diff --git a/.mailmap b/.mailmap
index 7c9dc3d..f0bc990 100644
--- a/.mailmap
+++ b/.mailmap
@@ -1,10 +1,18 @@
-Han-Wen Nienhuys <hanwen@google.com>         Han-Wen NIenhuys <hanwen@google.com>
-Mark Ingram <markdingram@gmail.com>          markdingram <markdingram@gmail.com>
-Roberto Tyley <roberto.tyley@guardian.co.uk> roberto <roberto.tyley@guardian.co.uk>
-Saša Živkov <sasa.zivkov@sap.com>            Sasa Zivkov <sasa.zivkov@sap.com>
-Saša Živkov <sasa.zivkov@sap.com>            Saša Živkov <zivkov@gmail.com>
-Saša Živkov <sasa.zivkov@sap.com>            Sasa Zivkov <zivkov@gmail.com>
-Shawn Pearce <spearce@spearce.org>           Shawn O. Pearce <sop@google.com>
-Shawn Pearce <spearce@spearce.org>           Shawn Pearce <sop@google.com>
-Shawn Pearce <spearce@spearce.org>           Shawn O. Pearce <spearce@spearce.org>
-Terry Parker <tparker@google.com>            tparker <tparker@google.com>
+Chris Aniszczyk <caniszczyk@gmail.com>                      Chris Aniszczyk <zx@eclipsesource.com>
+Christian Halstrick <christian.halstrick@sap.com>           Christian Halstrick <christian.halstrick@gmail.com>
+Dani Megert <Daniel_Megert@ch.ibm.com>                      Daniel Megert <daniel_megert@ch.ibm.com>
+David Pursehouse <david.pursehouse@gmail.com>               David Pursehouse <david.pursehouse@sonymobile.com>
+Han-Wen Nienhuys <hanwen@google.com>                        Han-Wen NIenhuys <hanwen@google.com>
+Hector Oswaldo Caballero <hector.caballero@ericsson.com>    Hector Caballero <hector.caballero@ericsson.com>
+Lars Vogel <Lars.Vogel@vogella.com>                         Lars Vogel <Lars.Vogel@gmail.com>
+Mark Ingram <markdingram@gmail.com>                         markdingram <markdingram@gmail.com>
+Markus Duft <markus.duft@ssi-schaefer.com>                  Markus Duft <markus.duft@salomon.at>
+Michael Keppler <michael.keppler@gmx.de>                    Michael Keppler <Michael.Keppler@gmx.de>
+Roberto Tyley <roberto.tyley@guardian.co.uk>                roberto <roberto.tyley@guardian.co.uk>
+Saša Živkov <sasa.zivkov@sap.com>                           Sasa Zivkov <sasa.zivkov@sap.com>
+Saša Živkov <sasa.zivkov@sap.com>                           Saša Živkov <zivkov@gmail.com>
+Saša Živkov <sasa.zivkov@sap.com>                           Sasa Zivkov <zivkov@gmail.com>
+Shawn Pearce <spearce@spearce.org>                          Shawn O. Pearce <sop@google.com>
+Shawn Pearce <spearce@spearce.org>                          Shawn Pearce <sop@google.com>
+Shawn Pearce <spearce@spearce.org>                          Shawn O. Pearce <spearce@spearce.org>
+Terry Parker <tparker@google.com>                           tparker <tparker@google.com>
diff --git a/WORKSPACE b/WORKSPACE
index 9d723d2..209550f 100644
--- a/WORKSPACE
+++ b/WORKSPACE
@@ -1,5 +1,18 @@
 workspace(name = "jgit")
 
+load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive")
+
+http_archive(
+    name = "bazel_skylib",
+    sha256 = "bbccf674aa441c266df9894182d80de104cabd19be98be002f6d478aaa31574d",
+    strip_prefix = "bazel-skylib-2169ae1c374aab4a09aa90e65efe1a3aad4e279b",
+    urls = ["https://github.com/bazelbuild/bazel-skylib/archive/2169ae1c374aab4a09aa90e65efe1a3aad4e279b.tar.gz"],
+)
+
+load("@bazel_skylib//:lib.bzl", "versions")
+
+versions.check(minimum_bazel_version = "0.17.1")
+
 load("//tools:bazlets.bzl", "load_bazlets")
 
 load_bazlets(commit = "3afbeab55ece585dbfc7a980bf7214b24ddbbe86")
diff --git a/lib/BUILD b/lib/BUILD
index ebba0da..7cd420a 100644
--- a/lib/BUILD
+++ b/lib/BUILD
@@ -23,7 +23,6 @@
 
 java_library(
     name = "commons-logging",
-    testonly = 1,
     visibility = ["//visibility:public"],
     exports = ["@commons-logging//jar"],
 )
diff --git a/org.eclipse.jgit.ant.test/.classpath b/org.eclipse.jgit.ant.test/.classpath
index eca7bdb..3e5654f 100644
--- a/org.eclipse.jgit.ant.test/.classpath
+++ b/org.eclipse.jgit.ant.test/.classpath
@@ -2,6 +2,10 @@
 <classpath>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
 	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
-	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="src" path="src">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="bin"/>
 </classpath>
diff --git a/org.eclipse.jgit.ant.test/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.ant.test/.settings/org.eclipse.jdt.core.prefs
index 794592d..2ca78ff 100644
--- a/org.eclipse.jgit.ant.test/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.ant.test/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.ant.test/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.ant.test/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.ant.test/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.ant.test/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.ant.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.ant.test/META-INF/MANIFEST.MF
index eed03d7..e6bef69 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
 Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: org.apache.tools.ant,
- org.eclipse.jgit.ant.tasks;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.junit;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)",
+ org.eclipse.jgit.ant.tasks;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.junit;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)",
  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 26bd15b..9526daf 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.ant.test</artifactId>
diff --git a/org.eclipse.jgit.ant/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.ant/.settings/org.eclipse.jdt.core.prefs
index 565b75c..94a1c4f 100644
--- a/org.eclipse.jgit.ant/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.ant/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.ant/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.ant/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.ant/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.ant/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.ant/META-INF/MANIFEST.MF b/org.eclipse.jgit.ant/META-INF/MANIFEST.MF
index 5778a05..d151b32 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: org.apache.tools.ant,
-  org.eclipse.jgit.storage.file;version="[5.1.4,5.2.0)"
+  org.eclipse.jgit.storage.file;version="[5.2.0,5.3.0)"
 Bundle-Localization: plugin
 Bundle-Vendor: %Provider-Name
-Export-Package: org.eclipse.jgit.ant.tasks;version="5.1.4";
+Export-Package: org.eclipse.jgit.ant.tasks;version="5.2.0";
  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 013d69e..445a2f5 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>5.1.4-SNAPSHOT</version>
+		<version>5.2.0-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>org.eclipse.jgit.ant</artifactId>
diff --git a/org.eclipse.jgit.archive/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.archive/.settings/org.eclipse.jdt.core.prefs
index 13c32a6..ef6f5e7 100644
--- a/org.eclipse.jgit.archive/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.archive/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.archive/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.archive/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.archive/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.archive/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.archive/META-INF/MANIFEST.MF b/org.eclipse.jgit.archive/META-INF/MANIFEST.MF
index f8bf17e..31875bb 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.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="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.nls;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)",
+ org.eclipse.jgit.api;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.nls;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)",
  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="5.1.4";
+Export-Package: org.eclipse.jgit.archive;version="5.2.0";
   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 7e7547e..7556798 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: 5.1.4.qualifier
-Eclipse-SourceBundle: org.eclipse.jgit.archive;version="5.1.4.qualifier";roots="."
+Bundle-Version: 5.2.0.qualifier
+Eclipse-SourceBundle: org.eclipse.jgit.archive;version="5.2.0.qualifier";roots="."
diff --git a/org.eclipse.jgit.archive/pom.xml b/org.eclipse.jgit.archive/pom.xml
index e8ce6f8..b374dbd 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.archive</artifactId>
diff --git a/org.eclipse.jgit.archive/src/org/eclipse/jgit/archive/TarFormat.java b/org.eclipse.jgit.archive/src/org/eclipse/jgit/archive/TarFormat.java
index 9ed60d9..aee80d8 100644
--- a/org.eclipse.jgit.archive/src/org/eclipse/jgit/archive/TarFormat.java
+++ b/org.eclipse.jgit.archive/src/org/eclipse/jgit/archive/TarFormat.java
@@ -42,7 +42,7 @@
  */
 package org.eclipse.jgit.archive;
 
-import static org.eclipse.jgit.lib.Constants.CHARACTER_ENCODING;
+import static java.nio.charset.StandardCharsets.UTF_8;
 
 import java.io.IOException;
 import java.io.OutputStream;
@@ -85,7 +85,7 @@ public ArchiveOutputStream createArchiveOutputStream(OutputStream s)
 	public ArchiveOutputStream createArchiveOutputStream(OutputStream s,
 			Map<String, Object> o) throws IOException {
 		TarArchiveOutputStream out = new TarArchiveOutputStream(s,
-				CHARACTER_ENCODING);
+				UTF_8.name());
 		out.setLongFileMode(TarArchiveOutputStream.LONGFILE_POSIX);
 		out.setBigNumberMode(TarArchiveOutputStream.BIGNUMBER_POSIX);
 		return applyFormatOptions(out, o);
@@ -99,8 +99,7 @@ public void putEntry(ArchiveOutputStream out,
 		if (mode == FileMode.SYMLINK) {
 			final TarArchiveEntry entry = new TarArchiveEntry(
 					path, TarConstants.LF_SYMLINK);
-			entry.setLinkName(new String(
-					loader.getCachedBytes(100), CHARACTER_ENCODING));
+			entry.setLinkName(new String(loader.getCachedBytes(100), UTF_8));
 			out.putArchiveEntry(entry);
 			out.closeArchiveEntry();
 			return;
diff --git a/org.eclipse.jgit.http.apache/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.http.apache/.settings/org.eclipse.jdt.core.prefs
index 565b75c..94a1c4f 100644
--- a/org.eclipse.jgit.http.apache/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.http.apache/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.http.apache/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.http.apache/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.http.apache/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.http.apache/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.http.apache/META-INF/MANIFEST.MF b/org.eclipse.jgit.http.apache/META-INF/MANIFEST.MF
index 750f71c..1e8842b 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Localization: plugin
 Bundle-Vendor: %Provider-Name
@@ -23,10 +23,10 @@
  org.apache.http.impl.client;version="[4.3.0,5.0.0)",
  org.apache.http.impl.conn;version="[4.3.0,5.0.0)",
  org.apache.http.params;version="[4.3.0,5.0.0)",
- org.eclipse.jgit.nls;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport.http;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)"
-Export-Package: org.eclipse.jgit.transport.http.apache;version="5.1.4";
+ org.eclipse.jgit.nls;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport.http;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)"
+Export-Package: org.eclipse.jgit.transport.http.apache;version="5.2.0";
   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 bc2297c..8aea887 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>5.1.4-SNAPSHOT</version>
+		<version>5.2.0-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>org.eclipse.jgit.http.apache</artifactId>
diff --git a/org.eclipse.jgit.http.server/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.http.server/.settings/org.eclipse.jdt.core.prefs
index 565b75c..94a1c4f 100644
--- a/org.eclipse.jgit.http.server/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.http.server/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.http.server/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.http.server/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.http.server/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.http.server/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.http.server/META-INF/MANIFEST.MF b/org.eclipse.jgit.http.server/META-INF/MANIFEST.MF
index 4520ed7..c85e496 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
-Export-Package: org.eclipse.jgit.http.server;version="5.1.4",
- org.eclipse.jgit.http.server.glue;version="5.1.4";
+Export-Package: org.eclipse.jgit.http.server;version="5.2.0",
+ org.eclipse.jgit.http.server.glue;version="5.2.0";
   uses:="javax.servlet,javax.servlet.http",
- org.eclipse.jgit.http.server.resolver;version="5.1.4";
+ org.eclipse.jgit.http.server.resolver;version="5.2.0";
   uses:="org.eclipse.jgit.transport.resolver,
    org.eclipse.jgit.lib,
    org.eclipse.jgit.transport,
@@ -18,12 +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="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.dfs;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.nls;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport.resolver;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)"
+ org.eclipse.jgit.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.dfs;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.transport.parser;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.nls;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport.resolver;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)"
diff --git a/org.eclipse.jgit.http.server/pom.xml b/org.eclipse.jgit.http.server/pom.xml
index be409e0..a5c1a1c 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-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 b9ca12b..ee4b32e 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.FirstWant;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.transport.PacketLineIn;
 import org.eclipse.jgit.transport.PacketLineOut;
@@ -246,9 +247,9 @@ private static boolean isUploadPackSideBand(HttpServletRequest req) {
 			// not have an UploadPack, or it might not have read any of the request.
 			// So, cheat and read the first line.
 			String line = new PacketLineIn(req.getInputStream()).readString();
-			UploadPack.FirstLine parsed = new UploadPack.FirstLine(line);
-			return (parsed.getOptions().contains(OPTION_SIDE_BAND)
-					|| parsed.getOptions().contains(OPTION_SIDE_BAND_64K));
+			FirstWant parsed = FirstWant.fromLine(line);
+			return (parsed.getCapabilities().contains(OPTION_SIDE_BAND)
+					|| parsed.getCapabilities().contains(OPTION_SIDE_BAND_64K));
 		} catch (IOException e) {
 			// Probably the connection is closed and a subsequent write will fail, but
 			// try it just in case.
diff --git a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/InfoRefsServlet.java b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/InfoRefsServlet.java
index 1a9d192..b084b0d 100644
--- a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/InfoRefsServlet.java
+++ b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/InfoRefsServlet.java
@@ -69,7 +69,7 @@ public void doGet(final HttpServletRequest req,
 		// Assume a dumb client and send back the dumb client
 		// version of the info/refs file.
 		rsp.setContentType(HttpSupport.TEXT_PLAIN);
-		rsp.setCharacterEncoding(Constants.CHARACTER_ENCODING);
+		rsp.setCharacterEncoding(UTF_8.name());
 
 		final Repository db = getRepository(req);
 		try (OutputStreamWriter out = new OutputStreamWriter(
diff --git a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ServletUtils.java b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ServletUtils.java
index 9601c8c..b6d73b5 100644
--- a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ServletUtils.java
+++ b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ServletUtils.java
@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.http.server;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.util.HttpSupport.ENCODING_GZIP;
 import static org.eclipse.jgit.util.HttpSupport.ENCODING_X_GZIP;
 import static org.eclipse.jgit.util.HttpSupport.HDR_ACCEPT_ENCODING;
@@ -191,9 +192,9 @@ public static void consumeRequestBody(InputStream in) {
 	public static void sendPlainText(final String content,
 			final HttpServletRequest req, final HttpServletResponse rsp)
 			throws IOException {
-		final byte[] raw = content.getBytes(Constants.CHARACTER_ENCODING);
+		final byte[] raw = content.getBytes(UTF_8);
 		rsp.setContentType(TEXT_PLAIN);
-		rsp.setCharacterEncoding(Constants.CHARACTER_ENCODING);
+		rsp.setCharacterEncoding(UTF_8.name());
 		send(raw, req, rsp);
 	}
 
diff --git a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/SmartOutputStream.java b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/SmartOutputStream.java
index ad5e8d4..06bdce6 100644
--- a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/SmartOutputStream.java
+++ b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/SmartOutputStream.java
@@ -105,6 +105,7 @@ public void close() throws IOException {
 			// If output hasn't started yet, the entire thing fit into our
 			// buffer. Try to use a proper Content-Length header, and also
 			// deflate the response with gzip if it will be smaller.
+			@SuppressWarnings("resource")
 			TemporaryBuffer out = this;
 
 			if (256 < out.length() && acceptsGzipEncoding(req)) {
diff --git a/org.eclipse.jgit.http.test/.classpath b/org.eclipse.jgit.http.test/.classpath
index e6014c7..b258380 100644
--- a/org.eclipse.jgit.http.test/.classpath
+++ b/org.eclipse.jgit.http.test/.classpath
@@ -2,7 +2,15 @@
 <classpath>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
 	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
-	<classpathentry kind="src" path="tst"/>
-	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="src" path="tst">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path="src">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="bin"/>
 </classpath>
diff --git a/org.eclipse.jgit.http.test/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.http.test/.settings/org.eclipse.jdt.core.prefs
index 794592d..2ca78ff 100644
--- a/org.eclipse.jgit.http.test/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.http.test/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.http.test/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.http.test/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.http.test/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.http.test/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.http.test/META-INF/MANIFEST.MF
index ac66b79..37a9549 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.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="[5.1.4,5.2.0)",
- org.eclipse.jgit.http.server;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.http.server.glue;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.http.server.resolver;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.dfs;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.reftable;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.junit;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.junit.http;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.nls;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport.http;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport.http.apache;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport.resolver;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)",
+ org.eclipse.jgit.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.http.server;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.http.server.glue;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.http.server.resolver;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.dfs;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.reftable;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.junit;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.junit.http;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.nls;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport.http;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport.http.apache;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport.resolver;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)",
  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 23a08aa..5bc342c 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.http.test</artifactId>
diff --git a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/FileResolverTest.java b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/FileResolverTest.java
index 82e79b8..553c340 100644
--- a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/FileResolverTest.java
+++ b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/FileResolverTest.java
@@ -147,6 +147,7 @@ public void testNotAGitRepository() throws IOException,
 
 		try {
 			resolver.open(null, name);
+			fail("opened non-git repository");
 		} catch (RepositoryNotFoundException e) {
 			assertEquals("repository not found: " + name, e.getMessage());
 
diff --git a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/RegexPipelineTest.java b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/RegexPipelineTest.java
index 725a590..59c2b4e 100644
--- a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/RegexPipelineTest.java
+++ b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/RegexPipelineTest.java
@@ -43,11 +43,14 @@
 
 package org.eclipse.jgit.http.test;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 
 import java.io.BufferedReader;
+import java.io.BufferedWriter;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.net.HttpURLConnection;
 import java.net.URI;
@@ -82,7 +85,8 @@ private Servlet(String name) {
 		protected void doGet(HttpServletRequest req, HttpServletResponse res)
 				throws IOException {
 			res.setStatus(200);
-			PrintWriter out = new PrintWriter(res.getOutputStream());
+			PrintWriter out = new PrintWriter(new BufferedWriter(
+					new OutputStreamWriter(res.getOutputStream(), UTF_8)));
 			out.write(name);
 			out.write("\n");
 			out.write(String.valueOf(req.getServletPath()));
@@ -120,7 +124,8 @@ public void testSimpleRegex() throws Exception {
 		c = ((HttpURLConnection) uri.resolve("/a").toURL()
 				.openConnection());
 		assertEquals(200, c.getResponseCode());
-		r = new BufferedReader(new InputStreamReader(c.getInputStream()));
+		r = new BufferedReader(
+				new InputStreamReader(c.getInputStream(), UTF_8));
 		assertEquals("test", r.readLine());
 		assertEquals("", r.readLine());
 		assertEquals("/a", r.readLine());
@@ -129,7 +134,8 @@ public void testSimpleRegex() throws Exception {
 		c = ((HttpURLConnection) uri.resolve("/b").toURL()
 				.openConnection());
 		assertEquals(200, c.getResponseCode());
-		r = new BufferedReader(new InputStreamReader(c.getInputStream()));
+		r = new BufferedReader(
+				new InputStreamReader(c.getInputStream(), UTF_8));
 		assertEquals("test", r.readLine());
 		assertEquals("", r.readLine());
 		assertEquals("/b", r.readLine());
@@ -155,7 +161,8 @@ public void testServeOrdering() throws Exception {
 		c = ((HttpURLConnection) uri.resolve("/a").toURL()
 				.openConnection());
 		assertEquals(200, c.getResponseCode());
-		r = new BufferedReader(new InputStreamReader(c.getInputStream()));
+		r = new BufferedReader(
+				new InputStreamReader(c.getInputStream(), UTF_8));
 		assertEquals("test1", r.readLine());
 		assertEquals("", r.readLine());
 		assertEquals("/a", r.readLine());
@@ -183,7 +190,8 @@ public void testRegexGroupFilter() throws Exception {
 		c = ((HttpURLConnection) uri.resolve("/a/b").toURL()
 				.openConnection());
 		assertEquals(200, c.getResponseCode());
-		r = new BufferedReader(new InputStreamReader(c.getInputStream()));
+		r = new BufferedReader(
+				new InputStreamReader(c.getInputStream(), UTF_8));
 		assertEquals("test1", r.readLine());
 		assertEquals("", r.readLine());
 		// No RegexGroupFilter defaults to first group.
@@ -193,7 +201,8 @@ public void testRegexGroupFilter() throws Exception {
 		c = ((HttpURLConnection) uri.resolve("/c/d").toURL()
 				.openConnection());
 		assertEquals(200, c.getResponseCode());
-		r = new BufferedReader(new InputStreamReader(c.getInputStream()));
+		r = new BufferedReader(
+				new InputStreamReader(c.getInputStream(), UTF_8));
 		assertEquals("test2", r.readLine());
 		assertEquals("", r.readLine());
 		assertEquals("/c", r.readLine());
@@ -202,7 +211,8 @@ public void testRegexGroupFilter() throws Exception {
 		c = ((HttpURLConnection) uri.resolve("/e/f/g").toURL()
 				.openConnection());
 		assertEquals(200, c.getResponseCode());
-		r = new BufferedReader(new InputStreamReader(c.getInputStream()));
+		r = new BufferedReader(
+				new InputStreamReader(c.getInputStream(), UTF_8));
 		assertEquals("test3", r.readLine());
 		assertEquals("/e/f", r.readLine());
 		assertEquals("/g", r.readLine());
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 51aa5f2..d1c7737 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
@@ -266,7 +266,7 @@ public void doFilter(ServletRequest request,
 					throws IOException, ServletException {
 				final HttpServletResponse r = (HttpServletResponse) response;
 				r.setContentType("text/plain");
-				r.setCharacterEncoding(Constants.CHARACTER_ENCODING);
+				r.setCharacterEncoding(UTF_8.name());
 				try (PrintWriter w = r.getWriter()) {
 					w.print("OK");
 				}
diff --git a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/transport/http/apache/HttpClientConnectionTest.java b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/transport/http/apache/HttpClientConnectionTest.java
index 72c4921..8a0d59c 100644
--- a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/transport/http/apache/HttpClientConnectionTest.java
+++ b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/transport/http/apache/HttpClientConnectionTest.java
@@ -76,7 +76,7 @@ public void testGetHeaderFieldsAllowMultipleValues()
 		assertTrue(headerValues.contains("NTLM"));
 	}
 
-	private class HttpResponseMock extends AbstractHttpMessage
+	private static class HttpResponseMock extends AbstractHttpMessage
 			implements HttpResponse {
 		@Override
 		public StatusLine getStatusLine() {
diff --git a/org.eclipse.jgit.junit.http/.classpath b/org.eclipse.jgit.junit.http/.classpath
index b862a29..3e5654f 100644
--- a/org.eclipse.jgit.junit.http/.classpath
+++ b/org.eclipse.jgit.junit.http/.classpath
@@ -1,7 +1,11 @@
-<?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"/>
-	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="output" path="bin"/>
-</classpath>
+<?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"/>
+	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+	<classpathentry kind="src" path="src">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="bin"/>
+</classpath>
diff --git a/org.eclipse.jgit.junit.http/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.junit.http/.settings/org.eclipse.jdt.core.prefs
index 794592d..2ca78ff 100644
--- a/org.eclipse.jgit.junit.http/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.junit.http/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.junit.http/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.junit.http/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.junit.http/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.junit.http/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.junit.http/META-INF/MANIFEST.MF b/org.eclipse.jgit.junit.http/META-INF/MANIFEST.MF
index b4a0d46..a95385a 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.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="[5.1.4,5.2.0)",
- org.eclipse.jgit.http.server;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.junit;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport.resolver;version="[5.1.4,5.2.0)",
+ org.eclipse.jgit.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.http.server;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.junit;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport.resolver;version="[5.2.0,5.3.0)",
  org.junit;version="[4.12,5.0.0)"
-Export-Package: org.eclipse.jgit.junit.http;version="5.1.4";
+Export-Package: org.eclipse.jgit.junit.http;version="5.2.0";
   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 9b5ed19..72ab8d3 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.junit.http</artifactId>
diff --git a/org.eclipse.jgit.junit/.classpath b/org.eclipse.jgit.junit/.classpath
index eca7bdb..3e5654f 100644
--- a/org.eclipse.jgit.junit/.classpath
+++ b/org.eclipse.jgit.junit/.classpath
@@ -2,6 +2,10 @@
 <classpath>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
 	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
-	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="src" path="src">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="bin"/>
 </classpath>
diff --git a/org.eclipse.jgit.junit/.settings/.api_filters b/org.eclipse.jgit.junit/.settings/.api_filters
deleted file mode 100644
index e5de787..0000000
--- a/org.eclipse.jgit.junit/.settings/.api_filters
+++ /dev/null
@@ -1,35 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<component id="org.eclipse.jgit.junit" version="2">
-    <resource path="src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java" type="org.eclipse.jgit.junit.LocalDiskRepositoryTestCase">
-        <filter comment="Don't care about non-API in tests." id="643842064">
-            <message_arguments>
-                <message_argument value="FileRepository"/>
-                <message_argument value="LocalDiskRepositoryTestCase"/>
-                <message_argument value="createBareRepository()"/>
-            </message_arguments>
-        </filter>
-        <filter comment="Don't care about non-API in tests." id="643842064">
-            <message_arguments>
-                <message_argument value="FileRepository"/>
-                <message_argument value="LocalDiskRepositoryTestCase"/>
-                <message_argument value="createRepository(boolean, boolean)"/>
-            </message_arguments>
-        </filter>
-        <filter comment="Don't care about non-API in tests." id="643842064">
-            <message_arguments>
-                <message_argument value="FileRepository"/>
-                <message_argument value="LocalDiskRepositoryTestCase"/>
-                <message_argument value="createWorkRepository()"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/junit/RepositoryTestCase.java" type="org.eclipse.jgit.junit.RepositoryTestCase">
-        <filter comment="Don't care about non-API in tests." id="627060751">
-            <message_arguments>
-                <message_argument value="FileRepository"/>
-                <message_argument value="RepositoryTestCase"/>
-                <message_argument value="db"/>
-            </message_arguments>
-        </filter>
-    </resource>
-</component>
diff --git a/org.eclipse.jgit.junit/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.junit/.settings/org.eclipse.jdt.core.prefs
index 794592d..2ca78ff 100644
--- a/org.eclipse.jgit.junit/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.junit/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.junit/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.junit/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.junit/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.junit/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.junit/META-INF/MANIFEST.MF b/org.eclipse.jgit.junit/META-INF/MANIFEST.MF
index e171965..9721c42 100644
--- a/org.eclipse.jgit.junit/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.junit/META-INF/MANIFEST.MF
@@ -3,31 +3,31 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.junit
 Bundle-SymbolicName: org.eclipse.jgit.junit
-Bundle-Version: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Import-Package: org.eclipse.jgit.api;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.api.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.dircache;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.pack;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.merge;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.treewalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.treewalk.filter;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util.io;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util.time;version="[5.1.4,5.2.0)",
+Import-Package: org.eclipse.jgit.api;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.api.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.dircache;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.pack;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.merge;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.treewalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.treewalk.filter;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util.io;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util.time;version="[5.2.0,5.3.0)",
  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)"
-Export-Package: org.eclipse.jgit.junit;version="5.1.4";
+Export-Package: org.eclipse.jgit.junit;version="5.2.0";
   uses:="org.eclipse.jgit.dircache,
    org.eclipse.jgit.lib,
    org.eclipse.jgit.revwalk,
@@ -36,4 +36,4 @@
    org.eclipse.jgit.util,
    org.eclipse.jgit.storage.file,
    org.eclipse.jgit.api",
- org.eclipse.jgit.junit.time;version="5.1.4"
+ org.eclipse.jgit.junit.time;version="5.2.0"
diff --git a/org.eclipse.jgit.junit/pom.xml b/org.eclipse.jgit.junit/pom.xml
index 50c1818..24e2c71 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.junit</artifactId>
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/MockSystemReader.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/MockSystemReader.java
index d3d7d68..8de386e 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/MockSystemReader.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/MockSystemReader.java
@@ -70,7 +70,7 @@
  * Mock {@link org.eclipse.jgit.util.SystemReader} for tests.
  */
 public class MockSystemReader extends SystemReader {
-	private final class MockConfig extends FileBasedConfig {
+	private static final class MockConfig extends FileBasedConfig {
 		private MockConfig(File cfgLocation, FS fs) {
 			super(cfgLocation, fs);
 		}
diff --git a/org.eclipse.jgit.lfs.server.test/.classpath b/org.eclipse.jgit.lfs.server.test/.classpath
index 4f9f6bf..f08af0a 100644
--- a/org.eclipse.jgit.lfs.server.test/.classpath
+++ b/org.eclipse.jgit.lfs.server.test/.classpath
@@ -2,6 +2,10 @@
 <classpath>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
 	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
-	<classpathentry kind="src" path="tst"/>
+	<classpathentry kind="src" path="tst">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="bin"/>
 </classpath>
diff --git a/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.jdt.core.prefs
index 794592d..2ca78ff 100644
--- a/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.mylyn.team.ui.prefs
index ce7a0f0..984263d 100644
--- a/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,2 +1,2 @@
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
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 8d6fe4c..8035403 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.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="[5.1.4,5.2.0)",
- org.eclipse.jgit.api.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.junit;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.junit.http;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.server;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.server.fs;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.test;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.treewalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.treewalk.filter;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)",
+ org.eclipse.jgit.api;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.api.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.junit;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.junit.http;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.server;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.server.fs;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.test;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.treewalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.treewalk.filter;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)",
  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 06e144a..5210d4f 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.lfs.server.test</artifactId>
diff --git a/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/PushTest.java b/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/PushTest.java
index b081a8e..4eb4a0d 100644
--- a/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/PushTest.java
+++ b/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/PushTest.java
@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.lfs.server.fs;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 
 import java.io.InputStream;
@@ -149,7 +150,7 @@ public void testPushSimple() throws Exception {
 							new String(IO
 									.readWholeStream(is,
 											(int) ldr.getSize())
-									.array()));
+									.array(), UTF_8));
 				}
 			}
 
diff --git a/org.eclipse.jgit.lfs.server/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.lfs.server/.settings/org.eclipse.jdt.core.prefs
index 89394ec..525ac67 100644
--- a/org.eclipse.jgit.lfs.server/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.lfs.server/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.lfs.server/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.lfs.server/.settings/org.eclipse.mylyn.team.ui.prefs
index ce7a0f0..984263d 100644
--- a/org.eclipse.jgit.lfs.server/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.lfs.server/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,2 +1,2 @@
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.lfs.server/META-INF/MANIFEST.MF b/org.eclipse.jgit.lfs.server/META-INF/MANIFEST.MF
index d4b2c03..2b6771c 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
-Export-Package: org.eclipse.jgit.lfs.server;version="5.1.4";
+Export-Package: org.eclipse.jgit.lfs.server;version="5.2.0";
   uses:="javax.servlet.http,
    org.eclipse.jgit.lfs.lib",
- org.eclipse.jgit.lfs.server.fs;version="5.1.4";
+ org.eclipse.jgit.lfs.server.fs;version="5.2.0";
   uses:="javax.servlet,
    javax.servlet.http,
    org.eclipse.jgit.lfs.server,
    org.eclipse.jgit.lfs.lib",
- org.eclipse.jgit.lfs.server.internal;version="5.1.4";x-internal:=true,
- org.eclipse.jgit.lfs.server.s3;version="5.1.4";
+ org.eclipse.jgit.lfs.server.internal;version="5.2.0";x-internal:=true,
+ org.eclipse.jgit.lfs.server.s3;version="5.2.0";
   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="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.internal;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.nls;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport.http;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport.http.apache;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)",
+ org.eclipse.jgit.annotations;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.internal;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.nls;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport.http;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport.http.apache;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)",
  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 ef4569f..6a708d5 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.lfs.server</artifactId>
diff --git a/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/LargeFileRepository.java b/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/LargeFileRepository.java
index cfa53af..4cb0277 100644
--- a/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/LargeFileRepository.java
+++ b/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/LargeFileRepository.java
@@ -82,7 +82,8 @@ public interface LargeFileRepository {
 	 * @return Action for verifying the object, or {@code null} if the server
 	 *         doesn't support or require verification
 	 */
-	public @Nullable Response.Action getVerifyAction(AnyLongObjectId id);
+	@Nullable
+	public Response.Action getVerifyAction(AnyLongObjectId id);
 
 	/**
 	 * Get size of an object
diff --git a/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/fs/FileLfsRepository.java b/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/fs/FileLfsRepository.java
index 55d9093..0a7c37c 100644
--- a/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/fs/FileLfsRepository.java
+++ b/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/fs/FileLfsRepository.java
@@ -99,7 +99,8 @@ public Action getUploadAction(AnyLongObjectId id, long size) {
 
 	/** {@inheritDoc} */
 	@Override
-	public @Nullable Action getVerifyAction(AnyLongObjectId id) {
+	@Nullable
+	public Action getVerifyAction(AnyLongObjectId id) {
 		return null;
 	}
 
diff --git a/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/s3/SignerV4.java b/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/s3/SignerV4.java
index b21c94e..7b76cec 100644
--- a/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/s3/SignerV4.java
+++ b/org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/s3/SignerV4.java
@@ -411,7 +411,8 @@ private static String urlEncode(String url, boolean keepPathSlash) {
 		String stringToSign = stringToSign(SCHEME, ALGORITHM, dateTimeStamp,
 				scope, canonicalRequest);
 
-		byte[] signature = (SCHEME + bucketConfig.getSecretKey()).getBytes();
+		byte[] signature = (SCHEME + bucketConfig.getSecretKey())
+				.getBytes(UTF_8);
 		signature = sign(dateStamp, signature);
 		signature = sign(bucketConfig.getRegion(), signature);
 		signature = sign(S3, signature);
diff --git a/org.eclipse.jgit.lfs.test/.classpath b/org.eclipse.jgit.lfs.test/.classpath
index e43ae76..e79b7c7 100644
--- a/org.eclipse.jgit.lfs.test/.classpath
+++ b/org.eclipse.jgit.lfs.test/.classpath
@@ -2,7 +2,15 @@
 <classpath>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
 	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="tst"/>
+	<classpathentry kind="src" path="src">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path="tst">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="bin"/>
 </classpath>
diff --git a/org.eclipse.jgit.lfs.test/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.lfs.test/.settings/org.eclipse.jdt.core.prefs
index 794592d..2ca78ff 100644
--- a/org.eclipse.jgit.lfs.test/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.lfs.test/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.lfs.test/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.lfs.test/.settings/org.eclipse.mylyn.team.ui.prefs
index ce7a0f0..984263d 100644
--- a/org.eclipse.jgit.lfs.test/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.lfs.test/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,2 +1,2 @@
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF
index 7d96ca2..19c9953 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
 Bundle-Vendor: %provider_name
 Bundle-Localization: plugin
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Import-Package: org.eclipse.jgit.internal.storage.dfs;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.junit;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.treewalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.treewalk.filter;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)",
+Import-Package: org.eclipse.jgit.internal.storage.dfs;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.junit;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.treewalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.treewalk.filter;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)",
  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="5.1.4";x-friends:="org.eclipse.jgit.lfs.server.test"
+Export-Package: org.eclipse.jgit.lfs.test;version="5.2.0";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 732193f..c04f916 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.lfs.test</artifactId>
diff --git a/org.eclipse.jgit.lfs.test/tst/org/eclipse/jgit/lfs/lib/LFSPointerTest.java b/org.eclipse.jgit.lfs.test/tst/org/eclipse/jgit/lfs/lib/LFSPointerTest.java
index a1283dd..146a25e 100644
--- a/org.eclipse.jgit.lfs.test/tst/org/eclipse/jgit/lfs/lib/LFSPointerTest.java
+++ b/org.eclipse.jgit.lfs.test/tst/org/eclipse/jgit/lfs/lib/LFSPointerTest.java
@@ -43,7 +43,7 @@
 
 package org.eclipse.jgit.lfs.lib;
 
