(' ');
+				}
+			} else if (ch == '\n') {
+				out.write('\n');
+				out.write(' ');
+			} else {
+				// sanity check
+				if (ch > 127)
+					throw new IllegalArgumentException(MessageFormat
+							.format(JGitText.get().notASCIIString, in));
+				out.write(ch);
+			}
+		}
+	}
+
+	/**
 	 * Format this builder's state as a commit object.
 	 *
 	 * @return this object in the canonical commit format, suitable for storage
@@ -377,6 +470,10 @@ public String toString() {
 		r.append(committer != null ? committer.toString() : "NOT_SET");
 		r.append("\n");
 
+		r.append("gpgSignature ");
+		r.append(gpgSignature != null ? gpgSignature.toString() : "NOT_SET");
+		r.append("\n");
+
 		if (encoding != null && encoding != UTF_8) {
 			r.append("encoding ");
 			r.append(encoding.name());
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/GpgSignature.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/GpgSignature.java
new file mode 100644
index 0000000..663f850
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/GpgSignature.java
@@ -0,0 +1,98 @@
+/*
+ * Copyright (C) 2018, Salesforce.
+ * 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 java.nio.charset.StandardCharsets.US_ASCII;
+
+import java.io.Serializable;
+
+import org.eclipse.jgit.annotations.NonNull;
+
+/**
+ * A structure for holding GPG signature together with additional related data.
+ *
+ * @since 5.3
+ */
+public class GpgSignature implements Serializable {
+
+	private static final long serialVersionUID = 1L;
+
+	private byte[] signature;
+
+	/**
+	 * Creates a new instance with the specified signature
+	 *
+	 * @param signature
+	 *            the signature
+	 */
+	public GpgSignature(@NonNull byte[] signature) {
+		this.signature = signature;
+	}
+
+	/**
+	 * Format for Git storage.
+	 * <p>
+	 * This returns the ASCII Armor as per
+	 * https://tools.ietf.org/html/rfc4880#section-6.2.
+	 * </p>
+	 *
+	 * @return a string of the signature ready to be embedded in a Git object
+	 */
+	public String toExternalString() {
+		return new String(signature, US_ASCII);
+	}
+
+	/** {@inheritDoc} */
+	@Override
+	@SuppressWarnings("nls")
+	public String toString() {
+		final StringBuilder r = new StringBuilder();
+
+		r.append("GpgSignature[");
+		r.append(
+				this.signature != null ? "length " + signature.length : "null");
+		r.append("]");
+
+		return r.toString();
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/GpgSigner.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/GpgSigner.java
new file mode 100644
index 0000000..99a23c6
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/GpgSigner.java
@@ -0,0 +1,138 @@
+/*
+ * Copyright (C) 2018, Salesforce.
+ * 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.annotations.NonNull;
+import org.eclipse.jgit.annotations.Nullable;
+import org.eclipse.jgit.api.errors.CanceledException;
+import org.eclipse.jgit.lib.internal.BouncyCastleGpgSigner;
+import org.eclipse.jgit.transport.CredentialsProvider;
+
+/**
+ * Creates GPG signatures for Git objects.
+ *
+ * @since 5.3
+ */
+public abstract class GpgSigner {
+
+	private static GpgSigner defaultSigner = new BouncyCastleGpgSigner();
+
+	/**
+	 * Get the default signer, or <code>null</code>.
+	 *
+	 * @return the default signer, or <code>null</code>.
+	 */
+	public static GpgSigner getDefault() {
+		return defaultSigner;
+	}
+
+	/**
+	 * Set the default signer.
+	 *
+	 * @param signer
+	 *            the new default signer, may be <code>null</code> to select no
+	 *            default.
+	 */
+	public static void setDefault(GpgSigner signer) {
+		GpgSigner.defaultSigner = signer;
+	}
+
+	/**
+	 * Signs the specified commit.
+	 *
+	 * <p>
+	 * Implementors should obtain the payload for signing from the specified
+	 * commit via {@link CommitBuilder#build()} and create a proper
+	 * {@link GpgSignature}. The generated signature must be set on the
+	 * specified {@code commit} (see
+	 * {@link CommitBuilder#setGpgSignature(GpgSignature)}).
+	 * </p>
+	 * <p>
+	 * Any existing signature on the commit must be discarded prior obtaining
+	 * the payload via {@link CommitBuilder#build()}.
+	 * </p>
+	 *
+	 * @param commit
+	 *            the commit to sign (must not be <code>null</code> and must be
+	 *            complete to allow proper calculation of payload)
+	 * @param gpgSigningKey
+	 *            the signing key to locate (passed as is to the GPG signing
+	 *            tool as is; eg., value of <code>user.signingkey</code>)
+	 * @param committer
+	 *            the signing identity (to help with key lookup in case signing
+	 *            key is not specified)
+	 * @param credentialsProvider
+	 *            provider to use when querying for signing key credentials (eg.
+	 *            passphrase)
+	 * @throws CanceledException
+	 *             when signing was canceled (eg., user aborted when entering
+	 *             passphrase)
+	 */
+	public abstract void sign(@NonNull CommitBuilder commit,
+			@Nullable String gpgSigningKey, @NonNull PersonIdent committer,
+			CredentialsProvider credentialsProvider) throws CanceledException;
+
+	/**
+	 * Indicates if a signing key is available for the specified committer
+	 * and/or signing key.
+	 *
+	 * @param gpgSigningKey
+	 *            the signing key to locate (passed as is to the GPG signing
+	 *            tool as is; eg., value of <code>user.signingkey</code>)
+	 * @param committer
+	 *            the signing identity (to help with key lookup in case signing
+	 *            key is not specified)
+	 * @param credentialsProvider
+	 *            provider to use when querying for signing key credentials (eg.
+	 *            passphrase)
+	 * @return <code>true</code> if a signing key is available,
+	 *         <code>false</code> otherwise
+	 * @throws CanceledException
+	 *             when signing was canceled (eg., user aborted when entering
+	 *             passphrase)
+	 */
+	public abstract boolean canLocateSigningKey(@Nullable String gpgSigningKey,
+			@NonNull PersonIdent committer,
+			CredentialsProvider credentialsProvider) throws CanceledException;
+
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectId.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectId.java
index 764f890..0e96138 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectId.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectId.java
@@ -49,6 +49,7 @@
 import java.io.ObjectOutputStream;
 import java.io.Serializable;
 
+import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.errors.InvalidObjectIdException;
 import org.eclipse.jgit.util.NB;
 import org.eclipse.jgit.util.RawParseUtils;
@@ -86,7 +87,10 @@ public static final ObjectId zeroId() {
 	 *            the string to test.
 	 * @return true if the string can converted into an ObjectId.
 	 */
-	public static final boolean isId(String id) {
+	public static final boolean isId(@Nullable String id) {
+		if (id == null) {
+			return false;
+		}
 		if (id.length() != Constants.OBJECT_ID_STRING_LENGTH)
 			return false;
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectIdRef.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectIdRef.java
index 22aaa3a..b791c64 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectIdRef.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectIdRef.java
@@ -67,7 +67,26 @@ public static class Unpeeled extends ObjectIdRef {
 		 */
 		public Unpeeled(@NonNull Storage st, @NonNull String name,
 				@Nullable ObjectId id) {
-			super(st, name, id);
+			super(st, name, id, -1);
+		}
+
+		/**
+		 * Create a new ref pairing with update index.
+		 *
+		 * @param st
+		 *            method used to store this ref.
+		 * @param name
+		 *            name of this ref.
+		 * @param id
+		 *            current value of the ref. May be {@code null} to indicate
+		 *            a ref that does not exist yet.
+		 * @param updateIndex
+		 *            number increasing with each update to the reference.
+		 * @since 5.3
+		 */
+		public Unpeeled(@NonNull Storage st, @NonNull String name,
+				@Nullable ObjectId id, long updateIndex) {
+			super(st, name, id, updateIndex);
 		}
 
 		@Override
@@ -100,7 +119,29 @@ public static class PeeledTag extends ObjectIdRef {
 		 */
 		public PeeledTag(@NonNull Storage st, @NonNull String name,
 				@Nullable ObjectId id, @NonNull ObjectId p) {
-			super(st, name, id);
+			super(st, name, id, -1);
+			peeledObjectId = p;
+		}
+
+		/**
+		 * Create a new ref pairing with update index.
+		 *
+		 * @param st
+		 *            method used to store this ref.
+		 * @param name
+		 *            name of this ref.
+		 * @param id
+		 *            current value of the ref. May be {@code null} to indicate
+		 *            a ref that does not exist yet.
+		 * @param p
+		 *            the first non-tag object that tag {@code id} points to.
+		 * @param updateIndex
+		 *            number increasing with each update to the reference.
+		 * @since 5.3
+		 */
+		public PeeledTag(@NonNull Storage st, @NonNull String name,
+				@Nullable ObjectId id, @NonNull ObjectId p, long updateIndex) {
+			super(st, name, id, updateIndex);
 			peeledObjectId = p;
 		}
 
@@ -131,7 +172,26 @@ public static class PeeledNonTag extends ObjectIdRef {
 		 */
 		public PeeledNonTag(@NonNull Storage st, @NonNull String name,
 				@Nullable ObjectId id) {
-			super(st, name, id);
+			super(st, name, id, -1);
+		}
+
+		/**
+		 * Create a new ref pairing with update index.
+		 *
+		 * @param st
+		 *            method used to store this ref.
+		 * @param name
+		 *            name of this ref.
+		 * @param id
+		 *            current value of the ref. May be {@code null} to indicate
+		 *            a ref that does not exist yet.
+		 * @param updateIndex
+		 *            number increasing with each update to the reference.
+		 * @since 5.3
+		 */
+		public PeeledNonTag(@NonNull Storage st, @NonNull String name,
+				@Nullable ObjectId id, long updateIndex) {
+			super(st, name, id, updateIndex);
 		}
 
 		@Override
@@ -152,6 +212,8 @@ public boolean isPeeled() {
 
 	private final ObjectId objectId;
 
+	private final long updateIndex;
+
 	/**
 	 * Create a new ref pairing.
 	 *
@@ -162,12 +224,17 @@ public boolean isPeeled() {
 	 * @param id
 	 *            current value of the ref. May be {@code null} to indicate a
 	 *            ref that does not exist yet.
+	 * @param updateIndex
+	 *            number that increases with each ref update. Set to -1 if the
+	 *            storage doesn't support versioning.
+	 * @since 5.3
 	 */
 	protected ObjectIdRef(@NonNull Storage st, @NonNull String name,
-			@Nullable ObjectId id) {
+			@Nullable ObjectId id, long updateIndex) {
 		this.name = name;
 		this.storage = st;
 		this.objectId = id;
+		this.updateIndex = updateIndex;
 	}
 
 	/** {@inheritDoc} */
@@ -211,6 +278,18 @@ public Storage getStorage() {
 		return storage;
 	}
 
+	/**
+	 * {@inheritDoc}
+	 * @since 5.3
+	 */
+	@Override
+	public long getUpdateIndex() {
+		if (updateIndex == -1) {
+			throw new UnsupportedOperationException();
+		}
+		return updateIndex;
+	}
+
 	/** {@inheritDoc} */
 	@NonNull
 	@Override
@@ -220,7 +299,9 @@ public String toString() {
 		r.append(getName());
 		r.append('=');
 		r.append(ObjectId.toString(getObjectId()));
-		r.append(']');
+		r.append('(');
+		r.append(updateIndex); // Print value, even if -1
+		r.append(")]"); //$NON-NLS-1$
 		return r.toString();
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Ref.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Ref.java
index faabbf8..32c8b06 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Ref.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Ref.java
@@ -217,4 +217,27 @@ public boolean isPacked() {
 	 */
 	@NonNull
 	Storage getStorage();
+
+	/**
+	 * Indicator of the relative order between updates of a specific reference
+	 * name. A number that increases when a reference is updated.
+	 * <p>
+	 * With symbolic references, the update index refers to updates of the
+	 * symbolic reference itself. For example, if HEAD points to
+	 * refs/heads/master, then the update index for exactRef("HEAD") will only
+	 * increase when HEAD changes to point to another ref, regardless of how
+	 * many times refs/heads/master is updated.
+	 * <p>
+	 * Should not be used unless the {@code RefDatabase} that instantiated the
+	 * ref supports versioning (see {@link RefDatabase#hasVersioning()})
+	 *
+	 * @return the update index (i.e. version) of this reference.
+	 * @throws UnsupportedOperationException
+	 *             if the creator of the instance (e.g. {@link RefDatabase})
+	 *             doesn't support versioning and doesn't override this method
+	 * @since 5.3
+	 */
+	default long getUpdateIndex() {
+		throw new UnsupportedOperationException();
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefDatabase.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefDatabase.java
index 68929b4..8777920 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefDatabase.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefDatabase.java
@@ -69,10 +69,10 @@ public abstract class RefDatabase {
 	/**
 	 * Order of prefixes to search when using non-absolute references.
 	 * <p>
-	 * The implementation's {@link #getRef(String)} method must take this search
-	 * space into consideration when locating a reference by name. The first
-	 * entry in the path is always {@code ""}, ensuring that absolute references
-	 * are resolved without further mangling.
+	 * {@link #findRef(String)} takes this search space into consideration
+	 * when locating a reference by name. The first entry in the path is
+	 * always {@code ""}, ensuring that absolute references are resolved
+	 * without further mangling.
 	 */
 	protected static final String[] SEARCH_PATH = { "", //$NON-NLS-1$
 			Constants.R_REFS, //
@@ -111,6 +111,19 @@ public abstract class RefDatabase {
 	public abstract void close();
 