-import static org.eclipse.jgit.lib.Constants.CHARACTER_ENCODING;
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 
 import java.io.ByteArrayOutputStream;
@@ -66,7 +66,7 @@ public void testEncoding() throws IOException {
 			assertEquals(
 					"version https://git-lfs.github.com/spec/v1\noid sha256:"
 							+ s + "\nsize 4\n",
-					baos.toString(CHARACTER_ENCODING));
+					baos.toString(UTF_8.name()));
 		}
 	}
 }
diff --git a/org.eclipse.jgit.lfs/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.lfs/.settings/org.eclipse.jdt.core.prefs
index 89394ec..525ac67 100644
--- a/org.eclipse.jgit.lfs/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.lfs/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.lfs/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.lfs/.settings/org.eclipse.mylyn.team.ui.prefs
index ce7a0f0..984263d 100644
--- a/org.eclipse.jgit.lfs/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.lfs/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,2 +1,2 @@
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF b/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF
index 2cf8e2f..f3ab7fc 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
-Export-Package: org.eclipse.jgit.lfs;version="5.1.4",
- org.eclipse.jgit.lfs.errors;version="5.1.4",
- org.eclipse.jgit.lfs.internal;version="5.1.4";x-friends:="org.eclipse.jgit.lfs.test,org.eclipse.jgit.lfs.server.fs,org.eclipse.jgit.lfs.server",
- org.eclipse.jgit.lfs.lib;version="5.1.4"
+Export-Package: org.eclipse.jgit.lfs;version="5.2.0",
+ org.eclipse.jgit.lfs.errors;version="5.2.0",
+ org.eclipse.jgit.lfs.internal;version="5.2.0";x-friends:="org.eclipse.jgit.lfs.test,org.eclipse.jgit.lfs.server.fs,org.eclipse.jgit.lfs.server",
+ org.eclipse.jgit.lfs.lib;version="5.2.0"
 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="[5.1.4,5.2.0)";resolution:=optional,
- org.eclipse.jgit.api.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.attributes;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.diff;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.hooks;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.nls;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.storage.pack;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport.http;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.treewalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.treewalk.filter;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util.io;version="[5.1.4,5.2.0)"
+ org.eclipse.jgit.annotations;version="[5.2.0,5.3.0)";resolution:=optional,
+ org.eclipse.jgit.api.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.attributes;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.diff;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.hooks;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.nls;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.storage.pack;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport.http;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.treewalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.treewalk.filter;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util.io;version="[5.2.0,5.3.0)"
diff --git a/org.eclipse.jgit.lfs/pom.xml b/org.eclipse.jgit.lfs/pom.xml
index b289a4f..f49b8b6 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.lfs</artifactId>
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/BuiltinLFS.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/BuiltinLFS.java
index 415caa9..56e3a12 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/BuiltinLFS.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/BuiltinLFS.java
@@ -99,7 +99,8 @@ public LfsInputStream applyCleanFilter(Repository db, InputStream input,
 	}
 
 	@Override
-	public @Nullable PrePushHook getPrePushHook(Repository repo,
+	@Nullable
+	public PrePushHook getPrePushHook(Repository repo,
 			PrintStream outputStream) {
 		if (isEnabled(repo)) {
 			return new LfsPrePushHook(repo, outputStream);
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/SmudgeFilter.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/SmudgeFilter.java
index fac87c1..7bacf49 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/SmudgeFilter.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/SmudgeFilter.java
@@ -222,7 +222,10 @@ public static Collection<Path> downloadLfsResource(Lfs lfs, Repository db,
 									Integer.valueOf(responseCode)));
 				}
 				Path path = lfs.getMediaFile(ptr.getOid());
-				path.getParent().toFile().mkdirs();
+				Path parent = path.getParent();
+				if (parent != null) {
+					parent.toFile().mkdirs();
+				}
 				try (InputStream contentIn = contentServerConn
 						.getInputStream()) {
 					long bytesCopied = Files.copy(contentIn, path);
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/AtomicObjectOutputStream.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/AtomicObjectOutputStream.java
index 0762ac5..317d68a 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/AtomicObjectOutputStream.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/AtomicObjectOutputStream.java
@@ -106,7 +106,8 @@ public AtomicObjectOutputStream(Path path) throws IOException {
 	 *         stream. May return {@code null} if called before closing this
 	 *         stream.
 	 */
-	public @Nullable AnyLongObjectId getId() {
+	@Nullable
+	public AnyLongObjectId getId() {
 		return id;
 	}
 
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/LfsConnectionFactory.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/LfsConnectionFactory.java
index 955eca0..feb8b4a 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/LfsConnectionFactory.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/LfsConnectionFactory.java
@@ -227,7 +227,8 @@ private static Protocol.ExpiringAction getSshAuthentication(
 	 * @throws IOException
 	 *             in case of any error.
 	 */
-	public static @NonNull HttpConnection getLfsContentConnection(
+	@NonNull
+	public static HttpConnection getLfsContentConnection(
 			Repository repo, Protocol.Action action, String method)
 			throws IOException {
 		URL contentUrl = new URL(action.href);
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
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 161604c..9343e36 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="5.1.4.qualifier"
+      version="5.2.0.qualifier"
       provider-name="%providerName">
 
    <description url="http://www.eclipse.org/jgit/">
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/pom.xml b/org.eclipse.jgit.packaging/org.eclipse.jgit.feature/pom.xml
index c74e22e..48e1a45 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.http.apache.feature/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.packaging/org.eclipse.jgit.http.apache.feature/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.http.apache.feature/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.http.apache.feature/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
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 1339610..10dc8a3 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="5.1.4.qualifier"
+      version="5.2.0.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 c9350f2..b833f98 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.junit.feature/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.packaging/org.eclipse.jgit.junit.feature/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.junit.feature/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.junit.feature/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
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 4339e85..cae4dd9 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="5.1.4.qualifier"
+      version="5.2.0.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 9228ad7..ad32702 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.lfs.feature/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.packaging/org.eclipse.jgit.lfs.feature/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.lfs.feature/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.lfs.feature/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
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 6beb73e..692d48c 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="5.1.4.qualifier"
+      version="5.2.0.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 8a98f4f..b88eba0 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.feature/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.feature/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.feature/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.feature/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
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 523668f..bbf0c6f 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="5.1.4.qualifier"
+      version="5.2.0.qualifier"
       provider-name="%providerName">
 
    <description url="http://www.eclipse.org/jgit/">
@@ -31,8 +31,8 @@
          version="0.0.0"/>
 
    <requires>
-      <import feature="org.eclipse.jgit" version="5.1.4" match="equivalent"/>
-      <import feature="org.eclipse.jgit.lfs" version="5.1.4" match="equivalent"/>
+      <import feature="org.eclipse.jgit" version="5.2.0" match="equivalent"/>
+      <import feature="org.eclipse.jgit.lfs" version="5.2.0" 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 e95dc4a..0854a57 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.source.feature/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.source.feature/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.source.feature/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.pgm.source.feature/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
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 7e572e0..a70e791 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="5.1.4.qualifier"
+      version="5.2.0.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 cb40a79..1287d05 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.repository/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.packaging/org.eclipse.jgit.repository/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.repository/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.repository/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
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 4555c81..c5681bd 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.repository</artifactId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.source.feature/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.packaging/org.eclipse.jgit.source.feature/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.source.feature/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.source.feature/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
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 f8b919e..1581663 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="5.1.4.qualifier"
+      version="5.2.0.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 0cdb2dd..82e055f 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <groupId>org.eclipse.jgit.feature</groupId>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/META-INF/MANIFEST.MF b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/META-INF/MANIFEST.MF
index 0734df9..ebe9a53 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
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 31542a3..7e5755f 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.target</artifactId>
diff --git a/org.eclipse.jgit.packaging/pom.xml b/org.eclipse.jgit.packaging/pom.xml
index 8894712..4d04a35 100644
--- a/org.eclipse.jgit.packaging/pom.xml
+++ b/org.eclipse.jgit.packaging/pom.xml
@@ -53,7 +53,7 @@
 
   <groupId>org.eclipse.jgit</groupId>
   <artifactId>jgit.tycho.parent</artifactId>
-  <version>5.1.4-SNAPSHOT</version>
+  <version>5.2.0-SNAPSHOT</version>
   <packaging>pom</packaging>
 
   <name>JGit Tycho Parent</name>
diff --git a/org.eclipse.jgit.pgm.test/.classpath b/org.eclipse.jgit.pgm.test/.classpath
index b26f4c4..1334739 100644
--- a/org.eclipse.jgit.pgm.test/.classpath
+++ b/org.eclipse.jgit.pgm.test/.classpath
@@ -1,7 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="tst"/>
-	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="src" path="tst">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path="src">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
 	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
 	<classpathentry kind="output" path="bin"/>
diff --git a/org.eclipse.jgit.pgm.test/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.pgm.test/.settings/org.eclipse.jdt.core.prefs
index 794592d..2ca78ff 100644
--- a/org.eclipse.jgit.pgm.test/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.pgm.test/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.pgm.test/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.pgm.test/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.pgm.test/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.pgm.test/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF
index 932e1da..f9e9984 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
 Bundle-Vendor: %provider_name
 Bundle-Localization: plugin
 Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Import-Package: org.eclipse.jgit.api;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.api.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.diff;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.dircache;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.file;version="5.1.4",
- org.eclipse.jgit.junit;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.merge;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.pgm;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.pgm.internal;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.pgm.opt;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.treewalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util.io;version="[5.1.4,5.2.0)",
+Import-Package: org.eclipse.jgit.api;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.api.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.diff;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.dircache;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.file;version="5.2.0",
+ org.eclipse.jgit.junit;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.merge;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.pgm;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.pgm.internal;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.pgm.opt;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.treewalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util.io;version="[5.2.0,5.3.0)",
  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 aa50962..6c8ce35 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.pgm.test</artifactId>
diff --git a/org.eclipse.jgit.pgm.test/src/org/eclipse/jgit/pgm/CLIGitCommand.java b/org.eclipse.jgit.pgm.test/src/org/eclipse/jgit/pgm/CLIGitCommand.java
index 81875f1..9ad22dd 100644
--- a/org.eclipse.jgit.pgm.test/src/org/eclipse/jgit/pgm/CLIGitCommand.java
+++ b/org.eclipse.jgit.pgm.test/src/org/eclipse/jgit/pgm/CLIGitCommand.java
@@ -42,11 +42,13 @@
  */
 package org.eclipse.jgit.pgm;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertNull;
 
 import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.IOException;
+import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.List;
@@ -153,7 +155,8 @@ private void run(String commandLine) throws Exception {
 
 	@Override
 	PrintWriter createErrorWriter() {
-		return new PrintWriter(result.err);
+		return new PrintWriter(new OutputStreamWriter(
+				result.err, UTF_8));
 	}
 
 	@Override
@@ -249,19 +252,19 @@ public static class Result {
 		}
 
 		public String outString() {
-			return out.toString();
+			return new String(out.toByteArray(), UTF_8);
 		}
 
 		public List<String> outLines() {
-			return IO.readLines(out.toString());
+			return IO.readLines(outString());
 		}
 
 		public String errString() {
-			return err.toString();
+			return new String(err.toByteArray(), UTF_8);
 		}
 
 		public List<String> errLines() {
-			return IO.readLines(err.toString());
+			return IO.readLines(errString());
 		}
 	}
 
diff --git a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ProxyConfigTest.java b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ProxyConfigTest.java
index 40a223d..42530f3 100644
--- a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ProxyConfigTest.java
+++ b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ProxyConfigTest.java
@@ -37,6 +37,7 @@
  */
 package org.eclipse.jgit.pgm;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 
 import java.io.ByteArrayOutputStream;
@@ -47,7 +48,6 @@
 import java.util.List;
 import java.util.Map;
 
-import org.eclipse.jgit.lib.Constants;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -204,7 +204,7 @@ private static String getOutput(Process p)
 			while ((length = inputStream.read(buffer)) != -1) {
 				result.write(buffer, 0, length);
 			}
-			return result.toString(Constants.CHARACTER_ENCODING);
+			return result.toString(UTF_8.name());
 		}
 	}
 }
diff --git a/org.eclipse.jgit.pgm/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.pgm/.settings/org.eclipse.jdt.core.prefs
index 13c32a6..ef6f5e7 100644
--- a/org.eclipse.jgit.pgm/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.pgm/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.pgm/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.pgm/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.pgm/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.pgm/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.pgm/BUILD b/org.eclipse.jgit.pgm/BUILD
index ddc84be..abd8556 100644
--- a/org.eclipse.jgit.pgm/BUILD
+++ b/org.eclipse.jgit.pgm/BUILD
@@ -7,6 +7,7 @@
     deps = [
         ":services",
         "//lib:args4j",
+        "//lib:commons-logging",
         "//lib:httpclient",
         "//lib:httpcore",
         "//lib:jetty-http",
diff --git a/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF b/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF
index 5279e5e..ecce3ba 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
 Bundle-Localization: plugin
@@ -28,49 +28,49 @@
  org.eclipse.jetty.util.log;version="[9.4.5,10.0.0)",
  org.eclipse.jetty.util.security;version="[9.4.5,10.0.0)",
  org.eclipse.jetty.util.thread;version="[9.4.5,10.0.0)",
- org.eclipse.jgit.api;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.api.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.archive;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.awtui;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.blame;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.diff;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.dircache;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.gitrepo;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.ketch;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.dfs;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.io;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.pack;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.reftable;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.reftree;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.server;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.server.fs;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs.server.s3;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.merge;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.nls;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.notes;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revplot;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk.filter;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.storage.pack;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport.http.apache;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport.resolver;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.treewalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.treewalk.filter;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util.io;version="[5.1.4,5.2.0)",
+ org.eclipse.jgit.api;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.api.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.archive;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.awtui;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.blame;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.diff;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.dircache;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.gitrepo;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.ketch;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.dfs;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.io;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.pack;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.reftable;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.reftree;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.server;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.server.fs;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs.server.s3;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.merge;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.nls;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.notes;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revplot;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk.filter;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.storage.pack;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport.http.apache;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport.resolver;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.treewalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.treewalk.filter;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util.io;version="[5.2.0,5.3.0)",
  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="5.1.4";
+Export-Package: org.eclipse.jgit.console;version="5.2.0";
   uses:="org.eclipse.jgit.transport,
    org.eclipse.jgit.util",
- org.eclipse.jgit.pgm;version="5.1.4";
+ org.eclipse.jgit.pgm;version="5.2.0";
   uses:="org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.pgm.opt,
@@ -81,11 +81,11 @@
    org.eclipse.jgit.treewalk,
    javax.swing,
    org.eclipse.jgit.transport",
- org.eclipse.jgit.pgm.debug;version="5.1.4";
+ org.eclipse.jgit.pgm.debug;version="5.2.0";
   uses:="org.eclipse.jgit.util.io,
    org.eclipse.jgit.pgm",
- org.eclipse.jgit.pgm.internal;version="5.1.4";x-friends:="org.eclipse.jgit.pgm.test,org.eclipse.jgit.test",
- org.eclipse.jgit.pgm.opt;version="5.1.4";
+ org.eclipse.jgit.pgm.internal;version="5.2.0";x-friends:="org.eclipse.jgit.pgm.test,org.eclipse.jgit.test",
+ org.eclipse.jgit.pgm.opt;version="5.2.0";
   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 de0d2af..c10ea77 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: 5.1.4.qualifier
-Eclipse-SourceBundle: org.eclipse.jgit.pgm;version="5.1.4.qualifier";roots="."
+Bundle-Version: 5.2.0.qualifier
+Eclipse-SourceBundle: org.eclipse.jgit.pgm;version="5.2.0.qualifier";roots="."
diff --git a/org.eclipse.jgit.pgm/pom.xml b/org.eclipse.jgit.pgm/pom.xml
index 1579a42..b229a8f 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.pgm</artifactId>
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 7e5b545..66c84af 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
@@ -44,6 +44,9 @@
 
 package org.eclipse.jgit.pgm;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_SECTION_I18N;
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_LOG_OUTPUT_ENCODING;
 import static org.eclipse.jgit.lib.Constants.R_HEADS;
 import static org.eclipse.jgit.lib.Constants.R_REMOTES;
 import static org.eclipse.jgit.lib.Constants.R_TAGS;
@@ -56,6 +59,7 @@
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.io.OutputStreamWriter;
+import java.nio.charset.Charset;
 import java.text.MessageFormat;
 import java.util.ResourceBundle;
 
@@ -168,6 +172,30 @@ public void initRaw(final Repository repository, final String gitDir,
 	}
 
 	/**
+	 * Get the log output encoding specified in the repository's
+	 * {@code i18n.logOutputEncoding} configuration.
+	 *
+	 * @param repository
+	 *            the repository.
+	 * @return Charset corresponding to {@code i18n.logOutputEncoding}, or
+	 *         {@code UTF_8}.
+	 */
+	private Charset getLogOutputEncodingCharset(Repository repository) {
+		if (repository != null) {
+			String logOutputEncoding = repository.getConfig().getString(
+					CONFIG_SECTION_I18N, null, CONFIG_KEY_LOG_OUTPUT_ENCODING);
+			if (logOutputEncoding != null) {
+				try {
+					return Charset.forName(logOutputEncoding);
+				} catch (IllegalArgumentException e) {
+					throw die(CLIText.get().cannotCreateOutputStream);
+				}
+			}
+		}
+		return UTF_8;
+	}
+
+	/**
 	 * Initialize the command to work with a repository.
 	 *
 	 * @param repository
@@ -177,32 +205,18 @@ public void initRaw(final Repository repository, final String gitDir,
 	 *            {@code repository} is null.
 	 */
 	protected void init(Repository repository, String gitDir) {
-		try {
-			final String outputEncoding = repository != null ? repository
-					.getConfig().getString("i18n", null, "logOutputEncoding") : null; //$NON-NLS-1$ //$NON-NLS-2$
-			if (ins == null)
-				ins = new FileInputStream(FileDescriptor.in);
-			if (outs == null)
-				outs = new FileOutputStream(FileDescriptor.out);
-			if (errs == null)
-				errs = new FileOutputStream(FileDescriptor.err);
-			BufferedWriter outbufw;
-			if (outputEncoding != null)
-				outbufw = new BufferedWriter(new OutputStreamWriter(outs,
-						outputEncoding));
-			else
-				outbufw = new BufferedWriter(new OutputStreamWriter(outs));
-			outw = new ThrowingPrintWriter(outbufw);
-			BufferedWriter errbufw;
-			if (outputEncoding != null)
-				errbufw = new BufferedWriter(new OutputStreamWriter(errs,
-						outputEncoding));
-			else
-				errbufw = new BufferedWriter(new OutputStreamWriter(errs));
-			errw = new ThrowingPrintWriter(errbufw);
-		} catch (IOException e) {
-			throw die(CLIText.get().cannotCreateOutputStream);
-		}
+		Charset charset = getLogOutputEncodingCharset(repository);
+
+		if (ins == null)
+			ins = new FileInputStream(FileDescriptor.in);
+		if (outs == null)
+			outs = new FileOutputStream(FileDescriptor.out);
+		if (errs == null)
+			errs = new FileOutputStream(FileDescriptor.err);
+		outw = new ThrowingPrintWriter(new BufferedWriter(
+				new OutputStreamWriter(outs, charset)));
+		errw = new ThrowingPrintWriter(new BufferedWriter(
+				new OutputStreamWriter(errs, charset)));
 
 		if (repository != null && repository.getDirectory() != null) {
 			db = repository;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java
index bb51b50..300a01d 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java
@@ -474,7 +474,7 @@ private static abstract class Fold {
 	}
 
 	/** Utility to help us identify unique lines in a file. */
-	private class Line {
+	private static class Line {
 		private final RawText txt;
 
 		private final int pos;
diff --git a/org.eclipse.jgit.test/.classpath b/org.eclipse.jgit.test/.classpath
index 84b5052..3b0dd26 100644
--- a/org.eclipse.jgit.test/.classpath
+++ b/org.eclipse.jgit.test/.classpath
@@ -1,9 +1,25 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry excluding="**/*.idx|**/*.pack" kind="src" path="tst"/>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="tst-rsrc"/>
-	<classpathentry kind="src" path="exttst"/>
+	<classpathentry excluding="**/*.idx|**/*.pack" kind="src" path="tst">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path="src">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path="tst-rsrc">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path="exttst">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
 	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
 	<classpathentry kind="output" path="bin"/>
diff --git a/org.eclipse.jgit.test/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.test/.settings/org.eclipse.jdt.core.prefs
index 794592d..2ca78ff 100644
--- a/org.eclipse.jgit.test/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.test/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.test/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.test/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.test/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.test/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
index c2159bd..6df9e39 100644
--- a/org.eclipse.jgit.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
@@ -3,58 +3,59 @@
 Bundle-Name: %plugin_name
 Automatic-Module-Name: org.eclipse.jgit.test
 Bundle-SymbolicName: org.eclipse.jgit.test
-Bundle-Version: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: com.googlecode.javaewah;version="[1.1.6,2.0.0)",
  com.jcraft.jsch;version="[0.1.54,0.2.0)",
- org.eclipse.jgit.api;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.api.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.attributes;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.awtui;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.blame;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.diff;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.dircache;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.events;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.fnmatch;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.gitrepo;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.hooks;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.ignore;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.ignore.internal;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.fsck;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.dfs;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.io;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.pack;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.reftable;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.internal.storage.reftree;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.junit;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lfs;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.merge;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.nls;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.notes;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.patch;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.pgm;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.pgm.internal;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revplot;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk.filter;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.storage.file;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.storage.pack;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.submodule;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport.http;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport.resolver;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.treewalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.treewalk.filter;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util.io;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util.sha1;version="[5.1.4,5.2.0)",
+ org.eclipse.jgit.api;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.api.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.attributes;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.awtui;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.blame;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.diff;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.dircache;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.events;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.fnmatch;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.gitrepo;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.hooks;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.ignore;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.ignore.internal;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.fsck;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.dfs;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.io;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.pack;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.reftable;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.storage.reftree;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.internal.transport.parser;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.junit;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lfs;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.merge;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.nls;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.notes;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.patch;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.pgm;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.pgm.internal;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revplot;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk.filter;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.storage.file;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.storage.pack;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.submodule;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport.http;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport.resolver;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.treewalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.treewalk.filter;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util.io;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util.sha1;version="[5.2.0,5.3.0)",
  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)",
diff --git a/org.eclipse.jgit.test/pom.xml b/org.eclipse.jgit.test/pom.xml
index 7a220d5..6aa34f5 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.test</artifactId>
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 911f659..16cec64 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
@@ -43,6 +43,7 @@
  */
 package org.eclipse.jgit.api;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.util.FileUtils.RECURSIVE;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
@@ -118,7 +119,7 @@ public void testAddNonExistingSingleFile() throws GitAPIException {
 	public void testAddExistingSingleFile() throws IOException, GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
@@ -489,7 +490,7 @@ public void testAddExistingSingleSmallFileWithNewLine() throws IOException,
 			GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("row1\r\nrow2");
 		}
 
@@ -519,7 +520,7 @@ public void testAddExistingSingleMediumSizeFileWithNewLine()
 			data.append("row1\r\nrow2");
 		}
 		String crData = data.toString();
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print(crData);
 		}
 		String lfData = data.toString().replaceAll("\r", "");
@@ -544,7 +545,7 @@ public void testAddExistingSingleBinaryFile() throws IOException,
 			GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("row1\r\nrow2\u0000");
 		}
 
@@ -570,7 +571,7 @@ public void testAddExistingSingleFileInSubDir() throws IOException,
 		FileUtils.mkdir(new File(db.getWorkTree(), "sub"));
 		File file = new File(db.getWorkTree(), "sub/a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
@@ -588,7 +589,7 @@ public void testAddExistingSingleFileTwice() throws IOException,
 			GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
@@ -597,7 +598,7 @@ public void testAddExistingSingleFileTwice() throws IOException,
 
 			dc.getEntry(0).getObjectId();
 
-			try (PrintWriter writer = new PrintWriter(file)) {
+			try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 				writer.print("other content");
 			}
 
@@ -613,7 +614,7 @@ public void testAddExistingSingleFileTwice() throws IOException,
 	public void testAddExistingSingleFileTwiceWithCommit() throws Exception {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
@@ -624,7 +625,7 @@ public void testAddExistingSingleFileTwiceWithCommit() throws Exception {
 
 			git.commit().setMessage("commit a.txt").call();
 
-			try (PrintWriter writer = new PrintWriter(file)) {
+			try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 				writer.print("other content");
 			}
 
@@ -640,7 +641,7 @@ public void testAddExistingSingleFileTwiceWithCommit() throws Exception {
 	public void testAddRemovedFile() throws Exception {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
@@ -663,7 +664,7 @@ public void testAddRemovedFile() throws Exception {
 	public void testAddRemovedCommittedFile() throws Exception {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
@@ -690,13 +691,13 @@ public void testAddWithConflicts() throws Exception {
 
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
 		File file2 = new File(db.getWorkTree(), "b.txt");
 		FileUtils.createNewFile(file2);
-		try (PrintWriter writer = new PrintWriter(file2)) {
+		try (PrintWriter writer = new PrintWriter(file2, UTF_8.name())) {
 			writer.print("content b");
 		}
 
@@ -707,12 +708,12 @@ public void testAddWithConflicts() throws Exception {
 		addEntryToBuilder("b.txt", file2, newObjectInserter, builder, 0);
 		addEntryToBuilder("a.txt", file, newObjectInserter, builder, 1);
 
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("other content");
 		}
 		addEntryToBuilder("a.txt", file, newObjectInserter, builder, 3);
 
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("our content");
 		}
 		addEntryToBuilder("a.txt", file, newObjectInserter, builder, 2)
@@ -743,13 +744,13 @@ public void testAddWithConflicts() throws Exception {
 	public void testAddTwoFiles() throws Exception  {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
 		File file2 = new File(db.getWorkTree(), "b.txt");
 		FileUtils.createNewFile(file2);
-		try (PrintWriter writer = new PrintWriter(file2)) {
+		try (PrintWriter writer = new PrintWriter(file2, UTF_8.name())) {
 			writer.print("content b");
 		}
 
@@ -767,13 +768,13 @@ public void testAddFolder() throws Exception  {
 		FileUtils.mkdir(new File(db.getWorkTree(), "sub"));
 		File file = new File(db.getWorkTree(), "sub/a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
 		File file2 = new File(db.getWorkTree(), "sub/b.txt");
 		FileUtils.createNewFile(file2);
-		try (PrintWriter writer = new PrintWriter(file2)) {
+		try (PrintWriter writer = new PrintWriter(file2, UTF_8.name())) {
 			writer.print("content b");
 		}
 
@@ -791,19 +792,19 @@ public void testAddIgnoredFile() throws Exception  {
 		FileUtils.mkdir(new File(db.getWorkTree(), "sub"));
 		File file = new File(db.getWorkTree(), "sub/a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
 		File ignoreFile = new File(db.getWorkTree(), ".gitignore");
 		FileUtils.createNewFile(ignoreFile);
-		try (PrintWriter writer = new PrintWriter(ignoreFile)) {
+		try (PrintWriter writer = new PrintWriter(ignoreFile, UTF_8.name())) {
 			writer.print("sub/b.txt");
 		}
 
 		File file2 = new File(db.getWorkTree(), "sub/b.txt");
 		FileUtils.createNewFile(file2);
-		try (PrintWriter writer = new PrintWriter(file2)) {
+		try (PrintWriter writer = new PrintWriter(file2, UTF_8.name())) {
 			writer.print("content b");
 		}
 
@@ -821,13 +822,13 @@ public void testAddWholeRepo() throws Exception  {
 		FileUtils.mkdir(new File(db.getWorkTree(), "sub"));
 		File file = new File(db.getWorkTree(), "sub/a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
 		File file2 = new File(db.getWorkTree(), "sub/b.txt");
 		FileUtils.createNewFile(file2);
-		try (PrintWriter writer = new PrintWriter(file2)) {
+		try (PrintWriter writer = new PrintWriter(file2, UTF_8.name())) {
 			writer.print("content b");
 		}
 
@@ -849,13 +850,13 @@ public void testAddWithoutParameterUpdate() throws Exception {
 		FileUtils.mkdir(new File(db.getWorkTree(), "sub"));
 		File file = new File(db.getWorkTree(), "sub/a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
 		File file2 = new File(db.getWorkTree(), "sub/b.txt");
 		FileUtils.createNewFile(file2);
-		try (PrintWriter writer = new PrintWriter(file2)) {
+		try (PrintWriter writer = new PrintWriter(file2, UTF_8.name())) {
 			writer.print("content b");
 		}
 
@@ -872,12 +873,12 @@ public void testAddWithoutParameterUpdate() throws Exception {
 			// new unstaged file sub/c.txt
 			File file3 = new File(db.getWorkTree(), "sub/c.txt");
 			FileUtils.createNewFile(file3);
-			try (PrintWriter writer = new PrintWriter(file3)) {
+			try (PrintWriter writer = new PrintWriter(file3, UTF_8.name())) {
 				writer.print("content c");
 			}
 
 			// file sub/a.txt is modified
-			try (PrintWriter writer = new PrintWriter(file)) {
+			try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 				writer.print("modified content");
 			}
 
@@ -904,13 +905,13 @@ public void testAddWithParameterUpdate() throws Exception {
 		FileUtils.mkdir(new File(db.getWorkTree(), "sub"));
 		File file = new File(db.getWorkTree(), "sub/a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
 		File file2 = new File(db.getWorkTree(), "sub/b.txt");
 		FileUtils.createNewFile(file2);
-		try (PrintWriter writer = new PrintWriter(file2)) {
+		try (PrintWriter writer = new PrintWriter(file2, UTF_8.name())) {
 			writer.print("content b");
 		}
 
@@ -927,12 +928,12 @@ public void testAddWithParameterUpdate() throws Exception {
 			// new unstaged file sub/c.txt
 			File file3 = new File(db.getWorkTree(), "sub/c.txt");
 			FileUtils.createNewFile(file3);
-			try (PrintWriter writer = new PrintWriter(file3)) {
+			try (PrintWriter writer = new PrintWriter(file3, UTF_8.name())) {
 				writer.print("content c");
 			}
 
 			// file sub/a.txt is modified
-			try (PrintWriter writer = new PrintWriter(file)) {
+			try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 				writer.print("modified content");
 			}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ArchiveCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ArchiveCommandTest.java
index 1300f98..1c41018 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ArchiveCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ArchiveCommandTest.java
@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.api;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNull;
 
@@ -190,7 +191,8 @@ public void archiveByDirectoryPath() throws GitAPIException, IOException {
 		}
 	}
 
-	private class MockFormat implements ArchiveCommand.Format<MockOutputStream> {
+	private static class MockFormat
+			implements ArchiveCommand.Format<MockOutputStream> {
 
 		private Map<String, String> entries = new HashMap<>();
 
@@ -230,7 +232,9 @@ public MockOutputStream createArchiveOutputStream(OutputStream s,
 
 		@Override
 		public void putEntry(MockOutputStream out, ObjectId tree, String path, FileMode mode, ObjectLoader loader) {
-			String content = mode != FileMode.TREE ? new String(loader.getBytes()) : null;
+			String content = mode != FileMode.TREE
+					? new String(loader.getBytes(), UTF_8)
+					: null;
 			entries.put(path, content);
 		}
 
@@ -240,7 +244,7 @@ public Iterable<String> suffixes() {
 		}
 	}
 
-	public class MockOutputStream extends OutputStream {
+	public static class MockOutputStream extends OutputStream {
 
 		private int foo;
 
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 0d7009d..6b5fe50 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
@@ -370,8 +370,7 @@ public void testCloneRepositoryWithTagName() throws Exception {
 	}
 
 	@Test
-	public void testCloneRepositoryOnlyOneBranch() throws IOException,
-			JGitInternalException, GitAPIException {
+	public void testCloneRepositoryOnlyOneBranch() throws Exception {
 		File directory = createTempDirectory("testCloneRepositoryWithBranch");
 		CloneCommand command = Git.cloneRepository();
 		command.setBranch("refs/heads/master");
@@ -382,25 +381,47 @@ public void testCloneRepositoryOnlyOneBranch() throws IOException,
 		Git git2 = command.call();
 		addRepoToClose(git2.getRepository());
 		assertNotNull(git2);
+		assertNull(git2.getRepository().resolve("tag-for-blob"));
+		assertNotNull(git2.getRepository().resolve("tag-initial"));
 		assertEquals(git2.getRepository().getFullBranch(), "refs/heads/master");
 		assertEquals("refs/remotes/origin/master", allRefNames(git2
 				.branchList().setListMode(ListMode.REMOTE).call()));
+		RemoteConfig cfg = new RemoteConfig(git2.getRepository().getConfig(),
+				Constants.DEFAULT_REMOTE_NAME);
+		List<RefSpec> specs = cfg.getFetchRefSpecs();
+		assertEquals(1, specs.size());
+		assertEquals(
+				new RefSpec("+refs/heads/master:refs/remotes/origin/master"),
+				specs.get(0));
+	}
 
+	@Test
+	public void testBareCloneRepositoryOnlyOneBranch() throws Exception {
 		// Same thing, but now test with bare repo
-		directory = createTempDirectory("testCloneRepositoryWithBranch_bare");
-		command = Git.cloneRepository();
+		File directory = createTempDirectory(
+				"testCloneRepositoryWithBranch_bare");
+		CloneCommand command = Git.cloneRepository();
 		command.setBranch("refs/heads/master");
 		command.setBranchesToClone(Collections
 				.singletonList("refs/heads/master"));
 		command.setDirectory(directory);
 		command.setURI(fileUri());
 		command.setBare(true);
-		git2 = command.call();
+		Git git2 = command.call();
 		addRepoToClose(git2.getRepository());
 		assertNotNull(git2);
+		assertNull(git2.getRepository().resolve("tag-for-blob"));
+		assertNotNull(git2.getRepository().resolve("tag-initial"));
 		assertEquals(git2.getRepository().getFullBranch(), "refs/heads/master");
 		assertEquals("refs/heads/master", allRefNames(git2.branchList()
 				.setListMode(ListMode.ALL).call()));
+		RemoteConfig cfg = new RemoteConfig(git2.getRepository().getConfig(),
+				Constants.DEFAULT_REMOTE_NAME);
+		List<RefSpec> specs = cfg.getFetchRefSpecs();
+		assertEquals(1, specs.size());
+		assertEquals(
+				new RefSpec("+refs/heads/master:refs/heads/master"),
+				specs.get(0));
 	}
 
 	public static String allRefNames(List<Ref> refs) {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitAndLogCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitAndLogCommandTest.java
index ca0630e..c028ca3 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitAndLogCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitAndLogCommandTest.java
@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.api;
 
+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.assertTrue;
@@ -120,7 +121,7 @@ public void testLogWithFilter() throws IOException, JGitInternalException,
 			// create first file
 			File file = new File(db.getWorkTree(), "a.txt");
 			FileUtils.createNewFile(file);
-			try (PrintWriter writer = new PrintWriter(file)) {
+			try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 				writer.print("content1");
 			}
 
@@ -131,7 +132,7 @@ public void testLogWithFilter() throws IOException, JGitInternalException,
 			// create second file
 			file = new File(db.getWorkTree(), "b.txt");
 			FileUtils.createNewFile(file);
-			try (PrintWriter writer = new PrintWriter(file)) {
+			try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 				writer.print("content2");
 			}
 
@@ -231,7 +232,7 @@ public void testAddUnstagedChanges() throws IOException,
 			JGitInternalException, GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
-		try (PrintWriter writer = new PrintWriter(file)) {
+		try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 			writer.print("content");
 		}
 
@@ -242,7 +243,7 @@ public void testAddUnstagedChanges() throws IOException,
 			assertEquals("6b584e8ece562ebffc15d38808cd6b98fc3d97ea",
 					tw.getObjectId(0).getName());
 
-			try (PrintWriter writer = new PrintWriter(file)) {
+			try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 				writer.print("content2");
 			}
 			commit = git.commit().setMessage("second commit").call();
@@ -265,7 +266,7 @@ public void testModeChange() throws IOException, GitAPIException {
 			// create file
 			File file = new File(db.getWorkTree(), "a.txt");
 			FileUtils.createNewFile(file);
-			try (PrintWriter writer = new PrintWriter(file)) {
+			try (PrintWriter writer = new PrintWriter(file, UTF_8.name())) {
 				writer.print("content1");
 			}
 
@@ -358,7 +359,7 @@ public void testInsertChangeId() throws JGitInternalException,
 					messageHeader + messageFooter)
 					.setInsertChangeId(true).call();
 			// we should find a real change id (at the end of the file)
-			byte[] chars = commit.getFullMessage().getBytes();
+			byte[] chars = commit.getFullMessage().getBytes(UTF_8);
 			int lastLineBegin = RawParseUtils.prevLF(chars, chars.length - 2);
 			String lastLine = RawParseUtils.decode(chars, lastLineBegin + 1,
 					chars.length);
@@ -371,7 +372,7 @@ public void testInsertChangeId() throws JGitInternalException,
 					.setInsertChangeId(true).call();
 			// we should find a real change id (in the line as dictated by the
 			// template)
-			chars = commit.getFullMessage().getBytes();
+			chars = commit.getFullMessage().getBytes(UTF_8);
 			int lineStart = 0;
 			int lineEnd = 0;
 			for (int i = 0; i < 4; i++) {
@@ -389,7 +390,7 @@ public void testInsertChangeId() throws JGitInternalException,
 					messageHeader + changeIdTemplate + messageFooter)
 					.setInsertChangeId(false).call();
 			// we should find the untouched template
-			chars = commit.getFullMessage().getBytes();
+			chars = commit.getFullMessage().getBytes(UTF_8);
 			lineStart = 0;
 			lineEnd = 0;
 			for (int i = 0; i < 4; i++) {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitOnlyTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitOnlyTest.java
index bbd6ec0..83181ee 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitOnlyTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitOnlyTest.java
@@ -43,6 +43,7 @@
  */
 package org.eclipse.jgit.api;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
@@ -1298,7 +1299,7 @@ static private String getHead(Git git, String path)
 				final TreeWalk tw = TreeWalk.forPath(repo, path,
 						rw.parseTree(headId));
 				return new String(tw.getObjectReader().open(tw.getObjectId(0))
-						.getBytes());
+						.getBytes(), UTF_8);
 			}
 		} catch (Exception e) {
 			return "";
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CrLfNativeTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CrLfNativeTest.java
new file mode 100644
index 0000000..c726128
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CrLfNativeTest.java
@@ -0,0 +1,181 @@
+/*
+ * Copyright (C) 2018, Thomas Wolf <thomas.wolf@paranor.ch>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.api;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.eclipse.jgit.api.ResetCommand.ResetType;
+import org.eclipse.jgit.junit.MockSystemReader;
+import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.lib.CoreConfig.EolStreamType;
+import org.eclipse.jgit.storage.file.FileBasedConfig;
+import org.eclipse.jgit.treewalk.FileTreeIterator;
+import org.eclipse.jgit.treewalk.TreeWalk;
+import org.eclipse.jgit.treewalk.TreeWalk.OperationType;
+import org.eclipse.jgit.util.SystemReader;
+import org.junit.Test;
+
+public class CrLfNativeTest extends RepositoryTestCase {
+
+	@Test
+	public void checkoutWithCrLfNativeUnix() throws Exception {
+		verifyNativeCheckout(new MockSystemReader() {
+			{
+				setUnix();
+			}
+		});
+	}
+
+	@Test
+	public void checkoutWithCrLfNativeWindows() throws Exception {
+		verifyNativeCheckout(new MockSystemReader() {
+			{
+				setWindows();
+			}
+		});
+	}
+
+	private void verifyNativeCheckout(SystemReader systemReader)
+			throws Exception {
+		SystemReader.setInstance(systemReader);
+		Git git = Git.wrap(db);
+		FileBasedConfig config = db.getConfig();
+		config.setString("core", null, "autocrlf", "false");
+		config.setString("core", null, "eol", "native");
+		config.save();
+		// core.eol is active only if text is set, or if text=auto
+		writeTrashFile(".gitattributes", "*.txt text\n");
+		File file = writeTrashFile("file.txt", "line 1\nline 2\n");
+		git.add().addFilepattern("file.txt").addFilepattern(".gitattributes")
+				.call();
+		git.commit().setMessage("Initial").call();
+		// Check-in with core.eol=native normalization
+		assertEquals(
+				"[.gitattributes, mode:100644, content:*.txt text\n]"
+						+ "[file.txt, mode:100644, content:line 1\nline 2\n]",
+				indexState(CONTENT));
+		writeTrashFile("file.txt", "something else");
+		git.add().addFilepattern("file.txt").call();
+		git.commit().setMessage("New commit").call();
+		git.reset().setMode(ResetType.HARD).setRef("HEAD~").call();
+		// Check-out should convert to the native line separator
+		checkFile(file, systemReader.isWindows() ? "line 1\r\nline 2\r\n"
+				: "line 1\nline 2\n");
+		Status status = git.status().call();
+		assertTrue("git status should be clean", status.isClean());
+	}
+
+	/**
+	 * Verifies the handling of the crlf attribute: crlf == text, -crlf ==
+	 * -text, crlf=input == eol=lf
+	 *
+	 * @throws Exception
+	 */
+	@Test
+	public void testCrLfAttribute() throws Exception {
+		FileBasedConfig config = db.getConfig();
+		config.setString("core", null, "autocrlf", "false");
+		config.setString("core", null, "eol", "crlf");
+		config.save();
+		writeTrashFile(".gitattributes",
+				"*.txt text\n*.crlf crlf\n*.bin -text\n*.nocrlf -crlf\n*.input crlf=input\n*.eol eol=lf");
+		writeTrashFile("foo.txt", "");
+		writeTrashFile("foo.crlf", "");
+		writeTrashFile("foo.bin", "");
+		writeTrashFile("foo.nocrlf", "");
+		writeTrashFile("foo.input", "");
+		writeTrashFile("foo.eol", "");
+		Map<String, EolStreamType> inTypes = new HashMap<>();
+		Map<String, EolStreamType> outTypes = new HashMap<>();
+		try (TreeWalk walk = new TreeWalk(db)) {
+			walk.addTree(new FileTreeIterator(db));
+			while (walk.next()) {
+				String path = walk.getPathString();
+				if (".gitattributes".equals(path)) {
+					continue;
+				}
+				EolStreamType in = walk
+						.getEolStreamType(OperationType.CHECKIN_OP);
+				EolStreamType out = walk
+						.getEolStreamType(OperationType.CHECKOUT_OP);
+				inTypes.put(path, in);
+				outTypes.put(path, out);
+			}
+		}
+		assertEquals("", checkTypes("check-in", inTypes));
+		assertEquals("", checkTypes("check-out", outTypes));
+	}
+
+	private String checkTypes(String prefix, Map<String, EolStreamType> types) {
+		StringBuilder result = new StringBuilder();
+		EolStreamType a = types.get("foo.crlf");
+		EolStreamType b = types.get("foo.txt");
+		report(result, prefix, "crlf != text", a, b);
+		a = types.get("foo.nocrlf");
+		b = types.get("foo.bin");
+		report(result, prefix, "-crlf != -text", a, b);
+		a = types.get("foo.input");
+		b = types.get("foo.eol");
+		report(result, prefix, "crlf=input != eol=lf", a, b);
+		return result.toString();
+	}
+
+	private void report(StringBuilder result, String prefix, String label,
+			EolStreamType a,
+			EolStreamType b) {
+		if (a == null || b == null || !a.equals(b)) {
+			result.append(prefix).append(' ').append(label).append(": ")
+					.append(toString(a)).append(" != ").append(toString(b))
+					.append('\n');
+		}
+	}
+
+	private String toString(EolStreamType type) {
+		return type == null ? "null" : type.name();
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/DescribeCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/DescribeCommandTest.java
index a422ef9..bb0714d 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/DescribeCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/DescribeCommandTest.java
@@ -42,13 +42,15 @@
  */
 package org.eclipse.jgit.api;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 
+import java.io.BufferedWriter;
 import java.io.File;
-import java.io.FileWriter;
 import java.io.IOException;
+import java.nio.file.Files;
 import java.util.Arrays;
 import java.util.Collection;
 
@@ -404,7 +406,7 @@ private void tag(String tag, boolean annotatedTag) throws GitAPIException {
 	}
 
 	private static void touch(File f, String contents) throws Exception {
-		try (FileWriter w = new FileWriter(f)) {
+		try (BufferedWriter w = Files.newBufferedWriter(f.toPath(), UTF_8)) {
 			w.write(contents);
 		}
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolRepositoryTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolRepositoryTest.java
index 48d3733..47806cb 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolRepositoryTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolRepositoryTest.java
@@ -38,6 +38,7 @@
  */
 package org.eclipse.jgit.api;
 
+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.assertTrue;
@@ -722,10 +723,10 @@ private void collectEntryContentAndAttributes(FileMode type, String pathName,
 			}
 			e.attrs = e.attrs.trim();
 			e.file = new String(
-					IO.readFully(new File(db.getWorkTree(), pathName)));
+					IO.readFully(new File(db.getWorkTree(), pathName)), UTF_8);
 			DirCacheEntry dce = dirCache.getEntry(pathName);
 			ObjectLoader open = walk.getObjectReader().open(dce.getObjectId());
-			e.index = new String(open.getBytes());
+			e.index = new String(open.getBytes(), UTF_8);
 			e.indexContentLength = dce.getLength();
 		}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java
index 2b97b30..9b12011 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java
@@ -82,6 +82,8 @@ public class ResetCommandTest extends RepositoryTestCase {
 
 	private File indexFile;
 
+	private File indexNestedFile;
+
 	private File untrackedFile;
 
 	private DirCacheEntry prestage;
@@ -97,7 +99,7 @@ public void setupRepository() throws IOException, JGitInternalException,
 		indexFile = writeTrashFile("a.txt", "content");
 
 		// create nested file
-		writeTrashFile("dir/b.txt", "content");
+		indexNestedFile = writeTrashFile("dir/b.txt", "content");
 
 		// add files and commit them
 		git.add().addFilepattern("a.txt").addFilepattern("dir/b.txt").call();
@@ -119,13 +121,16 @@ public void testHardReset() throws JGitInternalException,
 			AmbiguousObjectException, IOException, GitAPIException {
 		setupRepository();
 		ObjectId prevHead = db.resolve(Constants.HEAD);
-		assertSameAsHead(git.reset().setMode(ResetType.HARD)
+		ResetCommand reset = git.reset();
+		assertSameAsHead(reset.setMode(ResetType.HARD)
 				.setRef(initialCommit.getName()).call());
+		assertFalse("reflog should be enabled", reset.isReflogDisabled());
 		// check if HEAD points to initial commit now
 		ObjectId head = db.resolve(Constants.HEAD);
 		assertEquals(initialCommit, head);
 		// check if files were removed
 		assertFalse(indexFile.exists());
+		assertFalse(indexNestedFile.exists());
 		assertTrue(untrackedFile.exists());
 		// fileInIndex must no longer be in HEAD and in the index
 		String fileInIndexPath = indexFile.getAbsolutePath();
@@ -148,6 +153,7 @@ public void testHardResetReflogDisabled() throws Exception {
 		assertEquals(initialCommit, head);
 		// check if files were removed
 		assertFalse(indexFile.exists());
+		assertFalse(indexNestedFile.exists());
 		assertTrue(untrackedFile.exists());
 		// fileInIndex must no longer be in HEAD and in the index
 		String fileInIndexPath = indexFile.getAbsolutePath();
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesNodeTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesNodeTest.java
index f0d3c36..f4ccf05 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesNodeTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesNodeTest.java
@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.attributes;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.attributes.Attribute.State.SET;
 import static org.eclipse.jgit.attributes.Attribute.State.UNSET;
 import static org.junit.Assert.assertEquals;
@@ -88,7 +89,7 @@ public void testBasic() throws IOException {
 		String attributeFileContent = "*.type1 A -B C=value\n"
 				+ "*.type2 -A B C=value2";
 
-		is = new ByteArrayInputStream(attributeFileContent.getBytes());
+		is = new ByteArrayInputStream(attributeFileContent.getBytes(UTF_8));
 		AttributesNode node = new AttributesNode();
 		node.parse(is);
 		assertAttribute("file.type1", node,
@@ -102,7 +103,7 @@ public void testNegativePattern() throws IOException {
 		String attributeFileContent = "!*.type1 A -B C=value\n"
 				+ "!*.type2 -A B C=value2";
 
-		is = new ByteArrayInputStream(attributeFileContent.getBytes());
+		is = new ByteArrayInputStream(attributeFileContent.getBytes(UTF_8));
 		AttributesNode node = new AttributesNode();
 		node.parse(is);
 		assertAttribute("file.type1", node, new Attributes());
@@ -113,7 +114,7 @@ public void testNegativePattern() throws IOException {
 	public void testEmptyNegativeAttributeKey() throws IOException {
 		String attributeFileContent = "*.type1 - \n" //
 				+ "*.type2 -   -A";
-		is = new ByteArrayInputStream(attributeFileContent.getBytes());
+		is = new ByteArrayInputStream(attributeFileContent.getBytes(UTF_8));
 		AttributesNode node = new AttributesNode();
 		node.parse(is);
 		assertAttribute("file.type1", node, new Attributes());
@@ -125,7 +126,7 @@ public void testEmptyValueKey() throws IOException {
 		String attributeFileContent = "*.type1 = \n" //
 				+ "*.type2 =value\n"//
 				+ "*.type3 attr=\n";
-		is = new ByteArrayInputStream(attributeFileContent.getBytes());
+		is = new ByteArrayInputStream(attributeFileContent.getBytes(UTF_8));
 		AttributesNode node = new AttributesNode();
 		node.parse(is);
 		assertAttribute("file.type1", node, new Attributes());
@@ -140,7 +141,7 @@ public void testEmptyLine() throws IOException {
 				+ "    \n" //
 				+ "*.type2 -A B C=value2";
 
-		is = new ByteArrayInputStream(attributeFileContent.getBytes());
+		is = new ByteArrayInputStream(attributeFileContent.getBytes(UTF_8));
 		AttributesNode node = new AttributesNode();
 		node.parse(is);
 		assertAttribute("file.type1", node,
@@ -156,7 +157,7 @@ public void testTabSeparator() throws IOException {
 				+ "*.type3  \t\t   B\n" //
 				+ "*.type3\t-A";//
 
-		is = new ByteArrayInputStream(attributeFileContent.getBytes());
+		is = new ByteArrayInputStream(attributeFileContent.getBytes(UTF_8));
 		AttributesNode node = new AttributesNode();
 		node.parse(is);
 		assertAttribute("file.type1", node,
@@ -170,7 +171,7 @@ public void testTabSeparator() throws IOException {
 	public void testDoubleAsteriskAtEnd() throws IOException {
 		String attributeFileContent = "dir/** \tA -B\tC=value";
 
-		is = new ByteArrayInputStream(attributeFileContent.getBytes());
+		is = new ByteArrayInputStream(attributeFileContent.getBytes(UTF_8));
 		AttributesNode node = new AttributesNode();
 		node.parse(is);
 		assertAttribute("dir", node,
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBuilderTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBuilderTest.java
index d12f302..b6291bf 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBuilderTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBuilderTest.java
@@ -89,6 +89,7 @@ public void testBuildRejectsUnsetFileMode() throws Exception {
 		assertEquals(0, e.getRawMode());
 		try {
 			b.add(e);
+			fail("did not reject unset file mode");
 		} catch (IllegalArgumentException err) {
 			assertEquals("FileMode not set for path a", err.getMessage());
 		}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/gitrepo/RepoCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/gitrepo/RepoCommandTest.java
index 92f0cf6..3b330ab 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/gitrepo/RepoCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/gitrepo/RepoCommandTest.java
@@ -52,9 +52,9 @@
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.File;
-import java.io.FileReader;
 import java.io.IOException;
 import java.net.URI;
+import java.nio.file.Files;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -139,7 +139,7 @@ public void setUp() throws Exception {
 		resolveRelativeUris();
 	}
 
-	class IndexedRepos implements RepoCommand.RemoteReader {
+	static class IndexedRepos implements RepoCommand.RemoteReader {
 		Map<String, Repository> uriRepoMap;
 		IndexedRepos() {
 			uriRepoMap = new HashMap<>();
@@ -474,8 +474,8 @@ public void testAddRepoManifest() throws Exception {
 			.call();
 		File hello = new File(db.getWorkTree(), "foo/hello.txt");
 		assertTrue("submodule should be checked out", hello.exists());
-		try (BufferedReader reader = new BufferedReader(
-				new FileReader(hello))) {
+		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
+				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("submodule content should be as expected",
 					"master world", content);
@@ -565,8 +565,8 @@ public void testRepoManifestCopyFile() throws Exception {
 		// The original file should exist
 		File hello = new File(localDb.getWorkTree(), "foo/hello.txt");
 		assertTrue("The original file should exist", hello.exists());
-		try (BufferedReader reader = new BufferedReader(
-				new FileReader(hello))) {
+		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
+				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("The original file should have expected content",
 					"master world", content);
@@ -574,8 +574,8 @@ public void testRepoManifestCopyFile() throws Exception {
 		// The dest file should also exist
 		hello = new File(localDb.getWorkTree(), "Hello");
 		assertTrue("The destination file should exist", hello.exists());
-		try (BufferedReader reader = new BufferedReader(
-				new FileReader(hello))) {
+		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
+				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("The destination file should have expected content",
 					"master world", content);
@@ -610,8 +610,8 @@ public void testBareRepo() throws Exception {
 			assertTrue("The .gitmodules file should exist",
 					gitmodules.exists());
 			// The first line of .gitmodules file should be expected
-			try (BufferedReader reader = new BufferedReader(
-					new FileReader(gitmodules))) {
+			try (BufferedReader reader = Files
+					.newBufferedReader(gitmodules.toPath(), UTF_8)) {
 				String content = reader.readLine();
 				assertEquals(
 						"The first line of .gitmodules file should be as expected",
@@ -644,8 +644,8 @@ public void testRevision() throws Exception {
 			.setURI(rootUri)
 			.call();
 		File hello = new File(db.getWorkTree(), "foo/hello.txt");
-		try (BufferedReader reader = new BufferedReader(
-				new FileReader(hello))) {
+		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
+				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("submodule content should be as expected",
 					"branch world", content);
@@ -671,8 +671,8 @@ public void testRevisionBranch() throws Exception {
 			.setURI(rootUri)
 			.call();
 		File hello = new File(db.getWorkTree(), "foo/hello.txt");
-		try (BufferedReader reader = new BufferedReader(
-				new FileReader(hello))) {
+		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
+				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("submodule content should be as expected",
 					"branch world", content);
@@ -698,8 +698,8 @@ public void testRevisionTag() throws Exception {
 			.setURI(rootUri)
 			.call();
 		File hello = new File(db.getWorkTree(), "foo/hello.txt");
-		try (BufferedReader reader = new BufferedReader(
-				new FileReader(hello))) {
+		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
+				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("submodule content should be as expected",
 					"branch world", content);
@@ -771,8 +771,8 @@ public void testCopyFileBare() throws Exception {
 			assertFalse("The foo/Hello file should be skipped",
 					foohello.exists());
 			// The content of Hello file should be expected
-			try (BufferedReader reader = new BufferedReader(
-					new FileReader(hello))) {
+			try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
+					UTF_8)) {
 				String content = reader.readLine();
 				assertEquals("The Hello file should have expected content",
 						"branch world", content);
@@ -829,8 +829,8 @@ public void testReplaceManifestBare() throws Exception {
 		// The .gitmodules file should have 'submodule "bar"' and shouldn't
 		// have
 		// 'submodule "foo"' lines.
-		try (BufferedReader reader = new BufferedReader(
-				new FileReader(dotmodules))) {
+		try (BufferedReader reader = Files
+				.newBufferedReader(dotmodules.toPath(), UTF_8)) {
 			boolean foo = false;
 			boolean bar = false;
 			while (true) {
@@ -879,8 +879,8 @@ public void testRemoveOverlappingBare() throws Exception {
 		}
 
 		// Check .gitmodules file
-		try (BufferedReader reader = new BufferedReader(
-				new FileReader(dotmodules))) {
+		try (BufferedReader reader = Files
+				.newBufferedReader(dotmodules.toPath(), UTF_8)) {
 			boolean foo = false;
 			boolean foobar = false;
 			boolean a = false;
@@ -935,8 +935,8 @@ public void testIncludeTag() throws Exception {
 			.call();
 		File hello = new File(localDb.getWorkTree(), "foo/hello.txt");
 		assertTrue("submodule should be checked out", hello.exists());
-		try (BufferedReader reader = new BufferedReader(
-				new FileReader(hello))) {
+		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
+				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("submodule content should be as expected",
 					"master world", content);
@@ -1074,8 +1074,9 @@ public void testRecordSubmoduleLabels() throws Exception {
 					".gitattributes");
 			assertTrue("The .gitattributes file should exist",
 					gitattributes.exists());
-			try (BufferedReader reader = new BufferedReader(
-					new FileReader(gitattributes));) {
+			try (BufferedReader reader = Files
+					.newBufferedReader(gitattributes.toPath(),
+					UTF_8)) {
 				String content = reader.readLine();
 				assertEquals(".gitattributes content should be as expected",
 						"/test a1 a2", content);
@@ -1142,8 +1143,8 @@ public void testRemoteRevision() throws Exception {
 			.setURI(rootUri)
 			.call();
 		File hello = new File(db.getWorkTree(), "foo/hello.txt");
-		try (BufferedReader reader = new BufferedReader(
-				new FileReader(hello))) {
+		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
+				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("submodule content should be as expected",
 					"branch world", content);
@@ -1169,8 +1170,8 @@ public void testDefaultRemoteRevision() throws Exception {
 			.setURI(rootUri)
 			.call();
 		File hello = new File(db.getWorkTree(), "foo/hello.txt");
-		try (BufferedReader reader = new BufferedReader(
-				new FileReader(hello))) {
+		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
+				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("submodule content should be as expected",
 					"branch world", content);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsFsckTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsFsckTest.java
index 804d744..c181125 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsFsckTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsFsckTest.java
@@ -266,4 +266,59 @@ public void testNonCommitHead() throws Exception {
 				"refs/heads/master");
 	}
 
+	private ObjectId insertGitModules(String contents) throws IOException {
+		ObjectId blobId = ins.insert(Constants.OBJ_BLOB,
+				Constants.encode(contents));
+
+		byte[] blobIdBytes = new byte[OBJECT_ID_LENGTH];
+		blobId.copyRawTo(blobIdBytes, 0);
+		byte[] data = concat(encodeASCII("100644 .gitmodules\0"), blobIdBytes);
+		ins.insert(Constants.OBJ_TREE, data);
+		ins.flush();
+
+		return blobId;
+	}
+
+	@Test
+	public void testInvalidGitModules() throws Exception {
+		String fakeGitmodules = new StringBuilder()
+				.append("[submodule \"test\"]\n")
+				.append("    path = xlib\n")
+				.append("    url = https://example.com/repo/xlib.git\n\n")
+				.append("[submodule \"test2\"]\n")
+				.append("    path = zlib\n")
+				.append("    url = -upayload.sh\n")
+				.toString();
+
+		ObjectId blobId = insertGitModules(fakeGitmodules);
+
+		DfsFsck fsck = new DfsFsck(repo);
+		FsckError errors = fsck.check(null);
+		assertEquals(errors.getCorruptObjects().size(), 1);
+
+		CorruptObject error = errors.getCorruptObjects().iterator().next();
+		assertEquals(error.getId(), blobId);
+		assertEquals(error.getType(), Constants.OBJ_BLOB);
+		assertEquals(error.getErrorType(), ErrorType.GITMODULES_URL);
+	}
+
+
+	@Test
+	public void testValidGitModules() throws Exception {
+		String fakeGitmodules = new StringBuilder()
+				.append("[submodule \"test\"]\n")
+				.append("    path = xlib\n")
+				.append("    url = https://example.com/repo/xlib.git\n\n")
+				.append("[submodule \"test2\"]\n")
+				.append("    path = zlib\n")
+				.append("    url = ok/path\n")
+				.toString();
+
+		insertGitModules(fakeGitmodules);
+
+		DfsFsck fsck = new DfsFsck(repo);
+		FsckError errors = fsck.check(null);
+		assertEquals(errors.getCorruptObjects().size(), 0);
+	}
+
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileRepositoryBuilderTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileRepositoryBuilderTest.java
index deffa04..f6cb558 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileRepositoryBuilderTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileRepositoryBuilderTest.java
@@ -43,14 +43,16 @@
 
 package org.eclipse.jgit.internal.storage.file;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
+import java.io.BufferedWriter;
 import java.io.File;
-import java.io.FileWriter;
 import java.io.IOException;
+import java.nio.file.Files;
 
 import org.eclipse.jgit.junit.LocalDiskRepositoryTestCase;
 import org.eclipse.jgit.lib.ConfigConstants;
@@ -120,18 +122,19 @@ public void absoluteGitDirRef() throws Exception {
 		Repository repo1 = createWorkRepository();
 		File dir = createTempDirectory("dir");
 		File dotGit = new File(dir, Constants.DOT_GIT);
-		try (FileWriter writer = new FileWriter(dotGit)) {
-			writer.append("gitdir: " + repo1.getDirectory().getAbsolutePath()).close();
-			FileRepositoryBuilder builder = new FileRepositoryBuilder();
-
-			builder.setWorkTree(dir);
-			builder.setMustExist(true);
-			Repository repo2 = builder.build();
-
-			assertEquals(repo1.getDirectory().getAbsolutePath(), repo2
-					.getDirectory().getAbsolutePath());
-			assertEquals(dir, repo2.getWorkTree());
+		try (BufferedWriter writer = Files.newBufferedWriter(dotGit.toPath(),
+				UTF_8)) {
+			writer.append("gitdir: " + repo1.getDirectory().getAbsolutePath());
 		}
+		FileRepositoryBuilder builder = new FileRepositoryBuilder();
+
+		builder.setWorkTree(dir);
+		builder.setMustExist(true);
+		Repository repo2 = builder.build();
+
+		assertEquals(repo1.getDirectory().getAbsolutePath(),
+				repo2.getDirectory().getAbsolutePath());
+		assertEquals(dir, repo2.getWorkTree());
 	}
 
 	@Test
@@ -140,20 +143,20 @@ public void relativeGitDirRef() throws Exception {
 		File dir = new File(repo1.getWorkTree(), "dir");
 		assertTrue(dir.mkdir());
 		File dotGit = new File(dir, Constants.DOT_GIT);
-		try (FileWriter writer = new FileWriter(dotGit)) {
-			writer.append("gitdir: ../" + Constants.DOT_GIT).close();
-
-			FileRepositoryBuilder builder = new FileRepositoryBuilder();
-			builder.setWorkTree(dir);
-			builder.setMustExist(true);
-			Repository repo2 = builder.build();
-
-			// The tmp directory may be a symlink so the actual path
-			// may not
-			assertEquals(repo1.getDirectory().getCanonicalPath(), repo2
-					.getDirectory().getCanonicalPath());
-			assertEquals(dir, repo2.getWorkTree());
+		try (BufferedWriter writer = Files.newBufferedWriter(dotGit.toPath(),
+				UTF_8)) {
+			writer.append("gitdir: ../" + Constants.DOT_GIT);
 		}
+		FileRepositoryBuilder builder = new FileRepositoryBuilder();
+		builder.setWorkTree(dir);
+		builder.setMustExist(true);
+		Repository repo2 = builder.build();
+
+		// The tmp directory may be a symlink so the actual path
+		// may not
+		assertEquals(repo1.getDirectory().getCanonicalPath(),
+				repo2.getDirectory().getCanonicalPath());
+		assertEquals(dir, repo2.getWorkTree());
 	}
 
 	@Test
@@ -161,22 +164,23 @@ public void scanWithGitDirRef() throws Exception {
 		Repository repo1 = createWorkRepository();
 		File dir = createTempDirectory("dir");
 		File dotGit = new File(dir, Constants.DOT_GIT);
-		try (FileWriter writer = new FileWriter(dotGit)) {
+		try (BufferedWriter writer = Files.newBufferedWriter(dotGit.toPath(),
+				UTF_8)) {
 			writer.append(
-					"gitdir: " + repo1.getDirectory().getAbsolutePath()).close();
-			FileRepositoryBuilder builder = new FileRepositoryBuilder();
-
-			builder.setWorkTree(dir);
-			builder.findGitDir(dir);
-			assertEquals(repo1.getDirectory().getAbsolutePath(), builder
-					.getGitDir().getAbsolutePath());
-			builder.setMustExist(true);
-			Repository repo2 = builder.build();
-
-			// The tmp directory may be a symlink
-			assertEquals(repo1.getDirectory().getCanonicalPath(), repo2
-					.getDirectory().getCanonicalPath());
-			assertEquals(dir, repo2.getWorkTree());
+					"gitdir: " + repo1.getDirectory().getAbsolutePath());
 		}
+		FileRepositoryBuilder builder = new FileRepositoryBuilder();
+
+		builder.setWorkTree(dir);
+		builder.findGitDir(dir);
+		assertEquals(repo1.getDirectory().getAbsolutePath(),
+				builder.getGitDir().getAbsolutePath());
+		builder.setMustExist(true);
+		Repository repo2 = builder.build();
+
+		// The tmp directory may be a symlink
+		assertEquals(repo1.getDirectory().getCanonicalPath(),
+				repo2.getDirectory().getCanonicalPath());
+		assertEquals(dir, repo2.getWorkTree());
 	}
 }
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 cbb73bb..3ca689a 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
@@ -42,6 +42,7 @@
 
 package org.eclipse.jgit.internal.storage.file;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 
@@ -189,7 +190,8 @@ public void testShallowFile()
 
 		String commit = "d3148f9410b071edd4a4c85d2a43d1fa2574b0d2";
 		try (PrintWriter writer = new PrintWriter(
-				new File(repository.getDirectory(), Constants.SHALLOW))) {
+				new File(repository.getDirectory(), Constants.SHALLOW),
+				UTF_8.name())) {
 			writer.println(commit);
 		}
 		Set<ObjectId> shallowCommits = dir.getShallowCommits();
@@ -205,7 +207,8 @@ public void testShallowFileCorrupt()
 
 		String commit = "X3148f9410b071edd4a4c85d2a43d1fa2574b0d2";
 		try (PrintWriter writer = new PrintWriter(
-				new File(repository.getDirectory(), Constants.SHALLOW))) {
+				new File(repository.getDirectory(), Constants.SHALLOW),
+				UTF_8.name())) {
 			writer.println(commit);
 		}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogReaderTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogReaderTest.java
index dc05eea..acdaf3a 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogReaderTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogReaderTest.java
@@ -44,6 +44,7 @@
 
 package org.eclipse.jgit.internal.storage.file;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
@@ -67,31 +68,31 @@
 public class ReflogReaderTest extends SampleDataRepositoryTestCase {
 
 	static byte[] oneLine = "da85355dfc525c9f6f3927b876f379f46ccf826e 3e7549db262d1e836d9bf0af7e22355468f1717c A O Thor Too <authortoo@wri.tr> 1243028200 +0200\tcommit: Add a toString for debugging to RemoteRefUpdate\n"
-			.getBytes();
+			.getBytes(UTF_8);
 
 	static byte[] twoLine = ("0000000000000000000000000000000000000000 c6734895958052a9dbc396cff4459dc1a25029ab A U Thor <thor@committer.au> 1243028201 -0100\tbranch: Created from rr/renamebranchv4\n"
 			+ "c6734895958052a9dbc396cff4459dc1a25029ab 54794942a18a237c57a80719afed44bb78172b10 Same A U Thor <same.author@example.com> 1243028202 +0100\trebase finished: refs/heads/rr/renamebranch5 onto c6e3b9fe2da0293f11eae202ec35fb343191a82d\n")
-			.getBytes();
+					.getBytes(UTF_8);
 
 	static byte[] twoLineWithAppendInProgress = ("0000000000000000000000000000000000000000 c6734895958052a9dbc396cff4459dc1a25029ab A U Thor <thor@committer.au> 1243028201 -0100\tbranch: Created from rr/renamebranchv4\n"
 			+ "c6734895958052a9dbc396cff4459dc1a25029ab 54794942a18a237c57a80719afed44bb78172b10 Same A U Thor <same.author@example.com> 1243028202 +0100\trebase finished: refs/heads/rr/renamebranch5 onto c6e3b9fe2da0293f11eae202ec35fb343191a82d\n"
 			+ "54794942a18a237c57a80719afed44bb78172b10 ")
-			.getBytes();
+					.getBytes(UTF_8);
 
 	static byte[] aLine = "1111111111111111111111111111111111111111 3e7549db262d1e836d9bf0af7e22355468f1717c A U Thor <thor@committer.au> 1243028201 -0100\tbranch: change to a\n"
-			.getBytes();
+			.getBytes(UTF_8);
 
 	static byte[] masterLine = "2222222222222222222222222222222222222222 3e7549db262d1e836d9bf0af7e22355468f1717c A U Thor <thor@committer.au> 1243028201 -0100\tbranch: change to master\n"
-			.getBytes();
+			.getBytes(UTF_8);
 
 	static byte[] headLine = "3333333333333333333333333333333333333333 3e7549db262d1e836d9bf0af7e22355468f1717c A U Thor <thor@committer.au> 1243028201 -0100\tbranch: change to HEAD\n"
-			.getBytes();
+			.getBytes(UTF_8);
 
 	static byte[] oneLineWithoutComment = "da85355dfc525c9f6f3927b876f379f46ccf826e 3e7549db262d1e836d9bf0af7e22355468f1717c A O Thor Too <authortoo@wri.tr> 1243028200 +0200\n"
-			.getBytes();
+			.getBytes(UTF_8);
 
 	static byte[] switchBranch = "0d43a6890a19fd657faad1c4cfbe3cb1b47851c3 4809df9c0d8bce5b00955563f77c5a9f25aa0d12 A O Thor Too <authortoo@wri.tr> 1315088009 +0200\tcheckout: moving from new/work to master\n"
-			.getBytes();
+			.getBytes(UTF_8);
 
 	@Test
 	public void testReadOneLine() throws Exception {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogWriterTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogWriterTest.java
index 1d188c3..a84be7e 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogWriterTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogWriterTest.java
@@ -42,6 +42,7 @@
  *******************************************************************************/
 package org.eclipse.jgit.internal.storage.file;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 
 import java.io.File;
@@ -73,9 +74,9 @@ public void shouldFilterLineFeedFromMessage() throws Exception {
 		writer.log("refs/heads/master", oldId, newId, ident,
 				"stash: Add\nmessage\r\nwith line feeds");
 
-		byte[] buffer = new byte[oneLine.getBytes().length];
+		byte[] buffer = new byte[oneLine.getBytes(UTF_8).length];
 		readReflog(buffer);
-		assertEquals(oneLine, new String(buffer));
+		assertEquals(oneLine, new String(buffer, UTF_8));
 	}
 
 	private void readReflog(byte[] buffer)
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 0207322..96caa01 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
@@ -333,9 +333,9 @@ public void test002_WriteEmptyTree2() throws IOException {
 	public void test002_CreateBadTree() throws Exception {
 		// We won't create a tree entry with an empty filename
 		//
+		final TreeFormatter formatter = new TreeFormatter();
 		expectedException.expect(IllegalArgumentException.class);
 		expectedException.expectMessage(JGitText.get().invalidTreeZeroLengthName);
-		final TreeFormatter formatter = new TreeFormatter();
 		formatter.append("", FileMode.TREE,
 				ObjectId.fromString("4b825dc642cb6eb9a060e54bf8d69288fbee4904"));
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/WindowCacheGetTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/WindowCacheGetTest.java
index 01426ee..9063b65 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/WindowCacheGetTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/WindowCacheGetTest.java
@@ -141,7 +141,7 @@ private void doCacheTests() throws IOException {
 		}
 	}
 