 	/**
+	 * With versioning, each reference has a version number that increases on
+	 * update. See {@link Ref#getUpdateIndex()}.
+	 *
+	 * @implSpec This method returns false by default. Implementations
+	 *           supporting versioning must override it to return true.
+	 * @return true if the implementation assigns update indices to references.
+	 * @since 5.3
+	 */
+	public boolean hasVersioning() {
+		return false;
+	}
+
+	/**
 	 * Determine if a proposed reference name overlaps with an existing one.
 	 * <p>
 	 * Reference names use '/' as a component separator, and may be stored in a
@@ -244,6 +257,23 @@ public boolean performsAtomicTransactions() {
 	}
 
 	/**
+	 * Compatibility synonym for {@link #findRef(String)}.
+	 *
+	 * @param name
+	 *            the name of the reference. May be a short name which must be
+	 *            searched for using the standard {@link #SEARCH_PATH}.
+	 * @return the reference (if it exists); else {@code null}.
+	 * @throws IOException
+	 *             the reference space cannot be accessed.
+	 * @deprecated Use {@link #findRef(String)} instead.
+	 */
+	@Deprecated
+	@Nullable
+	public final Ref getRef(String name) throws IOException {
+		return findRef(name);
+	}
+
+	/**
 	 * Read a single reference.
 	 * <p>
 	 * Aside from taking advantage of {@link #SEARCH_PATH}, this method may be
@@ -259,14 +289,21 @@ public boolean performsAtomicTransactions() {
 	 * @return the reference (if it exists); else {@code null}.
 	 * @throws java.io.IOException
 	 *             the reference space cannot be accessed.
+	 * @since 5.3
 	 */
 	@Nullable
-	public abstract Ref getRef(String name) throws IOException;
+	public final Ref findRef(String name) throws IOException {
+		String[] names = new String[SEARCH_PATH.length];
+		for (int i = 0; i < SEARCH_PATH.length; i++) {
+			names[i] = SEARCH_PATH[i] + name;
+		}
+		return firstExactRef(names);
+	}
 
 	/**
 	 * Read a single reference.
 	 * <p>
-	 * Unlike {@link #getRef}, this method expects an unshortened reference
+	 * Unlike {@link #findRef}, this method expects an unshortened reference
 	 * name and does not search using the standard {@link #SEARCH_PATH}.
 	 *
 	 * @param name
@@ -277,13 +314,7 @@ public boolean performsAtomicTransactions() {
 	 * @since 4.1
 	 */
 	@Nullable
-	public Ref exactRef(String name) throws IOException {
-		Ref ref = getRef(name);
-		if (ref == null || !name.equals(ref.getName())) {
-			return null;
-		}
-		return ref;
-	}
+	public abstract Ref exactRef(String name) throws IOException;
 
 	/**
 	 * Read the specified references.
@@ -462,7 +493,7 @@ public boolean hasRefs() throws IOException {
 	 * <p>
 	 * The result list includes non-ref items such as MERGE_HEAD and
 	 * FETCH_RESULT cast to be refs. The names of these refs are not returned by
-	 * <code>getRefs()</code> but are accepted by {@link #getRef(String)}
+	 * <code>getRefs()</code> but are accepted by {@link #findRef(String)}
 	 * and {@link #exactRef(String)}.
 	 *
 	 * @return a list of additional refs
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefRename.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefRename.java
index a05daa0..0bd34b5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefRename.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefRename.java
@@ -184,7 +184,7 @@ public Result rename() throws IOException {
 	 *             the current value of {@code HEAD} cannot be read.
 	 */
 	protected boolean needToUpdateHEAD() throws IOException {
-		Ref head = source.getRefDatabase().getRef(Constants.HEAD);
+		Ref head = source.getRefDatabase().exactRef(Constants.HEAD);
 		if (head != null && head.isSymbolic()) {
 			head = head.getTarget();
 			return head.getName().equals(source.getName());
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 fc3ea84..1ce1528 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefUpdate.java
@@ -665,7 +665,7 @@ public Result delete(RevWalk walk) throws IOException {
 				: getRef().getLeaf().getName();
 		if (myName.startsWith(Constants.R_HEADS) && !getRepository().isBare()) {
 			// Don't allow the currently checked out branch to be deleted.
-			Ref head = getRefDatabase().getRef(Constants.HEAD);
+			Ref head = getRefDatabase().exactRef(Constants.HEAD);
 			while (head != null && head.isSymbolic()) {
 				head = head.getTarget();
 				if (myName.equals(head.getName()))
@@ -708,7 +708,7 @@ public Result link(String target) throws IOException {
 			if (!tryLock(false))
 				return Result.LOCK_FAILURE;
 
-			final Ref old = getRefDatabase().getRef(getName());
+			final Ref old = getRefDatabase().exactRef(getName());
 			if (old != null && old.isSymbolic()) {
 				final Ref dst = old.getTarget();
 				if (target.equals(dst.getName()))
@@ -718,7 +718,7 @@ public Result link(String target) throws IOException {
 			if (old != null && old.getObjectId() != null)
 				setOldObjectId(old.getObjectId());
 
-			final Ref dst = getRefDatabase().getRef(target);
+			final Ref dst = getRefDatabase().exactRef(target);
 			if (dst != null && dst.getObjectId() != null)
 				setNewObjectId(dst.getObjectId());
 
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 77d268a..a61897a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
@@ -57,6 +57,7 @@
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.io.UncheckedIOException;
 import java.net.URISyntaxException;
 import java.text.MessageFormat;
 import java.util.Collection;
@@ -297,7 +298,7 @@ public ObjectReader newObjectReader() {
 	/**
 	 * Get the used file system abstraction.
 	 *
-	 * @return the used file system abstraction, or or {@code null} if
+	 * @return the used file system abstraction, or {@code null} if
 	 *         repository isn't local.
 	 */
 	/*
@@ -319,13 +320,14 @@ public FS getFS() {
 	 *            a {@link org.eclipse.jgit.lib.AnyObjectId} object.
 	 * @return true if the specified object is stored in this repo or any of the
 	 *         known shared repositories.
+	 * @deprecated use {@code getObjectDatabase().has(objectId)}
 	 */
+	@Deprecated
 	public boolean hasObject(AnyObjectId objectId) {
 		try {
 			return getObjectDatabase().has(objectId);
 		} catch (IOException e) {
-			// Legacy API, assume error means "no"
-			return false;
+			throw new UncheckedIOException(e);
 		}
 	}
 
@@ -849,7 +851,7 @@ private ObjectId resolveSimple(String revstr) throws IOException {
 			return ObjectId.fromString(revstr);
 
 		if (Repository.isValidRefName("x/" + revstr)) { //$NON-NLS-1$
-			Ref r = getRefDatabase().getRef(revstr);
+			Ref r = getRefDatabase().findRef(revstr);
 			if (r != null)
 				return r.getObjectId();
 		}
@@ -1079,7 +1081,7 @@ public final Ref exactRef(String name) throws IOException {
 	 *
 	 * @param name
 	 *            the name of the ref to lookup. May be a short-hand form, e.g.
-	 *            "master" which is is automatically expanded to
+	 *            "master" which is automatically expanded to
 	 *            "refs/heads/master" if "refs/heads/master" already exists.
 	 * @return the Ref with the given name, or {@code null} if it does not exist
 	 * @throws java.io.IOException
@@ -1087,7 +1089,7 @@ public final Ref exactRef(String name) throws IOException {
 	 */
 	@Nullable
 	public final Ref findRef(String name) throws IOException {
-		return getRefDatabase().getRef(name);
+		return getRefDatabase().findRef(name);
 	}
 
 	/**
@@ -1103,7 +1105,7 @@ public Map<String, Ref> getAllRefs() {
 		try {
 			return getRefDatabase().getRefs(RefDatabase.ALL);
 		} catch (IOException e) {
-			return new HashMap<>();
+			throw new UncheckedIOException(e);
 		}
 	}
 
@@ -1121,7 +1123,7 @@ public Map<String, Ref> getTags() {
 		try {
 			return getRefDatabase().getRefs(Constants.R_TAGS);
 		} catch (IOException e) {
-			return new HashMap<>();
+			throw new UncheckedIOException(e);
 		}
 	}
 
@@ -1320,9 +1322,7 @@ public RepositoryState getRepositoryState() {
 					return RepositoryState.MERGING_RESOLVED;
 				}
 			} catch (IOException e) {
-				// Can't decide whether unmerged paths exists. Return
-				// MERGING state to be on the safe side (in state MERGING
-				// you are not allow to do anything)
+				throw new UncheckedIOException(e);
 			}
 			return RepositoryState.MERGING;
 		}
@@ -1337,7 +1337,7 @@ public RepositoryState getRepositoryState() {
 					return RepositoryState.CHERRY_PICKING_RESOLVED;
 				}
 			} catch (IOException e) {
-				// fall through to CHERRY_PICKING
+				throw new UncheckedIOException(e);
 			}
 
 			return RepositoryState.CHERRY_PICKING;
@@ -1350,7 +1350,7 @@ public RepositoryState getRepositoryState() {
 					return RepositoryState.REVERTING_RESOLVED;
 				}
 			} catch (IOException e) {
-				// fall through to REVERTING
+				throw new UncheckedIOException(e);
 			}
 
 			return RepositoryState.REVERTING;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/SymbolicRef.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/SymbolicRef.java
index d4b83b0..00fcf52 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/SymbolicRef.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/SymbolicRef.java
@@ -58,6 +58,8 @@ public class SymbolicRef implements Ref {
 
 	private final Ref target;
 
+	private final long updateIndex;
+
 	/**
 	 * Create a new ref pairing.
 	 *
@@ -69,6 +71,25 @@ public class SymbolicRef implements Ref {
 	public SymbolicRef(@NonNull String refName, @NonNull Ref target) {
 		this.name = refName;
 		this.target = target;
+		this.updateIndex = -1;
+	}
+
+	/**
+	 * Create a new ref pairing.
+	 *
+	 * @param refName
+	 *            name of this ref.
+	 * @param target
+	 *            the ref we reference and derive our value from.
+	 * @param updateIndex
+	 *            index that increases with each update of the reference
+	 * @since 5.3
+	 */
+	public SymbolicRef(@NonNull String refName, @NonNull Ref target,
+			long updateIndex) {
+		this.name = refName;
+		this.target = target;
+		this.updateIndex = updateIndex;
 	}
 
 	/** {@inheritDoc} */
@@ -128,6 +149,18 @@ public boolean isPeeled() {
 		return getLeaf().isPeeled();
 	}
 