-	private class TestObject {
+	private static class TestObject {
 		ObjectId id;
 
 		int type;
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/transport/parser/FirstWantTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/transport/parser/FirstWantTest.java
new file mode 100644
index 0000000..627079e
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/transport/parser/FirstWantTest.java
@@ -0,0 +1,121 @@
+/*
+ * 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 org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.eclipse.jgit.errors.PackProtocolException;
+import org.junit.Test;
+
+public class FirstWantTest {
+
+	@Test
+	public void testFirstWantWithOptions() throws PackProtocolException {
+		String line = "want b9d4d1eb2f93058814480eae9e1b67550f46ee38 "
+				+ "no-progress include-tag ofs-delta agent=JGit/unknown";
+
+		FirstWant r = FirstWant.fromLine(line);
+		assertEquals("want b9d4d1eb2f93058814480eae9e1b67550f46ee38",
+				r.getLine());
+		Set<String> capabilities = r.getCapabilities();
+		Set<String> expectedCapabilities = new HashSet<>(
+				Arrays.asList("no-progress", "include-tag", "ofs-delta",
+						"agent=JGit/unknown"));
+		assertEquals(expectedCapabilities, capabilities);
+	}
+
+	@Test
+	public void testFirstWantWithoutOptions() throws PackProtocolException {
+		String line = "want b9d4d1eb2f93058814480eae9e1b67550f46ee38";
+
+		FirstWant r = FirstWant.fromLine(line);
+		assertEquals("want b9d4d1eb2f93058814480eae9e1b67550f46ee38",
+				r.getLine());
+		assertTrue(r.getCapabilities().isEmpty());
+	}
+
+	private String makeFirstWantLine(String capability) {
+		return String.format("want b9d4d1eb2f93058814480eae9e1b67550f46ee38 %s", capability);
+	}
+
+	@Test
+	public void testFirstWantNoWhitespace() {
+		try {
+			FirstWant.fromLine(
+					"want b9d4d1eb2f93058814480eae9e1b67550f400000capability");
+			fail("Accepting first want line without SP between oid and first capability");
+		} catch (PackProtocolException e) {
+			// pass
+		}
+	}
+
+	@Test
+	public void testFirstWantOnlyWhitespace() throws PackProtocolException {
+		FirstWant r = FirstWant
+				.fromLine("want b9d4d1eb2f93058814480eae9e1b67550f46ee38 ");
+		assertEquals("want b9d4d1eb2f93058814480eae9e1b67550f46ee38",
+				r.getLine());
+	}
+
+	@Test
+	public void testFirstWantValidCapabilityNames()
+			throws PackProtocolException {
+		List<String> validNames = Arrays.asList(
+				"c", "cap", "C", "CAP", "1", "1cap", "cap-64k_test",
+				"-", "-cap",
+				"_", "_cap", "agent=pack.age/Version");
+
+		for (String capability: validNames) {
+			FirstWant r = FirstWant.fromLine(makeFirstWantLine(capability));
+			assertEquals(r.getCapabilities().size(), 1);
+			assertTrue(r.getCapabilities().contains(capability));
+		}
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java
index c4c4da8..21d8d66 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java
@@ -48,6 +48,7 @@
 
 package org.eclipse.jgit.lib;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static java.util.concurrent.TimeUnit.DAYS;
 import static java.util.concurrent.TimeUnit.HOURS;
 import static java.util.concurrent.TimeUnit.MILLISECONDS;
@@ -66,11 +67,15 @@
 import java.io.IOException;
 import java.nio.file.Files;
 import java.text.MessageFormat;
+import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.Iterator;
 import java.util.LinkedList;
+import java.util.List;
 import java.util.Set;
 import java.util.concurrent.TimeUnit;
+import java.util.function.Consumer;
 
 import org.eclipse.jgit.api.MergeCommand.FastForwardMode;
 import org.eclipse.jgit.errors.ConfigInvalidException;
@@ -78,6 +83,7 @@
 import org.eclipse.jgit.junit.MockSystemReader;
 import org.eclipse.jgit.merge.MergeConfig;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
+import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.SystemReader;
 import org.junit.After;
@@ -94,6 +100,12 @@ public class ConfigTest {
 	// A non-ASCII whitespace character: U+2002 EN QUAD.
 	private static final char WS = '\u2002';
 
+	private static final String REFS_ORIGIN = "+refs/heads/*:refs/remotes/origin/*";
+
+	private static final String REFS_UPSTREAM = "+refs/heads/*:refs/remotes/upstream/*";
+
+	private static final String REFS_BACKUP = "+refs/heads/*:refs/remotes/backup/*";
+
 	@Rule
 	public ExpectedException expectedEx = ExpectedException.none();
 
@@ -690,11 +702,7 @@ public void testExplicitlySetEmptyString() throws Exception {
 
 		assertEquals("", c.getString("a", null, "y"));
 		assertArrayEquals(new String[]{""}, c.getStringList("a", null, "y"));
-		try {
-			c.getInt("a", null, "y", 1);
-		} catch (IllegalArgumentException e) {
-			assertEquals("Invalid integer value: a.y=", e.getMessage());
-		}
+		assertEquals(1, c.getInt("a", null, "y", 1));
 
 		assertNull(c.getString("a", null, "z"));
 		assertArrayEquals(new String[]{}, c.getStringList("a", null, "z"));
@@ -711,11 +719,7 @@ public void testParsedEmptyString() throws Exception {
 
 		assertNull(c.getString("a", null, "y"));
 		assertArrayEquals(new String[]{null}, c.getStringList("a", null, "y"));
-		try {
-			c.getInt("a", null, "y", 1);
-		} catch (IllegalArgumentException e) {
-			assertEquals("Invalid integer value: a.y=", e.getMessage());
-		}
+		assertEquals(1, c.getInt("a", null, "y", 1));
 
 		assertNull(c.getString("a", null, "z"));
 		assertArrayEquals(new String[]{}, c.getStringList("a", null, "z"));
@@ -801,11 +805,9 @@ public void testIncludeValuePathRelative() throws ConfigInvalidException {
 	public void testIncludeTooManyRecursions() throws IOException {
 		File config = tmp.newFile("config");
 		String include = "[include]\npath=" + pathToString(config) + "\n";
-		Files.write(config.toPath(), include.getBytes());
-		FileBasedConfig fbConfig = new FileBasedConfig(null, config,
-				FS.DETECTED);
+		Files.write(config.toPath(), include.getBytes(UTF_8));
 		try {
-			fbConfig.load();
+			loadConfig(config);
 			fail();
 		} catch (ConfigInvalidException cie) {
 			for (Throwable t = cie; t != null; t = t.getCause()) {
@@ -824,7 +826,7 @@ public void testIncludeIsNoop() throws IOException, ConfigInvalidException {
 		File config = tmp.newFile("config");
 
 		String fooBar = "[foo]\nbar=true\n";
-		Files.write(config.toPath(), fooBar.getBytes());
+		Files.write(config.toPath(), fooBar.getBytes(UTF_8));
 
 		Config parsed = parse("[include]\npath=" + pathToString(config) + "\n");
 		assertFalse(parsed.getBoolean("foo", "bar", false));
@@ -835,15 +837,13 @@ public void testIncludeCaseInsensitiveSection()
 			throws IOException, ConfigInvalidException {
 		File included = tmp.newFile("included");
 		String content = "[foo]\nbar=true\n";
-		Files.write(included.toPath(), content.getBytes());
+		Files.write(included.toPath(), content.getBytes(UTF_8));
 
 		File config = tmp.newFile("config");
 		content = "[Include]\npath=" + pathToString(included) + "\n";
-		Files.write(config.toPath(), content.getBytes());
+		Files.write(config.toPath(), content.getBytes(UTF_8));
 
-		FileBasedConfig fbConfig = new FileBasedConfig(null, config,
-				FS.DETECTED);
-		fbConfig.load();
+		FileBasedConfig fbConfig = loadConfig(config);
 		assertTrue(fbConfig.getBoolean("foo", "bar", false));
 	}
 
@@ -852,15 +852,13 @@ public void testIncludeCaseInsensitiveKey()
 			throws IOException, ConfigInvalidException {
 		File included = tmp.newFile("included");
 		String content = "[foo]\nbar=true\n";
-		Files.write(included.toPath(), content.getBytes());
+		Files.write(included.toPath(), content.getBytes(UTF_8));
 
 		File config = tmp.newFile("config");
 		content = "[include]\nPath=" + pathToString(included) + "\n";
-		Files.write(config.toPath(), content.getBytes());
+		Files.write(config.toPath(), content.getBytes(UTF_8));
 
-		FileBasedConfig fbConfig = new FileBasedConfig(null, config,
-				FS.DETECTED);
-		fbConfig.load();
+		FileBasedConfig fbConfig = loadConfig(config);
 		assertTrue(fbConfig.getBoolean("foo", "bar", false));
 	}
 
@@ -881,15 +879,13 @@ public void testIncludeExceptionContainsFile() throws IOException {
 		File included = tmp.newFile("included");
 		String includedPath = pathToString(included);
 		String content = "[include]\npath=\n";
-		Files.write(included.toPath(), content.getBytes());
+		Files.write(included.toPath(), content.getBytes(UTF_8));
 
 		File config = tmp.newFile("config");
 		String include = "[include]\npath=" + includedPath + "\n";
-		Files.write(config.toPath(), include.getBytes());
-		FileBasedConfig fbConfig = new FileBasedConfig(null, config,
-				FS.DETECTED);
+		Files.write(config.toPath(), include.getBytes(UTF_8));
 		try {
-			fbConfig.load();
+			loadConfig(config);
 			fail("Expected ConfigInvalidException");
 		} catch (ConfigInvalidException e) {
 			// Check that there is some exception in the chain that contains
@@ -904,6 +900,306 @@ public void testIncludeExceptionContainsFile() throws IOException {
 		}
 	}
 
+	@Test
+	public void testIncludeSetValueMustNotTouchIncludedLines1()
+			throws IOException, ConfigInvalidException {
+		File includedFile = createAllTypesIncludedContent();
+
+		File configFile = tmp.newFile("config");
+		String content = createAllTypesSampleContent("Alice Parker", false, 11,
+				21, 31, CoreConfig.AutoCRLF.FALSE,
+				"+refs/heads/*:refs/remotes/origin/*") + "\n[include]\npath="
+				+ pathToString(includedFile);
+		Files.write(configFile.toPath(), content.getBytes(UTF_8));
+
+		FileBasedConfig fbConfig = loadConfig(configFile);
+		assertValuesAsIncluded(fbConfig, REFS_ORIGIN, REFS_UPSTREAM);
+		assertSections(fbConfig, "user", "core", "remote", "include");
+
+		setAllValuesNew(fbConfig);
+		assertValuesAsIsSaveLoad(fbConfig, config -> {
+			assertValuesAsIncluded(config, REFS_BACKUP, REFS_UPSTREAM);
+			assertSections(fbConfig, "user", "core", "remote", "include");
+		});
+	}
+
+	@Test
+	public void testIncludeSetValueMustNotTouchIncludedLines2()
+			throws IOException, ConfigInvalidException {
+		File includedFile = createAllTypesIncludedContent();
+
+		File configFile = tmp.newFile("config");
+		String content = "[include]\npath=" + pathToString(includedFile) + "\n"
+				+ createAllTypesSampleContent("Alice Parker", false, 11, 21, 31,
+						CoreConfig.AutoCRLF.FALSE,
+						"+refs/heads/*:refs/remotes/origin/*");
+		Files.write(configFile.toPath(), content.getBytes(UTF_8));
+
+		FileBasedConfig fbConfig = loadConfig(configFile);
+		assertValuesAsConfig(fbConfig, REFS_UPSTREAM, REFS_ORIGIN);
+		assertSections(fbConfig, "include", "user", "core", "remote");
+
+		setAllValuesNew(fbConfig);
+		assertValuesAsIsSaveLoad(fbConfig, config -> {
+			assertValuesAsNew(config, REFS_UPSTREAM, REFS_BACKUP);
+			assertSections(fbConfig, "include", "user", "core", "remote");
+		});
+	}
+
+	@Test
+	public void testIncludeSetValueOnFileWithJustContainsInclude()
+			throws IOException, ConfigInvalidException {
+		File includedFile = createAllTypesIncludedContent();
+
+		File configFile = tmp.newFile("config");
+		String content = "[include]\npath=" + pathToString(includedFile);
+		Files.write(configFile.toPath(), content.getBytes(UTF_8));
+
+		FileBasedConfig fbConfig = loadConfig(configFile);
+		assertValuesAsIncluded(fbConfig, REFS_UPSTREAM);
+		assertSections(fbConfig, "include", "user", "core", "remote");
+
+		setAllValuesNew(fbConfig);
+		assertValuesAsIsSaveLoad(fbConfig, config -> {
+			assertValuesAsNew(config, REFS_UPSTREAM, REFS_BACKUP);
+			assertSections(fbConfig, "include", "user", "core", "remote");
+		});
+	}
+
+	@Test
+	public void testIncludeSetValueOnFileWithJustEmptySection1()
+			throws IOException, ConfigInvalidException {
+		File includedFile = createAllTypesIncludedContent();
+
+		File configFile = tmp.newFile("config");
+		String content = "[user]\n[include]\npath="
+				+ pathToString(includedFile);
+		Files.write(configFile.toPath(), content.getBytes(UTF_8));
+
+		FileBasedConfig fbConfig = loadConfig(configFile);
+		assertValuesAsIncluded(fbConfig, REFS_UPSTREAM);
+		assertSections(fbConfig, "user", "include", "core", "remote");
+
+		setAllValuesNew(fbConfig);
+		assertValuesAsIsSaveLoad(fbConfig, config -> {
+			assertValuesAsNewWithName(config, "Alice Muller", REFS_UPSTREAM,
+					REFS_BACKUP);
+			assertSections(fbConfig, "user", "include", "core", "remote");
+		});
+	}
+
+	@Test
+	public void testIncludeSetValueOnFileWithJustEmptySection2()
+			throws IOException, ConfigInvalidException {
+		File includedFile = createAllTypesIncludedContent();
+
+		File configFile = tmp.newFile("config");
+		String content = "[include]\npath=" + pathToString(includedFile)
+				+ "\n[user]";
+		Files.write(configFile.toPath(), content.getBytes(UTF_8));
+
+		FileBasedConfig fbConfig = loadConfig(configFile);
+		assertValuesAsIncluded(fbConfig, REFS_UPSTREAM);
+		assertSections(fbConfig, "include", "user", "core", "remote");
+
+		setAllValuesNew(fbConfig);
+		assertValuesAsIsSaveLoad(fbConfig, config -> {
+			assertValuesAsNew(config, REFS_UPSTREAM, REFS_BACKUP);
+			assertSections(fbConfig, "include", "user", "core", "remote");
+		});
+	}
+
+	@Test
+	public void testIncludeSetValueOnFileWithJustExistingSection1()
+			throws IOException, ConfigInvalidException {
+		File includedFile = createAllTypesIncludedContent();
+
+		File configFile = tmp.newFile("config");
+		String content = "[user]\nemail=alice@home\n[include]\npath="
+				+ pathToString(includedFile);
+		Files.write(configFile.toPath(), content.getBytes(UTF_8));
+
+		FileBasedConfig fbConfig = loadConfig(configFile);
+		assertValuesAsIncluded(fbConfig, REFS_UPSTREAM);
+		assertSections(fbConfig, "user", "include", "core", "remote");
+
+		setAllValuesNew(fbConfig);
+		assertValuesAsIsSaveLoad(fbConfig, config -> {
+			assertValuesAsNewWithName(config, "Alice Muller", REFS_UPSTREAM,
+					REFS_BACKUP);
+			assertSections(fbConfig, "user", "include", "core", "remote");
+		});
+	}
+
+	@Test
+	public void testIncludeSetValueOnFileWithJustExistingSection2()
+			throws IOException, ConfigInvalidException {
+		File includedFile = createAllTypesIncludedContent();
+
+		File configFile = tmp.newFile("config");
+		String content = "[include]\npath=" + pathToString(includedFile)
+				+ "\n[user]\nemail=alice@home\n";
+		Files.write(configFile.toPath(), content.getBytes(UTF_8));
+
+		FileBasedConfig fbConfig = loadConfig(configFile);
+		assertValuesAsIncluded(fbConfig, REFS_UPSTREAM);
+		assertSections(fbConfig, "include", "user", "core", "remote");
+
+		setAllValuesNew(fbConfig);
+		assertValuesAsIsSaveLoad(fbConfig, config -> {
+			assertValuesAsNew(config, REFS_UPSTREAM, REFS_BACKUP);
+			assertSections(fbConfig, "include", "user", "core", "remote");
+		});
+	}
+
+	@Test
+	public void testIncludeUnsetSectionMustNotTouchIncludedLines()
+			throws IOException, ConfigInvalidException {
+		File includedFile = tmp.newFile("included");
+		RefSpec includedRefSpec = new RefSpec(REFS_UPSTREAM);
+		String includedContent = "[remote \"origin\"]\n" + "fetch="
+				+ includedRefSpec;
+		Files.write(includedFile.toPath(), includedContent.getBytes(UTF_8));
+
+		File configFile = tmp.newFile("config");
+		RefSpec refSpec = new RefSpec(REFS_ORIGIN);
+		String content = "[include]\npath=" + pathToString(includedFile) + "\n"
+				+ "[remote \"origin\"]\n" + "fetch=" + refSpec;
+		Files.write(configFile.toPath(), content.getBytes(UTF_8));
+
+		FileBasedConfig fbConfig = loadConfig(configFile);
+
+		Consumer<FileBasedConfig> assertion = config -> {
+			assertEquals(Arrays.asList(includedRefSpec, refSpec),
+					config.getRefSpecs("remote", "origin", "fetch"));
+		};
+		assertion.accept(fbConfig);
+
+		fbConfig.unsetSection("remote", "origin");
+		assertValuesAsIsSaveLoad(fbConfig, config -> {
+			assertEquals(Collections.singletonList(includedRefSpec),
+					config.getRefSpecs("remote", "origin", "fetch"));
+		});
+	}
+
+	private File createAllTypesIncludedContent() throws IOException {
+		File includedFile = tmp.newFile("included");
+		String includedContent = createAllTypesSampleContent("Alice Muller",
+				true, 10, 20, 30, CoreConfig.AutoCRLF.TRUE,
+				"+refs/heads/*:refs/remotes/upstream/*");
+		Files.write(includedFile.toPath(), includedContent.getBytes(UTF_8));
+		return includedFile;
+	}
+
+	private static void assertValuesAsIsSaveLoad(FileBasedConfig fbConfig,
+			Consumer<FileBasedConfig> assertion)
+			throws IOException, ConfigInvalidException {
+		assertion.accept(fbConfig);
+
+		fbConfig.save();
+		assertion.accept(fbConfig);
+
+		fbConfig = loadConfig(fbConfig.getFile());
+		assertion.accept(fbConfig);
+	}
+
+	private static void setAllValuesNew(Config config) {
+		config.setString("user", null, "name", "Alice Bauer");
+		config.setBoolean("core", null, "fileMode", false);
+		config.setInt("core", null, "deltaBaseCacheLimit", 12);
+		config.setLong("core", null, "packedGitLimit", 22);
+		config.setLong("core", null, "repositoryCacheExpireAfter", 32);
+		config.setEnum("core", null, "autocrlf", CoreConfig.AutoCRLF.FALSE);
+		config.setString("remote", "origin", "fetch",
+				"+refs/heads/*:refs/remotes/backup/*");
+	}
+
+	private static void assertValuesAsIncluded(Config config, String... refs) {
+		assertAllTypesSampleContent("Alice Muller", true, 10, 20, 30,
+				CoreConfig.AutoCRLF.TRUE, config, refs);
+	}
+
+	private static void assertValuesAsConfig(Config config, String... refs) {
+		assertAllTypesSampleContent("Alice Parker", false, 11, 21, 31,
+				CoreConfig.AutoCRLF.FALSE, config, refs);
+	}
+
+	private static void assertValuesAsNew(Config config, String... refs) {
+		assertValuesAsNewWithName(config, "Alice Bauer", refs);
+	}
+
+	private static void assertValuesAsNewWithName(Config config, String name,
+			String... refs) {
+		assertAllTypesSampleContent(name, false, 12, 22, 32,
+				CoreConfig.AutoCRLF.FALSE, config, refs);
+	}
+
+	private static void assertSections(Config config, String... sections) {
+		assertEquals(Arrays.asList(sections),
+				new ArrayList<>(config.getSections()));
+	}
+
+	private static String createAllTypesSampleContent(String name,
+			boolean fileMode, int deltaBaseCacheLimit, long packedGitLimit,
+			long repositoryCacheExpireAfter, CoreConfig.AutoCRLF autoCRLF,
+			String fetchRefSpec) {
+		final StringBuilder builder = new StringBuilder();
+		builder.append("[user]\n");
+		builder.append("name=");
+		builder.append(name);
+		builder.append("\n");
+
+		builder.append("[core]\n");
+		builder.append("fileMode=");
+		builder.append(fileMode);
+		builder.append("\n");
+
+		builder.append("deltaBaseCacheLimit=");
+		builder.append(deltaBaseCacheLimit);
+		builder.append("\n");
+
+		builder.append("packedGitLimit=");
+		builder.append(packedGitLimit);
+		builder.append("\n");
+
+		builder.append("repositoryCacheExpireAfter=");
+		builder.append(repositoryCacheExpireAfter);
+		builder.append("\n");
+
+		builder.append("autocrlf=");
+		builder.append(autoCRLF.name());
+		builder.append("\n");
+
+		builder.append("[remote \"origin\"]\n");
+		builder.append("fetch=");
+		builder.append(fetchRefSpec);
+		builder.append("\n");
+		return builder.toString();
+	}
+
+	private static void assertAllTypesSampleContent(String name,
+			boolean fileMode, int deltaBaseCacheLimit, long packedGitLimit,
+			long repositoryCacheExpireAfter, CoreConfig.AutoCRLF autoCRLF,
+			Config config, String... fetchRefSpecs) {
+		assertEquals(name, config.getString("user", null, "name"));
+		assertEquals(fileMode,
+				config.getBoolean("core", "fileMode", !fileMode));
+		assertEquals(deltaBaseCacheLimit,
+				config.getInt("core", "deltaBaseCacheLimit", -1));
+		assertEquals(packedGitLimit,
+				config.getLong("core", "packedGitLimit", -1));
+		assertEquals(repositoryCacheExpireAfter, config.getTimeUnit("core",
+				null, "repositoryCacheExpireAfter", -1, MILLISECONDS));
+		assertEquals(autoCRLF, config.getEnum("core", null, "autocrlf",
+				CoreConfig.AutoCRLF.INPUT));
+		final List<RefSpec> refspecs = new ArrayList<>();
+		for (String fetchRefSpec : fetchRefSpecs) {
+			refspecs.add(new RefSpec(fetchRefSpec));
+		}
+
+		assertEquals(refspecs, config.getRefSpecs("remote", "origin", "fetch"));
+	}
+
 	private static void assertReadLong(long exp) throws ConfigInvalidException {
 		assertReadLong(exp, String.valueOf(exp));
 	}
@@ -1217,4 +1513,12 @@ private static void assertInvalidSubsection(String expectedMessage,
 			assertEquals(expectedMessage, e.getMessage());
 		}
 	}
+
+	private static FileBasedConfig loadConfig(File file)
+			throws IOException, ConfigInvalidException {
+		final FileBasedConfig config = new FileBasedConfig(null, file,
+				FS.DETECTED);
+		config.load();
+		return config;
+	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutMaliciousPathTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutMaliciousPathTest.java
index 32a1ec9..057e0c8 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutMaliciousPathTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutMaliciousPathTest.java
@@ -37,6 +37,7 @@
  */
 package org.eclipse.jgit.lib;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
@@ -343,7 +344,7 @@ private void testMaliciousPath(boolean good, boolean secondCheckout,
 			ObjectInserter newObjectInserter;
 			newObjectInserter = git.getRepository().newObjectInserter();
 			ObjectId blobId = newObjectInserter.insert(Constants.OBJ_BLOB,
-					"data".getBytes());
+					"data".getBytes(UTF_8));
 			newObjectInserter = git.getRepository().newObjectInserter();
 			FileMode mode = FileMode.REGULAR_FILE;
 			ObjectId insertId = blobId;
@@ -366,8 +367,8 @@ private void testMaliciousPath(boolean good, boolean secondCheckout,
 			insertId = blobId;
 			for (int i = path.length - 1; i >= 0; --i) {
 				TreeFormatter treeFormatter = new TreeFormatter();
-				treeFormatter.append(path[i].getBytes(), 0,
-							path[i].getBytes().length,
+				treeFormatter.append(path[i].getBytes(UTF_8), 0,
+						path[i].getBytes(UTF_8).length,
 							mode, insertId, true);
 				insertId = newObjectInserter.insert(treeFormatter);
 				mode = FileMode.TREE;
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 eb87827..534b323 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
@@ -40,6 +40,7 @@
  */
 package org.eclipse.jgit.lib;
 
+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;
@@ -310,7 +311,7 @@ private void assertIndex(HashMap<String, String> i)
 			assertTrue("unexpected content for path " + path
 					+ " in index. Expected: <" + expectedValue + ">",
 					Arrays.equals(db.open(read.getEntry(j).getObjectId())
-							.getCachedBytes(), i.get(path).getBytes()));
+							.getCachedBytes(), i.get(path).getBytes(UTF_8)));
 		}
 	}
 
@@ -405,7 +406,7 @@ private ObjectId buildTree(HashMap<String, String> headEntries)
 
 	ObjectId genSha1(String data) {
 		try (ObjectInserter w = db.newObjectInserter()) {
-			ObjectId id = w.insert(Constants.OBJ_BLOB, data.getBytes());
+			ObjectId id = w.insert(Constants.OBJ_BLOB, data.getBytes(UTF_8));
 			w.flush();
 			return id;
 		} catch (IOException e) {
@@ -928,6 +929,7 @@ public void testCheckoutHierarchy() throws IOException {
 						"e/g3"));
 		try {
 			checkout();
+			fail("did not throw CheckoutConflictException");
 		} catch (CheckoutConflictException e) {
 			assertWorkDir(mkmap("a", "a", "b/c", "b/c", "d", "d", "e/f",
 					"e/f", "e/g", "e/g3"));
@@ -2048,7 +2050,7 @@ public void assertWorkDir(Map<String, String> i)
 						assertArrayEquals(
 								"unexpected content for path " + path
 										+ " in workDir. ",
-								buffer, i.get(path).getBytes());
+								buffer, i.get(path).getBytes(UTF_8));
 					}
 					nrFiles++;
 				} else if (file.isDirectory()) {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/MergeHeadMsgTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/MergeHeadMsgTest.java
index 347883f..abf7d56 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/MergeHeadMsgTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/MergeHeadMsgTest.java
@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.lib;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 
@@ -72,7 +73,9 @@ public void testReadWriteMergeHeads() throws IOException {
 		// same test again, this time with lower-level io
 		try (FileOutputStream fos = new FileOutputStream(
 				new File(db.getDirectory(), "MERGE_HEAD"));) {
-			fos.write("0000000000000000000000000000000000000000\n1c6db447abdbb291b25f07be38ea0b1bf94947c5\n".getBytes(Constants.CHARACTER_ENCODING));
+			fos.write(
+					"0000000000000000000000000000000000000000\n1c6db447abdbb291b25f07be38ea0b1bf94947c5\n"
+							.getBytes(UTF_8));
 		}
 		assertEquals(db.readMergeHeads().size(), 2);
 		assertEquals(db.readMergeHeads().get(0), ObjectId.zeroId());
@@ -82,7 +85,7 @@ public void testReadWriteMergeHeads() throws IOException {
 		assertEquals(db.readMergeHeads(), null);
 		try (FileOutputStream fos = new FileOutputStream(
 				new File(db.getDirectory(), "MERGE_HEAD"))) {
-			fos.write(sampleId.getBytes(Constants.CHARACTER_ENCODING));
+			fos.write(sampleId.getBytes(UTF_8));
 		}
 		assertEquals(db.readMergeHeads().size(), 1);
 		assertEquals(db.readMergeHeads().get(0), ObjectId.fromString(sampleId));
@@ -100,7 +103,7 @@ public void testReadWriteMergeMsg() throws IOException {
 		assertFalse(new File(db.getDirectory(), "MERGE_MSG").exists());
 		try (FileOutputStream fos = new FileOutputStream(
 				new File(db.getDirectory(), Constants.MERGE_MSG))) {
-			fos.write(mergeMsg.getBytes(Constants.CHARACTER_ENCODING));
+			fos.write(mergeMsg.getBytes(UTF_8));
 		}
 		assertEquals(db.readMergeCommitMsg(), mergeMsg);
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ObjectLoaderTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ObjectLoaderTest.java
index 83e61d9..055e66e 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ObjectLoaderTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ObjectLoaderTest.java
@@ -260,6 +260,12 @@ public int read() throws IOException {
 						fail("never should have reached read");
 						return -1;
 					}
+
+					@Override
+					public int read(byte b[], int off, int len) {
+						fail("never should have reached read");
+						return -1;
+					}
 				};
 			}
 		};
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RacyGitTests.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RacyGitTests.java
index 3542dfa..bb24994 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RacyGitTests.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RacyGitTests.java
@@ -43,6 +43,7 @@
 package org.eclipse.jgit.lib;
 
 import static java.lang.Long.valueOf;
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assume.assumeTrue;
@@ -181,7 +182,7 @@ public void testRacyGitDetection() throws Exception {
 	private File addToWorkDir(String path, String content) throws IOException {
 		File f = new File(db.getWorkTree(), path);
 		try (FileOutputStream fos = new FileOutputStream(f)) {
-			fos.write(content.getBytes(Constants.CHARACTER_ENCODING));
+			fos.write(content.getBytes(UTF_8));
 			return f;
 		}
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RefTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RefTest.java
index a42027b..7d2c4a2 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RefTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RefTest.java
@@ -45,6 +45,7 @@
 
 package org.eclipse.jgit.lib;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.junit.Assert.assertEquals;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
@@ -261,7 +262,7 @@ public void testReadLoosePackedRef() throws IOException,
 		assertEquals(Storage.PACKED, ref.getStorage());
 		try (FileOutputStream os = new FileOutputStream(
 				new File(db.getDirectory(), "refs/heads/master"))) {
-			os.write(ref.getObjectId().name().getBytes());
+			os.write(ref.getObjectId().name().getBytes(UTF_8));
 			os.write('\n');
 		}
 
@@ -333,4 +334,17 @@ public void testGetRefsByPrefix() throws IOException {
 		assertEquals(1, refs.size());
 		checkContainsRef(refs, db.exactRef("refs/heads/prefix/a"));
 	}
+
+	@Test
+	public void testGetRefsByPrefixes() throws IOException {
+		List<Ref> refs = db.getRefDatabase().getRefsByPrefix();
+		assertEquals(0, refs.size());
+
+		refs = db.getRefDatabase().getRefsByPrefix("refs/heads/p",
+				"refs/tags/A");
+		assertEquals(3, refs.size());
+		checkContainsRef(refs, db.exactRef("refs/heads/pa"));
+		checkContainsRef(refs, db.exactRef("refs/heads/prefix/a"));
+		checkContainsRef(refs, db.exactRef("refs/tags/A"));
+	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/SquashCommitMsgTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/SquashCommitMsgTest.java
index 203c00e..f58ab06 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/SquashCommitMsgTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/SquashCommitMsgTest.java
@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.lib;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 
@@ -68,7 +69,7 @@ public void testReadWriteMergeMsg() throws IOException {
 		assertFalse(new File(db.getDirectory(), Constants.SQUASH_MSG).exists());
 		try (FileOutputStream fos = new FileOutputStream(
 				new File(db.getDirectory(), Constants.SQUASH_MSG))) {
-			fos.write(squashMsg.getBytes(Constants.CHARACTER_ENCODING));
+			fos.write(squashMsg.getBytes(UTF_8));
 		}
 		assertEquals(db.readSquashCommitMsg(), squashMsg);
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ValidRefNameTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ValidRefNameTest.java
index 87e901f..df5079a 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ValidRefNameTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ValidRefNameTest.java
@@ -270,8 +270,8 @@ public void testWindowsReservedNames() {
 
 	@Test
 	public void testNormalizeBranchName() {
-		assertEquals(true, Repository.normalizeBranchName(null) == "");
-		assertEquals(true, Repository.normalizeBranchName("").equals(""));
+		assertEquals("", Repository.normalizeBranchName(null));
+		assertEquals("", Repository.normalizeBranchName(""));
 		assertNormalized("Bug 12345::::Hello World", "Bug_12345-Hello_World");
 		assertNormalized("Bug 12345 :::: Hello World", "Bug_12345_Hello_World");
 		assertNormalized("Bug 12345 :::: Hello::: World",
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergeAlgorithmTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergeAlgorithmTest.java
index 5af62b6..3da779b 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergeAlgorithmTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergeAlgorithmTest.java
@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.merge;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 
 import java.io.ByteArrayOutputStream;
@@ -301,8 +302,8 @@ private String merge(String commonBase, String ours, String theirs) throws IOExc
 		MergeResult r = new MergeAlgorithm().merge(RawTextComparator.DEFAULT,
 				T(commonBase), T(ours), T(theirs));
 		ByteArrayOutputStream bo=new ByteArrayOutputStream(50);
-		fmt.formatMerge(bo, r, "B", "O", "T", Constants.CHARACTER_ENCODING);
-		return new String(bo.toByteArray(), Constants.CHARACTER_ENCODING);
+		fmt.formatMerge(bo, r, "B", "O", "T", UTF_8);
+		return new String(bo.toByteArray(), UTF_8);
 	}
 
 	public String t(String text) {
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 8f12dd7..8ca5d45 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
@@ -839,7 +839,7 @@ public ObjectReader newReader() {
 	/**
 	 * Throws an exception if reading beyond limit.
 	 */
-	class BigReadForbiddenStream extends ObjectStream.Filter {
+	static class BigReadForbiddenStream extends ObjectStream.Filter {
 		int limit;
 
 		BigReadForbiddenStream(ObjectStream orig, int limit) {
@@ -878,7 +878,7 @@ public int read(byte[] b, int off, int len) throws IOException {
 		}
 	}
 
-	class BigReadForbiddenReader extends ObjectReader.Filter {
+	static class BigReadForbiddenReader extends ObjectReader.Filter {
 		ObjectReader delegate;
 		int limit;
 
@@ -972,7 +972,7 @@ public void checkContentMergeConflict_noTree(MergeStrategy strategy)
 			merger.getMergeResults().get("file");
 			try (ByteArrayOutputStream out = new ByteArrayOutputStream()) {
 				fmt.formatMerge(out, merger.getMergeResults().get("file"),
-						"BASE", "OURS", "THEIRS", UTF_8.name());
+						"BASE", "OURS", "THEIRS", UTF_8);
 				String expected = "<<<<<<< OURS\n"
 						+ "1master\n"
 						+ "=======\n"
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/revplot/PlotCommitListTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/revplot/PlotCommitListTest.java
index 9a6043f..7297de3 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/revplot/PlotCommitListTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/revplot/PlotCommitListTest.java
@@ -56,7 +56,7 @@
 
 public class PlotCommitListTest extends RevWalkTestCase {
 
-	class CommitListAssert {
+	static class CommitListAssert {
 		private PlotCommitList<PlotLane> pcl;
 		private PlotCommit<PlotLane> current;
 		private int nextIndex = 0;
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/FileBasedConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/FileBasedConfigTest.java
index 7f0d602..b401d2b 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/FileBasedConfigTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/FileBasedConfigTest.java
@@ -52,6 +52,7 @@
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.util.StringTokenizer;
 
 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.util.FS;
@@ -67,16 +68,23 @@ public class FileBasedConfigTest {
 
 	private static final String NAME = "name";
 
+	private static final String EMAIL = "email";
+
 	private static final String ALICE = "Alice";
 
 	private static final String BOB = "Bob";
 
+	private static final String ALICE_EMAIL = "alice@home";
+
 	private static final String CONTENT1 = "[" + USER + "]\n\t" + NAME + " = "
 			+ ALICE + "\n";
 
 	private static final String CONTENT2 = "[" + USER + "]\n\t" + NAME + " = "
 			+ BOB + "\n";
 
+	private static final String CONTENT3 = "[" + USER + "]\n\t" + NAME + " = "
+			+ ALICE + "\n" + "[" + USER + "]\n\t" + EMAIL + " = " + ALICE_EMAIL;
+
 	private File trash;
 
 	@Before
@@ -93,14 +101,14 @@ public void tearDown() throws Exception {
 
 	@Test
 	public void testSystemEncoding() throws IOException, ConfigInvalidException {
-		final File file = createFile(CONTENT1.getBytes());
+		final File file = createFile(CONTENT1.getBytes(UTF_8));
 		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
 		config.load();
 		assertEquals(ALICE, config.getString(USER, null, NAME));
 
 		config.setString(USER, null, NAME, BOB);
 		config.save();
-		assertArrayEquals(CONTENT2.getBytes(), IO.readFully(file));
+		assertArrayEquals(CONTENT2.getBytes(UTF_8), IO.readFully(file));
 	}
 
 	@Test
@@ -112,7 +120,7 @@ public void testUTF8withoutBOM() throws IOException, ConfigInvalidException {
 
 		config.setString(USER, null, NAME, BOB);
 		config.save();
-		assertArrayEquals(CONTENT2.getBytes(), IO.readFully(file));
+		assertArrayEquals(CONTENT2.getBytes(UTF_8), IO.readFully(file));
 	}
 
 	@Test
@@ -142,8 +150,8 @@ public void testUTF8withBOM() throws IOException, ConfigInvalidException {
 	@Test
 	public void testLeadingWhitespaces() throws IOException, ConfigInvalidException {
 		final ByteArrayOutputStream bos1 = new ByteArrayOutputStream();
-		bos1.write(" \n\t".getBytes());
-		bos1.write(CONTENT1.getBytes());
+		bos1.write(" \n\t".getBytes(UTF_8));
+		bos1.write(CONTENT1.getBytes(UTF_8));
 
 		final File file = createFile(bos1.toByteArray());
 		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
@@ -154,18 +162,18 @@ public void testLeadingWhitespaces() throws IOException, ConfigInvalidException
 		config.save();
 
 		final ByteArrayOutputStream bos2 = new ByteArrayOutputStream();
-		bos2.write(" \n\t".getBytes());
-		bos2.write(CONTENT2.getBytes());
+		bos2.write(" \n\t".getBytes(UTF_8));
+		bos2.write(CONTENT2.getBytes(UTF_8));
 		assertArrayEquals(bos2.toByteArray(), IO.readFully(file));
 	}
 
 	@Test
 	public void testIncludeAbsolute()
 			throws IOException, ConfigInvalidException {
-		final File includedFile = createFile(CONTENT1.getBytes());
+		final File includedFile = createFile(CONTENT1.getBytes(UTF_8));
 		final ByteArrayOutputStream bos = new ByteArrayOutputStream();
-		bos.write("[include]\npath=".getBytes());
-		bos.write(pathToString(includedFile).getBytes());
+		bos.write("[include]\npath=".getBytes(UTF_8));
+		bos.write(pathToString(includedFile).getBytes(UTF_8));
 
 		final File file = createFile(bos.toByteArray());
 		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
@@ -176,10 +184,10 @@ public void testIncludeAbsolute()
 	@Test
 	public void testIncludeRelativeDot()
 			throws IOException, ConfigInvalidException {
-		final File includedFile = createFile(CONTENT1.getBytes(), "dir1");
+		final File includedFile = createFile(CONTENT1.getBytes(UTF_8), "dir1");
 		final ByteArrayOutputStream bos = new ByteArrayOutputStream();
-		bos.write("[include]\npath=".getBytes());
-		bos.write(("./" + includedFile.getName()).getBytes());
+		bos.write("[include]\npath=".getBytes(UTF_8));
+		bos.write(("./" + includedFile.getName()).getBytes(UTF_8));
 
 		final File file = createFile(bos.toByteArray(), "dir1");
 		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
@@ -190,11 +198,11 @@ public void testIncludeRelativeDot()
 	@Test
 	public void testIncludeRelativeDotDot()
 			throws IOException, ConfigInvalidException {
-		final File includedFile = createFile(CONTENT1.getBytes(), "dir1");
+		final File includedFile = createFile(CONTENT1.getBytes(UTF_8), "dir1");
 		final ByteArrayOutputStream bos = new ByteArrayOutputStream();
-		bos.write("[include]\npath=".getBytes());
+		bos.write("[include]\npath=".getBytes(UTF_8));
 		bos.write(("../" + includedFile.getParentFile().getName() + "/"
-				+ includedFile.getName()).getBytes());
+				+ includedFile.getName()).getBytes(UTF_8));
 
 		final File file = createFile(bos.toByteArray(), "dir2");
 		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
@@ -205,10 +213,10 @@ public void testIncludeRelativeDotDot()
 	@Test
 	public void testIncludeRelativeDotDotNotFound()
 			throws IOException, ConfigInvalidException {
-		final File includedFile = createFile(CONTENT1.getBytes());
+		final File includedFile = createFile(CONTENT1.getBytes(UTF_8));
 		final ByteArrayOutputStream bos = new ByteArrayOutputStream();
-		bos.write("[include]\npath=".getBytes());
-		bos.write(("../" + includedFile.getName()).getBytes());
+		bos.write("[include]\npath=".getBytes(UTF_8));
+		bos.write(("../" + includedFile.getName()).getBytes(UTF_8));
 
 		final File file = createFile(bos.toByteArray());
 		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
@@ -219,10 +227,10 @@ public void testIncludeRelativeDotDotNotFound()
 	@Test
 	public void testIncludeWithTilde()
 			throws IOException, ConfigInvalidException {
-		final File includedFile = createFile(CONTENT1.getBytes(), "home");
+		final File includedFile = createFile(CONTENT1.getBytes(UTF_8), "home");
 		final ByteArrayOutputStream bos = new ByteArrayOutputStream();
-		bos.write("[include]\npath=".getBytes());
-		bos.write(("~/" + includedFile.getName()).getBytes());
+		bos.write("[include]\npath=".getBytes(UTF_8));
+		bos.write(("~/" + includedFile.getName()).getBytes(UTF_8));
 
 		final File file = createFile(bos.toByteArray(), "repo");
 		final FS fs = FS.DETECTED.newInstance();
@@ -233,6 +241,50 @@ public void testIncludeWithTilde()
 		assertEquals(ALICE, config.getString(USER, null, NAME));
 	}
 
+	@Test
+	public void testIncludeDontInlineIncludedLinesOnSave()
+			throws IOException, ConfigInvalidException {
+		// use a content with multiple sections and multiple key/value pairs
+		// because code for first line works different than for subsequent lines
+		final File includedFile = createFile(CONTENT3.getBytes(UTF_8), "dir1");
+
+		final File file = createFile(new byte[0], "dir2");
+		FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
+		config.setString("include", null, "path",
+				("../" + includedFile.getParentFile().getName() + "/"
+						+ includedFile.getName()));
+
+		// just by setting the include.path, it won't be included
+		assertEquals(null, config.getString(USER, null, NAME));
+		assertEquals(null, config.getString(USER, null, EMAIL));
+		config.save();
+
+		// and it won't be included after saving
+		assertEquals(null, config.getString(USER, null, NAME));
+		assertEquals(null, config.getString(USER, null, EMAIL));
+
+		final String expectedText = config.toText();
+		assertEquals(2,
+				new StringTokenizer(expectedText, "\n", false).countTokens());
+
+		config = new FileBasedConfig(file, FS.DETECTED);
+		config.load();
+
+		String actualText = config.toText();
+		assertEquals(expectedText, actualText);
+		// but it will be included after (re)loading
+		assertEquals(ALICE, config.getString(USER, null, NAME));
+		assertEquals(ALICE_EMAIL, config.getString(USER, null, EMAIL));
+
+		config.save();
+
+		actualText = config.toText();
+		assertEquals(expectedText, actualText);
+		// and of course preserved after saving
+		assertEquals(ALICE, config.getString(USER, null, NAME));
+		assertEquals(ALICE_EMAIL, config.getString(USER, null, EMAIL));
+	}
+
 	private File createFile(byte[] content) throws IOException {
 		return createFile(content, null);
 	}
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 fed22c0..a0cd37e 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
@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.submodule;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_PATH;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_URL;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_SUBMODULE_SECTION;
@@ -52,9 +53,10 @@
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 
+import java.io.BufferedWriter;
 import java.io.File;
-import java.io.FileWriter;
 import java.io.IOException;
+import java.nio.file.Files;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.Status;
@@ -155,10 +157,12 @@ public void repositoryWithRootLevelSubmoduleAbsoluteRef()
 		if (!dotGit.getParentFile().exists())
 			dotGit.getParentFile().mkdirs();
 
-		File modulesGitDir = new File(db.getDirectory(), "modules"
-				+ File.separatorChar + path);
-		new FileWriter(dotGit).append(
-				"gitdir: " + modulesGitDir.getAbsolutePath()).close();
+		File modulesGitDir = new File(db.getDirectory(),
+				"modules" + File.separatorChar + path);
+		try (BufferedWriter fw = Files.newBufferedWriter(dotGit.toPath(),
+				UTF_8)) {
+			fw.append("gitdir: " + modulesGitDir.getAbsolutePath());
+		}
 		FileRepositoryBuilder builder = new FileRepositoryBuilder();
 		builder.setWorkTree(new File(db.getWorkTree(), path));
 		builder.build().create();
@@ -209,9 +213,11 @@ public void repositoryWithRootLevelSubmoduleRelativeRef()
 
 		File modulesGitDir = new File(db.getDirectory(), "modules"
 				+ File.separatorChar + path);
-		new FileWriter(dotGit).append(
-				"gitdir: " + "../" + Constants.DOT_GIT + "/modules/" + path)
-				.close();
+		try (BufferedWriter fw = Files.newBufferedWriter(dotGit.toPath(),
+				UTF_8)) {
+			fw.append("gitdir: " + "../" + Constants.DOT_GIT + "/modules/"
+					+ path);
+		}
 		FileRepositoryBuilder builder = new FileRepositoryBuilder();
 		builder.setWorkTree(new File(db.getWorkTree(), path));
 		builder.build().create();
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PacketLineOutTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PacketLineOutTest.java
index 391a701..ad8ae42 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PacketLineOutTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PacketLineOutTest.java
@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.transport;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.fail;
 
@@ -50,7 +51,6 @@
 import java.io.IOException;
 import java.io.OutputStream;
 
-import org.eclipse.jgit.lib.Constants;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -173,8 +173,8 @@ public void flush() throws IOException {
 		assertEquals(1, flushCnt[0]);
 	}
 
-	private void assertBuffer(String exp) throws IOException {
+	private void assertBuffer(String exp) {
 		assertEquals(exp, new String(rawOut.toByteArray(),
-				Constants.CHARACTER_ENCODING));
+				UTF_8));
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/ProtocolV2ParserTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/ProtocolV2ParserTest.java
index 4d11508..7cfe66f 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/ProtocolV2ParserTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/ProtocolV2ParserTest.java
@@ -45,6 +45,7 @@
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.hasItems;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.assertTrue;
 
@@ -162,15 +163,15 @@ public void testFetchBasicArguments()
 				ConfigBuilder.getDefault());
 		FetchV2Request request = parser.parseFetchRequest(pckIn,
 				testRepo.getRepository().getRefDatabase());
-		assertTrue(request.getOptions()
+		assertTrue(request.getClientCapabilities()
 				.contains(GitProtocolConstants.OPTION_THIN_PACK));
-		assertTrue(request.getOptions()
+		assertTrue(request.getClientCapabilities()
 				.contains(GitProtocolConstants.OPTION_NO_PROGRESS));
-		assertTrue(request.getOptions()
+		assertTrue(request.getClientCapabilities()
 				.contains(GitProtocolConstants.OPTION_INCLUDE_TAG));
-		assertTrue(request.getOptions()
+		assertTrue(request.getClientCapabilities()
 				.contains(GitProtocolConstants.CAPABILITY_OFS_DELTA));
-		assertThat(objIdsAsStrings(request.getWantsIds()),
+		assertThat(objIdsAsStrings(request.getWantIds()),
 				hasItems("4624442d68ee402a94364191085b77137618633e",
 						"f900c8326a43303685c46b279b9f70411bff1a4b"));
 		assertThat(objIdsAsStrings(request.getPeerHas()),
@@ -198,7 +199,7 @@ public void testFetchWithShallow_deepen() throws IOException {
 						"145e683b229dcab9d0e2ccb01b386f9ecc17d29d"));
 		assertTrue(request.getDeepenNotRefs().isEmpty());
 		assertEquals(15, request.getDepth());
-		assertTrue(request.getOptions()
+		assertTrue(request.getClientCapabilities()
 				.contains(GitProtocolConstants.OPTION_DEEPEN_RELATIVE));
 	}
 
@@ -263,25 +264,26 @@ public void testFetchWithBlobSizeFilter() throws IOException {
 
 	@Test
 	public void testFetchMustNotHaveMultipleFilters() throws IOException {
-		thrown.expect(PackProtocolException.class);
 		PacketLineIn pckIn = formatAsPacketLine(PacketLineIn.DELIM,
 				"filter blob:none",
 				"filter blob:limit=12",
 				PacketLineIn.END);
 		ProtocolV2Parser parser = new ProtocolV2Parser(
 				ConfigBuilder.start().allowFilter().done());
-		FetchV2Request request = parser.parseFetchRequest(pckIn,
+
+		thrown.expect(PackProtocolException.class);
+		parser.parseFetchRequest(pckIn,
 				testRepo.getRepository().getRefDatabase());
-		assertEquals(0, request.getFilterBlobLimit());
 	}
 
 	@Test
 	public void testFetchFilterWithoutAllowFilter() throws IOException {
-		thrown.expect(PackProtocolException.class);
 		PacketLineIn pckIn = formatAsPacketLine(PacketLineIn.DELIM,
 				"filter blob:limit=12", PacketLineIn.END);
 		ProtocolV2Parser parser = new ProtocolV2Parser(
 				ConfigBuilder.getDefault());
+
+		thrown.expect(PackProtocolException.class);
 		parser.parseFetchRequest(pckIn,
 				testRepo.getRepository().getRefDatabase());
 	}
@@ -306,17 +308,14 @@ public void testFetchWithRefInWant() throws Exception {
 		assertEquals(1, request.getWantedRefs().size());
 		assertThat(request.getWantedRefs().keySet(),
 				hasItems("refs/heads/branchA"));
-		assertEquals(2, request.getWantsIds().size());
-		assertThat(objIdsAsStrings(request.getWantsIds()),
+		assertEquals(2, request.getWantIds().size());
+		assertThat(objIdsAsStrings(request.getWantIds()),
 				hasItems("e4980cdc48cfa1301493ca94eb70523f6788b819",
 						one.getName()));
 	}
 
 	@Test
 	public void testFetchWithRefInWantUnknownRef() throws Exception {
-		thrown.expect(PackProtocolException.class);
-		thrown.expectMessage(containsString("refs/heads/branchC"));
-
 		PacketLineIn pckIn = formatAsPacketLine(PacketLineIn.DELIM,
 				"want e4980cdc48cfa1301493ca94eb70523f6788b819",
 				"want-ref refs/heads/branchC",
@@ -329,8 +328,66 @@ public void testFetchWithRefInWantUnknownRef() throws Exception {
 		testRepo.update("branchA", one);
 		testRepo.update("branchB", two);
 
+		thrown.expect(PackProtocolException.class);
+		thrown.expectMessage(containsString("refs/heads/branchC"));
 		parser.parseFetchRequest(pckIn,
 				testRepo.getRepository().getRefDatabase());
 	}
 
+	@Test
+	public void testLsRefsMinimalReq() throws IOException {
+		PacketLineIn pckIn = formatAsPacketLine(PacketLineIn.DELIM,
+				PacketLineIn.END);
+
+		ProtocolV2Parser parser = new ProtocolV2Parser(
+				ConfigBuilder.getDefault());
+		LsRefsV2Request req = parser.parseLsRefsRequest(pckIn);
+		assertFalse(req.getPeel());
+		assertFalse(req.getSymrefs());
+		assertEquals(0, req.getRefPrefixes().size());
+	}
+
+	@Test
+	public void testLsRefsSymrefs() throws IOException {
+		PacketLineIn pckIn = formatAsPacketLine(PacketLineIn.DELIM, "symrefs",
+				PacketLineIn.END);
+
+		ProtocolV2Parser parser = new ProtocolV2Parser(
+				ConfigBuilder.getDefault());
+		LsRefsV2Request req = parser.parseLsRefsRequest(pckIn);
+		assertFalse(req.getPeel());
+		assertTrue(req.getSymrefs());
+		assertEquals(0, req.getRefPrefixes().size());
+
+	}
+
+	@Test
+	public void testLsRefsPeel() throws IOException {
+		PacketLineIn pckIn = formatAsPacketLine(
+				PacketLineIn.DELIM,
+				"peel",
+				PacketLineIn.END);
+
+		ProtocolV2Parser parser = new ProtocolV2Parser(
+				ConfigBuilder.getDefault());
+		LsRefsV2Request req = parser.parseLsRefsRequest(pckIn);
+		assertTrue(req.getPeel());
+		assertFalse(req.getSymrefs());
+		assertEquals(0, req.getRefPrefixes().size());
+	}
+
+	@Test
+	public void testLsRefsRefPrefixes() throws IOException {
+		PacketLineIn pckIn = formatAsPacketLine(PacketLineIn.DELIM,
+				"ref-prefix refs/for", "ref-prefix refs/heads",
+				PacketLineIn.END);
+
+		ProtocolV2Parser parser = new ProtocolV2Parser(
+				ConfigBuilder.getDefault());
+		LsRefsV2Request req = parser.parseLsRefsRequest(pckIn);
+		assertFalse(req.getPeel());
+		assertFalse(req.getSymrefs());
+		assertEquals(2, req.getRefPrefixes().size());
+		assertThat(req.getRefPrefixes(), hasItems("refs/for", "refs/heads"));
+	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushCertificateParserTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushCertificateParserTest.java
index 0647167..4bf26b6 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushCertificateParserTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushCertificateParserTest.java
@@ -42,6 +42,7 @@
 
 package org.eclipse.jgit.transport;
 
+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;
@@ -334,7 +335,7 @@ public void testParseMultipleFromStream() throws Exception {
 		assertFalse(input.contains(PushCertificateParser.END_CERT));
 		input += input;
 		Reader reader = new InputStreamReader(
-				new ByteArrayInputStream(Constants.encode(input)));
+				new ByteArrayInputStream(Constants.encode(input)), UTF_8);
 
 		assertNotNull(PushCertificateParser.fromReader(reader));
 		assertNotNull(PushCertificateParser.fromReader(reader));
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushCertificateStoreTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushCertificateStoreTest.java
index 68e0129..fa4fd65 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushCertificateStoreTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushCertificateStoreTest.java
@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.transport;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.lib.ObjectId.zeroId;
 import static org.eclipse.jgit.lib.RefUpdate.Result.FAST_FORWARD;
 import static org.eclipse.jgit.lib.RefUpdate.Result.LOCK_FAILURE;
@@ -96,7 +97,9 @@ private static PushCertificate newCert(String... updateLines) {
 				+ "-----END PGP SIGNATURE-----\n");
 		try {
 			return PushCertificateParser.fromReader(new InputStreamReader(
-					new ByteArrayInputStream(Constants.encode(cert.toString()))));
+					new ByteArrayInputStream(
+							Constants.encode(cert.toString())),
+					UTF_8));
 		} catch (IOException e) {
 			throw new IllegalArgumentException(e);
 		}
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 c959f6c..dfa50b6 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
@@ -492,9 +492,8 @@ public void testIncludesInvalidGitmodules() throws Exception {
 		assertSame(PacketLineIn.END, r.readString());
 
 		String errorLine = r.readString();
-		System.out.println(errorLine);
-		assertTrue(errorLine.startsWith(
-				"unpack error Invalid submodule URL '-"));
+		assertTrue(errorLine.startsWith("unpack error"));
+		assertTrue(errorLine.contains("Invalid submodule URL '-"));
 		assertEquals("ng refs/heads/s n/a (unpacker error)", r.readString());
 		assertSame(PacketLineIn.END, r.readString());
 	}
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 4d3e162..b6cf356 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
@@ -44,6 +44,7 @@
 package org.eclipse.jgit.transport;
 
 import static java.lang.Integer.valueOf;
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.transport.SideBandOutputStream.CH_DATA;
 import static org.eclipse.jgit.transport.SideBandOutputStream.CH_ERROR;
 import static org.eclipse.jgit.transport.SideBandOutputStream.CH_PROGRESS;
@@ -59,7 +60,6 @@
 import java.text.MessageFormat;
 
 import org.eclipse.jgit.internal.JGitText;
-import org.eclipse.jgit.lib.Constants;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -259,8 +259,7 @@ public void testConstructor_RejectsBadBufferSize() throws Exception {
 		}
 	}
 
-	private void assertBuffer(String exp) throws IOException {
-		assertEquals(exp, new String(rawOut.toByteArray(),
-				Constants.CHARACTER_ENCODING));
+	private void assertBuffer(String exp) {
+		assertEquals(exp, new String(rawOut.toByteArray(), UTF_8));
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/TestProtocolTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/TestProtocolTest.java
index 953c9fc..1c4d0cf 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/TestProtocolTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/TestProtocolTest.java
@@ -46,6 +46,7 @@
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -238,6 +239,7 @@ public UploadPack create(User req, Repository db)
 						.setRemote(user1Uri.toString())
 						.setRefSpecs(MASTER)
 						.call();
+				fail("accepted not permitted fetch");
 			} catch (InvalidRemoteException expected) {
 				// Expected.
 			}
@@ -282,6 +284,7 @@ public ReceivePack create(User req, Repository db)
 						.setRemote(user1Uri.toString())
 						.setRefSpecs(HEADS)
 						.call();
+				fail("accepted not permitted push");
 			} catch (TransportException expected) {
 				assertTrue(expected.getMessage().contains(
 						JGitText.get().pushNotPermitted));
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 317ac32..aaef458 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
@@ -7,6 +7,7 @@
 import static org.hamcrest.Matchers.theInstance;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
@@ -27,6 +28,7 @@
 import org.eclipse.jgit.internal.storage.dfs.InMemoryRepository;
 import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.lib.NullProgressMonitor;
+import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
@@ -484,6 +486,8 @@ private static class TestV2Hook implements ProtocolV2Hook {
 
 		private LsRefsV2Request lsRefsRequest;
 
+		private FetchV2Request fetchRequest;
+
 		@Override
 		public void onCapabilities(CapabilitiesV2Request req) {
 			capabilitiesRequest = req;
@@ -493,6 +497,11 @@ public void onCapabilities(CapabilitiesV2Request req) {
 		public void onLsRefs(LsRefsV2Request req) {
 			lsRefsRequest = req;
 		}
+
+		@Override
+		public void onFetch(FetchV2Request req) {
+			fetchRequest = req;
+		}
 	}
 
 	@Test
@@ -501,18 +510,18 @@ public void testV2Capabilities() throws Exception {
 		ByteArrayInputStream recvStream =
 				uploadPackV2Setup(null, null, hook, PacketLineIn.END);
 		PacketLineIn pckIn = new PacketLineIn(recvStream);
-
 		assertThat(hook.capabilitiesRequest, notNullValue());
 		assertThat(pckIn.readString(), is("version 2"));
 		assertThat(
-			Arrays.asList(pckIn.readString(), pckIn.readString()),
-			// TODO(jonathantanmy) This check is written this way
-			// to make it simple to see that we expect this list of
-			// capabilities, but probably should be loosened to
-			// allow additional commands to be added to the list,
-			// and additional capabilities to be added to existing
-			// commands without requiring test changes.
-			hasItems("ls-refs", "fetch=shallow"));
+				Arrays.asList(pckIn.readString(), pckIn.readString(),
+						pckIn.readString()),
+				// TODO(jonathantanmy) This check is written this way
+				// to make it simple to see that we expect this list of
+				// capabilities, but probably should be loosened to
+				// allow additional commands to be added to the list,
+				// and additional capabilities to be added to existing
+				// commands without requiring test changes.
+				hasItems("ls-refs", "fetch=shallow", "server-option"));
 		assertTrue(pckIn.readString() == PacketLineIn.END);
 	}
 
@@ -525,10 +534,11 @@ public void testV2CapabilitiesAllowFilter() throws Exception {
 
 		assertThat(pckIn.readString(), is("version 2"));
 		assertThat(
-			Arrays.asList(pckIn.readString(), pckIn.readString()),
-			// TODO(jonathantanmy) This check overspecifies the
-			// order of the capabilities of "fetch".
-			hasItems("ls-refs", "fetch=filter shallow"));
+				Arrays.asList(pckIn.readString(), pckIn.readString(),
+						pckIn.readString()),
+				// TODO(jonathantanmy) This check overspecifies the
+				// order of the capabilities of "fetch".
+				hasItems("ls-refs", "fetch=filter shallow", "server-option"));
 		assertTrue(pckIn.readString() == PacketLineIn.END);
 	}
 
@@ -541,10 +551,12 @@ public void testV2CapabilitiesRefInWant() throws Exception {
 
 		assertThat(pckIn.readString(), is("version 2"));
 		assertThat(
-			Arrays.asList(pckIn.readString(), pckIn.readString()),
-			// TODO(jonathantanmy) This check overspecifies the
-			// order of the capabilities of "fetch".
-			hasItems("ls-refs", "fetch=ref-in-want shallow"));
+				Arrays.asList(pckIn.readString(), pckIn.readString(),
+						pckIn.readString()),
+				// TODO(jonathantanmy) This check overspecifies the
+				// order of the capabilities of "fetch".
+				hasItems("ls-refs", "fetch=ref-in-want shallow",
+						"server-option"));
 		assertTrue(pckIn.readString() == PacketLineIn.END);
 	}
 
@@ -557,8 +569,9 @@ public void testV2CapabilitiesRefInWantNotAdvertisedIfUnallowed() throws Excepti
 
 		assertThat(pckIn.readString(), is("version 2"));
 		assertThat(
-			Arrays.asList(pckIn.readString(), pckIn.readString()),
-			hasItems("ls-refs", "fetch=shallow"));
+				Arrays.asList(pckIn.readString(), pckIn.readString(),
+						pckIn.readString()),
+				hasItems("ls-refs", "fetch=shallow", "server-option"));
 		assertTrue(pckIn.readString() == PacketLineIn.END);
 	}
 
@@ -572,8 +585,9 @@ public void testV2CapabilitiesRefInWantNotAdvertisedIfAdvertisingForbidden() thr
 
 		assertThat(pckIn.readString(), is("version 2"));
 		assertThat(
-			Arrays.asList(pckIn.readString(), pckIn.readString()),
-			hasItems("ls-refs", "fetch=shallow"));
+				Arrays.asList(pckIn.readString(), pckIn.readString(),
+						pckIn.readString()),
+				hasItems("ls-refs", "fetch=shallow", "server-option"));
 		assertTrue(pckIn.readString() == PacketLineIn.END);
 	}
 
@@ -718,6 +732,21 @@ public void testV2LsRefsUnrecognizedArgument() throws Exception {
 			PacketLineIn.END);
 	}
 
+	@Test
+	public void testV2LsRefsServerOptions() throws Exception {
+		String[] lines = { "command=ls-refs\n",
+				"server-option=one\n", "server-option=two\n",
+				PacketLineIn.DELIM,
+				PacketLineIn.END };
+
+		TestV2Hook testHook = new TestV2Hook();
+		uploadPackV2Setup(null, null, testHook, lines);
+
+		LsRefsV2Request req = testHook.lsRefsRequest;
+		assertEquals(2, req.getServerOptions().size());
+		assertThat(req.getServerOptions(), hasItems("one", "two"));
+	}
+
 	/*
 	 * Parse multiplexed packfile output from upload-pack using protocol V2
 	 * into the client repository.
@@ -1191,6 +1220,59 @@ public void testV2FetchDeepenWithoutDone() throws Exception {
 	}
 
 	@Test
+	public void testV2FetchShallowSince() throws Exception {
+		PersonIdent person = new PersonIdent(remote.getRepository());
+
+		RevCommit beyondBoundary = remote.commit()
+			.committer(new PersonIdent(person, 1510000000, 0)).create();
+		RevCommit boundary = remote.commit().parent(beyondBoundary)
+			.committer(new PersonIdent(person, 1520000000, 0)).create();
+		RevCommit tooOld = remote.commit()
+			.committer(new PersonIdent(person, 1500000000, 0)).create();
+		RevCommit merge = remote.commit().parent(boundary).parent(tooOld)
+			.committer(new PersonIdent(person, 1530000000, 0)).create();
+
+		remote.update("branch1", merge);
+
+		// Report that we only have "boundary" as a shallow boundary.
+		ByteArrayInputStream recvStream = uploadPackV2(
+			"command=fetch\n",
+			PacketLineIn.DELIM,
+			"shallow " + boundary.toObjectId().getName() + "\n",
+			"deepen-since 1510000\n",
+			"want " + merge.toObjectId().getName() + "\n",
+			"have " + boundary.toObjectId().getName() + "\n",
+			"done\n",
+			PacketLineIn.END);
+		PacketLineIn pckIn = new PacketLineIn(recvStream);
+		assertThat(pckIn.readString(), is("shallow-info"));
+
+		// "merge" is shallow because one of its parents is committed
+		// earlier than the given deepen-since time.
+		assertThat(pckIn.readString(), is("shallow " + merge.toObjectId().getName()));
+
+		// "boundary" is unshallow because its parent committed at or
+		// later than the given deepen-since time.
+		assertThat(pckIn.readString(), is("unshallow " + boundary.toObjectId().getName()));
+
+		assertThat(pckIn.readString(), theInstance(PacketLineIn.DELIM));
+		assertThat(pckIn.readString(), is("packfile"));
+		parsePack(recvStream);
+
+		// The server does not send this because it is committed
+		// earlier than the given deepen-since time.
+		assertFalse(client.hasObject(tooOld.toObjectId()));
+
+		// The server does not send this because the client claims to
+		// have it.
+		assertFalse(client.hasObject(boundary.toObjectId()));
+
+		// The server sends both these commits.
+		assertTrue(client.hasObject(beyondBoundary.toObjectId()));
+		assertTrue(client.hasObject(merge.toObjectId()));
+	}
+
+	@Test
 	public void testV2FetchUnrecognizedArgument() throws Exception {
 		thrown.expect(PackProtocolException.class);
 		thrown.expectMessage("unexpected invalid-argument");
@@ -1202,6 +1284,21 @@ public void testV2FetchUnrecognizedArgument() throws Exception {
 	}
 
 	@Test
+	public void testV2FetchServerOptions() throws Exception {
+		String[] lines = { "command=fetch\n", "server-option=one\n",
+				"server-option=two\n", PacketLineIn.DELIM,
+				PacketLineIn.END };
+
+		TestV2Hook testHook = new TestV2Hook();
+		uploadPackV2Setup(null, null, testHook, lines);
+
+		FetchV2Request req = testHook.fetchRequest;
+		assertNotNull(req);
+		assertEquals(2, req.getServerOptions().size());
+		assertThat(req.getServerOptions(), hasItems("one", "two"));
+	}
+
+	@Test
 	public void testV2FetchFilter() throws Exception {
 		RevBlob big = remote.blob("foobar");
 		RevBlob small = remote.blob("fooba");
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/WalkEncryptionTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/WalkEncryptionTest.java
index f2fb022..4750d15 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/WalkEncryptionTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/WalkEncryptionTest.java
@@ -651,7 +651,8 @@ static void configCreate(String algorithm) throws Exception {
 			Properties props = Props.discover();
 			props.put(AmazonS3.Keys.PASSWORD, JGIT_PASS);
 			props.put(AmazonS3.Keys.CRYPTO_ALG, algorithm);
-			try (PrintWriter writer = new PrintWriter(JGIT_CONF_FILE)) {
+			try (PrintWriter writer = new PrintWriter(JGIT_CONF_FILE,
+					UTF_8.name())) {
 				props.store(writer, "JGIT S3 connection configuration file.");
 			}
 		}
@@ -665,7 +666,8 @@ static void configCreate(String algorithm) throws Exception {
 		static void configCreate(Properties source) throws Exception {
 			Properties target = Props.discover();
 			target.putAll(source);
-			try (PrintWriter writer = new PrintWriter(JGIT_CONF_FILE)) {
+			try (PrintWriter writer = new PrintWriter(JGIT_CONF_FILE,
+					UTF_8.name())) {
 				target.store(writer, "JGIT S3 connection configuration file.");
 			}
 		}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/AbstractTreeIteratorTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/AbstractTreeIteratorTest.java
index 934984f..8afd49a 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/AbstractTreeIteratorTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/AbstractTreeIteratorTest.java
@@ -66,7 +66,7 @@ private static String prefix(String path) {
 		return s > 0 ? path.substring(0, s) : "";
 	}
 
-	public class FakeTreeIterator extends WorkingTreeIterator {
+	public static class FakeTreeIterator extends WorkingTreeIterator {
 		public FakeTreeIterator(String pathName, FileMode fileMode) {
 			super(prefix(pathName), new Config().get(WorkingTreeOptions.KEY));
 			mode = fileMode.getBits();
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/InterIndexDiffFilterTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/InterIndexDiffFilterTest.java
index cba35d8..ea5db09 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/InterIndexDiffFilterTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/InterIndexDiffFilterTest.java
@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.treewalk.filter;
 
+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.assertTrue;
@@ -114,7 +115,7 @@ public void apply(DirCacheEntry ent) {
 	}
 
 	private ObjectId id(String data) {
-		byte[] bytes = data.getBytes();
+		byte[] bytes = data.getBytes(UTF_8);
 		return db.newObjectInserter().idFor(Constants.OBJ_BLOB, bytes);
 	}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/BlockListTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/BlockListTest.java
index 0a3de85..dca9c57 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/BlockListTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/BlockListTest.java
@@ -47,6 +47,7 @@
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertSame;
 import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
 
 import java.util.Iterator;
 
@@ -84,18 +85,21 @@ public void testGet() {
 
 		try {
 			list.get(-1);
+			fail("accepted out-of-bounds index");
 		} catch (IndexOutOfBoundsException badIndex) {
 			assertEquals(String.valueOf(-1), badIndex.getMessage());
 		}
 
 		try {
 			list.get(0);
+			fail("accepted out-of-bounds index");
 		} catch (IndexOutOfBoundsException badIndex) {
 			assertEquals(String.valueOf(0), badIndex.getMessage());
 		}
 
 		try {
 			list.get(4);
+			fail("accepted out-of-bounds index");
 		} catch (IndexOutOfBoundsException badIndex) {
 			assertEquals(String.valueOf(4), badIndex.getMessage());
 		}
@@ -114,6 +118,7 @@ public void testGet() {
 
 		try {
 			list.get(3);
+			fail("accepted out-of-bounds index");
 		} catch (IndexOutOfBoundsException badIndex) {
 			assertEquals(String.valueOf(3), badIndex.getMessage());
 		}
@@ -125,18 +130,21 @@ public void testSet() {
 
 		try {
 			list.set(-1, "foo");
+			fail("accepted out-of-bounds index");
 		} catch (IndexOutOfBoundsException badIndex) {
 			assertEquals(String.valueOf(-1), badIndex.getMessage());
 		}
 
 		try {
 			list.set(0, "foo");
+			fail("accepted out-of-bounds index");
 		} catch (IndexOutOfBoundsException badIndex) {
 			assertEquals(String.valueOf(0), badIndex.getMessage());
 		}
 
 		try {
 			list.set(4, "foo");
+			fail("accepted out-of-bounds index");
 		} catch (IndexOutOfBoundsException badIndex) {
 			assertEquals(String.valueOf(4), badIndex.getMessage());
 		}
@@ -161,6 +169,7 @@ public void testSet() {
 
 		try {
 			list.set(3, "bar");
+			fail("accepted out-of-bounds index");
 		} catch (IndexOutOfBoundsException badIndex) {
 			assertEquals(String.valueOf(3), badIndex.getMessage());
 		}
@@ -323,12 +332,14 @@ public void testAddRejectsBadIndexes() {
 
 		try {
 			list.add(-1, Integer.valueOf(42));
+			fail("accepted out-of-bounds index");
 		} catch (IndexOutOfBoundsException badIndex) {
 			assertEquals(String.valueOf(-1), badIndex.getMessage());
 		}
 
 		try {
 			list.add(4, Integer.valueOf(42));
+			fail("accepted out-of-bounds index");
 		} catch (IndexOutOfBoundsException badIndex) {
 			assertEquals(String.valueOf(4), badIndex.getMessage());
 		}
@@ -341,12 +352,14 @@ public void testRemoveRejectsBadIndexes() {
 
 		try {
 			list.remove(-1);
+			fail("accepted out-of-bounds index");
 		} catch (IndexOutOfBoundsException badIndex) {
 			assertEquals(String.valueOf(-1), badIndex.getMessage());
 		}
 
 		try {
 			list.remove(4);
+			fail("accepted out-of-bounds index");
 		} catch (IndexOutOfBoundsException badIndex) {
 			assertEquals(String.valueOf(4), badIndex.getMessage());
 		}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/IOReadLineTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/IOReadLineTest.java
index 928fb2e..fa303ec 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/IOReadLineTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/IOReadLineTest.java
@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.util;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 
 import java.io.BufferedReader;
@@ -105,7 +106,7 @@ private String readLine(Reader r) throws Exception {
 
 	private Reader newReader(String in) {
 		Reader r = new InputStreamReader(
-				new ByteArrayInputStream(Constants.encode(in)));
+				new ByteArrayInputStream(Constants.encode(in)), UTF_8);
 		if (buffered) {
 			r = new BufferedReader(r);
 		}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/RunExternalScriptTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/RunExternalScriptTest.java
index 7c0985e..19af836 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/RunExternalScriptTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/RunExternalScriptTest.java
@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.util;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 
 import java.io.ByteArrayInputStream;
@@ -75,10 +76,10 @@ public void testCopyStdIn() throws IOException, InterruptedException {
 		File script = writeTempFile("cat -");
 		int rc = FS.DETECTED.runProcess(
 				new ProcessBuilder("sh", script.getPath()), out, err,
-				new ByteArrayInputStream(inputStr.getBytes()));
+				new ByteArrayInputStream(inputStr.getBytes(UTF_8)));
 		assertEquals(0, rc);
-		assertEquals(inputStr, new String(out.toByteArray()));
-		assertEquals("", new String(err.toByteArray()));
+		assertEquals(inputStr, new String(out.toByteArray(), UTF_8));
+		assertEquals("", new String(err.toByteArray(), UTF_8));
 	}
 