+	/**
+	 * {@inheritDoc}
+	 * @since 5.3
+	 */
+	@Override
+	public long getUpdateIndex() {
+		if (updateIndex == -1) {
+			throw new UnsupportedOperationException();
+		}
+		return updateIndex;
+	}
+
 	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
@@ -143,7 +176,9 @@ public String toString() {
 		r.append(cur.getName());
 		r.append('=');
 		r.append(ObjectId.toString(cur.getObjectId()));
-		r.append("]");
+		r.append("(");
+		r.append(updateIndex); // Print value, even if -1
+		r.append(")]");
 		return r.toString();
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/internal/BouncyCastleGpgKey.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/internal/BouncyCastleGpgKey.java
new file mode 100644
index 0000000..ef9d7ee
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/internal/BouncyCastleGpgKey.java
@@ -0,0 +1,71 @@
+/*
+ * Copyright (C) 2018, Salesforce.
+ * 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.internal;
+
+import java.nio.file.Path;
+
+import org.bouncycastle.openpgp.PGPSecretKey;
+
+/**
+ * Container which holds a {@link #getSecretKey()} together with the
+ * {@link #getOrigin() path it was loaded from}.
+ */
+class BouncyCastleGpgKey {
+
+	private PGPSecretKey secretKey;
+
+	private Path origin;
+
+	public BouncyCastleGpgKey(PGPSecretKey secretKey, Path origin) {
+		this.secretKey = secretKey;
+		this.origin = origin;
+	}
+
+	public PGPSecretKey getSecretKey() {
+		return secretKey;
+	}
+
+	public Path getOrigin() {
+		return origin;
+	}
+}
\ No newline at end of file
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/internal/BouncyCastleGpgKeyLocator.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/internal/BouncyCastleGpgKeyLocator.java
new file mode 100644
index 0000000..091667d
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/internal/BouncyCastleGpgKeyLocator.java
@@ -0,0 +1,373 @@
+/*
+ * Copyright (C) 2018, Salesforce.
+ * 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.internal;
+
+import static java.nio.file.Files.exists;
+import static java.nio.file.Files.newInputStream;
+
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.InvalidPathException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.text.MessageFormat;
+import java.util.Iterator;
+import java.util.Locale;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import org.bouncycastle.gpg.SExprParser;
+import org.bouncycastle.gpg.keybox.BlobType;
+import org.bouncycastle.gpg.keybox.KeyBlob;
+import org.bouncycastle.gpg.keybox.KeyBox;
+import org.bouncycastle.gpg.keybox.KeyInformation;
+import org.bouncycastle.gpg.keybox.PublicKeyRingBlob;
+import org.bouncycastle.gpg.keybox.UserID;
+import org.bouncycastle.openpgp.PGPException;
+import org.bouncycastle.openpgp.PGPPublicKey;
+import org.bouncycastle.openpgp.PGPSecretKey;
+import org.bouncycastle.openpgp.PGPSecretKeyRing;
+import org.bouncycastle.openpgp.PGPSecretKeyRingCollection;
+import org.bouncycastle.openpgp.PGPUtil;
+import org.bouncycastle.openpgp.operator.PBEProtectionRemoverFactory;
+import org.bouncycastle.openpgp.operator.PGPDigestCalculatorProvider;
+import org.bouncycastle.openpgp.operator.jcajce.JcaKeyFingerprintCalculator;
+import org.bouncycastle.openpgp.operator.jcajce.JcaPGPDigestCalculatorProviderBuilder;
+import org.bouncycastle.openpgp.operator.jcajce.JcePBEProtectionRemoverFactory;
+import org.bouncycastle.util.encoders.Hex;
+import org.eclipse.jgit.annotations.NonNull;
+import org.eclipse.jgit.api.errors.CanceledException;
+import org.eclipse.jgit.errors.UnsupportedCredentialItem;
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.util.SystemReader;
+
+/**
+ * Locates GPG keys from either <code>~/.gnupg/private-keys-v1.d</code> or
+ * <code>~/.gnupg/secring.gpg</code>
+ */
+class BouncyCastleGpgKeyLocator {
+
+	private static final Path GPG_DIRECTORY = findGpgDirectory();
+
+	private static final Path USER_KEYBOX_PATH = GPG_DIRECTORY
+			.resolve("pubring.kbx"); //$NON-NLS-1$
+
+	private static final Path USER_SECRET_KEY_DIR = GPG_DIRECTORY
+			.resolve("private-keys-v1.d"); //$NON-NLS-1$
+
+	private static final Path USER_PGP_LEGACY_SECRING_FILE = GPG_DIRECTORY
+			.resolve("secring.gpg"); //$NON-NLS-1$
+
+	private final String signingKey;
+
+	private BouncyCastleGpgKeyPassphrasePrompt passphrasePrompt;
+
+	private static Path findGpgDirectory() {
+		SystemReader system = SystemReader.getInstance();
+		if (system.isWindows()) {
+			// On Windows prefer %APPDATA%\gnupg if it exists, even if Cygwin is
+			// used.
+			String appData = system.getenv("APPDATA"); //$NON-NLS-1$
+			if (appData != null && !appData.isEmpty()) {
+				try {
+					Path directory = Paths.get(appData).resolve("gnupg"); //$NON-NLS-1$
+					if (Files.isDirectory(directory)) {
+						return directory;
+					}
+				} catch (SecurityException | InvalidPathException e) {
+					// Ignore and return the default location below.
+				}
+			}
+		}
+		// All systems, including Cygwin and even Windows if
+		// %APPDATA%\gnupg doesn't exist: ~/.gnupg
+		File home = FS.DETECTED.userHome();
+		if (home == null) {
+			// Oops. What now?
+			home = new File(".").getAbsoluteFile(); //$NON-NLS-1$
+		}
+		return home.toPath().resolve(".gnupg"); //$NON-NLS-1$
+	}
+
+	/**
+	 * Create a new key locator for the specified signing key.
+	 * <p>
+	 * The signing key must either be a hex representation of a specific key or
+	 * a user identity substring (eg., email address). All keys in the KeyBox
+	 * will be looked up in the order as returned by the KeyBox. A key id will
+	 * be searched before attempting to find a key by user id.
+	 * </p>
+	 *
+	 * @param signingKey
+	 *            the signing key to search for
+	 * @param passphrasePrompt
+	 *            the provider to use when asking for key passphrase
+	 */
+	public BouncyCastleGpgKeyLocator(String signingKey,
+			@NonNull BouncyCastleGpgKeyPassphrasePrompt passphrasePrompt) {
+		this.signingKey = signingKey;
+		this.passphrasePrompt = passphrasePrompt;
+	}
+
+	private PGPSecretKey attemptParseSecretKey(Path keyFile,
+			PGPDigestCalculatorProvider calculatorProvider,
+			PBEProtectionRemoverFactory passphraseProvider,
+			PGPPublicKey publicKey) throws IOException {
+		try (InputStream in = newInputStream(keyFile)) {
+			return new SExprParser(calculatorProvider).parseSecretKey(
+					new BufferedInputStream(in), passphraseProvider, publicKey);
+		} catch (PGPException | ClassCastException e) {
+			return null;
+		}
+	}
+
+	private boolean containsSigningKey(String userId) {
+		return userId.toLowerCase(Locale.ROOT)
+				.contains(signingKey.toLowerCase(Locale.ROOT));
+	}
+
+	private PGPPublicKey findPublicKeyByKeyId(KeyBlob keyBlob)
+			throws IOException {
+		for (KeyInformation keyInfo : keyBlob.getKeyInformation()) {
+			if (signingKey.toLowerCase(Locale.ROOT)
+					.equals(Hex.toHexString(keyInfo.getKeyID())
+							.toLowerCase(Locale.ROOT))) {
+				return getFirstPublicKey(keyBlob);
+			}
+		}
+		return null;
+	}
+
+	private PGPPublicKey findPublicKeyByUserId(KeyBlob keyBlob)
+			throws IOException {
+		for (UserID userID : keyBlob.getUserIds()) {
+			if (containsSigningKey(userID.getUserIDAsString())) {
+				return getFirstPublicKey(keyBlob);
+			}
+		}
+		return null;
+	}
+
+	/**
+	 * Finds a public key associated with the signing key.
+	 *
+	 * @param keyboxFile
+	 *            the KeyBox file
+	 * @return publicKey the public key (maybe <code>null</code>)
+	 * @throws IOException
+	 *             in case of problems reading the file
+	 */
+	private PGPPublicKey findPublicKeyInKeyBox(Path keyboxFile)
+			throws IOException {
+		KeyBox keyBox = readKeyBoxFile(keyboxFile);
+		for (KeyBlob keyBlob : keyBox.getKeyBlobs()) {
+			if (keyBlob.getType() == BlobType.OPEN_PGP_BLOB) {
+				PGPPublicKey key = findPublicKeyByKeyId(keyBlob);
+				if (key != null) {
+					return key;
+				}
+				key = findPublicKeyByUserId(keyBlob);
+				if (key != null) {
+					return key;
+				}
+			}
+		}
+		return null;
+	}
+
+	/**
+	 * Use pubring.kbx when available, if not fallback to secring.gpg or secret
+	 * key path provided to parse and return secret key
+	 *
+	 * @return the secret key
+	 * @throws IOException
+	 *             in case of issues reading key files
+	 * @throws PGPException
+	 *             in case of issues finding a key
+	 * @throws CanceledException
+	 * @throws URISyntaxException
+	 * @throws UnsupportedCredentialItem
+	 */
+	public BouncyCastleGpgKey findSecretKey()
+			throws IOException, PGPException, CanceledException,
+			UnsupportedCredentialItem, URISyntaxException {
+		if (exists(USER_KEYBOX_PATH)) {
+			PGPPublicKey publicKey = //
+					findPublicKeyInKeyBox(USER_KEYBOX_PATH);
+
+			if (publicKey != null) {
+				return findSecretKeyForKeyBoxPublicKey(publicKey,
+						USER_KEYBOX_PATH);
+			}
+
+			throw new PGPException(MessageFormat
+					.format(JGitText.get().gpgNoPublicKeyFound, signingKey));
+		} else if (exists(USER_PGP_LEGACY_SECRING_FILE)) {
+			PGPSecretKey secretKey = findSecretKeyInLegacySecring(signingKey,
+					USER_PGP_LEGACY_SECRING_FILE);
+
+			if (secretKey != null) {
+				return new BouncyCastleGpgKey(secretKey, USER_PGP_LEGACY_SECRING_FILE);
+			}
+
+			throw new PGPException(MessageFormat.format(
+					JGitText.get().gpgNoKeyInLegacySecring, signingKey));
+		}
+
+		throw new PGPException(JGitText.get().gpgNoKeyring);
+	}
+
+	private BouncyCastleGpgKey findSecretKeyForKeyBoxPublicKey(
+			PGPPublicKey publicKey, Path userKeyboxPath)
+			throws PGPException, CanceledException, UnsupportedCredentialItem,
+			URISyntaxException {
+		/*
+		 * this is somewhat brute-force but there doesn't seem to be another
+		 * way; we have to walk all private key files we find and try to open
+		 * them
+		 */
+
+		PGPDigestCalculatorProvider calculatorProvider = new JcaPGPDigestCalculatorProviderBuilder()
+				.build();
+
+		PBEProtectionRemoverFactory passphraseProvider = new JcePBEProtectionRemoverFactory(
+				passphrasePrompt.getPassphrase(publicKey.getFingerprint(),
+						userKeyboxPath));
+
+		try (Stream<Path> keyFiles = Files.walk(USER_SECRET_KEY_DIR)) {
+			for (Path keyFile : keyFiles.filter(Files::isRegularFile)
+					.collect(Collectors.toList())) {
+				PGPSecretKey secretKey = attemptParseSecretKey(keyFile,
+						calculatorProvider, passphraseProvider, publicKey);
+				if (secretKey != null) {
+					return new BouncyCastleGpgKey(secretKey, userKeyboxPath);
+				}
+			}
+
+			passphrasePrompt.clear();
+			throw new PGPException(MessageFormat.format(
+					JGitText.get().gpgNoSecretKeyForPublicKey,
+					Long.toHexString(publicKey.getKeyID())));
+		} catch (RuntimeException e) {
+			passphrasePrompt.clear();
+			throw e;
+		} catch (IOException e) {
+			passphrasePrompt.clear();
+			throw new PGPException(MessageFormat.format(
+					JGitText.get().gpgFailedToParseSecretKey,
+					USER_SECRET_KEY_DIR.toAbsolutePath()), e);
+		}
+	}
+
+	/**
+	 * Return the first suitable key for signing in the key ring collection. For
+	 * this case we only expect there to be one key available for signing.
+	 * </p>
+	 *
+	 * @param signingkey
+	 * @param secringFile
+	 *
+	 * @return the first suitable PGP secret key found for signing
+	 * @throws IOException
+	 *             on I/O related errors
+	 * @throws PGPException
+	 *             on BouncyCastle errors
+	 */
+	private PGPSecretKey findSecretKeyInLegacySecring(String signingkey,
+			Path secringFile) throws IOException, PGPException {
+
+		try (InputStream in = newInputStream(secringFile)) {
+			PGPSecretKeyRingCollection pgpSec = new PGPSecretKeyRingCollection(
+					PGPUtil.getDecoderStream(new BufferedInputStream(in)),
+					new JcaKeyFingerprintCalculator());
+
+			Iterator<PGPSecretKeyRing> keyrings = pgpSec.getKeyRings();
+			while (keyrings.hasNext()) {
+				PGPSecretKeyRing keyRing = keyrings.next();
+				Iterator<PGPSecretKey> keys = keyRing.getSecretKeys();
+				while (keys.hasNext()) {
+					PGPSecretKey key = keys.next();
+					// try key id
+					String fingerprint = Hex
+							.toHexString(key.getPublicKey().getFingerprint())
+							.toLowerCase(Locale.ROOT);
+					if (fingerprint
+							.endsWith(signingkey.toLowerCase(Locale.ROOT))) {
+						return key;
+					}
+					// try user id
+					Iterator<String> userIDs = key.getUserIDs();
+					while (userIDs.hasNext()) {
+						String userId = userIDs.next();
+						if (containsSigningKey(userId)) {
+							return key;
+						}
+					}
+				}
+			}
+		}
+		return null;
+	}
+
+	private PGPPublicKey getFirstPublicKey(KeyBlob keyBlob) throws IOException {
+		return ((PublicKeyRingBlob) keyBlob).getPGPPublicKeyRing()
+				.getPublicKey();
+	}
+
+	private KeyBox readKeyBoxFile(Path keyboxFile) throws IOException {
+		KeyBox keyBox;
+		try (InputStream in = new BufferedInputStream(
+				newInputStream(keyboxFile))) {
+			// note: KeyBox constructor reads in the whole InputStream at once
+			// this code will change in 1.61 to
+			// either 'new BcKeyBox(in)' or 'new JcaKeyBoxBuilder().build(in)'
+			keyBox = new KeyBox(in, new JcaKeyFingerprintCalculator());
+		}
+		return keyBox;
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/internal/BouncyCastleGpgKeyPassphrasePrompt.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/internal/BouncyCastleGpgKeyPassphrasePrompt.java
new file mode 100644
index 0000000..2efe962
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/internal/BouncyCastleGpgKeyPassphrasePrompt.java
@@ -0,0 +1,134 @@
+/*-
+ * Copyright (C) 2019, Salesforce.
+ * 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.internal;
+
+import java.net.URISyntaxException;
+import java.nio.file.Path;
+import java.text.MessageFormat;
+
+import org.bouncycastle.openpgp.PGPException;
+import org.bouncycastle.util.encoders.Hex;
+import org.eclipse.jgit.api.errors.CanceledException;
+import org.eclipse.jgit.errors.UnsupportedCredentialItem;
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.transport.CredentialItem.CharArrayType;
+import org.eclipse.jgit.transport.CredentialItem.InformationalMessage;
+import org.eclipse.jgit.transport.CredentialsProvider;
+import org.eclipse.jgit.transport.URIish;
+
+/**
+ * Prompts for a passphrase and caches it until {@link #clear() cleared}.
+ * <p>
+ * Implements {@link AutoCloseable} so it can be used within a
+ * try-with-resources block.
+ * </p>
+ */
+class BouncyCastleGpgKeyPassphrasePrompt implements AutoCloseable {
+
+	private CharArrayType passphrase;
+
+	private CredentialsProvider credentialsProvider;
+
+	public BouncyCastleGpgKeyPassphrasePrompt(
+			CredentialsProvider credentialsProvider) {
+		this.credentialsProvider = credentialsProvider;
+	}
+
+	/**
+	 * Clears any cached passphrase
+	 */
+	public void clear() {
+		if (passphrase != null) {
+			passphrase.clear();
+			passphrase = null;
+		}
+	}
+
+	@Override
+	public void close() {
+		clear();
+	}
+
+	private URIish createURI(Path keyLocation) throws URISyntaxException {
+		return new URIish(keyLocation.toUri().toString());
+	}
+
+	/**
+	 * Prompts use for a passphrase unless one was cached from a previous
+	 * prompt.
+	 *
+	 * @param keyFingerprint
+	 *            the fingerprint to show to the user during prompting
+	 * @param keyLocation
+	 *            the location the key was loaded from
+	 * @return the passphrase (maybe <code>null</code>)
+	 * @throws PGPException
+	 * @throws CanceledException
+	 *             in case passphrase was not entered by user
+	 * @throws URISyntaxException
+	 * @throws UnsupportedCredentialItem
+	 */
+	public char[] getPassphrase(byte[] keyFingerprint, Path keyLocation)
+			throws PGPException, CanceledException, UnsupportedCredentialItem,
+			URISyntaxException {
+		if (passphrase == null) {
+			passphrase = new CharArrayType(JGitText.get().credentialPassphrase,
+					true);
+		}
+
+		if (credentialsProvider == null) {
+			throw new PGPException(JGitText.get().gpgNoCredentialsProvider);
+		}
+
+		if (passphrase.getValue() == null
+				&& !credentialsProvider.get(createURI(keyLocation),
+						new InformationalMessage(
+								MessageFormat.format(JGitText.get().gpgKeyInfo,
+										Hex.toHexString(keyFingerprint))),
+						passphrase)) {
+			throw new CanceledException(JGitText.get().gpgSigningCancelled);
+		}
+		return passphrase.getValue();
+	}
+
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/internal/BouncyCastleGpgSigner.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/internal/BouncyCastleGpgSigner.java
new file mode 100644
index 0000000..4d696dd
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/internal/BouncyCastleGpgSigner.java
@@ -0,0 +1,160 @@
+/*
+ * Copyright (C) 2018, Salesforce.
+ * 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.internal;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.security.Security;
+
+import org.bouncycastle.bcpg.ArmoredOutputStream;
+import org.bouncycastle.bcpg.BCPGOutputStream;
+import org.bouncycastle.bcpg.HashAlgorithmTags;
+import org.bouncycastle.jce.provider.BouncyCastleProvider;
+import org.bouncycastle.openpgp.PGPException;
+import org.bouncycastle.openpgp.PGPPrivateKey;
+import org.bouncycastle.openpgp.PGPSecretKey;
+import org.bouncycastle.openpgp.PGPSignature;
+import org.bouncycastle.openpgp.PGPSignatureGenerator;
+import org.bouncycastle.openpgp.operator.jcajce.JcaPGPContentSignerBuilder;
+import org.bouncycastle.openpgp.operator.jcajce.JcePBESecretKeyDecryptorBuilder;
+import org.eclipse.jgit.annotations.NonNull;
+import org.eclipse.jgit.annotations.Nullable;
+import org.eclipse.jgit.api.errors.CanceledException;
+import org.eclipse.jgit.api.errors.JGitInternalException;
+import org.eclipse.jgit.errors.UnsupportedCredentialItem;
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.lib.CommitBuilder;
+import org.eclipse.jgit.lib.GpgSignature;
+import org.eclipse.jgit.lib.GpgSigner;
+import org.eclipse.jgit.lib.PersonIdent;
+import org.eclipse.jgit.transport.CredentialsProvider;
+
+/**
+ * GPG Signer using BouncyCastle library
+ */
+public class BouncyCastleGpgSigner extends GpgSigner {
+
+	private static void registerBouncyCastleProviderIfNecessary() {
+		if (Security.getProvider(BouncyCastleProvider.PROVIDER_NAME) == null) {
+			Security.addProvider(new BouncyCastleProvider());
+		}
+	}
+
+	/**
+	 * Create a new instance.
+	 * <p>
+	 * The BounceCastleProvider will be registered if necessary.
+	 * </p>
+	 */
+	public BouncyCastleGpgSigner() {
+		registerBouncyCastleProviderIfNecessary();
+	}
+
+	@Override
+	public boolean canLocateSigningKey(@Nullable String gpgSigningKey,
+			PersonIdent committer, CredentialsProvider credentialsProvider)
+			throws CanceledException {
+		try (BouncyCastleGpgKeyPassphrasePrompt passphrasePrompt = new BouncyCastleGpgKeyPassphrasePrompt(
+				credentialsProvider)) {
+			BouncyCastleGpgKey gpgKey = locateSigningKey(gpgSigningKey,
+					committer, passphrasePrompt);
+			return gpgKey != null;
+		} catch (PGPException | IOException | URISyntaxException e) {
+			return false;
+		}
+	}
+
+	private BouncyCastleGpgKey locateSigningKey(@Nullable String gpgSigningKey,
+			PersonIdent committer,
+			BouncyCastleGpgKeyPassphrasePrompt passphrasePrompt)
+			throws CanceledException, UnsupportedCredentialItem, IOException,
+			PGPException, URISyntaxException {
+		if (gpgSigningKey == null || gpgSigningKey.isEmpty()) {
+			gpgSigningKey = committer.getEmailAddress();
+		}
+
+		BouncyCastleGpgKeyLocator keyHelper = new BouncyCastleGpgKeyLocator(
+				gpgSigningKey, passphrasePrompt);
+
+		return keyHelper.findSecretKey();
+	}
+
+	@Override
+	public void sign(@NonNull CommitBuilder commit,
+			@Nullable String gpgSigningKey, @NonNull PersonIdent committer,
+			CredentialsProvider credentialsProvider) throws CanceledException {
+		try (BouncyCastleGpgKeyPassphrasePrompt passphrasePrompt = new BouncyCastleGpgKeyPassphrasePrompt(
+				credentialsProvider)) {
+			BouncyCastleGpgKey gpgKey = locateSigningKey(gpgSigningKey,
+					committer, passphrasePrompt);
+			PGPSecretKey secretKey = gpgKey.getSecretKey();
+			if (secretKey == null) {
+				throw new JGitInternalException(
+						JGitText.get().unableToSignCommitNoSecretKey);
+			}
+			char[] passphrase = passphrasePrompt.getPassphrase(
+					secretKey.getPublicKey().getFingerprint(),
+					gpgKey.getOrigin());
+			PGPPrivateKey privateKey = secretKey
+					.extractPrivateKey(new JcePBESecretKeyDecryptorBuilder()
+							.setProvider(BouncyCastleProvider.PROVIDER_NAME)
+							.build(passphrase));
+			PGPSignatureGenerator signatureGenerator = new PGPSignatureGenerator(
+					new JcaPGPContentSignerBuilder(
+							secretKey.getPublicKey().getAlgorithm(),
+							HashAlgorithmTags.SHA256).setProvider(
+									BouncyCastleProvider.PROVIDER_NAME));
+			signatureGenerator.init(PGPSignature.BINARY_DOCUMENT, privateKey);
+			ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+			try (BCPGOutputStream out = new BCPGOutputStream(
+					new ArmoredOutputStream(buffer))) {
+				signatureGenerator.update(commit.build());
+				signatureGenerator.generate().encode(out);
+			}
+			commit.setGpgSignature(new GpgSignature(buffer.toByteArray()));
+		} catch (PGPException | IOException | URISyntaxException e) {
+			throw new JGitInternalException(e.getMessage(), e);
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeResult.java b/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeResult.java
index 062d86f..a533bf5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeResult.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeResult.java
@@ -119,7 +119,7 @@ public void add(int srcIdx, int begin, int end, ConflictState conflictState) {
 
 	/**
 	 * Returns the common predecessor sequence and the merged sequence in one
-	 * list. The common predecessor is is the first element in the list
+	 * list. The common predecessor is the first element in the list
 	 *
 	 * @return the common predecessor at position 0 followed by the merged
 	 *         sequences.
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 909f3b1..75334dd 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
@@ -1027,13 +1027,16 @@ private TemporaryBuffer doMerge(MergeResult<RawText> result)
 			throws IOException {
 		TemporaryBuffer.LocalFile buf = new TemporaryBuffer.LocalFile(
 				db != null ? nonNullRepo().getDirectory() : null, inCoreLimit);
+		boolean success = false;
 		try {
 			new MergeFormatter().formatMerge(buf, result,
 					Arrays.asList(commitNames), UTF_8);
 			buf.close();
-		} catch (IOException e) {
-			buf.destroy();
-			throw e;
+			success = true;
+		} finally {
+			if (!success) {
+				buf.destroy();
+			}
 		}
 		return buf;
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/nls/NLS.java b/org.eclipse.jgit/src/org/eclipse/jgit/nls/NLS.java
index 89a87af..375cd32 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/nls/NLS.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/nls/NLS.java
@@ -79,7 +79,7 @@ public class NLS {
 	/**
 	 * Sets the locale for the calling thread.
 	 * <p>
-	 * The {@link #getBundleFor(Class)} method will honor this setting if if it
+	 * The {@link #getBundleFor(Class)} method will honor this setting if it
 	 * is supported by the provided resource bundle property files. Otherwise,
 	 * it will use a fall back locale as described in the
 	 * {@link TranslationBundle}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotCommitList.java b/org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotCommitList.java
index 5e15316..45508ce 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotCommitList.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotCommitList.java
@@ -141,7 +141,8 @@ protected void enter(int index, PlotCommit<L> currCommit) {
 			final PlotCommit<L> c = currCommit.children[0];
 			currCommit.lane = c.lane;
 			Integer len = laneLength.get(currCommit.lane);
-			len = Integer.valueOf(len.intValue() + 1);
+			len = len != null ? Integer.valueOf(len.intValue() + 1)
+					: Integer.valueOf(0);
 			laneLength.put(currCommit.lane, len);
 		} else {
 			// More than one child, or our child is a merge.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/ObjectWalk.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/ObjectWalk.java
index e5903c9..fd578da 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/ObjectWalk.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/ObjectWalk.java
@@ -330,11 +330,11 @@ public RevCommit next() throws MissingObjectException,
 	 *
 	 * @return next most recent object; null if traversal is over.
 	 * @throws org.eclipse.jgit.errors.MissingObjectException
-	 *             one or or more of the next objects are not available from the
+	 *             one or more of the next objects are not available from the
 	 *             object database, but were thought to be candidates for
 	 *             traversal. This usually indicates a broken link.
 	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
-	 *             one or or more of the objects in a tree do not match the type
+	 *             one or more of the objects in a tree do not match the type
 	 *             indicated.
 	 * @throws java.io.IOException
 	 *             a pack file or loose object could not be read.
@@ -534,11 +534,11 @@ private static int parseMode(byte[] buf, int startPtr, int recEndPtr, TreeVisit
 	 * provides some detail about the connectivity failure.
 	 *
 	 * @throws org.eclipse.jgit.errors.MissingObjectException
-	 *             one or or more of the next objects are not available from the
+	 *             one or more of the next objects are not available from the
 	 *             object database, but were thought to be candidates for
 	 *             traversal. This usually indicates a broken link.
 	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
-	 *             one or or more of the objects in a tree do not match the type
+	 *             one or more of the objects in a tree do not match the type
 	 *             indicated.
 	 * @throws java.io.IOException
 	 *             a pack file or loose object could not be read.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevWalk.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevWalk.java
index 400ea33..0a43e8f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevWalk.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevWalk.java
@@ -394,11 +394,11 @@ public void markUninteresting(RevCommit c)
 	 *         <code>base</code> (and thus <code>base</code> is fully merged
 	 *         into <code>tip</code>); false otherwise.
 	 * @throws org.eclipse.jgit.errors.MissingObjectException
-	 *             one or or more of the next commit's parents are not available
+	 *             one or more of the next commit's parents are not available
 	 *             from the object database, but were thought to be candidates
 	 *             for traversal. This usually indicates a broken link.
 	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
-	 *             one or or more of the next commit's parents are not actually
+	 *             one or more of the next commit's parents are not actually
 	 *             commit objects.
 	 * @throws java.io.IOException
 	 *             a pack file or loose object could not be read.
@@ -431,11 +431,11 @@ public boolean isMergedInto(RevCommit base, RevCommit tip)
 	 *
 	 * @return next most recent commit; null if traversal is over.
 	 * @throws org.eclipse.jgit.errors.MissingObjectException
-	 *             one or or more of the next commit's parents are not available
+	 *             one or more of the next commit's parents are not available
 	 *             from the object database, but were thought to be candidates
 	 *             for traversal. This usually indicates a broken link.
 	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
-	 *             one or or more of the next commit's parents are not actually
+	 *             one or more of the next commit's parents are not actually
 	 *             commit objects.
 	 * @throws java.io.IOException
 	 *             a pack file or loose object could not be read.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/WindowCacheConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/WindowCacheConfig.java
index c2e6a42..ff49976 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/WindowCacheConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/WindowCacheConfig.java
@@ -251,7 +251,7 @@ public WindowCacheConfig fromConfig(Config rc) {
 	 * Install this configuration as the live settings.
 	 * <p>
 	 * The new configuration is applied immediately. If the new limits are
-	 * smaller than what what is currently cached, older entries will be purged
+	 * smaller than what is currently cached, older entries will be purged
 	 * as soon as possible to allow the cache to meet the new limit.
 	 *
 	 * @since 3.0
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 6bd32dd..6722e9b 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
@@ -1100,7 +1100,7 @@ public void setBitmapExcessiveBranchCount(int count) {
 	}
 
 	/**
-	 * Get the the age in days that marks a branch as "inactive".
+	 * Get the age in days that marks a branch as "inactive".
 	 *
 	 * Default setting: {@value #DEFAULT_BITMAP_INACTIVE_BRANCH_AGE_IN_DAYS}
 	 *
@@ -1112,7 +1112,7 @@ public int getBitmapInactiveBranchAgeInDays() {
 	}
 