 	@Test
@@ -88,8 +89,8 @@ public void testCopyNullStdIn() throws IOException, InterruptedException {
 				new ProcessBuilder("sh", script.getPath()), out, err,
 				(InputStream) null);
 		assertEquals(0, rc);
-		assertEquals("", new String(out.toByteArray()));
-		assertEquals("", new String(err.toByteArray()));
+		assertEquals("", new String(out.toByteArray(), UTF_8));
+		assertEquals("", new String(err.toByteArray(), UTF_8));
 	}
 
 	@Test
@@ -99,8 +100,8 @@ public void testArguments() throws IOException, InterruptedException {
 				new ProcessBuilder("sh",
 				script.getPath(), "a", "b", "c"), out, err, (InputStream) null);
 		assertEquals(0, rc);
-		assertEquals("3,a,b,c,,,\n", new String(out.toByteArray()));
-		assertEquals("", new String(err.toByteArray()));
+		assertEquals("3,a,b,c,,,\n", new String(out.toByteArray(), UTF_8));
+		assertEquals("", new String(err.toByteArray(), UTF_8));
 	}
 
 	@Test
@@ -110,8 +111,8 @@ public void testRc() throws IOException, InterruptedException {
 				new ProcessBuilder("sh", script.getPath(), "a", "b", "c"),
 				out, err, (InputStream) null);
 		assertEquals(3, rc);
-		assertEquals("", new String(out.toByteArray()));
-		assertEquals("", new String(err.toByteArray()));
+		assertEquals("", new String(out.toByteArray(), UTF_8));
+		assertEquals("", new String(err.toByteArray(), UTF_8));
 	}
 
 	@Test
@@ -121,8 +122,8 @@ public void testNullStdout() throws IOException, InterruptedException {
 				new ProcessBuilder("sh", script.getPath()), null, err,
 				(InputStream) null);
 		assertEquals(0, rc);
-		assertEquals("", new String(out.toByteArray()));
-		assertEquals("", new String(err.toByteArray()));
+		assertEquals("", new String(out.toByteArray(), UTF_8));
+		assertEquals("", new String(err.toByteArray(), UTF_8));
 	}
 
 	@Test
@@ -132,8 +133,8 @@ public void testStdErr() throws IOException, InterruptedException {
 				new ProcessBuilder("sh", script.getPath()), null, err,
 				(InputStream) null);
 		assertEquals(0, rc);
-		assertEquals("", new String(out.toByteArray()));
-		assertEquals("hi" + LF, new String(err.toByteArray()));
+		assertEquals("", new String(out.toByteArray(), UTF_8));
+		assertEquals("hi" + LF, new String(err.toByteArray(), UTF_8));
 	}
 
 	@Test
@@ -142,10 +143,10 @@ public void testAllTogetherBin() throws IOException, InterruptedException {
 		File script = writeTempFile("echo $#,$1,$2,$3,$4,$5,$6 >&2 ; cat -; exit 5");
 		int rc = FS.DETECTED.runProcess(
 				new ProcessBuilder("sh", script.getPath(), "a", "b", "c"),
-				out, err, new ByteArrayInputStream(inputStr.getBytes()));
+				out, err, new ByteArrayInputStream(inputStr.getBytes(UTF_8)));
 		assertEquals(5, rc);
-		assertEquals(inputStr, new String(out.toByteArray()));
-		assertEquals("3,a,b,c,,," + LF, new String(err.toByteArray()));
+		assertEquals(inputStr, new String(out.toByteArray(), UTF_8));
+		assertEquals("3,a,b,c,,," + LF, new String(err.toByteArray(), UTF_8));
 	}
 
 	@Test(expected = IOException.class)
@@ -172,10 +173,11 @@ public void testCopyStdInExecute()
 		File script = writeTempFile("cat -");
 		ProcessBuilder pb = new ProcessBuilder("sh", script.getPath());
 		ExecutionResult res = FS.DETECTED.execute(pb,
-				new ByteArrayInputStream(inputStr.getBytes()));
+				new ByteArrayInputStream(inputStr.getBytes(UTF_8)));
 		assertEquals(0, res.getRc());
-		assertEquals(inputStr, new String(res.getStdout().toByteArray()));
-		assertEquals("", new String(res.getStderr().toByteArray()));
+		assertEquals(inputStr,
+				new String(res.getStdout().toByteArray(), UTF_8));
+		assertEquals("", new String(res.getStderr().toByteArray(), UTF_8));
 	}
 
 	@Test
@@ -184,8 +186,9 @@ public void testStdErrExecute() throws IOException, InterruptedException {
 		ProcessBuilder pb = new ProcessBuilder("sh", script.getPath());
 		ExecutionResult res = FS.DETECTED.execute(pb, null);
 		assertEquals(0, res.getRc());
-		assertEquals("", new String(res.getStdout().toByteArray()));
-		assertEquals("hi" + LF, new String(res.getStderr().toByteArray()));
+		assertEquals("", new String(res.getStdout().toByteArray(), UTF_8));
+		assertEquals("hi" + LF,
+				new String(res.getStderr().toByteArray(), UTF_8));
 	}
 
 	@Test
@@ -197,11 +200,12 @@ public void testAllTogetherBinExecute()
 		ProcessBuilder pb = new ProcessBuilder("sh", script.getPath(), "a",
 				"b", "c");
 		ExecutionResult res = FS.DETECTED.execute(pb,
-				new ByteArrayInputStream(inputStr.getBytes()));
+				new ByteArrayInputStream(inputStr.getBytes(UTF_8)));
 		assertEquals(5, res.getRc());
-		assertEquals(inputStr, new String(res.getStdout().toByteArray()));
+		assertEquals(inputStr,
+				new String(res.getStdout().toByteArray(), UTF_8));
 		assertEquals("3,a,b,c,,," + LF,
-				new String(res.getStderr().toByteArray()));
+				new String(res.getStderr().toByteArray(), UTF_8));
 	}
 
 	private File writeTempFile(String body) throws IOException {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoCRLFInputStreamTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoCRLFInputStreamTest.java
index 1272e16..8f77c55 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoCRLFInputStreamTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoCRLFInputStreamTest.java
@@ -43,6 +43,8 @@
 
 package org.eclipse.jgit.util.io;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
+
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
@@ -89,8 +91,8 @@ private void assertNoCrLf(String string, String string2) throws IOException {
 
 	private void assertNoCrLfHelper(String expect, String input)
 			throws IOException {
-		byte[] inbytes = input.getBytes();
-		byte[] expectBytes = expect.getBytes();
+		byte[] inbytes = input.getBytes(UTF_8);
+		byte[] expectBytes = expect.getBytes(UTF_8);
 		for (int i = 0; i < 5; ++i) {
 			byte[] buf = new byte[i];
 			try (ByteArrayInputStream bis = new ByteArrayInputStream(inbytes);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoCRLFOutputStreamTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoCRLFOutputStreamTest.java
index 0655827..3a3dc81 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoCRLFOutputStreamTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/AutoCRLFOutputStreamTest.java
@@ -44,6 +44,8 @@
 
 package org.eclipse.jgit.util.io;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
+
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
@@ -91,8 +93,8 @@ private void assertNoCrLf(String string, String string2) throws IOException {
 
 	private void assertNoCrLfHelper(String expect, String input)
 			throws IOException {
-		byte[] inbytes = input.getBytes();
-		byte[] expectBytes = expect.getBytes();
+		byte[] inbytes = input.getBytes(UTF_8);
+		byte[] expectBytes = expect.getBytes(UTF_8);
 		for (int i = -4; i < 5; ++i) {
 			int size = Math.abs(i);
 			byte[] buf = new byte[size];
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/TimeoutOutputStreamTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/TimeoutOutputStreamTest.java
index a63b1cb..c35f90c 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/TimeoutOutputStreamTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/io/TimeoutOutputStreamTest.java
@@ -282,7 +282,7 @@ private static long now() {
 		return System.currentTimeMillis();
 	}
 
-	private final class FullPipeInputStream extends PipedInputStream {
+	private static final class FullPipeInputStream extends PipedInputStream {
 		FullPipeInputStream(PipedOutputStream src) throws IOException {
 			super(src);
 			src.write(new byte[PIPE_SIZE]);
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 b824fae..a6e0eed 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
@@ -167,6 +167,8 @@ public void testSkip() throws IOException {
 
 		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;
 			}
@@ -259,6 +261,11 @@ public void testNonBlockingPartialRead() throws Exception {
 			public int read() throws IOException {
 				throw new IOException("Expected");
 			}
+
+			@Override
+			public int read(byte b[], int off, int len) throws IOException {
+				throw new IOException("Expected");
+			}
 		};
 		@SuppressWarnings("resource" /* java 7 */)
 		final UnionInputStream u = new UnionInputStream(
diff --git a/org.eclipse.jgit.ui/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.ui/.settings/org.eclipse.jdt.core.prefs
index 89394ec..525ac67 100644
--- a/org.eclipse.jgit.ui/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit.ui/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit.ui/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit.ui/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit.ui/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit.ui/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit.ui/META-INF/MANIFEST.MF b/org.eclipse.jgit.ui/META-INF/MANIFEST.MF
index 9b94df9..889a629 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
 Bundle-Vendor: %provider_name
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Export-Package: org.eclipse.jgit.awtui;version="5.1.4"
-Import-Package: org.eclipse.jgit.errors;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.lib;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.nls;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revplot;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.revwalk;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.transport;version="[5.1.4,5.2.0)",
- org.eclipse.jgit.util;version="[5.1.4,5.2.0)"
+Export-Package: org.eclipse.jgit.awtui;version="5.2.0"
+Import-Package: org.eclipse.jgit.errors;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.lib;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.nls;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revplot;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.revwalk;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.transport;version="[5.2.0,5.3.0)",
+ org.eclipse.jgit.util;version="[5.2.0,5.3.0)"
diff --git a/org.eclipse.jgit.ui/pom.xml b/org.eclipse.jgit.ui/pom.xml
index 9e47b24..08f9c10 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-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 f96336d..e4b7ba7 100644
--- a/org.eclipse.jgit/.settings/.api_filters
+++ b/org.eclipse.jgit/.settings/.api_filters
@@ -1,13 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <component id="org.eclipse.jgit" version="2">
-    <resource path="META-INF/MANIFEST.MF">
-        <filter id="924844039">
-            <message_arguments>
-                <message_argument value="5.1.3"/>
-                <message_argument value="5.1.0"/>
-            </message_arguments>
-        </filter>
-    </resource>
     <resource path="src/org/eclipse/jgit/lib/GitmoduleEntry.java" type="org.eclipse.jgit.lib.GitmoduleEntry">
         <filter id="1109393411">
             <message_arguments>
@@ -24,4 +16,12 @@
             </message_arguments>
         </filter>
     </resource>
+    <resource path="src/org/eclipse/jgit/revwalk/DepthWalk.java" type="org.eclipse.jgit.revwalk.DepthWalk">
+        <filter id="404000815">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.revwalk.DepthWalk"/>
+                <message_argument value="getDeepenSince()"/>
+            </message_arguments>
+        </filter>
+    </resource>
 </component>
diff --git a/org.eclipse.jgit/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit/.settings/org.eclipse.jdt.core.prefs
index 13c32a6..ef6f5e7 100644
--- a/org.eclipse.jgit/.settings/org.eclipse.jdt.core.prefs
+++ b/org.eclipse.jgit/.settings/org.eclipse.jdt.core.prefs
@@ -91,7 +91,7 @@
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
diff --git a/org.eclipse.jgit/.settings/org.eclipse.mylyn.team.ui.prefs b/org.eclipse.jgit/.settings/org.eclipse.mylyn.team.ui.prefs
index 0cba949..2fca432 100644
--- a/org.eclipse.jgit/.settings/org.eclipse.mylyn.team.ui.prefs
+++ b/org.eclipse.jgit/.settings/org.eclipse.mylyn.team.ui.prefs
@@ -1,3 +1,3 @@
 #Tue Jul 19 20:11:28 CEST 2011
-commit.comment.template=${task.description} \n\nBug\: ${task.key}
+commit.comment.template=${task.description}\n\nBug\: ${task.key}
 eclipse.preferences.version=1
diff --git a/org.eclipse.jgit/META-INF/MANIFEST.MF b/org.eclipse.jgit/META-INF/MANIFEST.MF
index c7fe72c..2b9ed08 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: 5.1.4.qualifier
+Bundle-Version: 5.2.0.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
-Export-Package: org.eclipse.jgit.annotations;version="5.1.4",
- org.eclipse.jgit.api;version="5.1.4";
+Export-Package: org.eclipse.jgit.annotations;version="5.2.0",
+ org.eclipse.jgit.api;version="5.2.0";
   uses:="org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.diff,
@@ -22,52 +22,52 @@
    org.eclipse.jgit.submodule,
    org.eclipse.jgit.transport,
    org.eclipse.jgit.merge",
- org.eclipse.jgit.api.errors;version="5.1.4";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.errors",
- org.eclipse.jgit.attributes;version="5.1.4",
- org.eclipse.jgit.blame;version="5.1.4";
+ org.eclipse.jgit.api.errors;version="5.2.0";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.errors",
+ org.eclipse.jgit.attributes;version="5.2.0",
+ org.eclipse.jgit.blame;version="5.2.0";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.diff",
- org.eclipse.jgit.diff;version="5.1.4";
+ org.eclipse.jgit.diff;version="5.2.0";
   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="5.1.4";
+ org.eclipse.jgit.dircache;version="5.2.0";
   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="5.1.4";
+ org.eclipse.jgit.errors;version="5.2.0";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.internal.storage.pack,
    org.eclipse.jgit.transport,
    org.eclipse.jgit.dircache",
- org.eclipse.jgit.events;version="5.1.4";uses:="org.eclipse.jgit.lib",
- org.eclipse.jgit.fnmatch;version="5.1.4",
- org.eclipse.jgit.gitrepo;version="5.1.4";
+ org.eclipse.jgit.events;version="5.2.0";uses:="org.eclipse.jgit.lib",
+ org.eclipse.jgit.fnmatch;version="5.2.0",
+ org.eclipse.jgit.gitrepo;version="5.2.0";
   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="5.1.4";x-internal:=true,
- org.eclipse.jgit.hooks;version="5.1.4";uses:="org.eclipse.jgit.lib",
- org.eclipse.jgit.ignore;version="5.1.4",
- org.eclipse.jgit.ignore.internal;version="5.1.4";x-friends:="org.eclipse.jgit.test",
- org.eclipse.jgit.internal;version="5.1.4";x-friends:="org.eclipse.jgit.test,org.eclipse.jgit.http.test",
- org.eclipse.jgit.internal.fsck;version="5.1.4";x-friends:="org.eclipse.jgit.test",
- org.eclipse.jgit.internal.ketch;version="5.1.4";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.internal.storage.dfs;version="5.1.4";
+ org.eclipse.jgit.gitrepo.internal;version="5.2.0";x-internal:=true,
+ org.eclipse.jgit.hooks;version="5.2.0";uses:="org.eclipse.jgit.lib",
+ org.eclipse.jgit.ignore;version="5.2.0",
+ org.eclipse.jgit.ignore.internal;version="5.2.0";x-friends:="org.eclipse.jgit.test",
+ org.eclipse.jgit.internal;version="5.2.0";x-friends:="org.eclipse.jgit.test,org.eclipse.jgit.http.test",
+ org.eclipse.jgit.internal.fsck;version="5.2.0";x-friends:="org.eclipse.jgit.test",
+ org.eclipse.jgit.internal.ketch;version="5.2.0";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.storage.dfs;version="5.2.0";
   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="5.1.4";
+ org.eclipse.jgit.internal.storage.file;version="5.2.0";
   x-friends:="org.eclipse.jgit.test,
    org.eclipse.jgit.junit,
    org.eclipse.jgit.junit.http,
@@ -75,12 +75,13 @@
    org.eclipse.jgit.lfs,
    org.eclipse.jgit.pgm,
    org.eclipse.jgit.pgm.test",
- org.eclipse.jgit.internal.storage.io;version="5.1.4";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.internal.storage.pack;version="5.1.4";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.internal.storage.reftable;version="5.1.4";
+ org.eclipse.jgit.internal.storage.io;version="5.2.0";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.storage.pack;version="5.2.0";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.storage.reftable;version="5.2.0";
   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="5.1.4";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.lib;version="5.1.4";
+ org.eclipse.jgit.internal.storage.reftree;version="5.2.0";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.transport.parser;version="5.2.0",
+ org.eclipse.jgit.lib;version="5.2.0";
   uses:="org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.util,
@@ -90,33 +91,33 @@
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.transport,
    org.eclipse.jgit.submodule",
- org.eclipse.jgit.lib.internal;version="5.1.4";x-internal:=true,
- org.eclipse.jgit.merge;version="5.1.4";
+ org.eclipse.jgit.lib.internal;version="5.2.0";x-internal:=true,
+ org.eclipse.jgit.merge;version="5.2.0";
   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="5.1.4",
- org.eclipse.jgit.notes;version="5.1.4";
+ org.eclipse.jgit.nls;version="5.2.0",
+ org.eclipse.jgit.notes;version="5.2.0";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.merge",
- org.eclipse.jgit.patch;version="5.1.4";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.diff",
- org.eclipse.jgit.revplot;version="5.1.4";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.revwalk",
- org.eclipse.jgit.revwalk;version="5.1.4";
+ org.eclipse.jgit.patch;version="5.2.0";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.diff",
+ org.eclipse.jgit.revplot;version="5.2.0";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.revwalk",
+ org.eclipse.jgit.revwalk;version="5.2.0";
   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="5.1.4";uses:="org.eclipse.jgit.revwalk,org.eclipse.jgit.lib,org.eclipse.jgit.util",
- org.eclipse.jgit.storage.file;version="5.1.4";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.util",
- org.eclipse.jgit.storage.pack;version="5.1.4";uses:="org.eclipse.jgit.lib",
- org.eclipse.jgit.submodule;version="5.1.4";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.treewalk.filter,org.eclipse.jgit.treewalk",
- org.eclipse.jgit.transport;version="5.1.4";
+ org.eclipse.jgit.revwalk.filter;version="5.2.0";uses:="org.eclipse.jgit.revwalk,org.eclipse.jgit.lib,org.eclipse.jgit.util",
+ org.eclipse.jgit.storage.file;version="5.2.0";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.util",
+ org.eclipse.jgit.storage.pack;version="5.2.0";uses:="org.eclipse.jgit.lib",
+ org.eclipse.jgit.submodule;version="5.2.0";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.treewalk.filter,org.eclipse.jgit.treewalk",
+ org.eclipse.jgit.transport;version="5.2.0";
   uses:="org.eclipse.jgit.transport.resolver,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.internal.storage.pack,
@@ -128,24 +129,24 @@
    org.eclipse.jgit.transport.http,
    org.eclipse.jgit.errors,
    org.eclipse.jgit.storage.pack",
- org.eclipse.jgit.transport.http;version="5.1.4";uses:="javax.net.ssl",
- org.eclipse.jgit.transport.resolver;version="5.1.4";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.transport",
- org.eclipse.jgit.treewalk;version="5.1.4";
+ org.eclipse.jgit.transport.http;version="5.2.0";uses:="javax.net.ssl",
+ org.eclipse.jgit.transport.resolver;version="5.2.0";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.transport",
+ org.eclipse.jgit.treewalk;version="5.2.0";
   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="5.1.4";uses:="org.eclipse.jgit.treewalk",
- org.eclipse.jgit.util;version="5.1.4";
+ org.eclipse.jgit.treewalk.filter;version="5.2.0";uses:="org.eclipse.jgit.treewalk",
+ org.eclipse.jgit.util;version="5.2.0";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.transport.http,
    org.eclipse.jgit.storage.file,
    org.ietf.jgss",
- org.eclipse.jgit.util.io;version="5.1.4",
- org.eclipse.jgit.util.sha1;version="5.1.4",
- org.eclipse.jgit.util.time;version="5.1.4"
+ org.eclipse.jgit.util.io;version="5.2.0",
+ org.eclipse.jgit.util.sha1;version="5.2.0",
+ org.eclipse.jgit.util.time;version="5.2.0"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: com.googlecode.javaewah;version="[1.1.6,2.0.0)",
  com.jcraft.jsch;version="[0.1.37,0.2.0)",
diff --git a/org.eclipse.jgit/META-INF/SOURCE-MANIFEST.MF b/org.eclipse.jgit/META-INF/SOURCE-MANIFEST.MF
index b9ff58c..53adf99 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: 5.1.4.qualifier
-Eclipse-SourceBundle: org.eclipse.jgit;version="5.1.4.qualifier";roots="."
+Bundle-Version: 5.2.0.qualifier
+Eclipse-SourceBundle: org.eclipse.jgit;version="5.2.0.qualifier";roots="."
diff --git a/org.eclipse.jgit/pom.xml b/org.eclipse.jgit/pom.xml
index b572145..0b31c46 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>5.1.4-SNAPSHOT</version>
+    <version>5.2.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit</artifactId>
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 3f1d212..b3f7b89 100644
--- a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
+++ b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
@@ -769,7 +769,9 @@
 uriNotFoundWithMessage={0} not found: {1}
 URINotSupported=URI not supported: {0}
 userConfigFileInvalid=User config file {0} invalid {1}
+validatingGitModules=Validating .gitmodules files
 walkFailure=Walk failure.
+wantNoSpaceWithCapabilities=No space between oid and first capability in first want line
 wantNotValid=want {0} not valid
 weeksAgo={0} weeks ago
 windowSizeMustBeLesserThanLimit=Window size must be < limit
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java
index 5b84032..c6f3c67 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java
@@ -42,11 +42,14 @@
  */
 package org.eclipse.jgit.api;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
+
 import java.io.File;
 import java.io.FileOutputStream;
-import java.io.FileWriter;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.OutputStreamWriter;
+import java.io.Writer;
 import java.nio.file.StandardCopyOption;
 import java.text.MessageFormat;
 import java.util.ArrayList;
@@ -258,7 +261,8 @@ private void apply(File f, FileHeader fh)
 		if (sb.length() > 0) {
 			sb.deleteCharAt(sb.length() - 1);
 		}
-		try (FileWriter fw = new FileWriter(f)) {
+		try (Writer fw = new OutputStreamWriter(new FileOutputStream(f),
+				UTF_8)) {
 			fw.write(sb.toString());
 		}
 
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 5c06bac..73af8ba 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
@@ -283,12 +283,11 @@ private FetchResult fetch(Repository clonedRepo, URIish u)
 		config.addURI(u);
 
 		final String dst = (bare ? Constants.R_HEADS : Constants.R_REMOTES
-				+ config.getName() + "/") + "*"; //$NON-NLS-1$//$NON-NLS-2$
-		RefSpec refSpec = new RefSpec();
-		refSpec = refSpec.setForceUpdate(true);
-		refSpec = refSpec.setSourceDestination(Constants.R_HEADS + "*", dst); //$NON-NLS-1$
+				+ config.getName() + '/') + '*';
+		boolean fetchAll = cloneAllBranches || branchesToClone == null
+				|| branchesToClone.isEmpty();
 
-		config.addFetchRefSpec(refSpec);
+		config.setFetchRefSpecs(calculateRefSpecs(fetchAll, dst));
 		config.update(clonedRepo.getConfig());
 
 		clonedRepo.getConfig().save();
@@ -297,27 +296,25 @@ private FetchResult fetch(Repository clonedRepo, URIish u)
 		FetchCommand command = new FetchCommand(clonedRepo);
 		command.setRemote(remote);
 		command.setProgressMonitor(monitor);
-		command.setTagOpt(TagOpt.FETCH_TAGS);
+		command.setTagOpt(fetchAll ? TagOpt.FETCH_TAGS : TagOpt.AUTO_FOLLOW);
 		configure(command);
 
-		List<RefSpec> specs = calculateRefSpecs(dst);
-		command.setRefSpecs(specs);
-
 		return command.call();
 	}
 
-	private List<RefSpec> calculateRefSpecs(String dst) {
+	private List<RefSpec> calculateRefSpecs(boolean fetchAll, String dst) {
 		RefSpec wcrs = new RefSpec();
 		wcrs = wcrs.setForceUpdate(true);
-		wcrs = wcrs.setSourceDestination(Constants.R_HEADS + "*", dst); //$NON-NLS-1$
+		wcrs = wcrs.setSourceDestination(Constants.R_HEADS + '*', dst);
 		List<RefSpec> specs = new ArrayList<>();
-		if (cloneAllBranches)
-			specs.add(wcrs);
-		else if (branchesToClone != null
-				&& branchesToClone.size() > 0) {
-			for (String selectedRef : branchesToClone)
-				if (wcrs.matchSource(selectedRef))
+		if (!fetchAll) {
+			for (String selectedRef : branchesToClone) {
+				if (wcrs.matchSource(selectedRef)) {
 					specs.add(wcrs.expandFromSource(selectedRef));
+				}
+			}
+		} else {
+			specs.add(wcrs);
 		}
 		return specs;
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/ListBranchCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/ListBranchCommand.java
index 28a27a9..29a51a0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ListBranchCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ListBranchCommand.java
@@ -44,6 +44,10 @@
  */
 package org.eclipse.jgit.api;
 
+import static org.eclipse.jgit.lib.Constants.HEAD;
+import static org.eclipse.jgit.lib.Constants.R_HEADS;
+import static org.eclipse.jgit.lib.Constants.R_REMOTES;
+
 import java.io.IOException;
 import java.text.MessageFormat;
 import java.util.ArrayList;
@@ -56,7 +60,6 @@
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.RefNotFoundException;
 import org.eclipse.jgit.internal.JGitText;
-import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
@@ -113,17 +116,18 @@ public List<Ref> call() throws GitAPIException {
 			Collection<Ref> refs = new ArrayList<>();
 
 			// Also return HEAD if it's detached
-			Ref head = repo.exactRef(Constants.HEAD);
-			if (head != null && head.getLeaf().getName().equals(Constants.HEAD))
+			Ref head = repo.exactRef(HEAD);
+			if (head != null && head.getLeaf().getName().equals(HEAD)) {
 				refs.add(head);
+			}
 
 			if (listMode == null) {
-				refs.addAll(getRefs(Constants.R_HEADS));
+				refs.addAll(repo.getRefDatabase().getRefsByPrefix(R_HEADS));
 			} else if (listMode == ListMode.REMOTE) {
-				refs.addAll(getRefs(Constants.R_REMOTES));
+				refs.addAll(repo.getRefDatabase().getRefsByPrefix(R_REMOTES));
 			} else {
-				refs.addAll(getRefs(Constants.R_HEADS));
-				refs.addAll(getRefs(Constants.R_REMOTES));
+				refs.addAll(repo.getRefDatabase().getRefsByPrefix(R_HEADS,
+						R_REMOTES));
 			}
 			resultRefs = new ArrayList<>(filterRefs(refs));
 		} catch (IOException e) {
@@ -185,8 +189,4 @@ public ListBranchCommand setContains(String containsCommitish) {
 		this.containsCommitish = containsCommitish;
 		return this;
 	}
-
-	private Collection<Ref> getRefs(String prefix) throws IOException {
-		return repo.getRefDatabase().getRefsByPrefix(prefix);
-	}
 }
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 1783c41..9653c36 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
@@ -43,6 +43,8 @@
  */
 package org.eclipse.jgit.api;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
+
 import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -1015,8 +1017,7 @@ private RebaseResult stop(RevCommit commitToPick, RebaseResult.Status status)
 			df.setRepository(repo);
 			df.format(commitToPick.getParent(0), commitToPick);
 		}
-		rebaseState.createFile(PATCH, new String(bos.toByteArray(),
-				Constants.CHARACTER_ENCODING));
+		rebaseState.createFile(PATCH, new String(bos.toByteArray(), UTF_8));
 		rebaseState.createFile(STOPPED_SHA,
 				repo.newObjectReader()
 				.abbreviate(
@@ -1733,7 +1734,7 @@ private static void createFile(File parentDir, String name,
 				throws IOException {
 			File file = new File(parentDir, name);
 			try (FileOutputStream fos = new FileOutputStream(file)) {
-				fos.write(content.getBytes(Constants.CHARACTER_ENCODING));
+				fos.write(content.getBytes(UTF_8));
 				fos.write('\n');
 			}
 		}
@@ -1741,7 +1742,7 @@ private static void createFile(File parentDir, String name,
 		private static void appendToFile(File file, String content)
 				throws IOException {
 			try (FileOutputStream fos = new FileOutputStream(file, true)) {
-				fos.write(content.getBytes(Constants.CHARACTER_ENCODING));
+				fos.write(content.getBytes(UTF_8));
 				fos.write('\n');
 			}
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleAddCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleAddCommand.java
index 244a156..f92455a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleAddCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleAddCommand.java
@@ -179,21 +179,6 @@ public Repository call() throws GitAPIException {
 			// Use the path as the default.
 			name = path;
 		}
-		if (name.contains("/../") || name.contains("\\..\\") //$NON-NLS-1$ //$NON-NLS-2$
-				|| name.startsWith("../") || name.startsWith("..\\") //$NON-NLS-1$ //$NON-NLS-2$
-				|| name.endsWith("/..") || name.endsWith("\\..")) { //$NON-NLS-1$ //$NON-NLS-2$
-			// Submodule names are used to store the submodule repositories
-			// under $GIT_DIR/modules. Having ".." in submodule names makes a
-			// vulnerability (CVE-2018-11235
-			// https://bugs.eclipse.org/bugs/show_bug.cgi?id=535027#c0)
-			// Reject the names with them. The callers need to make sure the
-			// names free from these. We don't automatically replace these
-			// characters or canonicalize by regarding the name as a file path.
-			// Since Path class is platform dependent, we manually check '/' and
-			// '\\' patterns here.
-			throw new IllegalArgumentException(MessageFormat
-					.format(JGitText.get().invalidNameContainsDotDot, name));
-		}
 
 		try {
 			SubmoduleValidator.assertValidSubmoduleName(name);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheIterator.java b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheIterator.java
index 19c916f..6196e75 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheIterator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheIterator.java
@@ -44,6 +44,8 @@
 
 package org.eclipse.jgit.dircache;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
+
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.Collections;
@@ -75,7 +77,7 @@
 public class DirCacheIterator extends AbstractTreeIterator {
 	/** Byte array holding ".gitattributes" string */
 	private static final byte[] DOT_GIT_ATTRIBUTES_BYTES = Constants.DOT_GIT_ATTRIBUTES
-			.getBytes();
+			.getBytes(UTF_8);
 
 	/** The cache this iterator was created to walk. */
 	protected final DirCache cache;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/events/WorkingTreeModifiedEvent.java b/org.eclipse.jgit/src/org/eclipse/jgit/events/WorkingTreeModifiedEvent.java
index 9fbcc4d..afd7889 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/events/WorkingTreeModifiedEvent.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/events/WorkingTreeModifiedEvent.java
@@ -94,7 +94,8 @@ public boolean isEmpty() {
 	 *
 	 * @return the set
 	 */
-	public @NonNull Collection<String> getModified() {
+	@NonNull
+	public Collection<String> getModified() {
 		Collection<String> result = modified;
 		if (result == null) {
 			result = Collections.emptyList();
@@ -109,7 +110,8 @@ public boolean isEmpty() {
 	 *
 	 * @return the set
 	 */
-	public @NonNull Collection<String> getDeleted() {
+	@NonNull
+	public Collection<String> getDeleted() {
 		Collection<String> result = deleted;
 		if (result == null) {
 			result = Collections.emptyList();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/ManifestParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/ManifestParser.java
index 26e783d..8e46341 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/ManifestParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/ManifestParser.java
@@ -358,7 +358,8 @@ public List<RepoProject> getProjects() {
 	 *
 	 * @return filtered projects list reference, never null
 	 */
-	public @NonNull List<RepoProject> getFilteredProjects() {
+	@NonNull
+	public List<RepoProject> getFilteredProjects() {
 		return filteredProjects;
 	}
 
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 45a239d..5a73cdc 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java
@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.gitrepo;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.lib.Constants.DEFAULT_REMOTE_NAME;
 import static org.eclipse.jgit.lib.Constants.R_REMOTES;
 
@@ -606,8 +607,7 @@ public RevCommit call() throws GitAPIException {
 							}
 
 							objectId = inserter.insert(Constants.OBJ_BLOB,
-								link.getBytes(
-									Constants.CHARACTER_ENCODING));
+									link.getBytes(UTF_8));
 							dcEntry = new DirCacheEntry(linkfile.dest);
 							dcEntry.setObjectId(objectId);
 							dcEntry.setFileMode(FileMode.SYMLINK);
@@ -620,7 +620,7 @@ public RevCommit call() throws GitAPIException {
 				// create a new DirCacheEntry for .gitmodules file.
 				final DirCacheEntry dcEntry = new DirCacheEntry(Constants.DOT_GIT_MODULES);
 				ObjectId objectId = inserter.insert(Constants.OBJ_BLOB,
-						content.getBytes(Constants.CHARACTER_ENCODING));
+						content.getBytes(UTF_8));
 				dcEntry.setObjectId(objectId);
 				dcEntry.setFileMode(FileMode.REGULAR_FILE);
 				builder.add(dcEntry);
@@ -629,7 +629,7 @@ public RevCommit call() throws GitAPIException {
 					// create a new DirCacheEntry for .gitattributes file.
 					final DirCacheEntry dcEntryAttr = new DirCacheEntry(Constants.DOT_GIT_ATTRIBUTES);
 					ObjectId attrId = inserter.insert(Constants.OBJ_BLOB,
-							attributes.toString().getBytes(Constants.CHARACTER_ENCODING));
+							attributes.toString().getBytes(UTF_8));
 					dcEntryAttr.setObjectId(attrId);
 					dcEntryAttr.setFileMode(FileMode.REGULAR_FILE);
 					builder.add(dcEntryAttr);
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 c11ae5a..9f0e3e0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
@@ -830,7 +830,9 @@ public static JGitText get() {
 	/***/ public String uriNotFoundWithMessage;
 	/***/ public String URINotSupported;
 	/***/ public String userConfigFileInvalid;
+	/***/ public String validatingGitModules;
 	/***/ public String walkFailure;
+	/***/ public String wantNoSpaceWithCapabilities;
 	/***/ public String wantNotValid;
 	/***/ public String weeksAgo;
 	/***/ public String windowSizeMustBeLesserThanLimit;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckError.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckError.java
index 131b004..335ac66 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckError.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckError.java
@@ -61,20 +61,21 @@ public static class CorruptObject {
 
 		final int type;
 