 	/**
-	 * Set the the age in days that marks a branch as "inactive".
+	 * Set the age in days that marks a branch as "inactive".
 	 *
 	 * Default setting: {@value #DEFAULT_BITMAP_INACTIVE_BRANCH_AGE_IN_DAYS}
 	 *
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHook.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHook.java
index 72b4255..8512f2d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHook.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHook.java
@@ -53,7 +53,7 @@ public interface AdvertiseRefsHook {
 	 * <p>
 	 * The method implementations do nothing to preserve the default behavior; see
 	 * {@link UploadPack#setAdvertisedRefs(java.util.Map)} and
-	 * {@link BaseReceivePack#setAdvertisedRefs(java.util.Map,java.util.Set)}.
+	 * {@link ReceivePack#setAdvertisedRefs(java.util.Map,java.util.Set)}.
 	 */
 	AdvertiseRefsHook DEFAULT = new AdvertiseRefsHook() {
 		@Override
@@ -85,7 +85,7 @@ void advertiseRefs(UploadPack uploadPack)
 	 *
 	 * @param receivePack
 	 *            instance on which to call
-	 *            {@link org.eclipse.jgit.transport.BaseReceivePack#setAdvertisedRefs(java.util.Map,java.util.Set)}
+	 *            {@link org.eclipse.jgit.transport.ReceivePack#setAdvertisedRefs(java.util.Map,java.util.Set)}
 	 *            if necessary.
 	 * @throws org.eclipse.jgit.transport.ServiceMayNotContinueException
 	 *             abort; the message will be sent to the user.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHookChain.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHookChain.java
index 4ef3e1a..12238a1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHookChain.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHookChain.java
@@ -52,7 +52,7 @@
  * Hooks are run in the order passed to the constructor. A hook may inspect or
  * modify the results of the previous hooks in the chain by calling
  * {@link org.eclipse.jgit.transport.UploadPack#getAdvertisedRefs()}, or
- * {@link org.eclipse.jgit.transport.BaseReceivePack#getAdvertisedRefs()} or
+ * {@link org.eclipse.jgit.transport.ReceivePack#getAdvertisedRefs()} or
  * {@link org.eclipse.jgit.transport.BaseReceivePack#getAdvertisedObjects()}.
  */
 public class AdvertiseRefsHookChain implements AdvertiseRefsHook {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackPushConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackPushConnection.java
index 69624ff..847e901 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackPushConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackPushConnection.java
@@ -338,7 +338,7 @@ private void writePack(final Map<String, RemoteRefUpdate> refUpdates,
 			for (Ref r : getRefs()) {
 				// only add objects that we actually have
 				ObjectId oid = r.getObjectId();
-				if (local.hasObject(oid))
+				if (local.getObjectDatabase().has(oid))
 					remoteObjects.add(oid);
 			}
 			remoteObjects.addAll(additionalHaves);
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 0376336..6f17620 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java
@@ -80,6 +80,7 @@
 import org.eclipse.jgit.internal.storage.file.PackLock;
 import org.eclipse.jgit.internal.submodule.SubmoduleValidator;
 import org.eclipse.jgit.internal.submodule.SubmoduleValidator.SubmoduleValidationException;
+import org.eclipse.jgit.internal.transport.parser.FirstCommand;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.BatchRefUpdate;
 import org.eclipse.jgit.lib.Config;
@@ -119,10 +120,14 @@
  * Subclasses compose these operations into full service implementations.
  */
 public abstract class BaseReceivePack {
-	/** Data in the first line of a request, the line itself plus capabilities. */
+	/**
+	 * Data in the first line of a request, the line itself plus capabilities.
+	 *
+	 * @deprecated Use {@link FirstCommand} instead.
+	 */
+	@Deprecated
 	public static class FirstLine {
-		private final String line;
-		private final Set<String> capabilities;
+		private final FirstCommand command;
 
 		/**
 		 * Parse the first line of a receive-pack request.
@@ -131,33 +136,25 @@ public static class FirstLine {
 		 *            line from the client.
 		 */
 		public FirstLine(String line) {
-			final HashSet<String> caps = new HashSet<>();
-			final int nul = line.indexOf('\0');
-			if (nul >= 0) {
-				for (String c : line.substring(nul + 1).split(" ")) //$NON-NLS-1$
-					caps.add(c);
-				this.line = line.substring(0, nul);
-			} else
-				this.line = line;
-			this.capabilities = Collections.unmodifiableSet(caps);
+			command = FirstCommand.fromLine(line);
 		}
 
 		/** @return non-capabilities part of the line. */
 		public String getLine() {
-			return line;
+			return command.getLine();
 		}
 
 		/** @return capabilities parsed from the line. */
 		public Set<String> getCapabilities() {
-			return capabilities;
+			return command.getCapabilities();
 		}
 	}
 
 	/** Database we write the stored objects into. */
-	private final Repository db;
+	final Repository db;
 
 	/** Revision traversal support over {@link #db}. */
-	private final RevWalk walk;
+	final RevWalk walk;
 
 	/**
 	 * Is the client connection a bi-directional socket or pipe?
@@ -207,7 +204,7 @@ public Set<String> getCapabilities() {
 	private AdvertiseRefsHook advertiseRefsHook;
 
 	/** Filter used while advertising the refs to the client. */
-	private RefFilter refFilter;
+	RefFilter refFilter;
 
 	/** Timeout in seconds to wait for client interaction. */
 	private int timeout;
@@ -242,10 +239,10 @@ public Set<String> getCapabilities() {
 	private PackParser parser;
 
 	/** The refs we advertised as existing at the start of the connection. */
-	private Map<String, Ref> refs;
+	Map<String, Ref> refs;
 
 	/** All SHA-1s shown to the client, which can be possible edges. */
-	private Set<ObjectId> advertisedHaves;
+	Set<ObjectId> advertisedHaves;
 
 	/** Capabilities requested by the client. */
 	private Set<String> enabledCapabilities;
@@ -278,7 +275,7 @@ public Set<String> getCapabilities() {
 
 	private PushCertificateParser pushCertificateParser;
 	private SignedPushConfig signedPushConfig;
-	private PushCertificate pushCert;
+	PushCertificate pushCert;
 	private ReceivedPackStatistics stats;
 
 	/**
@@ -289,10 +286,10 @@ public Set<String> getCapabilities() {
 	 * @return the parsed certificate, or null if push certificates are disabled
 	 *         or no cert was presented by the client.
 	 * @since 4.1
+	 * @deprecated use {@link ReceivePack#getPushCertificate}.
 	 */
-	public PushCertificate getPushCertificate() {
-		return pushCert;
-	}
+	@Deprecated
+	public abstract PushCertificate getPushCertificate();
 
 	/**
 	 * Set the push certificate used to verify the pusher's identity.
@@ -303,10 +300,10 @@ public PushCertificate getPushCertificate() {
 	 * @param cert
 	 *            the push certificate to set.
 	 * @since 4.1
+	 * @deprecated use {@link ReceivePack#setPushCertificate(PushCertificate)}.
 	 */
-	public void setPushCertificate(PushCertificate cert) {
-		pushCert = cert;
-	}
+	@Deprecated
+	public abstract void setPushCertificate(PushCertificate cert);
 
 	/**
 	 * Create a new pack receive for an open repository.
@@ -424,29 +421,29 @@ public void flush() {
 	 * Get the repository this receive completes into.
 	 *
 	 * @return the repository this receive completes into.
+	 * @deprecated use {@link ReceivePack#getRepository}
 	 */
-	public final Repository getRepository() {
-		return db;
-	}
+	@Deprecated
+	public abstract Repository getRepository();
 
 	/**
 	 * Get the RevWalk instance used by this connection.
 	 *
 	 * @return the RevWalk instance used by this connection.
+	 * @deprecated use {@link ReceivePack#getRevWalk}
 	 */
-	public final RevWalk getRevWalk() {
-		return walk;
-	}
+	@Deprecated
+	public abstract RevWalk getRevWalk();
 
 	/**
 	 * Get refs which were advertised to the client.
 	 *
 	 * @return all refs which were advertised to the client, or null if
 	 *         {@link #setAdvertisedRefs(Map, Set)} has not been called yet.
+	 * @deprecated use {@link ReceivePack#getAdvertisedRefs}
 	 */
-	public final Map<String, Ref> getAdvertisedRefs() {
-		return refs;
-	}
+	@Deprecated
+	public abstract Map<String, Ref> getAdvertisedRefs();
 
 	/**
 	 * Set the refs advertised by this ReceivePack.
@@ -464,25 +461,10 @@ public final Map<String, Ref> getAdvertisedRefs() {
 	 *            explicit set of additional haves to claim as advertised. If
 	 *            null, assumes the default set of additional haves from the
 	 *            repository.
+	 * @deprecated use {@link ReceivePack#setAdvertisedRefs}
 	 */
-	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())
-			refs.remove(Constants.HEAD);
-
-		for (Ref ref : refs.values()) {
-			if (ref.getObjectId() != null)
-				advertisedHaves.add(ref.getObjectId());
-		}
-		if (additionalHaves != null)
-			advertisedHaves.addAll(additionalHaves);
-		else
-			advertisedHaves.addAll(db.getAdditionalHaves());
-	}
+	@Deprecated
+	public abstract void setAdvertisedRefs(Map<String, Ref> allRefs, Set<ObjectId> additionalHaves);
 
 	/**
 	 * Get objects advertised to the client.
@@ -1310,7 +1292,7 @@ protected void recvCommands() throws IOException {
 
 				if (firstPkt) {
 					firstPkt = false;
-					FirstLine firstLine = new FirstLine(line);
+					FirstCommand firstLine = FirstCommand.fromLine(line);
 					enabledCapabilities = firstLine.getCapabilities();
 					line = firstLine.getLine();
 					enableCapabilities();
@@ -1606,7 +1588,7 @@ private void checkConnectivity() throws IOException {
 						throw new MissingObjectException(o, o.getType());
 				}
 
-				if (o instanceof RevBlob && !db.hasObject(o))
+				if (o instanceof RevBlob && !db.getObjectDatabase().has(o))
 					throw new MissingObjectException(o, Constants.TYPE_BLOB);
 			}
 			checking.endTask();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleFetchConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleFetchConnection.java
index 4b20f6c..84a0972 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleFetchConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleFetchConnection.java
@@ -50,6 +50,7 @@
 import static java.nio.charset.StandardCharsets.UTF_8;
 
 import java.io.BufferedInputStream;
+import java.io.EOFException;
 import java.io.IOException;
 import java.io.InputStream;
 import java.text.MessageFormat;
@@ -165,9 +166,13 @@ private String readLine(byte[] hdrbuf) throws IOException {
 		while (!done) {
 			bin.mark(hdrbuf.length);
 			final int cnt = bin.read(hdrbuf);
+			if (cnt < 0) {
+				throw new EOFException(JGitText.get().shortReadOfBlock);
+			}
 			int lf = 0;
-			while (lf < cnt && hdrbuf[lf] != '\n')
+			while (lf < cnt && hdrbuf[lf] != '\n') {
 				lf++;
+			}
 			bin.reset();
 			IO.skipFully(bin, lf);
 			if (lf < cnt && hdrbuf[lf] == '\n') {
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 211707e..681ae12 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
@@ -181,7 +181,7 @@ else if (tagopt == TagOpt.FETCH_TAGS)
 					ObjectId id = r.getPeeledObjectId();
 					if (id == null)
 						id = r.getObjectId();
-					if (transport.local.hasObject(id))
+					if (localHasObject(id))
 						wantTag(r);
 				}
 
@@ -393,6 +393,18 @@ private void expandSingle(RefSpec spec, Set<Ref> matched)
 		}
 	}
 
+	private boolean localHasObject(ObjectId id) throws TransportException {
+		try {
+			return transport.local.getObjectDatabase().has(id);
+		} catch (IOException err) {
+			throw new TransportException(
+					MessageFormat.format(
+							JGitText.get().readingObjectsFromLocalRepositoryFailed,
+							err.getMessage()),
+					err);
+		}
+	}
+
 	private Collection<Ref> expandAutoFollowTags() throws TransportException {
 		final Collection<Ref> additionalTags = new ArrayList<>();
 		final Map<String, Ref> haveRefs = localRefs();
@@ -410,7 +422,7 @@ private Collection<Ref> expandAutoFollowTags() throws TransportException {
 			if (obj == null)
 				obj = r.getObjectId();
 
-			if (askFor.containsKey(obj) || transport.local.hasObject(obj))
+			if (askFor.containsKey(obj) || localHasObject(obj))
 				wantTag(r);
 			else
 				additionalTags.add(r);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/InternalHttpServerGlue.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/InternalHttpServerGlue.java
index fe7aaf7..075cc9c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/InternalHttpServerGlue.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/InternalHttpServerGlue.java
@@ -44,7 +44,7 @@
 package org.eclipse.jgit.transport;
 
 /**
- * Internal API to to assist {@code org.eclipse.jgit.http.server}.
+ * Internal API to assist {@code org.eclipse.jgit.http.server}.
  * <p>
  * <b>Do not call.</b>
  *
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NonceGenerator.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NonceGenerator.java
index fc22034..c573d12 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NonceGenerator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NonceGenerator.java
@@ -81,7 +81,7 @@ String createNonce(Repository db, long timestamp)
 	 *            such that the pusher cannot forge nonces by pushing to another
 	 *            repository at the same time as well and reusing the nonce.
 	 * @param allowSlop
-	 *            If the receiving backend is is able to generate slop. This is
+	 *            If the receiving backend is able to generate slop. This is
 	 *            the case for serving via http protocol using more than one
 	 *            http frontend. The client would talk to different http
 	 *            frontends, which may have a slight difference of time due to
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 49acb4d..2b2795f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackParser.java
@@ -1237,7 +1237,7 @@ void use(int cnt) {
 		bAvail -= cnt;
 	}
 
-	// Ensure at least need bytes are available in in {@link #buf}.
+	// Ensure at least need bytes are available in {@link #buf}.
 	int fill(Source src, int need) throws IOException {
 		while (bAvail < need) {
 			int next = bOffset + bAvail;
@@ -1568,7 +1568,7 @@ protected abstract void onBeginWholeObject(long streamPosition, int type,
 			long inflatedSize) throws IOException;
 
 	/**
-	 * Event notifying the the current object.
+	 * Event notifying the current object.
 	 *
 	 *@param info
 	 *            object information.
@@ -1616,7 +1616,7 @@ protected abstract void onBeginRefDelta(long deltaStreamPosition,
 			AnyObjectId baseId, long inflatedSize) throws IOException;
 
 	/**
-	 * Event notifying the the current object.
+	 * Event notifying the current object.
 	 *
 	 *@return object information that must be populated with at least the
 	 *         offset.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java
index 577aaf4..4652c3f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java
@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.transport;
 
+import static org.eclipse.jgit.lib.Constants.HEAD;
 import static org.eclipse.jgit.transport.GitProtocolConstants.CAPABILITY_ATOMIC;
 import static org.eclipse.jgit.transport.GitProtocolConstants.CAPABILITY_PUSH_OPTIONS;
 import static org.eclipse.jgit.transport.GitProtocolConstants.CAPABILITY_REPORT_STATUS;
@@ -53,13 +54,18 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
 import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.errors.UnpackException;
 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.Ref;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.transport.ReceiveCommand.Result;
 import org.eclipse.jgit.transport.RefAdvertiser.PacketLineOutRefAdvertiser;
 
@@ -93,6 +99,106 @@ public ReceivePack(Repository into) {
 	}
 
 	/**
+	 * Get the repository this receive completes into.
+	 *
+	 * @return the repository this receive completes into.
+	 */
+	@Override
+	public final Repository getRepository() {
+		return db;
+	}
+
+	/**
+	 * Get the RevWalk instance used by this connection.
+	 *
+	 * @return the RevWalk instance used by this connection.
+	 */
+	@Override
+	public final RevWalk getRevWalk() {
+		return walk;
+	}
+
+	/**
+	 * Get refs which were advertised to the client.
+	 *
+	 * @return all refs which were advertised to the client, or null if
+	 *         {@link #setAdvertisedRefs(Map, Set)} has not been called yet.
+	 */
+	@Override
+	public final Map<String, Ref> getAdvertisedRefs() {
+		return refs;
+	}
+
+	/**
+	 * Set the refs advertised by this ReceivePack.
+	 * <p>
+	 * Intended to be called from a
+	 * {@link org.eclipse.jgit.transport.PreReceiveHook}.
+	 *
+	 * @param allRefs
+	 *            explicit set of references to claim as advertised by this
+	 *            ReceivePack instance. This overrides any references that may
+	 *            exist in the source repository. The map is passed to the
+	 *            configured {@link #getRefFilter()}. If null, assumes all refs
+	 *            were advertised.
+	 * @param additionalHaves
+	 *            explicit set of additional haves to claim as advertised. If
+	 *            null, assumes the default set of additional haves from the
+	 *            repository.
+	 */
+	@Override
+	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(HEAD);
+		if (head != null && head.isSymbolic()) {
+			refs.remove(HEAD);
+		}
+
+		for (Ref ref : refs.values()) {
+			if (ref.getObjectId() != null) {
+				advertisedHaves.add(ref.getObjectId());
+			}
+		}
+		if (additionalHaves != null) {
+			advertisedHaves.addAll(additionalHaves);
+		} else {
+			advertisedHaves.addAll(db.getAdditionalHaves());
+		}
+	}
+
+	/**
+	 * Get the push certificate used to verify the pusher's identity.
+	 * <p>
+	 * Only valid after commands are read from the wire.
+	 *
+	 * @return the parsed certificate, or null if push certificates are disabled
+	 *         or no cert was presented by the client.
+	 * @since 4.1
+	 */
+	@Override
+	public PushCertificate getPushCertificate() {
+		return pushCert;
+	}
+
+	/**
+	 * Set the push certificate used to verify the pusher's identity.
+	 * <p>
+	 * Should only be called if reconstructing an instance without going through
+	 * the normal {@link #recvCommands()} flow.
+	 *
+	 * @param cert
+	 *            the push certificate to set.
+	 * @since 4.1
+	 */
+	@Override
+	public void setPushCertificate(PushCertificate cert) {
+		pushCert = cert;
+	}
+
+	/**
 	 * Gets an unmodifiable view of the option strings associated with the push.
 	 *
 	 * @return an unmodifiable view of pushOptions, or null (if pushOptions is).
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteRefUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteRefUpdate.java
index 9a67f0f..c34e3b8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteRefUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteRefUpdate.java
@@ -293,7 +293,7 @@ public RemoteRefUpdate(final Repository localDb, final String srcRef,
 			final boolean forceUpdate, final String localName,
 			final ObjectId expectedOldObjectId) throws IOException {
 		if (remoteName == null)
-			throw new IllegalArgumentException(JGitText.get().remoteNameCantBeNull);
+			throw new IllegalArgumentException(JGitText.get().remoteNameCannotBeNull);
 		if (srcId == null && srcRef != null)
 			throw new IOException(MessageFormat.format(
 					JGitText.get().sourceRefDoesntResolveToAnyObject, srcRef));
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 2fbcaa2..1d0f836 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java
@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.transport;
 
+import static java.util.Collections.unmodifiableMap;
 import static java.util.function.Function.identity;
 import static java.util.stream.Collectors.toMap;
 import static org.eclipse.jgit.lib.Constants.R_TAGS;
@@ -79,9 +80,11 @@
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import java.util.Set;
 import java.util.TreeMap;
 
+import org.eclipse.jgit.annotations.NonNull;
 import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.errors.CorruptObjectException;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
@@ -421,7 +424,7 @@ public final Map<String, Ref> getAdvertisedRefs() {
 	 *            configured {@link #getRefFilter()}. If null, assumes all refs
 	 *            were advertised.
 	 */
-	public void setAdvertisedRefs(Map<String, Ref> allRefs) {
+	public void setAdvertisedRefs(@Nullable Map<String, Ref> allRefs) {
 		if (allRefs != null)
 			refs = allRefs;
 		else
@@ -545,7 +548,7 @@ public void setRequestPolicy(RequestPolicy policy) {
 	 *            custom validator for client want list.
 	 * @since 3.1
 	 */
-	public void setRequestValidator(RequestValidator validator) {
+	public void setRequestValidator(@Nullable RequestValidator validator) {
 		requestValidator = validator != null ? validator
 				: new AdvertisedRequestValidator();
 	}
@@ -579,21 +582,21 @@ public RefFilter getRefFilter() {
 	 * @param advertiseRefsHook
 	 *            the hook; may be null to show all refs.
 	 */
-	public void setAdvertiseRefsHook(AdvertiseRefsHook advertiseRefsHook) {
-		if (advertiseRefsHook != null)
-			this.advertiseRefsHook = advertiseRefsHook;
-		else
-			this.advertiseRefsHook = AdvertiseRefsHook.DEFAULT;
+	public void setAdvertiseRefsHook(
+			@Nullable AdvertiseRefsHook advertiseRefsHook) {
+		this.advertiseRefsHook = advertiseRefsHook != null ? advertiseRefsHook
+				: AdvertiseRefsHook.DEFAULT;
 	}
 
 	/**
 	 * Set the protocol V2 hook.
 	 *
 	 * @param hook
+	 *            the hook; if null no special actions are taken.
 	 * @since 5.1
 	 */
-	public void setProtocolV2Hook(ProtocolV2Hook hook) {
-		this.protocolV2Hook = hook;
+	public void setProtocolV2Hook(@Nullable ProtocolV2Hook hook) {
+		this.protocolV2Hook = hook != null ? hook : ProtocolV2Hook.DEFAULT;
 	}
 
 	/**
@@ -608,7 +611,7 @@ public void setProtocolV2Hook(ProtocolV2Hook hook) {
 	 * @param refFilter
 	 *            the filter; may be null to show all refs.
 	 */
-	public void setRefFilter(RefFilter refFilter) {
+	public void setRefFilter(@Nullable RefFilter refFilter) {
 		this.refFilter = refFilter != null ? refFilter : RefFilter.DEFAULT;
 	}
 
@@ -627,7 +630,7 @@ public PreUploadHook getPreUploadHook() {
 	 * @param hook
 	 *            the hook; if null no special actions are taken.
 	 */
-	public void setPreUploadHook(PreUploadHook hook) {
+	public void setPreUploadHook(@Nullable PreUploadHook hook) {
 		preUploadHook = hook != null ? hook : PreUploadHook.NULL;
 	}
 
@@ -648,7 +651,7 @@ public PostUploadHook getPostUploadHook() {
 	 *            the hook; if null no special actions are taken.
 	 * @since 4.1
 	 */
-	public void setPostUploadHook(PostUploadHook hook) {
+	public void setPostUploadHook(@Nullable PostUploadHook hook) {
 		postUploadHook = hook != null ? hook : PostUploadHook.NULL;
 	}
 
@@ -659,7 +662,7 @@ public void setPostUploadHook(PostUploadHook hook) {
 	 *            configuration controlling packing parameters. If null the
 	 *            source repository's settings will be used.
 	 */
-	public void setPackConfig(PackConfig pc) {
+	public void setPackConfig(@Nullable PackConfig pc) {
 		this.packConfig = pc;
 	}
 
@@ -671,7 +674,7 @@ public void setPackConfig(PackConfig pc) {
 	 *            repository's settings will be used.
 	 * @since 3.1
 	 */
-	public void setTransferConfig(TransferConfig tc) {
+	public void setTransferConfig(@Nullable TransferConfig tc) {
 		this.transferConfig = tc != null ? tc : new TransferConfig(db);
 		if (transferConfig.isAllowTipSha1InWant()) {
 			setRequestPolicy(transferConfig.isAllowReachableSha1InWant()
@@ -849,22 +852,46 @@ private Map<String, Ref> getFilteredRefs(Collection<String> refPrefixes)
 	}
 
 	/**
-	 * Read a ref on behalf of the client.
+	 * Returns the specified references.
 	 * <p>
-	 * This checks that the ref is present in the ref advertisement since
-	 * otherwise the client might not be supposed to be able to read it.
+	 * This produces an immutable map containing whatever subset of the
+	 * refs named by the caller are present in the supplied {@code refs}
+	 * map.
 	 *
-	 * @param name
-	 *            the unabbreviated name of the reference.
-	 * @return the requested Ref, or {@code null} if it is not visible or
-	 *         does not exist.
-	 * @throws java.io.IOException
-	 *            on failure to read the ref or check it for visibility.
+	 * @param refs
+	 *            Map to search for refs to return.
+	 * @param names
+	 *            which refs to search for in {@code refs}.
+	 * @return the requested Refs, omitting any that are null or missing.
 	 */
-	@Nullable
-	private Ref getRef(String name) throws IOException {
+	@NonNull
+	private static Map<String, Ref> mapRefs(
+			Map<String, Ref> refs, List<String> names) {
+		return unmodifiableMap(
+				names.stream()
+					.map(refs::get)
+					.filter(Objects::nonNull)
+					.collect(toMap(Ref::getName, identity(), (a, b) -> b)));
+	}
+
+	/**
+	 * Read refs on behalf of the client.
+	 * <p>
+	 * This checks whether the refs are present in the ref advertisement
+	 * since otherwise the client might not be supposed to be able to
+	 * read them.
+	 *
+	 * @param names
+	 *            unabbreviated names of references.
+	 * @return the requested Refs, omitting any that are not visible or
+	 *         do not exist.
+	 * @throws java.io.IOException
+	 *            on failure to read a ref or check it for visibility.
+	 */
+	@NonNull
+	private Map<String, Ref> exactRefs(List<String> names) throws IOException {
 		if (refs != null) {
-			return refs.get(name);
+			return mapRefs(refs, names);
 		}
 		if (!advertiseRefsHookCalled) {
 			advertiseRefsHook.advertiseRefs(this);
@@ -874,9 +901,10 @@ private Ref getRef(String name) throws IOException {
 				refFilter == RefFilter.DEFAULT &&
 				transferConfig.hasDefaultRefFilter()) {
 			// Fast path: no ref filtering is needed.
-			return db.getRefDatabase().exactRef(name);
+			String[] ns = names.toArray(new String[0]);
+			return unmodifiableMap(db.getRefDatabase().exactRef(ns));
 		}
-		return getAdvertisedOrDefaultRefs().get(name);
+		return mapRefs(getAdvertisedOrDefaultRefs(), names);
 	}
 
 	/**
@@ -906,7 +934,7 @@ private Ref findRef(String name) throws IOException {
 				refFilter == RefFilter.DEFAULT &&
 				transferConfig.hasDefaultRefFilter()) {
 			// Fast path: no ref filtering is needed.
-			return db.getRefDatabase().getRef(name);
+			return db.getRefDatabase().findRef(name);
 		}
 		return RefDatabase.findRef(getAdvertisedOrDefaultRefs(), name);
 	}
@@ -1042,6 +1070,31 @@ private void lsRefsV2() throws IOException {
 		adv.end();
 	}
 
+	// Resolves ref names from the request's want-ref lines to
+	// object ids, throwing PackProtocolException if any are missing.
+	private Map<String, ObjectId> wantedRefs(FetchV2Request req)
+			throws IOException {
+		Map<String, ObjectId> result = new TreeMap<>();
+
+		List<String> wanted = req.getWantedRefs();
+		Map<String, Ref> resolved = exactRefs(wanted);
+
+		for (String refName : wanted) {
+			Ref ref = resolved.get(refName);
+			if (ref == null) {
+				throw new PackProtocolException(MessageFormat
+						.format(JGitText.get().invalidRefName, refName));
+			}
+			ObjectId oid = ref.getObjectId();
+			if (oid == null) {
+				throw new PackProtocolException(MessageFormat
+						.format(JGitText.get().invalidRefName, refName));
+			}
+			result.put(refName, oid);
+		}
+		return result;
+	}
+
 	private void fetchV2() throws IOException {
 		// Depending on the requestValidator, #processHaveLines may
 		// require that advertised be set. Set it only in the required
@@ -1074,22 +1127,9 @@ private void fetchV2() throws IOException {
 			deepenNots.add(ref.getObjectId());
 		}
 