-		ObjectChecker.ErrorType errorType;
+		@Nullable
+		final ObjectChecker.ErrorType errorType;
 
 		/**
 		 * @param id
 		 *            the object identifier.
 		 * @param type
 		 *            type of the object.
+		 * @param errorType
+		 *            kind of error
 		 */
-		public CorruptObject(ObjectId id, int type) {
+		public CorruptObject(ObjectId id, int type,
+				@Nullable ObjectChecker.ErrorType errorType) {
 			this.id = id;
 			this.type = type;
-		}
-
-		void setErrorType(ObjectChecker.ErrorType errorType) {
 			this.errorType = errorType;
 		}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckPackParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckPackParser.java
index 5397ba4..50594df 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckPackParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/fsck/FsckPackParser.java
@@ -174,12 +174,8 @@ protected void verifySafeObject(final AnyObjectId id, final int type,
 		try {
 			super.verifySafeObject(id, type, data);
 		} catch (CorruptObjectException e) {
-			// catch the exception and continue parse the pack file
-			CorruptObject o = new CorruptObject(id.toObjectId(), type);
-			if (e.getErrorType() != null) {
-				o.setErrorType(e.getErrorType());
-			}
-			corruptObjects.add(o);
+			corruptObjects.add(
+					new CorruptObject(id.toObjectId(), type, e.getErrorType()));
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsFsck.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsFsck.java
index 3f96d09..c0e24c0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsFsck.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsFsck.java
@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.internal.storage.dfs;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.internal.storage.pack.PackExt.INDEX;
 import static org.eclipse.jgit.internal.storage.pack.PackExt.PACK;
 
@@ -54,12 +55,18 @@
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.internal.fsck.FsckError;
 import org.eclipse.jgit.internal.fsck.FsckError.CorruptIndex;
+import org.eclipse.jgit.internal.fsck.FsckError.CorruptObject;
 import org.eclipse.jgit.internal.fsck.FsckPackParser;
 import org.eclipse.jgit.internal.storage.dfs.DfsObjDatabase.PackSource;
+import org.eclipse.jgit.internal.submodule.SubmoduleValidator;
+import org.eclipse.jgit.internal.submodule.SubmoduleValidator.SubmoduleValidationException;
+import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.GitmoduleEntry;
 import org.eclipse.jgit.lib.NullProgressMonitor;
 import org.eclipse.jgit.lib.ObjectChecker;
 import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectLoader;
 import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.revwalk.ObjectWalk;
@@ -102,6 +109,7 @@ public FsckError check(ProgressMonitor pm) throws IOException {
 
 		FsckError errors = new FsckError();
 		if (!connectivityOnly) {
+			objChecker.reset();
 			checkPacks(pm, errors);
 		}
 		checkConnectivity(pm, errors);
@@ -128,6 +136,8 @@ private void checkPacks(ProgressMonitor pm, FsckError errors)
 				}
 			}
 		}
+
+		checkGitModules(pm, errors);
 	}
 
 	private void verifyPack(ProgressMonitor pm, FsckError errors, DfsReader ctx,
@@ -142,6 +152,28 @@ private void verifyPack(ProgressMonitor pm, FsckError errors, DfsReader ctx,
 		fpp.verifyIndex(pack.getPackIndex(ctx));
 	}
 
+	private void checkGitModules(ProgressMonitor pm, FsckError errors)
+			throws IOException {
+		pm.beginTask(JGitText.get().validatingGitModules,
+				objChecker.getGitsubmodules().size());
+		for (GitmoduleEntry entry : objChecker.getGitsubmodules()) {
+			AnyObjectId blobId = entry.getBlobId();
+			ObjectLoader blob = objdb.open(blobId, Constants.OBJ_BLOB);
+
+			try {
+				SubmoduleValidator.assertValidGitModulesFile(
+						new String(blob.getBytes(), UTF_8));
+			} catch (SubmoduleValidationException e) {
+				CorruptObject co = new FsckError.CorruptObject(
+						blobId.toObjectId(), Constants.OBJ_BLOB,
+						e.getFsckMessageId());
+				errors.getCorruptObjects().add(co);
+			}
+			pm.update(1);
+		}
+		pm.endTask();
+	}
+
 	private void checkConnectivity(ProgressMonitor pm, FsckError errors)
 			throws IOException {
 		pm.beginTask(JGitText.get().countingObjects, ProgressMonitor.UNKNOWN);
@@ -179,6 +211,9 @@ private void checkConnectivity(ProgressMonitor pm, FsckError errors)
 	 * Use a customized object checker instead of the default one. Caller can
 	 * specify a skip list to ignore some errors.
 	 *
+	 * It will be reset at the start of each {{@link #check(ProgressMonitor)}
+	 * call.
+	 *
 	 * @param objChecker
 	 *            A customized object checker.
 	 */
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 24723d8..4d5c1c0 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
@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.internal.storage.file;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.internal.storage.pack.PackExt.INDEX;
 import static org.eclipse.jgit.internal.storage.pack.PackExt.PACK;
 
@@ -50,7 +51,6 @@
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.IOException;
 import java.nio.file.AtomicMoveNotSupportedException;
 import java.nio.file.Files;
@@ -1034,8 +1034,8 @@ Set<AlternateHandle.Id> addMe(Set<AlternateHandle.Id> skips) {
 	}
 
 	private static BufferedReader open(File f)
-			throws FileNotFoundException {
-		return new BufferedReader(new FileReader(f));
+			throws IOException, FileNotFoundException {
+		return Files.newBufferedReader(f.toPath(), UTF_8);
 	}
 
 	private AlternateHandle openAlternate(String location)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexRemapper.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexRemapper.java
index 7069588..964cc4d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexRemapper.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackBitmapIndexRemapper.java
@@ -207,7 +207,7 @@ public EWAHCompressedBitmap getBitmap(AnyObjectId objectId) {
 	}
 
 	/** An entry in the old PackBitmapIndex. */
-	public final class Entry extends ObjectId {
+	public static final class Entry extends ObjectId {
 		private final int flags;
 
 		Entry(AnyObjectId src, int flags) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackOutputStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackOutputStream.java
index 7f38a7b..eb777be 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackOutputStream.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackOutputStream.java
@@ -187,6 +187,7 @@ public final void writeObject(ObjectToPack otp) throws IOException {
 	 * @throws java.io.IOException
 	 *             the underlying stream refused to accept the header.
 	 */
+	@SuppressWarnings("ShortCircuitBoolean")
 	public final void writeHeader(ObjectToPack otp, long rawLength)
 			throws IOException {
 		ObjectToPack b = otp.getDeltaBase();
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 3651631..7b872b1 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
@@ -45,13 +45,17 @@
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_PATH;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_URL;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_SUBMODULE_SECTION;
+import static org.eclipse.jgit.lib.ObjectChecker.ErrorType.GITMODULES_NAME;
+import static org.eclipse.jgit.lib.ObjectChecker.ErrorType.GITMODULES_PARSE;
+import static org.eclipse.jgit.lib.ObjectChecker.ErrorType.GITMODULES_PATH;
+import static org.eclipse.jgit.lib.ObjectChecker.ErrorType.GITMODULES_URL;
 
-import java.io.IOException;
 import java.text.MessageFormat;
 
 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Config;
+import org.eclipse.jgit.lib.ObjectChecker;
 
 /**
  * Validations for the git submodule fields (name, path, uri).
@@ -66,15 +70,30 @@ public class SubmoduleValidator {
 	 */
 	public static class SubmoduleValidationException extends Exception {
 
+		private static final long serialVersionUID = 1L;
+
+		private final ObjectChecker.ErrorType fsckMessageId;
+
 		/**
 		 * @param message
 		 *            Description of the problem
+		 * @param fsckMessageId
+		 *            Error identifier, following the git fsck fsck.<msg-id>
+		 *            format
 		 */
-		public SubmoduleValidationException(String message) {
+		SubmoduleValidationException(String message,
+				ObjectChecker.ErrorType fsckMessageId) {
 			super(message);
+			this.fsckMessageId = fsckMessageId;
 		}
 
-		private static final long serialVersionUID = 1L;
+
+		/**
+		 * @return the error identifier
+		 */
+		public ObjectChecker.ErrorType getFsckMessageId() {
+			return fsckMessageId;
+		}
 	}
 
 	/**
@@ -100,13 +119,15 @@ public static void assertValidSubmoduleName(String name)
 			// Since Path class is platform dependent, we manually check '/' and
 			// '\\' patterns here.
 			throw new SubmoduleValidationException(MessageFormat
-					.format(JGitText.get().invalidNameContainsDotDot, name));
+					.format(JGitText.get().invalidNameContainsDotDot, name),
+					GITMODULES_NAME);
 		}
 
 		if (name.startsWith("-")) { //$NON-NLS-1$
 			throw new SubmoduleValidationException(
 					MessageFormat.format(
-							JGitText.get().submoduleNameInvalid, name));
+							JGitText.get().submoduleNameInvalid, name),
+					GITMODULES_NAME);
 		}
 	}
 
@@ -123,7 +144,8 @@ public static void assertValidSubmoduleUri(String uri)
 		if (uri.startsWith("-")) { //$NON-NLS-1$
 			throw new SubmoduleValidationException(
 					MessageFormat.format(
-							JGitText.get().submoduleUrlInvalid, uri));
+							JGitText.get().submoduleUrlInvalid, uri),
+					GITMODULES_URL);
 		}
 	}
 
@@ -140,19 +162,22 @@ public static void assertValidSubmodulePath(String path)
 		if (path.startsWith("-")) { //$NON-NLS-1$
 			throw new SubmoduleValidationException(
 					MessageFormat.format(
-							JGitText.get().submodulePathInvalid, path));
+							JGitText.get().submodulePathInvalid, path),
+					GITMODULES_PATH);
 		}
 	}
 
 	/**
+	 * Validate a .gitmodules file
+	 *
 	 * @param gitModulesContents
 	 *            Contents of a .gitmodule file. They will be parsed internally.
-	 * @throws IOException
-	 *             If the contents
+	 * @throws SubmoduleValidationException
+	 *             if the contents don't look like a configuration file or field
+	 *             values are not valid
 	 */
 	public static void assertValidGitModulesFile(String gitModulesContents)
-			throws IOException {
-		// Validate .gitmodules file
+			throws SubmoduleValidationException {
 		Config c = new Config();
 		try {
 			c.fromText(gitModulesContents);
@@ -173,12 +198,9 @@ public static void assertValidGitModulesFile(String gitModulesContents)
 				}
 			}
 		} catch (ConfigInvalidException e) {
-			throw new IOException(
-					MessageFormat.format(
-							JGitText.get().invalidGitModules,
-							e));
-		} catch (SubmoduleValidationException e) {
-			throw new IOException(e.getMessage(), e);
+			throw new SubmoduleValidationException(
+					JGitText.get().invalidGitModules,
+					GITMODULES_PARSE);
 		}
 	}
 }
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
new file mode 100644
index 0000000..1ac9b18
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/parser/FirstWant.java
@@ -0,0 +1,120 @@
+/*
+ * 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 java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.eclipse.jgit.errors.PackProtocolException;
+import org.eclipse.jgit.internal.JGitText;
+
+/**
+ * In the pack negotiation phase (protocol v0/v1), the client sends a list of
+ * wants. The first "want" line is special, as it (can) have a list of
+ * capabilities appended.
+ *
+ * E.g. "want oid cap1 cap2 cap3"
+ *
+ * Do not confuse this line with the first one in the reference advertisement,
+ * which is sent by the server, looks like
+ * "b8f7c471373b8583ced0025cfad8c9916c484b76 HEAD\0 cap1 cap2 cap3" and is
+ * parsed by the BasePackConnection.readAdvertisedRefs method.
+ *
+ * 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;
+
+	private final Set<String> capabilities;
+
+	/**
+	 * Parse the first want line in the protocol v0/v1 pack negotiation.
+	 *
+	 * @param line
+	 *            line from the client.
+	 * @return an instance of FirstWant
+	 * @throws PackProtocolException
+	 *             if the line doesn't follow the protocol format.
+	 */
+	public static FirstWant fromLine(String line) throws PackProtocolException {
+		String wantLine;
+		Set<String> capabilities;
+
+		if (line.length() > 45) {
+			String opt = line.substring(45);
+			if (!opt.startsWith(" ")) { //$NON-NLS-1$
+				throw new PackProtocolException(JGitText.get().wantNoSpaceWithCapabilities);
+			}
+			opt = opt.substring(1);
+			HashSet<String> opts = new HashSet<>(
+					Arrays.asList(opt.split(" "))); //$NON-NLS-1$
+			wantLine = line.substring(0, 45);
+			capabilities = Collections.unmodifiableSet(opts);
+		} else {
+			wantLine = line;
+			capabilities = Collections.emptySet();
+		}
+
+		return new FirstWant(wantLine, capabilities);
+	}
+
+	private FirstWant(String line, Set<String> capabilities) {
+		this.line = line;
+		this.capabilities = capabilities;
+	}
+
+	/** @return non-capabilities part of the line. */
+	public String getLine() {
+		return line;
+	}
+
+	/** @return capabilities parsed from the line as an immutable set. */
+	public Set<String> getCapabilities() {
+		return capabilities;
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
index b666f21..4726975 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
@@ -62,7 +62,6 @@
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.atomic.AtomicReference;
 
-import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.events.ConfigChangedEvent;
 import org.eclipse.jgit.events.ConfigChangedListener;
@@ -868,7 +867,7 @@ private ConfigSnapshot unsetSection(final ConfigSnapshot srcState,
 
 		boolean lastWasMatch = false;
 		for (ConfigLine e : srcState.entryList) {
-			if (e.match(section, subsection)) {
+			if (e.includedFrom == null && e.match(section, subsection)) {
 				// Skip this record, it's for the section we are removing.
 				lastWasMatch = true;
 				continue;
@@ -923,7 +922,7 @@ private ConfigSnapshot replaceStringList(final ConfigSnapshot srcState,
 		//
 		while (entryIndex < entries.size() && valueIndex < values.size()) {
 			final ConfigLine e = entries.get(entryIndex);
-			if (e.match(section, subsection, name)) {
+			if (e.includedFrom == null && e.match(section, subsection, name)) {
 				entries.set(entryIndex, e.forValue(values.get(valueIndex++)));
 				insertPosition = entryIndex + 1;
 			}
@@ -935,7 +934,8 @@ private ConfigSnapshot replaceStringList(final ConfigSnapshot srcState,
 		if (valueIndex == values.size() && entryIndex < entries.size()) {
 			while (entryIndex < entries.size()) {
 				final ConfigLine e = entries.get(entryIndex++);
-				if (e.match(section, subsection, name))
+				if (e.includedFrom == null
+						&& e.match(section, subsection, name))
 					entries.remove(--entryIndex);
 			}
 		}
@@ -948,7 +948,8 @@ private ConfigSnapshot replaceStringList(final ConfigSnapshot srcState,
 				// is already a section available that matches. Insert
 				// after the last key of that section.
 				//
-				insertPosition = findSectionEnd(entries, section, subsection);
+				insertPosition = findSectionEnd(entries, section, subsection,
+						true);
 			}
 			if (insertPosition < 0) {
 				// We didn't find any matching section header for this key,
@@ -985,9 +986,14 @@ private static List<ConfigLine> copy(final ConfigSnapshot src,
 	}
 
 	private static int findSectionEnd(final List<ConfigLine> entries,
-			final String section, final String subsection) {
+			final String section, final String subsection,
+			boolean skipIncludedLines) {
 		for (int i = 0; i < entries.size(); i++) {
 			ConfigLine e = entries.get(i);
+			if (e.includedFrom != null && skipIncludedLines) {
+				continue;
+			}
+
 			if (e.match(section, subsection, null)) {
 				i++;
 				while (i < entries.size()) {
@@ -1011,6 +1017,8 @@ private static int findSectionEnd(final List<ConfigLine> entries,
 	public String toText() {
 		final StringBuilder out = new StringBuilder();
 		for (ConfigLine e : state.get().entryList) {
+			if (e.includedFrom != null)
+				continue;
 			if (e.prefix != null)
 				out.append(e.prefix);
 			if (e.section != null && e.name == null) {
@@ -1060,11 +1068,11 @@ public String toText() {
 	 *             made to {@code this}.
 	 */
 	public void fromText(String text) throws ConfigInvalidException {
-		state.set(newState(fromTextRecurse(text, 1)));
+		state.set(newState(fromTextRecurse(text, 1, null)));
 	}
 
-	private List<ConfigLine> fromTextRecurse(String text, int depth)
-			throws ConfigInvalidException {
+	private List<ConfigLine> fromTextRecurse(String text, int depth,
+			String includedFrom) throws ConfigInvalidException {
 		if (depth > MAX_DEPTH) {
 			throw new ConfigInvalidException(
 					JGitText.get().tooManyIncludeRecursions);
@@ -1073,6 +1081,7 @@ private List<ConfigLine> fromTextRecurse(String text, int depth)
 		final StringReader in = new StringReader(text);
 		ConfigLine last = null;
 		ConfigLine e = new ConfigLine();
+		e.includedFrom = includedFrom;
 		for (;;) {
 			int input = in.read();
 			if (-1 == input) {
@@ -1088,7 +1097,7 @@ private List<ConfigLine> fromTextRecurse(String text, int depth)
 				if (e.section != null)
 					last = e;
 				e = new ConfigLine();
-
+				e.includedFrom = includedFrom;
 			} else if (e.suffix != null) {
 				// Everything up until the end-of-line is in the suffix.
 				e.suffix += c;
@@ -1148,7 +1157,6 @@ private List<ConfigLine> fromTextRecurse(String text, int depth)
 	 *             if something went wrong while reading the config
 	 * @since 4.10
 	 */
-	@Nullable
 	protected byte[] readIncludedConfig(String relPath)
 			throws ConfigInvalidException {
 		return null;
@@ -1173,7 +1181,7 @@ private void addIncludedConfig(final List<ConfigLine> newEntries,
 			decoded = RawParseUtils.decode(bytes);
 		}
 		try {
-			newEntries.addAll(fromTextRecurse(decoded, depth + 1));
+			newEntries.addAll(fromTextRecurse(decoded, depth + 1, line.value));
 		} catch (ConfigInvalidException e) {
 			throw new ConfigInvalidException(MessageFormat
 					.format(JGitText.get().cannotReadFile, line.value), e);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
index d4a0280..196ce64 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
@@ -432,4 +432,18 @@ public final class ConfigConstants {
 	 * @since 4.11
 	 */
 	public static final String CONFIG_SECTION_LFS = "lfs";
+
+	/**
+	 * The "i18n" section
+	 *
+	 * @since 5.2
+	 */
+	public static final String CONFIG_SECTION_I18N = "i18n";
+
+	/**
+	 * The "logOutputEncoding" key
+	 *
+	 * @since 5.2
+	 */
+	public static final String CONFIG_KEY_LOG_OUTPUT_ENCODING = "logOutputEncoding";
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigLine.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigLine.java
index 937ba92..e623a8c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigLine.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigLine.java
@@ -73,6 +73,9 @@ class ConfigLine {
 	/** The text content after entry. */
 	String suffix;
 
+	/** The source from which this line was included from. */
+	String includedFrom;
+
 	ConfigLine forValue(String newValue) {
 		final ConfigLine e = new ConfigLine();
 		e.prefix = prefix;
@@ -81,6 +84,7 @@ ConfigLine forValue(String newValue) {
 		e.name = name;
 		e.value = newValue;
 		e.suffix = suffix;
+		e.includedFrom = includedFrom;
 		return e;
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java
index ed00554..4c55196 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java
@@ -232,11 +232,17 @@ public final class Constants {
 	 *
 	 * @deprecated Use {@link java.nio.charset.StandardCharsets#UTF_8} directly
 	 *             instead.
-	 **/
+	 */
 	@Deprecated
 	public static final Charset CHARSET;
 
-	/** Native character encoding for commit messages, file names... */
+	/**
+	 * Native character encoding for commit messages, file names...
+	 *
+	 * @deprecated Use {@link java.nio.charset.StandardCharsets#UTF_8} directly
+	 *             instead.
+	 */
+	@Deprecated
 	public static final String CHARACTER_ENCODING;
 
 	/** Default main branch name */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java
index 891c7f2..6a66cf6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java
@@ -293,7 +293,8 @@ private static IllegalArgumentException notTimeUnit(String section,
 
 	/** {@inheritDoc} */
 	@Override
-	public @NonNull List<RefSpec> getRefSpecs(Config config, String section,
+	@NonNull
+	public List<RefSpec> getRefSpecs(Config config, String section,
 			String subsection, String name) {
 		String[] values = config.getStringList(section, subsection, name);
 		List<RefSpec> result = new ArrayList<>(values.length);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectChecker.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectChecker.java
index d37fb21..127f019 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectChecker.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectChecker.java
@@ -109,7 +109,8 @@
  * the caller can provide both of these validations on its own.
  * <p>
  * Instances of this class are not thread safe, but they may be reused to
- * perform multiple object validations.
+ * perform multiple object validations, calling {@link #reset()} between them to
+ * clear the internal state (e.g. {@link #getGitsubmodules()})
  */
 public class ObjectChecker {
 	/** Header "tree " */
@@ -173,6 +174,13 @@ public enum ErrorType {
 		/***/ BAD_TIMEZONE,
 		/***/ MISSING_EMAIL,
 		/***/ MISSING_SPACE_BEFORE_DATE,
+		/** @since 5.2 */ GITMODULES_BLOB,
+		/** @since 5.2 */ GITMODULES_LARGE,
+		/** @since 5.2 */ GITMODULES_NAME,
+		/** @since 5.2 */ GITMODULES_PARSE,
+		/** @since 5.2 */ GITMODULES_PATH,
+		/** @since 5.2 */ GITMODULES_SYMLINK,
+		/** @since 5.2 */ GITMODULES_URL,
 		/***/ UNKNOWN_TYPE,
 
 		// These are unique to JGit.
@@ -1251,4 +1259,19 @@ private String normalize(byte[] raw, int ptr, int end) {
 	public List<GitmoduleEntry> getGitsubmodules() {
 		return gitsubmodules;
 	}
+
+	/**
+	 * Reset the invocation-specific state from this instance. Specifically this
+	 * clears the list of .gitmodules files encountered (see
+	 * {@link #getGitsubmodules()})
+	 *
+	 * Configurations like errors to filter, skip lists or the specified O.S.
+	 * (set via {@link #setSafeForMacOS(boolean)} or
+	 * {@link #setSafeForWindows(boolean)}) are NOT cleared.
+	 *
+	 * @since 5.2
+	 */
+	public void reset() {
+		gitsubmodules.clear();
+	}
 }
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 3170787..68929b4 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefDatabase.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefDatabase.java
@@ -415,6 +415,31 @@ public List<Ref> getRefsByPrefix(String prefix) throws IOException {
 	}
 
 	/**
+	 * Returns refs whose names start with one of the given prefixes.
+	 * <p>
+	 * The default implementation uses {@link #getRefsByPrefix(String)}.
+	 * Implementors of {@link RefDatabase} should override this method directly
+	 * if a better implementation is possible.
+	 *
+	 * @param prefixes
+	 *            strings that names of refs should start with.
+	 * @return immutable list of refs whose names start with one of
+	 *         {@code prefixes}. Refs can be unsorted and may contain duplicates
+	 *         if the prefixes overlap.
+	 * @throws java.io.IOException
+	 *             the reference space cannot be accessed.
+	 * @since 5.2
+	 */
+	@NonNull
+	public List<Ref> getRefsByPrefix(String... prefixes) throws IOException {
+		List<Ref> result = new ArrayList<>();
+		for (String prefix : prefixes) {
+			result.addAll(getRefsByPrefix(prefix));
+		}
+		return Collections.unmodifiableList(result);
+	}
+
+	/**
 	 * Check if any refs exist in the ref database.
 	 * <p>
 	 * This uses the same definition of refs as {@link #getRefs()}. In
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 5cd593e..fc3ea84 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefUpdate.java
@@ -823,7 +823,7 @@ private static RevObject safeParseOld(RevWalk rw, AnyObjectId oldId)
 	 * Handle the abstraction of storing a ref update. This is because both
 	 * updating and deleting of a ref have merge testing in common.
 	 */
-	private abstract class Store {
+	private static abstract class Store {
 		abstract Result execute(Result status) throws IOException;
 	}
 }
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 d73c05e..77d268a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
@@ -49,6 +49,7 @@
 package org.eclipse.jgit.lib;
 
 import static org.eclipse.jgit.lib.Constants.LOCK_SUFFIX;
+import static java.nio.charset.StandardCharsets.UTF_8;
 
 import java.io.BufferedOutputStream;
 import java.io.File;
@@ -1965,7 +1966,7 @@ private String readCommitMsgFile(String msgFilename) throws IOException {
 	private void writeCommitMsg(File msgFile, String msg) throws IOException {
 		if (msg != null) {
 			try (FileOutputStream fos = new FileOutputStream(msgFile)) {
-				fos.write(msg.getBytes(Constants.CHARACTER_ENCODING));
+				fos.write(msg.getBytes(UTF_8));
 			}
 		} else {
 			FileUtils.delete(msgFile, FileUtils.SKIP_MISSING);
@@ -1980,7 +1981,6 @@ private void writeCommitMsg(File msgFile, String msg) throws IOException {
 	 *         empty
 	 * @throws IOException
 	 */
-	@Nullable
 	private byte[] readGitDirectoryFile(String filename) throws IOException {
 		File file = new File(getDirectory(), filename);
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeFormatter.java b/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeFormatter.java
index 036917e..4796708 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeFormatter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeFormatter.java
@@ -45,6 +45,7 @@
 
 import java.io.IOException;
 import java.io.OutputStream;
+import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -63,7 +64,7 @@ public class MergeFormatter {
 	 * that are LF-separated lines.
 	 *
 	 * @param out
-	 *            the outputstream where to write the textual presentation
+	 *            the output stream where to write the textual presentation
 	 * @param res
 	 *            the merge result which should be presented
 	 * @param seqName
@@ -72,13 +73,44 @@ public class MergeFormatter {
 	 *            " or "&gt;&gt;&gt;&gt;&gt;&gt;&gt; " conflict markers. The
 	 *            names for the sequences are given in this list
 	 * @param charsetName
-	 *            the name of the characterSet used when writing conflict
+	 *            the name of the character set used when writing conflict
 	 *            metadata
 	 * @throws java.io.IOException
+	 * @deprecated Use
+	 *             {@link #formatMerge(OutputStream, MergeResult, List, Charset)}
+	 *             instead.
 	 */
+	@Deprecated
 	public void formatMerge(OutputStream out, MergeResult<RawText> res,
 			List<String> seqName, String charsetName) throws IOException {
-		new MergeFormatterPass(out, res, seqName, charsetName).formatMerge();
+		formatMerge(out, res, seqName, Charset.forName(charsetName));
+	}
+
+	/**
+	 * Formats the results of a merge of {@link org.eclipse.jgit.diff.RawText}
+	 * objects in a Git conformant way. This method also assumes that the
+	 * {@link org.eclipse.jgit.diff.RawText} objects being merged are line
+	 * oriented files which use LF as delimiter. This method will also use LF to
+	 * separate chunks and conflict metadata, therefore it fits only to texts
+	 * that are LF-separated lines.
+	 *
+	 * @param out
+	 *            the output stream where to write the textual presentation
+	 * @param res
+	 *            the merge result which should be presented
+	 * @param seqName
+	 *            When a conflict is reported each conflicting range will get a
+	 *            name. This name is following the "&lt;&lt;&lt;&lt;&lt;&lt;&lt;
+	 *            " or "&gt;&gt;&gt;&gt;&gt;&gt;&gt; " conflict markers. The
+	 *            names for the sequences are given in this list
+	 * @param charset
+	 *            the character set used when writing conflict metadata
+	 * @throws java.io.IOException
+	 * @since 5.2
+	 */
+	public void formatMerge(OutputStream out, MergeResult<RawText> res,
+			List<String> seqName, Charset charset) throws IOException {
+		new MergeFormatterPass(out, res, seqName, charset).formatMerge();
 	}
 
 	/**
@@ -100,17 +132,51 @@ public void formatMerge(OutputStream out, MergeResult<RawText> res,
 	 * @param theirsName
 	 *            the name ranges from theirs should get
 	 * @param charsetName
-	 *            the name of the characterSet used when writing conflict
+	 *            the name of the character set used when writing conflict
 	 *            metadata
 	 * @throws java.io.IOException
+	 * @deprecated use
+	 *             {@link #formatMerge(OutputStream, MergeResult, String, String, String, Charset)}
+	 *             instead.
+	 */
+	@Deprecated
+	public void formatMerge(OutputStream out, MergeResult res, String baseName,
+			String oursName, String theirsName, String charsetName) throws IOException {
+		formatMerge(out, res, baseName, oursName, theirsName,
+				Charset.forName(charsetName));
+	}
+
+	/**
+	 * Formats the results of a merge of exactly two
+	 * {@link org.eclipse.jgit.diff.RawText} objects in a Git conformant way.
+	 * This convenience method accepts the names for the three sequences (base
+	 * and the two merged sequences) as explicit parameters and doesn't require
+	 * the caller to specify a List
+	 *
+	 * @param out
+	 *            the {@link java.io.OutputStream} where to write the textual
+	 *            presentation
+	 * @param res
+	 *            the merge result which should be presented
+	 * @param baseName
+	 *            the name ranges from the base should get
+	 * @param oursName
+	 *            the name ranges from ours should get
+	 * @param theirsName
+	 *            the name ranges from theirs should get
+	 * @param charset
+	 *            the character set used when writing conflict metadata
+	 * @throws java.io.IOException
+	 * @since 5.2
 	 */
 	@SuppressWarnings("unchecked")
 	public void formatMerge(OutputStream out, MergeResult res, String baseName,
-			String oursName, String theirsName, String charsetName) throws IOException {
+			String oursName, String theirsName, Charset charset)
+			throws IOException {
 		List<String> names = new ArrayList<>(3);
 		names.add(baseName);
 		names.add(oursName);
 		names.add(theirsName);
-		formatMerge(out, res, names, charsetName);
+		formatMerge(out, res, names, charset);
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeFormatterPass.java b/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeFormatterPass.java
index 060f068..e1a8d31 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeFormatterPass.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeFormatterPass.java
@@ -46,6 +46,7 @@
 
 import java.io.IOException;
 import java.io.OutputStream;
+import java.nio.charset.Charset;
 import java.util.List;
 
 import org.eclipse.jgit.diff.RawText;
@@ -59,19 +60,33 @@ class MergeFormatterPass {
 
 	private final List<String> seqName;
 
-	private final String charsetName;
+	private final Charset charset;
 
 	private final boolean threeWayMerge;
 
 	private String lastConflictingName; // is set to non-null whenever we are in
 										// a conflict
 
-	MergeFormatterPass(OutputStream out, MergeResult<RawText> res, List<String> seqName,
-			String charsetName) {
+	/**
+	 * @param out
+	 *            the {@link java.io.OutputStream} where to write the textual
+	 *            presentation
+	 * @param res
+	 *            the merge result which should be presented
+	 * @param seqName
+	 *            When a conflict is reported each conflicting range will get a
+	 *            name. This name is following the "&lt;&lt;&lt;&lt;&lt;&lt;&lt;
+	 *            " or "&gt;&gt;&gt;&gt;&gt;&gt;&gt; " conflict markers. The
+	 *            names for the sequences are given in this list
+	 * @param charset
+	 *            the character set used when writing conflict metadata
+	 */
+	MergeFormatterPass(OutputStream out, MergeResult<RawText> res,
+			List<String> seqName, Charset charset) {
 		this.out = new EolAwareOutputStream(out);
 		this.res = res;
 		this.seqName = seqName;
-		this.charsetName = charsetName;
+		this.charset = charset;
 		this.threeWayMerge = (res.getSequences().size() == 3);
 	}
 
@@ -133,7 +148,7 @@ private void writeConflictChange(MergeChunk chunk) throws IOException {
 
 	private void writeln(String s) throws IOException {
 		out.beginln();
-		out.write((s + "\n").getBytes(charsetName)); //$NON-NLS-1$
+		out.write((s + "\n").getBytes(charset)); //$NON-NLS-1$
 	}
 
 	private void writeLine(RawText seq, int i) throws IOException {
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 f60c95f..412d9bb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
@@ -46,10 +46,10 @@
  */
 package org.eclipse.jgit.merge;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.diff.DiffAlgorithm.SupportedAlgorithm.HISTOGRAM;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_DIFF_SECTION;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_ALGORITHM;
-import static org.eclipse.jgit.lib.Constants.CHARACTER_ENCODING;
 import static org.eclipse.jgit.lib.Constants.OBJ_BLOB;
 
 import java.io.BufferedOutputStream;
@@ -1026,7 +1026,7 @@ private TemporaryBuffer doMerge(MergeResult<RawText> result)
 				db != null ? nonNullRepo().getDirectory() : null, inCoreLimit);
 		try {
 			new MergeFormatter().formatMerge(buf, result,
-					Arrays.asList(commitNames), CHARACTER_ENCODING);
+					Arrays.asList(commitNames), UTF_8);
 			buf.close();
 		} catch (IOException e) {
 			buf.destroy();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/DepthGenerator.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/DepthGenerator.java
index eaec305..6c6cc95 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/DepthGenerator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/DepthGenerator.java
@@ -59,6 +59,8 @@ class DepthGenerator extends Generator {
 
 	private final int depth;
 
+	private final int deepenSince;
+
 	private final RevWalk walk;
 
 	/**
@@ -91,6 +93,7 @@ class DepthGenerator extends Generator {
 		walk = (RevWalk)w;
 
 		this.depth = w.getDepth();
+		this.deepenSince = w.getDeepenSince();
 		this.UNSHALLOW = w.getUnshallowFlag();
 		this.REINTERESTING = w.getReinterestingFlag();
 
@@ -142,12 +145,24 @@ RevCommit next() throws MissingObjectException,
 				// this depth is guaranteed to be the smallest value that
 				// any path could produce.
 				if (dp.depth == -1) {
+					boolean failsDeepenSince = false;
+					if (deepenSince != 0) {
+						if ((p.flags & RevWalk.PARSED) == 0) {
+							p.parseHeaders(walk);
+						}
+						failsDeepenSince =
+							p.getCommitTime() < deepenSince;
+					}
+
 					dp.depth = newDepth;
 
 					// If the parent is not too deep, add it to the queue
 					// so that we can produce it later
-					if (newDepth <= depth)
+					if (newDepth <= depth && !failsDeepenSince) {
 						pending.add(p);
+					} else {
+						c.isBoundary = true;
+					}
 				}
 
 				// If the current commit has become unshallowed, everything
@@ -160,8 +175,7 @@ RevCommit next() throws MissingObjectException,
 				}
 			}
 
-			// Produce all commits less than the depth cutoff
-			boolean produce = c.depth <= depth;
+			boolean produce = true;
 
 			// Unshallow commits are uninteresting, but still need to be sent
 			// up to the PackWriter so that it will exclude objects correctly.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/DepthWalk.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/DepthWalk.java
index 06a5272..3499572 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/DepthWalk.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/DepthWalk.java
@@ -63,6 +63,15 @@ public interface DepthWalk {
 	 */
 	public int getDepth();
 
+	/**
+	 * @return the deepen-since value; if not 0, this walk only returns commits
+	 *         whose commit time is at or after this limit
+	 * @since 5.2
+	 */
+	public default int getDeepenSince() {
+		return 0;
+	}
+
 	/** @return flag marking commits that should become unshallow. */
 	/**
 	 * Get flag marking commits that should become unshallow.
@@ -83,12 +92,23 @@ public static class Commit extends RevCommit {
 		/** Depth of this commit in the graph, via shortest path. */
 		int depth;
 
+		boolean isBoundary;
+
 		/** @return depth of this commit, as found by the shortest path. */
 		public int getDepth() {
 			return depth;
 		}
 
 		/**
+		 * @return true if at least one of this commit's children was excluded
+		 *         due to a depth or shallow-since restriction, false otherwise
+		 * @since 5.2
+		 */
+		public boolean isBoundary() {
+			return isBoundary;
+		}
+
+		/**
 		 * Initialize a new commit.
 		 *
 		 * @param id
@@ -104,6 +124,8 @@ protected Commit(AnyObjectId id) {
 	public class RevWalk extends org.eclipse.jgit.revwalk.RevWalk implements DepthWalk {
 		private final int depth;
 