-		Map<String, ObjectId> wantedRefs = new TreeMap<>();
-		for (String refName : req.getWantedRefs()) {
-			Ref ref = getRef(refName);
-			if (ref == null) {
-				throw new PackProtocolException(MessageFormat
-						.format(JGitText.get().invalidRefName, refName));
-			}
-			ObjectId oid = ref.getObjectId();
-			if (oid == null) {
-				throw new PackProtocolException(MessageFormat
-						.format(JGitText.get().invalidRefName, refName));
-			}
-			// TODO(ifrade): Avoid mutating the parsed request.
-			req.getWantIds().add(oid);
-			wantedRefs.put(refName, oid);
-		}
+		Map<String, ObjectId> wantedRefs = wantedRefs(req);
+		// TODO(ifrade): Avoid mutating the parsed request.
+		req.getWantIds().addAll(wantedRefs.values());
 		wantIds = req.getWantIds();
 
 		boolean sectionSent = false;
@@ -1486,6 +1526,20 @@ public int getDepth() {
 	}
 
 	/**
+	 * Returns the filter blob limit for the current request. Valid only after
+	 * calling recvWants(). A limit -1 means no limit.
+	 *
+	 * @return filter blob limit requested by the client, or -1 if no limit
+	 * @since 5.3
+	 */
+	public long getFilterBlobLimit() {
+		if (currentRequest == null) {
+			throw new RequestNotYetReadException();
+		}
+		return currentRequest.getFilterBlobLimit();
+	}
+
+	/**
 	 * Get the user agent of the client.
 	 * <p>
 	 * If the client is new enough to use {@code agent=} capability that value
@@ -2080,6 +2134,7 @@ else if (ref.getName().startsWith(Constants.R_HEADS))
 						: req.getDepth() - 1;
 				pw.setShallowPack(req.getDepth(), unshallowCommits);
 
+				@SuppressWarnings("resource") // Ownership is transferred below
 				DepthWalk.RevWalk dw = new DepthWalk.RevWalk(
 						walk.getObjectReader(), walkDepth);
 				dw.setDeepenSince(req.getDeepenSince());
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkFetchConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkFetchConnection.java
index 9307914..2bb5814 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkFetchConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkFetchConnection.java
@@ -555,10 +555,10 @@ private boolean downloadPackedObject(final ProgressMonitor monitor,
 				continue;
 			} finally {
 				// If the pack was good its in the local repository
-				// and Repository.hasObject(id) will succeed in the
-				// future, so we do not need this data anymore. If
-				// it failed the index and pack are unusable and we
-				// shouldn't consult them again.
+				// and Repository.getObjectDatabase().has(id) will
+				// succeed in the future, so we do not need this
+				// data any more. If it failed the index and pack
+				// are unusable and we shouldn't consult them again.
 				//
 				try {
 					if (pack.tmpIdx != null)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkRemoteObjectDatabase.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkRemoteObjectDatabase.java
index 6d4df4f..5c67253 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkRemoteObjectDatabase.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkRemoteObjectDatabase.java
@@ -348,7 +348,7 @@ void writeInfoPacks(Collection<String> packNames) throws IOException {
 	/**
 	 * Open a buffered reader around a file.
 	 * <p>
-	 * This method is suitable for for reading line-oriented resources like
+	 * This method is suitable for reading line-oriented resources like
 	 * <code>info/packs</code>, <code>info/refs</code>, and the alternates list.
 	 *
 	 * @return a stream to read from the file. Never null.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
index b2d91f8..53fa3bc 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
@@ -75,6 +75,7 @@
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.dircache.DirCacheIterator;
 import org.eclipse.jgit.errors.CorruptObjectException;
+import org.eclipse.jgit.errors.LargeObjectException;
 import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.errors.NoWorkTreeException;
 import org.eclipse.jgit.ignore.FastIgnoreRule;
@@ -1499,9 +1500,18 @@ public EolStreamType getEolStreamType() throws IOException {
 	private EolStreamType getEolStreamType(OperationType opType)
 			throws IOException {
 		if (eolStreamTypeHolder == null) {
-			EolStreamType type=null;
+			EolStreamType type = null;
 			if (state.walk != null) {
 				type = state.walk.getEolStreamType(opType);
+				OperationType operationType = opType != null ? opType
+						: state.walk.getOperationType();
+				if (OperationType.CHECKIN_OP.equals(operationType)
+						&& EolStreamType.AUTO_LF.equals(type)
+						&& hasCrLfInIndex(getDirCacheIterator())) {
+					// If text=auto (or core.autocrlf=true) and the file has
+					// already been committed with CR/LF, then don't convert.
+					type = EolStreamType.DIRECT;
+				}
 			} else {
 				switch (getOptions().getAutoCRLF()) {
 				case FALSE:
@@ -1518,6 +1528,59 @@ private EolStreamType getEolStreamType(OperationType opType)
 		return eolStreamTypeHolder.get();
 	}
 
+	/**
+	 * Determines whether the file was committed un-normalized. If the iterator
+	 * points to a conflict entry, checks the "ours" version.
+	 *
+	 * @param dirCache
+	 *            iterator pointing to the current entry for the file in the
+	 *            index
+	 * @return {@code true} if the file in the index is not binary and has CR/LF
+	 *         line endings, {@code false} otherwise
+	 */
+	private boolean hasCrLfInIndex(DirCacheIterator dirCache) {
+		if (dirCache == null) {
+			return false;
+		}
+		// Read blob from index and check for CR/LF-delimited text.
+		DirCacheEntry entry = dirCache.getDirCacheEntry();
+		if (FileMode.REGULAR_FILE.equals(entry.getFileMode())) {
+			ObjectId blobId = entry.getObjectId();
+			if (entry.getStage() > 0
+					&& entry.getStage() != DirCacheEntry.STAGE_2) {
+				// Merge conflict: check ours (stage 2)
+				byte[] name = entry.getRawPath();
+				int i = 0;
+				while (!dirCache.eof()) {
+					dirCache.next(1);
+					i++;
+					entry = dirCache.getDirCacheEntry();
+					if (!Arrays.equals(name, entry.getRawPath())) {
+						break;
+					}
+					if (entry.getStage() == DirCacheEntry.STAGE_2) {
+						blobId = entry.getObjectId();
+						break;
+					}
+				}
+				dirCache.back(i);
+			}
+			try (ObjectReader reader = repository.newObjectReader()) {
+				ObjectLoader loader = reader.open(blobId, Constants.OBJ_BLOB);
+				try {
+					return RawText.isCrLfText(loader.getCachedBytes());
+				} catch (LargeObjectException e) {
+					try (InputStream in = loader.openStream()) {
+						return RawText.isCrLfText(in);
+					}
+				}
+			} catch (IOException e) {
+				// Ignore and return false below
+			}
+		}
+		return false;
+	}
+
 	private boolean isDirectoryIgnored(String pathRel) throws IOException {
 		final int pOff = 0 < pathOffset ? pathOffset - 1 : pathOffset;
 		final String base = TreeWalk.pathOf(this.path, 0, pOff);
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 eda8afb..eda0fae 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
@@ -51,6 +51,7 @@
 import java.io.InputStreamReader;
 import java.io.PrintStream;
 import java.nio.charset.Charset;
+import java.nio.file.AccessDeniedException;
 import java.nio.file.FileAlreadyExistsException;
 import java.nio.file.Files;
 import java.nio.file.InvalidPathException;
@@ -386,8 +387,9 @@ public boolean createNewFile(File lock) throws IOException {
 			Integer nlink = (Integer) (Files.getAttribute(lockPath,
 					"unix:nlink")); //$NON-NLS-1$
 			if (nlink > 2) {
-				LOG.warn("nlink of link to lock file {} was not 2 but {}", //$NON-NLS-1$
-						lock.getPath(), nlink);
+				LOG.warn(MessageFormat.format(
+						JGitText.get().failedAtomicFileCreation, lockPath,
+						nlink));
 				return false;
 			} else if (nlink < 2) {
 				supportsUnixNLink = false;
@@ -453,7 +455,8 @@ public LockToken createNewFileAtomic(File file) throws IOException {
 				supportsUnixNLink = false;
 			}
 			return token(true, link);
-		} catch (UnsupportedOperationException | IllegalArgumentException e) {
+		} catch (UnsupportedOperationException | IllegalArgumentException
+				| AccessDeniedException | SecurityException e) {
 			supportsUnixNLink = false;
 			return token(true, link);
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/IO.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/IO.java
index e88e7a3..a07a4fd 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/IO.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/IO.java
@@ -203,12 +203,13 @@ public static ByteBuffer readWholeStream(InputStream in, int sizeHint)
 		if (last < 0)
 			return ByteBuffer.wrap(out, 0, pos);
 
-		@SuppressWarnings("resource" /* java 7 */)
-		TemporaryBuffer.Heap tmp = new TemporaryBuffer.Heap(Integer.MAX_VALUE);
-		tmp.write(out);
-		tmp.write(last);
-		tmp.copy(in);
-		return ByteBuffer.wrap(tmp.toByteArray());
+		try (TemporaryBuffer.Heap tmp = new TemporaryBuffer.Heap(
+				Integer.MAX_VALUE)) {
+			tmp.write(out);
+			tmp.write(last);
+			tmp.copy(in);
+			return ByteBuffer.wrap(tmp.toByteArray());
+		}
 	}
 
 	/**
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 a440cb2..2081bac 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/RawParseUtils.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/RawParseUtils.java
@@ -75,7 +75,9 @@ public final class RawParseUtils {
 	 * UTF-8 charset constant.
 	 *
 	 * @since 2.2
+	 * @deprecated use {@link java.nio.charset.StandardCharsets#UTF_8} instead
 	 */
+	@Deprecated
 	public static final Charset UTF8_CHARSET = UTF_8;
 
 	private static final byte[] digits10;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoCRLFInputStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoCRLFInputStream.java
index 08377e6..4c60862 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoCRLFInputStream.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoCRLFInputStream.java
@@ -144,9 +144,18 @@ public void close() throws IOException {
 	}
 
 	private boolean fillBuffer() throws IOException {
-		cnt = in.read(buf, 0, buf.length);
-		if (cnt < 1)
+		cnt = 0;
+		while (cnt < buf.length) {
+			int n = in.read(buf, cnt, buf.length - cnt);
+			if (n < 0) {
+				break;
+			}
+			cnt += n;
+		}
+		if (cnt < 1) {
+			cnt = -1;
 			return false;
+		}
 		if (detectBinary) {
 			isBinary = RawText.isBinary(buf, cnt);
 			detectBinary = false;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFInputStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFInputStream.java
index ff28161..280cf7e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFInputStream.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/AutoLFInputStream.java
@@ -189,9 +189,18 @@ public void close() throws IOException {
 	}
 
 	private boolean fillBuffer() throws IOException {
-		cnt = in.read(buf, 0, buf.length);
-		if (cnt < 1)
+		cnt = 0;
+		while (cnt < buf.length) {
+			int n = in.read(buf, cnt, buf.length - cnt);
+			if (n < 0) {
+				break;
+			}
+			cnt += n;
+		}
+		if (cnt < 1) {
+			cnt = -1;
 			return false;
+		}
 		if (detectBinary) {
 			isBinary = RawText.isBinary(buf, cnt);
 			detectBinary = false;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/sha1/SHA1.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/sha1/SHA1.java
index 9fe01f1..1ad6602 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/sha1/SHA1.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/sha1/SHA1.java
@@ -48,8 +48,10 @@
 import static java.lang.Integer.rotateLeft;
 import static java.lang.Integer.rotateRight;
 
+import java.text.MessageFormat;
 import java.util.Arrays;
 
+import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.MutableObjectId;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.util.NB;
@@ -497,7 +499,8 @@ private void finish() {
 
 		if (foundCollision) {
 			ObjectId id = h.toObjectId();
-			LOG.warn("possible SHA-1 collision " + id.name()); //$NON-NLS-1$
+			LOG.warn(MessageFormat.format(JGitText.get().sha1CollisionDetected,
+					id.name()));
 			throw new Sha1CollisionException(id);
 		}
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/sha1/Sha1CollisionException.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/sha1/Sha1CollisionException.java
index dcefe95..0e5c919 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/sha1/Sha1CollisionException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/sha1/Sha1CollisionException.java
@@ -65,7 +65,7 @@ public class Sha1CollisionException extends RuntimeException {
 	 */
 	public Sha1CollisionException(ObjectId id) {
 		super(MessageFormat.format(
-				JGitText.get().sha1CollisionDetected1,
+				JGitText.get().sha1CollisionDetected,
 				id.name()));
 	}
 }
diff --git a/pom.xml b/pom.xml
index 732308b..fe25c02 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>5.2.3-SNAPSHOT</version>
+  <version>5.3.6-SNAPSHOT</version>
 
   <name>JGit - Parent</name>
   <url>${jgit-url}</url>
@@ -182,7 +182,7 @@
     <maven.build.timestamp.format>yyyyMMddHHmm</maven.build.timestamp.format>
     <bundle-manifest>${project.build.directory}/META-INF/MANIFEST.MF</bundle-manifest>
 
-    <jgit-last-release-version>5.1.0.201809111528-r</jgit-last-release-version>
+    <jgit-last-release-version>5.2.0.201812061821-r</jgit-last-release-version>
     <apache-sshd-version>2.0.0</apache-sshd-version>
     <jsch-version>0.1.55</jsch-version>
     <jzlib-version>1.1.1</jzlib-version>
@@ -193,7 +193,7 @@
     <commons-compress-version>1.18</commons-compress-version>
     <osgi-core-version>4.3.1</osgi-core-version>
     <servlet-api-version>3.1.0</servlet-api-version>
-    <jetty-version>9.4.11.v20180605</jetty-version>
+    <jetty-version>9.4.14.v20181114</jetty-version>
     <japicmp-version>0.14.1</japicmp-version>
     <httpclient-version>4.5.6</httpclient-version>
     <httpcore-version>4.4.10</httpcore-version>
@@ -202,6 +202,8 @@
     <maven-javadoc-plugin-version>3.1.0</maven-javadoc-plugin-version>
     <tycho-extras-version>1.3.0</tycho-extras-version>
     <gson-version>2.8.2</gson-version>
+    <bouncycastle-version>1.60</bouncycastle-version>
+    <spotbugs-maven-plugin-version>3.1.11</spotbugs-maven-plugin-version>
     <maven-project-info-reports-plugin-version>3.0.0</maven-project-info-reports-plugin-version>
     <maven-jxr-plugin-version>3.0.0</maven-jxr-plugin-version>
     <spotbugs-maven-plugin-version>3.1.12</spotbugs-maven-plugin-version>
@@ -212,7 +214,7 @@
     <!-- Properties to enable jacoco code coverage analysis -->
     <sonar.core.codeCoveragePlugin>jacoco</sonar.core.codeCoveragePlugin>
     <sonar.dynamicAnalysis>reuseReports</sonar.dynamicAnalysis>
-    <sonar.jacoco.reportPath>../target/jacoco.exec</sonar.jacoco.reportPath>
+    <sonar.jacoco.reportPath>${project.build.directory}/jacoco.exec</sonar.jacoco.reportPath>
   </properties>
 
   <repositories>
@@ -298,6 +300,7 @@
           <configuration>
             <forkCount>${test-fork-count}</forkCount>
             <reuseForks>true</reuseForks>
+            <argLine>@{argLine}</argLine>
           </configuration>
         </plugin>
 
@@ -375,7 +378,7 @@
             <dependency><!-- add support for ssh/scp -->
               <groupId>org.apache.maven.wagon</groupId>
               <artifactId>wagon-ssh</artifactId>
-              <version>3.2.0</version>
+              <version>3.3.2</version>
             </dependency>
           </dependencies>
         </plugin>
@@ -414,6 +417,11 @@
           <artifactId>maven-resources-plugin</artifactId>
           <version>3.1.0</version>
         </plugin>
+        <plugin>
+          <groupId>org.springframework.boot</groupId>
+          <artifactId>spring-boot-maven-plugin</artifactId>
+          <version>2.1.2.RELEASE</version>
+        </plugin>
       </plugins>
     </pluginManagement>
 
@@ -519,6 +527,7 @@
         <artifactId>jacoco-maven-plugin</artifactId>
         <executions>
           <execution>
+            <id>default-prepare-agent</id>
             <goals>
               <goal>prepare-agent</goal>
             </goals>
@@ -533,6 +542,38 @@
               <append>true</append>
             </configuration>
           </execution>
+          <execution>
+            <id>default-report</id>
+            <goals>
+              <goal>report</goal>
+            </goals>
+          </execution>
+          <execution>
+            <id>default-check</id>
+            <goals>
+              <goal>check</goal>
+            </goals>
+            <configuration>
+            <haltOnFailure>false</haltOnFailure>
+            <rules>
+              <rule>
+                <element>BUNDLE</element>
+                  <limits>
+                    <limit>
+                      <counter>INSTRUCTION</counter>
+                      <value>COVEREDRATIO</value>
+                      <minimum>50%</minimum>
+                    </limit>
+                    <limit>
+                      <counter>CLASS</counter>
+                      <value>MISSEDCOUNT</value>
+                      <maximum>10</maximum>
+                    </limit>
+                  </limits>
+                </rule>
+              </rules>
+            </configuration>
+          </execution>
         </executions>
       </plugin>
       <plugin>
@@ -610,6 +651,24 @@
           </reportSet>
         </reportSets>
       </plugin>
+      <plugin>
+        <groupId>org.jacoco</groupId>
+        <artifactId>jacoco-maven-plugin</artifactId>
+        <reportSets>
+          <reportSet>
+            <reports>
+              <report>report</report>
+            </reports>
+          </reportSet>
+          <reportSet>
+            <id>aggregate</id>
+            <inherited>false</inherited>
+            <reports>
+              <report>report-aggregate</report>
+            </reports>
+          </reportSet>
+        </reportSets>
+      </plugin>
     </plugins>
   </reporting>
 
@@ -660,7 +719,7 @@
       <dependency>
         <groupId>org.tukaani</groupId>
         <artifactId>xz</artifactId>
-        <version>1.6</version>
+        <version>1.8</version>
         <optional>true</optional>
       </dependency>
 
@@ -729,6 +788,25 @@
         <artifactId>gson</artifactId>
         <version>${gson-version}</version>
       </dependency>
+
+      <dependency>
+        <groupId>org.bouncycastle</groupId>
+        <artifactId>bcpg-jdk15on</artifactId>
+        <version>${bouncycastle-version}</version>
+      </dependency>
+
+      <dependency>
+        <groupId>org.bouncycastle</groupId>
+        <artifactId>bcprov-jdk15on</artifactId>
+        <version>${bouncycastle-version}</version>
+      </dependency>
+
+      <dependency>
+        <groupId>org.bouncycastle</groupId>
+        <artifactId>bcpkix-jdk15on</artifactId>
+        <version>${bouncycastle-version}</version>
+      </dependency>
+
     </dependencies>
   </dependencyManagement>
 
@@ -959,6 +1037,8 @@
     <module>org.eclipse.jgit.lfs.test</module>
     <module>org.eclipse.jgit.lfs.server.test</module>
     <module>org.eclipse.jgit.ssh.apache.test</module>
+
+    <module>org.eclipse.jgit.coverage</module>
   </modules>
 
 </project>
diff --git a/tools/BUILD b/tools/BUILD
index f1b1536..6741d23 100644
--- a/tools/BUILD
+++ b/tools/BUILD
@@ -1,9 +1,9 @@
-load("@rules_java//java:defs.bzl", "java_package_configuration")
 load(
     "@bazel_tools//tools/jdk:default_java_toolchain.bzl",
     "JDK9_JVM_OPTS",
     "default_java_toolchain",
 )
+load("@rules_java//java:defs.bzl", "java_package_configuration")
 
 default_java_toolchain(
     name = "error_prone_warnings_toolchain",
@@ -15,8 +15,10 @@
     visibility = ["//visibility:public"],
 )
 
-# This EP warnings list borrowed from here:
+# Error Prone errors enabled by default; see ../.bazelrc for how this is
+# enabled. This warnings list is originally based on:
 # https://github.com/bazelbuild/BUILD_file_generator/blob/master/tools/bazel_defs/java.bzl
+# However, feel free to add any additional errors. Thus far they have all been pretty useful.
 java_package_configuration(
     name = "error_prone",
     javacopts = [
@@ -24,61 +26,61 @@
         "-Xep:MissingCasesInEnumSwitch:ERROR",
         "-Xep:ReferenceEquality:WARN",
         "-Xep:StringEquality:WARN",
-        "-Xep:WildcardImport:WARN",
+        "-Xep:WildcardImport:ERROR",
         "-Xep:AmbiguousMethodReference:WARN",
-        "-Xep:BadAnnotationImplementation:WARN",
+        "-Xep:BadAnnotationImplementation:ERROR",
         "-Xep:BadComparable:WARN",
         "-Xep:BoxedPrimitiveConstructor:ERROR",
-        "-Xep:CannotMockFinalClass:WARN",
+        "-Xep:CannotMockFinalClass:ERROR",
         "-Xep:ClassCanBeStatic:ERROR",
         "-Xep:ClassNewInstance:WARN",
         "-Xep:DefaultCharset:ERROR",
-        "-Xep:DoubleCheckedLocking:WARN",
-        "-Xep:ElementsCountedInLoop:WARN",
-        "-Xep:EqualsHashCode:WARN",
-        "-Xep:EqualsIncompatibleType:WARN",
+        "-Xep:DoubleCheckedLocking:ERROR",
+        "-Xep:ElementsCountedInLoop:ERROR",
+        "-Xep:EqualsHashCode:ERROR",
+        "-Xep:EqualsIncompatibleType:ERROR",
         "-Xep:ExpectedExceptionChecker:ERROR",
         "-Xep:Finally:WARN",
-        "-Xep:FloatingPointLiteralPrecision:WARN",
-        "-Xep:FragmentInjection:WARN",
-        "-Xep:FragmentNotInstantiable:WARN",
-        "-Xep:FunctionalInterfaceClash:WARN",
+        "-Xep:FloatingPointLiteralPrecision:ERROR",
+        "-Xep:FragmentInjection:ERROR",
+        "-Xep:FragmentNotInstantiable:ERROR",
+        "-Xep:FunctionalInterfaceClash:ERROR",
         "-Xep:FutureReturnValueIgnored:WARN",
-        "-Xep:GetClassOnEnum:WARN",
-        "-Xep:ImmutableAnnotationChecker:WARN",
+        "-Xep:GetClassOnEnum:ERROR",
+        "-Xep:ImmutableAnnotationChecker:ERROR",
         "-Xep:ImmutableEnumChecker:WARN",
-        "-Xep:IncompatibleModifiers:WARN",
-        "-Xep:InjectOnConstructorOfAbstractClass:WARN",
-        "-Xep:InputStreamSlowMultibyteRead:WARN",
-        "-Xep:IterableAndIterator:WARN",
-        "-Xep:JUnit3FloatingPointComparisonWithoutDelta:WARN",
-        "-Xep:JUnitAmbiguousTestClass:WARN",
-        "-Xep:LiteralClassName:WARN",
+        "-Xep:IncompatibleModifiers:ERROR",
+        "-Xep:InjectOnConstructorOfAbstractClass:ERROR",
+        "-Xep:InputStreamSlowMultibyteRead:ERROR",
+        "-Xep:IterableAndIterator:ERROR",
+        "-Xep:JUnit3FloatingPointComparisonWithoutDelta:ERROR",
+        "-Xep:JUnitAmbiguousTestClass:ERROR",
+        "-Xep:LiteralClassName:ERROR",
         "-Xep:MissingFail:ERROR",
-        "-Xep:MissingOverride:WARN",
-        "-Xep:MutableConstantField:WARN",
+        "-Xep:MissingOverride:ERROR",
+        "-Xep:MutableConstantField:ERROR",
         "-Xep:NarrowingCompoundAssignment:WARN",
-        "-Xep:NonAtomicVolatileUpdate:WARN",
+        "-Xep:NonAtomicVolatileUpdate:ERROR",
         "-Xep:NonOverridingEquals:WARN",
-        "-Xep:NullableConstructor:WARN",
-        "-Xep:NullablePrimitive:WARN",
-        "-Xep:NullableVoid:WARN",
+        "-Xep:NullableConstructor:ERROR",
+        "-Xep:NullablePrimitive:ERROR",
+        "-Xep:NullableVoid:ERROR",
         "-Xep:OperatorPrecedence:WARN",
-        "-Xep:OverridesGuiceInjectableMethod:WARN",
-        "-Xep:PreconditionsInvalidPlaceholder:WARN",
-        "-Xep:ProtoFieldPreconditionsCheckNotNull:WARN",
-        "-Xep:ProtocolBufferOrdinal:WARN",
-        "-Xep:RequiredModifiers:WARN",
+        "-Xep:OverridesGuiceInjectableMethod:ERROR",
+        "-Xep:PreconditionsInvalidPlaceholder:ERROR",
+        "-Xep:ProtoFieldPreconditionsCheckNotNull:ERROR",
+        "-Xep:ProtocolBufferOrdinal:ERROR",
+        "-Xep:RequiredModifiers:ERROR",
         "-Xep:ShortCircuitBoolean:WARN",
-        "-Xep:SimpleDateFormatConstant:WARN",
-        "-Xep:StaticGuardedByInstance:WARN",
-        "-Xep:SynchronizeOnNonFinalField:WARN",
-        "-Xep:TruthConstantAsserts:WARN",
-        "-Xep:TypeParameterShadowing:WARN",
+        "-Xep:SimpleDateFormatConstant:ERROR",
+        "-Xep:StaticGuardedByInstance:ERROR",
+        "-Xep:SynchronizeOnNonFinalField:ERROR",
+        "-Xep:TruthConstantAsserts:ERROR",
+        "-Xep:TypeParameterShadowing:ERROR",
         "-Xep:TypeParameterUnusedInFormals:WARN",
-        "-Xep:URLEqualsHashCode:WARN",
-        "-Xep:UnsynchronizedOverridesSynchronized:WARN",
-        "-Xep:WaitNotInLoop:WARN",
+        "-Xep:URLEqualsHashCode:ERROR",
+        "-Xep:UnsynchronizedOverridesSynchronized:ERROR",
+        "-Xep:WaitNotInLoop:ERROR",
     ],
     packages = ["error_prone_packages"],
 )
diff --git a/tools/version.sh b/tools/version.sh
index e5c98ec..8b8095d 100755
--- a/tools/version.sh
+++ b/tools/version.sh
@@ -161,6 +161,17 @@
 		$seen_version = 0;
 		$old_argv = $ARGV;
 	}
+	if ($seen_version < 18) {
+			$seen_version++ if
+		s{<(version)>.*</\1>}{<${1}>'"$POM_V"'</${1}>};
+	}
+	' org.eclipse.jgit.coverage/pom.xml
+
+perl -pi~ -e '
+	if ($ARGV ne $old_argv) {
+		$seen_version = 0;
+		$old_argv = $ARGV;
+	}
 	if (!$seen_version) {
 		$seen_version = 1 if
 		s{<(version)>.*</\1>}{<${1}>'"$POM_V"'</${1}>};