+		private int deepenSince;
+
 		private final RevFlag UNSHALLOW;
 
 		private final RevFlag REINTERESTING;
@@ -159,6 +181,22 @@ public int getDepth() {
 		}
 
 		@Override
+		public int getDeepenSince() {
+			return deepenSince;
+		}
+
+		/**
+		 * Sets the deepen-since value.
+		 *
+		 * @param limit
+		 *            new deepen-since value
+		 * @since 5.2
+		 */
+		public void setDeepenSince(int limit) {
+			deepenSince = limit;
+		}
+
+		@Override
 		public RevFlag getUnshallowFlag() {
 			return UNSHALLOW;
 		}
@@ -174,6 +212,7 @@ public RevFlag getReinterestingFlag() {
 		@Override
 		public ObjectWalk toObjectWalkWithSameObjects() {
 			ObjectWalk ow = new ObjectWalk(reader, depth);
+			ow.deepenSince = deepenSince;
 			ow.objects = objects;
 			ow.freeFlags = freeFlags;
 			return ow;
@@ -184,6 +223,8 @@ public ObjectWalk toObjectWalkWithSameObjects() {
 	public class ObjectWalk extends org.eclipse.jgit.revwalk.ObjectWalk implements DepthWalk {
 		private final int depth;
 
+		private int deepenSince;
+
 		private final RevFlag UNSHALLOW;
 
 		private final RevFlag REINTERESTING;
@@ -263,6 +304,11 @@ public int getDepth() {
 		}
 
 		@Override
+		public int getDeepenSince() {
+			return deepenSince;
+		}
+
+		@Override
 		public RevFlag getUnshallowFlag() {
 			return UNSHALLOW;
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevCommit.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevCommit.java
index 86ecd8e..af4ec1f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevCommit.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevCommit.java
@@ -407,7 +407,7 @@ public final RevCommit getParent(int nth) {
 	 * @return contents of the gpg signature; null if the commit was not signed.
 	 * @since 5.1
 	 */
-	public final @Nullable byte[] getRawGpgSignature() {
+	public final byte[] getRawGpgSignature() {
 		final byte[] raw = buffer;
 		final byte[] header = {'g', 'p', 'g', 's', 'i', 'g'};
 		final int start = RawParseUtils.headerStart(header, raw, 0);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java
index 93b3baa..2b31ebd 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java
@@ -57,7 +57,6 @@
 import java.io.IOException;
 import java.text.MessageFormat;
 
-import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.errors.LockFailedException;
 import org.eclipse.jgit.internal.JGitText;
@@ -281,7 +280,6 @@ public boolean isOutdated() {
 	 * @since 4.10
 	 */
 	@Override
-	@Nullable
 	protected byte[] readIncludedConfig(String relPath)
 			throws ConfigInvalidException {
 		final File file;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AmazonS3.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AmazonS3.java
index f6ec4b9..c5661e5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AmazonS3.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AmazonS3.java
@@ -542,7 +542,7 @@ IOException error(final String action, final String key,
 			}
 			buf = b.toByteArray();
 			if (buf.length > 0) {
-				err.initCause(new IOException("\n" + new String(buf))); //$NON-NLS-1$
+				err.initCause(new IOException("\n" + new String(buf, UTF_8))); //$NON-NLS-1$
 			}
 		}
 		return err;
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 d3419bc..0376336 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java
@@ -72,12 +72,14 @@
 
 import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.errors.InvalidObjectIdException;
+import org.eclipse.jgit.errors.LargeObjectException;
 import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.errors.PackProtocolException;
 import org.eclipse.jgit.errors.TooLargePackException;
 import org.eclipse.jgit.internal.JGitText;
 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.lib.AnyObjectId;
 import org.eclipse.jgit.lib.BatchRefUpdate;
 import org.eclipse.jgit.lib.Config;
@@ -1528,8 +1530,12 @@ private void checkSubmodules()
 			AnyObjectId blobId = entry.getBlobId();
 			ObjectLoader blob = odb.open(blobId, Constants.OBJ_BLOB);
 
-			SubmoduleValidator.assertValidGitModulesFile(
-					new String(blob.getBytes(), UTF_8));
+			try {
+				SubmoduleValidator.assertValidGitModulesFile(
+						new String(blob.getBytes(), UTF_8));
+			} catch (LargeObjectException | SubmoduleValidationException e) {
+				throw new IOException(e);
+			}
 		}
 	}
 
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 c43ab18..211707e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
@@ -44,6 +44,7 @@
 
 package org.eclipse.jgit.transport;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.transport.ReceiveCommand.Result.NOT_ATTEMPTED;
 import static org.eclipse.jgit.transport.ReceiveCommand.Result.OK;
 import static org.eclipse.jgit.transport.ReceiveCommand.Result.REJECTED_NONFASTFORWARD;
@@ -337,7 +338,7 @@ private void updateFETCH_HEAD(FetchResult result) throws IOException {
 		try {
 			if (lock.lock()) {
 				try (Writer w = new OutputStreamWriter(
-						lock.getOutputStream())) {
+						lock.getOutputStream(), UTF_8)) {
 					for (FetchHeadRecord h : fetchHeadUpdates) {
 						h.write(w);
 						result.add(h);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchRequest.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchRequest.java
new file mode 100644
index 0000000..5d28a4d
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchRequest.java
@@ -0,0 +1,174 @@
+/*
+ * 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.transport;
+
+import static java.util.Objects.requireNonNull;
+
+import java.util.List;
+import java.util.Set;
+
+import org.eclipse.jgit.annotations.NonNull;
+import org.eclipse.jgit.lib.ObjectId;
+
+/**
+ * Common fields between v0/v1/v2 fetch requests.
+ */
+abstract class FetchRequest {
+
+	final Set<ObjectId> wantIds;
+
+	final int depth;
+
+	final Set<ObjectId> clientShallowCommits;
+
+	final long filterBlobLimit;
+
+	final Set<String> clientCapabilities;
+
+	final int deepenSince;
+
+	final List<String> deepenNotRefs;
+
+	/**
+	 * Initialize the common fields of a fetch request.
+	 *
+	 * @param wantIds
+	 *            list of want ids
+	 * @param depth
+	 *            how deep to go in the tree
+	 * @param clientShallowCommits
+	 *            commits the client has without history
+	 * @param filterBlobLimit
+	 *            to exclude blobs on certain conditions
+	 * @param clientCapabilities
+	 *            capabilities sent in the request
+	 * @param deepenNotRefs
+	 *            Requests that the shallow clone/fetch should be cut at these
+	 *            specific revisions instead of a depth.
+	 * @param deepenSince
+	 *            Requests that the shallow clone/fetch should be cut at a
+	 *            specific time, instead of depth
+	 */
+	FetchRequest(@NonNull Set<ObjectId> wantIds, int depth,
+			@NonNull Set<ObjectId> clientShallowCommits, long filterBlobLimit,
+			@NonNull Set<String> clientCapabilities, int deepenSince,
+			@NonNull List<String> deepenNotRefs) {
+		this.wantIds = requireNonNull(wantIds);
+		this.depth = depth;
+		this.clientShallowCommits = requireNonNull(clientShallowCommits);
+		this.filterBlobLimit = filterBlobLimit;
+		this.clientCapabilities = requireNonNull(clientCapabilities);
+		this.deepenSince = deepenSince;
+		this.deepenNotRefs = requireNonNull(deepenNotRefs);
+	}
+
+	/**
+	 * @return object ids in the "want" (and "want-ref") lines of the request
+	 */
+	@NonNull
+	Set<ObjectId> getWantIds() {
+		return wantIds;
+	}
+
+	/**
+	 * @return the depth set in a "deepen" line. 0 by default.
+	 */
+	int getDepth() {
+		return depth;
+	}
+
+	/**
+	 * Shallow commits the client already has.
+	 *
+	 * These are sent by the client in "shallow" request lines.
+	 *
+	 * @return set of commits the client has declared as shallow.
+	 */
+	@NonNull
+	Set<ObjectId> getClientShallowCommits() {
+		return clientShallowCommits;
+	}
+
+	/**
+	 * @return the blob limit set in a "filter" line (-1 if not set)
+	 */
+	long getFilterBlobLimit() {
+		return filterBlobLimit;
+	}
+
+	/**
+	 * Capabilities that the client wants enabled from the server.
+	 *
+	 * Capabilities are options that tune the expected response from the server,
+	 * like "thin-pack", "no-progress" or "ofs-delta". This list should be a
+	 * subset of the capabilities announced by the server in its first response.
+	 *
+	 * These options are listed and well-defined in the git protocol
+	 * specification.
+	 *
+	 * @return capabilities sent by the client
+	 */
+	@NonNull
+	Set<String> getClientCapabilities() {
+		return clientCapabilities;
+	}
+
+	/**
+	 * The value in a "deepen-since" line in the request, indicating the
+	 * timestamp where to stop fetching/cloning.
+	 *
+	 * @return timestamp in seconds since the epoch, where to stop the shallow
+	 *         fetch/clone. Defaults to 0 if not set in the request.
+	 */
+	int getDeepenSince() {
+		return deepenSince;
+	}
+
+	/**
+	 * @return refs received in "deepen-not" lines.
+	 */
+	@NonNull
+	List<String> getDeepenNotRefs() {
+		return deepenNotRefs;
+	}
+}
\ No newline at end of file
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchV0Request.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchV0Request.java
new file mode 100644
index 0000000..bb358c8
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchV0Request.java
@@ -0,0 +1,133 @@
+/*
+ * 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.transport;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.eclipse.jgit.annotations.NonNull;
+import org.eclipse.jgit.lib.ObjectId;
+
+/**
+ * Fetch request in the V0/V1 protocol.
+ */
+final class FetchV0Request extends FetchRequest {
+
+	FetchV0Request(@NonNull Set<ObjectId> wantIds, int depth,
+			@NonNull Set<ObjectId> clientShallowCommits, long filterBlobLimit,
+			@NonNull Set<String> clientCapabilities) {
+		super(wantIds, depth, clientShallowCommits, filterBlobLimit,
+				clientCapabilities, 0, Collections.emptyList());
+	}
+
+	static final class Builder {
+
+		int depth;
+
+		final Set<ObjectId> wantIds = new HashSet<>();
+
+		final Set<ObjectId> clientShallowCommits = new HashSet<>();
+
+		long filterBlobLimit = -1;
+
+		final Set<String> clientCaps = new HashSet<>();
+
+		/**
+		 * @param objectId
+		 *            object id received in a "want" line
+		 * @return this builder
+		 */
+		Builder addWantId(ObjectId objectId) {
+			wantIds.add(objectId);
+			return this;
+		}
+
+		/**
+		 * @param d
+		 *            depth set in a "deepen" line
+		 * @return this builder
+		 */
+		Builder setDepth(int d) {
+			depth = d;
+			return this;
+		}
+
+		/**
+		 * @param shallowOid
+		 *            object id received in a "shallow" line
+		 * @return this builder
+		 */
+		Builder addClientShallowCommit(ObjectId shallowOid) {
+			clientShallowCommits.add(shallowOid);
+			return this;
+		}
+
+		/**
+		 * @param clientCapabilities
+		 *            client capabilities sent by the client in the first want
+		 *            line of the request
+		 * @return this builder
+		 */
+		Builder addClientCapabilities(Collection<String> clientCapabilities) {
+			clientCaps.addAll(clientCapabilities);
+			return this;
+		}
+
+		/**
+		 * @param filterBlobLim
+		 *            blob limit set in a "filter" line
+		 * @return this builder
+		 */
+		Builder setFilterBlobLimit(long filterBlobLim) {
+			filterBlobLimit = filterBlobLim;
+			return this;
+		}
+
+		FetchV0Request build() {
+			return new FetchV0Request(wantIds, depth, clientShallowCommits,
+					filterBlobLimit, clientCaps);
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchV2Request.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchV2Request.java
index 853d969..951d2d7 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchV2Request.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchV2Request.java
@@ -42,7 +42,10 @@
  */
 package org.eclipse.jgit.transport;
 
+import static java.util.Objects.requireNonNull;
+
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -50,121 +53,61 @@
 import java.util.TreeMap;
 
 import org.eclipse.jgit.annotations.NonNull;
+import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.lib.ObjectId;
 
 /**
- * fetch protocol v2 request.
+ * Fetch request from git protocol v2.
  *
  * <p>
  * This is used as an input to {@link ProtocolV2Hook}.
  *
  * @since 5.1
  */
-public final class FetchV2Request {
+public final class FetchV2Request extends FetchRequest {
 	private final List<ObjectId> peerHas;
 
 	private final TreeMap<String, ObjectId> wantedRefs;
 
-	private final Set<ObjectId> wantsIds;
-
-	private final Set<ObjectId> clientShallowCommits;
-
-	private final int deepenSince;
-
-	private final List<String> deepenNotRefs;
-
-	private final int depth;
-
-	private final long filterBlobLimit;
-
-	private final Set<String> options;
-
 	private final boolean doneReceived;
 
-	private FetchV2Request(List<ObjectId> peerHas,
-			TreeMap<String, ObjectId> wantedRefs, Set<ObjectId> wantsIds,
-			Set<ObjectId> clientShallowCommits, int deepenSince,
-			List<String> deepenNotRefs, int depth, long filterBlobLimit,
-			boolean doneReceived, Set<String> options) {
-		this.peerHas = peerHas;
-		this.wantedRefs = wantedRefs;
-		this.wantsIds = wantsIds;
-		this.clientShallowCommits = clientShallowCommits;
-		this.deepenSince = deepenSince;
-		this.deepenNotRefs = deepenNotRefs;
-		this.depth = depth;
-		this.filterBlobLimit = filterBlobLimit;
+	@Nullable
+	private final String agent;
+
+	@NonNull
+	private final List<String> serverOptions;
+
+	FetchV2Request(@NonNull List<ObjectId> peerHas,
+			@NonNull TreeMap<String, ObjectId> wantedRefs,
+			@NonNull Set<ObjectId> wantIds,
+			@NonNull Set<ObjectId> clientShallowCommits, int deepenSince,
+			@NonNull List<String> deepenNotRefs, int depth,
+			long filterBlobLimit,
+			boolean doneReceived, @NonNull Set<String> clientCapabilities,
+			@Nullable String agent, @NonNull List<String> serverOptions) {
+		super(wantIds, depth, clientShallowCommits, filterBlobLimit,
+				clientCapabilities, deepenSince, deepenNotRefs);
+		this.peerHas = requireNonNull(peerHas);
+		this.wantedRefs = requireNonNull(wantedRefs);
 		this.doneReceived = doneReceived;
-		this.options = options;
+		this.agent = agent;
+		this.serverOptions = requireNonNull(serverOptions);
 	}
 
 	/**
-	 * @return object ids in the "have" lines of the request
+	 * @return object ids received in the "have" lines
 	 */
 	@NonNull
 	List<ObjectId> getPeerHas() {
-		return this.peerHas;
+		return peerHas;
 	}
 
 	/**
-	 * @return list of references in the "want-ref" lines of the request
+	 * @return list of references received in "want-ref" lines
 	 */
 	@NonNull
 	Map<String, ObjectId> getWantedRefs() {
-		return this.wantedRefs;
-	}
-
-	/**
-	 * @return object ids in the "want" (and "want-ref") lines of the request
-	 */
-	@NonNull
-	Set<ObjectId> getWantsIds() {
-		return wantsIds;
-	}
-
-	/**
-	 * Shallow commits the client already has.
-	 *
-	 * These are sent by the client in "shallow" request lines.
-	 *
-	 * @return set of commits the client has declared as shallow.
-	 */
-	@NonNull
-	Set<ObjectId> getClientShallowCommits() {
-		return clientShallowCommits;
-	}
-
-	/**
-	 * The value in a "deepen-since" line in the request, indicating the
-	 * timestamp where to stop fetching/cloning.
-	 *
-	 * @return timestamp in seconds since the epoch, where to stop the shallow
-	 *         fetch/clone. Defaults to 0 if not set in the request.
-	 */
-	int getDeepenSince() {
-		return deepenSince;
-	}
-
-	/**
-	 * @return the refs in "deepen-not" lines in the request.
-	 */
-	@NonNull
-	List<String> getDeepenNotRefs() {
-		return deepenNotRefs;
-	}
-
-	/**
-	 * @return the depth set in a "deepen" line. 0 by default.
-	 */
-	int getDepth() {
-		return depth;
-	}
-
-	/**
-	 * @return the blob limit set in a "filter" line (-1 if not set)
-	 */
-	long getFilterBlobLimit() {
-		return filterBlobLimit;
+		return wantedRefs;
 	}
 
 	/**
@@ -175,17 +118,25 @@ boolean wasDoneReceived() {
 	}
 
 	/**
-	 * Options that tune the expected response from the server, like
-	 * "thin-pack", "no-progress" or "ofs-delta"
+	 * @return string identifying the agent (as sent in the request body by the
+	 *         client)
+	 */
+	@Nullable
+	String getAgent() {
+		return agent;
+	}
+
+	/**
+	 * Options received in server-option lines. The caller can choose to act on
+	 * these in an application-specific way
 	 *
-	 * These are options listed and well-defined in the git protocol
-	 * specification
+	 * @return Immutable list of server options received in the request
 	 *
-	 * @return options found in the request lines
+	 * @since 5.2
 	 */
 	@NonNull
-	Set<String> getOptions() {
-		return options;
+	public List<String> getServerOptions() {
+		return serverOptions;
 	}
 
 	/** @return A builder of {@link FetchV2Request}. */
@@ -193,20 +144,19 @@ static Builder builder() {
 		return new Builder();
 	}
 
-
 	/** A builder for {@link FetchV2Request}. */
 	static final class Builder {
-		List<ObjectId> peerHas = new ArrayList<>();
+		final List<ObjectId> peerHas = new ArrayList<>();
 
-		TreeMap<String, ObjectId> wantedRefs = new TreeMap<>();
+		final TreeMap<String, ObjectId> wantedRefs = new TreeMap<>();
 
-		Set<ObjectId> wantsIds = new HashSet<>();
+		final Set<ObjectId> wantIds = new HashSet<>();
 
-		Set<ObjectId> clientShallowCommits = new HashSet<>();
+		final Set<ObjectId> clientShallowCommits = new HashSet<>();
 
-		List<String> deepenNotRefs = new ArrayList<>();
+		final List<String> deepenNotRefs = new ArrayList<>();
 
-		Set<String> options = new HashSet<>();
+		final Set<String> clientCapabilities = new HashSet<>();
 
 		int depth;
 
@@ -216,13 +166,18 @@ static final class Builder {
 
 		boolean doneReceived;
 
+		@Nullable
+		String agent;
+
+		final List<String> serverOptions = new ArrayList<>();
+
 		private Builder() {
 		}
 
 		/**
 		 * @param objectId
-		 *            from a "have" line in a fetch request
-		 * @return the builder
+		 *            object id received in a "have" line
+		 * @return this builder
 		 */
 		Builder addPeerHas(ObjectId objectId) {
 			peerHas.add(objectId);
@@ -230,13 +185,13 @@ Builder addPeerHas(ObjectId objectId) {
 		}
 
 		/**
-		 * From a "want-ref" line in a fetch request
+		 * Ref received in "want-ref" line and the object-id it refers to
 		 *
 		 * @param refName
 		 *            reference name
 		 * @param oid
-		 *            object id
-		 * @return the builder
+		 *            object id the reference is pointing at
+		 * @return this builder
 		 */
 		Builder addWantedRef(String refName, ObjectId oid) {
 			wantedRefs.put(refName, oid);
@@ -244,42 +199,42 @@ Builder addWantedRef(String refName, ObjectId oid) {
 		}
 
 		/**
-		 * @param option
-		 *            fetch request lines acting as options
-		 * @return the builder
+		 * @param clientCapability
+		 *            capability line sent by the client
+		 * @return this builder
 		 */
-		Builder addOption(String option) {
-			options.add(option);
+		Builder addClientCapability(String clientCapability) {
+			clientCapabilities.add(clientCapability);
 			return this;
 		}
 
 		/**
-		 * @param objectId
-		 *            from a "want" line in a fetch request
-		 * @return the builder
+		 * @param wantId
+		 *            object id received in a "want" line
+		 * @return this builder
 		 */
-		Builder addWantsIds(ObjectId objectId) {
-			wantsIds.add(objectId);
+		Builder addWantId(ObjectId wantId) {
+			wantIds.add(wantId);
 			return this;
 		}
 
 		/**
 		 * @param shallowOid
-		 *            from a "shallow" line in the fetch request
-		 * @return the builder
+		 *            object id received in a "shallow" line
+		 * @return this builder
 		 */
 		Builder addClientShallowCommit(ObjectId shallowOid) {
-			this.clientShallowCommits.add(shallowOid);
+			clientShallowCommits.add(shallowOid);
 			return this;
 		}
 
 		/**
 		 * @param d
-		 *            from a "deepen" line in the fetch request
-		 * @return the builder
+		 *            Depth received in a "deepen" line
+		 * @return this builder
 		 */
 		Builder setDepth(int d) {
-			this.depth = d;
+			depth = d;
 			return this;
 		}
 
@@ -288,32 +243,34 @@ Builder setDepth(int d) {
 		 *         0 if not set.
 		 */
 		int getDepth() {
-			return this.depth;
+			return depth;
 		}
 
 		/**
-		 * @return if there has been any "deepen not" line in the request
+		 * @return true if there has been at least one "deepen not" line in the
+		 *         request so far
 		 */
 		boolean hasDeepenNotRefs() {
 			return !deepenNotRefs.isEmpty();
 		}
 
 		/**
-		 * @param deepenNotRef reference in a "deepen not" line
-		 * @return the builder
+		 * @param deepenNotRef
+		 *            reference received in a "deepen not" line
+		 * @return this builder
 		 */
 		Builder addDeepenNotRef(String deepenNotRef) {
-			this.deepenNotRefs.add(deepenNotRef);
+			deepenNotRefs.add(deepenNotRef);
 			return this;
 		}
 
 		/**
 		 * @param value
 		 *            Unix timestamp received in a "deepen since" line
-		 * @return the builder
+		 * @return this builder
 		 */
 		Builder setDeepenSince(int value) {
-			this.deepenSince = value;
+			deepenSince = value;
 			return this;
 		}
 
@@ -322,35 +279,66 @@ Builder setDeepenSince(int value) {
 		 *         by default.
 		 */
 		int getDeepenSince() {
-			return this.deepenSince;
+			return deepenSince;
 		}
 
 		/**
-		 * @param filterBlobLimit
+		 * @param filterBlobLim
 		 *            set in a "filter" line
-		 * @return the builder
+		 * @return this builder
 		 */
-		Builder setFilterBlobLimit(long filterBlobLimit) {
-			this.filterBlobLimit = filterBlobLimit;
+		Builder setFilterBlobLimit(long filterBlobLim) {
+			filterBlobLimit = filterBlobLim;
 			return this;
 		}
 
 		/**
 		 * Mark that the "done" line has been received.
 		 *
-		 * @return the builder
+		 * @return this builder
 		 */
 		Builder setDoneReceived() {
-			this.doneReceived = true;
+			doneReceived = true;
 			return this;
 		}
+
+		/**
+		 * Value of an agent line received after the command and before the
+		 * arguments. E.g. "agent=a.b.c/1.0" should set "a.b.c/1.0".
+		 *
+		 * @param agentValue
+		 *            the client-supplied agent capability, without the leading
+		 *            "agent="
+		 * @return this builder
+		 */
+		Builder setAgent(@Nullable String agentValue) {
+			agent = agentValue;
+			return this;
+		}
+
+		/**
+		 * Records an application-specific option supplied in a server-option
+		 * line, for later retrieval with
+		 * {@link FetchV2Request#getServerOptions}.
+		 *
+		 * @param value
+		 *            the client-supplied server-option capability, without
+		 *            leading "server-option=".
+		 * @return this builder
+		 */
+		Builder addServerOption(@NonNull String value) {
+			serverOptions.add(value);
+			return this;
+		}
+
 		/**
 		 * @return Initialized fetch request
 		 */
 		FetchV2Request build() {
-			return new FetchV2Request(peerHas, wantedRefs, wantsIds,
+			return new FetchV2Request(peerHas, wantedRefs, wantIds,
 					clientShallowCommits, deepenSince, deepenNotRefs,
-					depth, filterBlobLimit, doneReceived, options);
+					depth, filterBlobLimit, doneReceived, clientCapabilities,
+					agent, Collections.unmodifiableList(serverOptions));
 		}
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/GitProtocolConstants.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/GitProtocolConstants.java
index 760ac6c..1561c93 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/GitProtocolConstants.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/GitProtocolConstants.java
@@ -245,6 +245,20 @@ public final class GitProtocolConstants {
 	public static final String CAPABILITY_REF_IN_WANT = "ref-in-want"; //$NON-NLS-1$
 
 	/**
+	 * The server supports arbitrary options
+	 *
+	 * @since 5.2
+	 */
+	public static final String CAPABILITY_SERVER_OPTION = "server-option"; //$NON-NLS-1$
+
+	/**
+	 * Option for passing application-specific options to the server.
+	 *
+	 * @since 5.2
+	 */
+	public static final String OPTION_SERVER_OPTION = "server-option"; //$NON-NLS-1$
+
+	/**
 	 * The server supports listing refs using protocol v2.
 	 *
 	 * @since 5.0
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/LsRefsV2Request.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/LsRefsV2Request.java
index 3aff584..add3731 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/LsRefsV2Request.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/LsRefsV2Request.java
@@ -42,9 +42,15 @@
  */
 package org.eclipse.jgit.transport;
 
+import static java.util.Objects.requireNonNull;
+
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
+import org.eclipse.jgit.annotations.NonNull;
+import org.eclipse.jgit.annotations.Nullable;
+
 /**
  * ls-refs protocol v2 request.
  *
@@ -60,11 +66,20 @@ public final class LsRefsV2Request {
 
 	private final boolean peel;
 
+	@Nullable
+	private final String agent;
+
+	@NonNull
+	private final List<String> serverOptions;
+
 	private LsRefsV2Request(List<String> refPrefixes, boolean symrefs,
-			boolean peel) {
+			boolean peel, @Nullable String agent,
+			@NonNull List<String> serverOptions) {
 		this.refPrefixes = refPrefixes;
 		this.symrefs = symrefs;
 		this.peel = peel;
+		this.agent = agent;
+		this.serverOptions = requireNonNull(serverOptions);
 	}
 
 	/** @return ref prefixes that the client requested. */
@@ -82,6 +97,34 @@ public boolean getPeel() {
 		return peel;
 	}
 
+	/**
+	 * @return agent as reported by the client
+	 *
+	 * @since 5.2
+	 */
+	@Nullable
+	public String getAgent() {
+		return agent;
+	}
+
+	/**
+	 * Get application-specific options provided by the client using
+	 * --server-option.
+	 * <p>
+	 * It returns just the content, without the "server-option=" prefix. E.g. a
+	 * request with server-option=A and server-option=B lines returns the list
+	 * [A, B].
+	 *
+	 * @return application-specific options from the client as an unmodifiable
+	 *         list
+	 *
+	 * @since 5.2
+	 */
+	@NonNull
+	public List<String> getServerOptions() {
+		return serverOptions;
+	}
+
 	/** @return A builder of {@link LsRefsV2Request}. */
 	public static Builder builder() {
 		return new Builder();
@@ -95,6 +138,10 @@ public static final class Builder {
 
 		private boolean peel;
 
+		private final List<String> serverOptions = new ArrayList<>();
+
+		private String agent;
+
 		private Builder() {
 		}
 
@@ -125,10 +172,43 @@ public Builder setPeel(boolean value) {
 			return this;
 		}
 
+		/**
+		 * Records an application-specific option supplied in a server-option
+		 * line, for later retrieval with
+		 * {@link LsRefsV2Request#getServerOptions}.
+		 *
+		 * @param value
+		 *            the client-supplied server-option capability, without
+		 *            leading "server-option=".
+		 * @return this builder
+		 * @since 5.2
+		 */
+		public Builder addServerOption(@NonNull String value) {
+			serverOptions.add(value);
+			return this;
+		}
+
+		/**
+		 * Value of an agent line received after the command and before the
+		 * arguments. E.g. "agent=a.b.c/1.0" should set "a.b.c/1.0".
+		 *
+		 * @param value
+		 *            the client-supplied agent capability, without leading
+		 *            "agent="
+		 * @return this builder
+		 *
+		 * @since 5.2
+		 */
+		public Builder setAgent(@Nullable String value) {
+			agent = value;
+			return this;
+		}
+
 		/** @return LsRefsV2Request */
 		public LsRefsV2Request build() {
 			return new LsRefsV2Request(
-					Collections.unmodifiableList(refPrefixes), symrefs, peel);
+					Collections.unmodifiableList(refPrefixes), symrefs, peel,
+					agent, Collections.unmodifiableList(serverOptions));
 		}
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java
index e688f63..8562376 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java
@@ -42,10 +42,13 @@
 
 package org.eclipse.jgit.transport;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
+
 import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileReader;
+import java.io.FileInputStream;
 import java.io.IOException;
+import java.io.InputStreamReader;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.Locale;
@@ -211,7 +214,8 @@ private void parse() {
 		this.hosts.clear();
 		this.lastModified = this.netrc.lastModified();
 
-		try (BufferedReader r = new BufferedReader(new FileReader(netrc))) {
+		try (BufferedReader r = new BufferedReader(
+				new InputStreamReader(new FileInputStream(netrc), UTF_8))) {
 			String line = null;
 
 			NetRCEntry entry = new NetRCEntry();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java
index 480055c..a5fa3fe 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java
@@ -43,6 +43,8 @@
 
 package org.eclipse.jgit.transport;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
@@ -241,7 +243,8 @@ private synchronized State refresh() {
 	private Map<String, HostEntry> parse(InputStream in)
 			throws IOException {
 		final Map<String, HostEntry> m = new LinkedHashMap<>();
-		final BufferedReader br = new BufferedReader(new InputStreamReader(in));
+		final BufferedReader br = new BufferedReader(
+				new InputStreamReader(in, UTF_8));
 		final List<HostEntry> current = new ArrayList<>(4);
 		String line;
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ProtocolV0Parser.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ProtocolV0Parser.java
new file mode 100644
index 0000000..60d5fff
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ProtocolV0Parser.java
@@ -0,0 +1,157 @@
+/*
+ * 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.transport;
+
+import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_FILTER;
+
+import java.io.EOFException;
+import java.io.IOException;
+import java.text.MessageFormat;
+
+import org.eclipse.jgit.errors.PackProtocolException;
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.internal.transport.parser.FirstWant;
+import org.eclipse.jgit.lib.ObjectId;
+
+/**
+ * Parser for git protocol versions 0 and 1.
+ *
+ * It reads the lines coming through the {@link PacketLineIn} and builds a
+ * {@link FetchV0Request} object.
+ *
+ * It requires a transferConfig object to know if the server supports filters.
+ */
+final class ProtocolV0Parser {
+
+	private final TransferConfig transferConfig;
+
+	ProtocolV0Parser(TransferConfig transferConfig) {
+		this.transferConfig = transferConfig;
+	}
+
+	/**
+	 * Parse an incoming protocol v1 upload request arguments from the wire.
+	 *
+	 * The incoming PacketLineIn is consumed until an END line, but the caller
+	 * is responsible for closing it (if needed).
+	 *
+	 * @param pckIn
+	 *            incoming lines. This method will read until an END line.
+	 * @return a FetchV0Request with the data received in the wire.
+	 * @throws PackProtocolException
+	 * @throws IOException
+	 */
+	FetchV0Request recvWants(PacketLineIn pckIn)
+			throws PackProtocolException, IOException {
+		FetchV0Request.Builder reqBuilder = new FetchV0Request.Builder();
+
+		boolean isFirst = true;
+		boolean filterReceived = false;
+
+		for (;;) {
+			String line;
+			try {
+				line = pckIn.readString();
+			} catch (EOFException eof) {
+				if (isFirst) {
+					break;
+				}
+				throw eof;
+			}
+
+			if (line == PacketLineIn.END) {
+				break;
+			}
+
+			if (line.startsWith("deepen ")) { //$NON-NLS-1$
+				int depth = Integer.parseInt(line.substring(7));
+				if (depth <= 0) {
+					throw new PackProtocolException(
+							MessageFormat.format(JGitText.get().invalidDepth,
+									Integer.valueOf(depth)));
+				}
+				reqBuilder.setDepth(depth);
+				continue;
+			}
+
+			if (line.startsWith("shallow ")) { //$NON-NLS-1$
+				reqBuilder.addClientShallowCommit(
+						ObjectId.fromString(line.substring(8)));
+				continue;
+			}
+
+			if (transferConfig.isAllowFilter()
+					&& line.startsWith(OPTION_FILTER + " ")) { //$NON-NLS-1$
+				String arg = line.substring(OPTION_FILTER.length() + 1);
+
+				if (filterReceived) {
+					throw new PackProtocolException(
+							JGitText.get().tooManyFilters);
+				}
+				filterReceived = true;
+
+				reqBuilder.setFilterBlobLimit(ProtocolV2Parser.filterLine(arg));
+				continue;
+			}
+
+			if (!line.startsWith("want ") || line.length() < 45) { //$NON-NLS-1$
+				throw new PackProtocolException(MessageFormat
+						.format(JGitText.get().expectedGot, "want", line)); //$NON-NLS-1$
+			}
+
+			if (isFirst) {
+				if (line.length() > 45) {
+					FirstWant firstLine = FirstWant.fromLine(line);
+					reqBuilder.addClientCapabilities(firstLine.getCapabilities());
+					line = firstLine.getLine();
+				}
+			}
+
+			reqBuilder.addWantId(ObjectId.fromString(line.substring(5)));
+			isFirst = false;
+		}
+
+		return reqBuilder.build();
+	}
+
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ProtocolV2Parser.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ProtocolV2Parser.java
index eae2c6e..a03f021 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ProtocolV2Parser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ProtocolV2Parser.java
@@ -44,15 +44,20 @@
 
 import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_DEEPEN_RELATIVE;
 import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_FILTER;
+import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_AGENT;
 import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_INCLUDE_TAG;
 import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_NO_PROGRESS;
 import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_OFS_DELTA;
+import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_SERVER_OPTION;
 import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_SIDE_BAND_64K;
 import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_THIN_PACK;
 import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_WANT_REF;
 
 import java.io.IOException;
 import java.text.MessageFormat;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.function.Consumer;
 
 import org.eclipse.jgit.errors.PackProtocolException;
 import org.eclipse.jgit.internal.JGitText;
@@ -75,6 +80,35 @@ final class ProtocolV2Parser {
 		this.transferConfig = transferConfig;
 	}
 
+	/*
+	 * Read lines until DELIM or END, calling the appropiate consumer.
+	 *
+	 * Returns the last read line (so caller can check if there is more to read
+	 * in the line).
+	 */
+	private static String consumeCapabilities(PacketLineIn pckIn,
+			Consumer<String> serverOptionConsumer,
+			Consumer<String> agentConsumer) throws IOException {
+
+		String serverOptionPrefix = OPTION_SERVER_OPTION + '=';
+		String agentPrefix = OPTION_AGENT + '=';
+
+		String line = pckIn.readString();
+		while (line != PacketLineIn.DELIM && line != PacketLineIn.END) {
+			if (line.startsWith(serverOptionPrefix)) {
+				serverOptionConsumer
+						.accept(line.substring(serverOptionPrefix.length()));
+			} else if (line.startsWith(agentPrefix)) {
+				agentConsumer.accept(line.substring(agentPrefix.length()));
+			} else {
+				// Unrecognized capability. Ignore it.
+			}
+			line = pckIn.readString();
+		}
+
+		return line;
+	}
+
 	/**
 	 * Parse the incoming fetch request arguments from the wire. The caller must
 	 * be sure that what is comings is a fetch request before coming here.
@@ -102,21 +136,26 @@ FetchV2Request parseFetchRequest(PacketLineIn pckIn, RefDatabase refdb)
 
 		// Packs are always sent multiplexed and using full 64K
 		// lengths.
-		reqBuilder.addOption(OPTION_SIDE_BAND_64K);
+		reqBuilder.addClientCapability(OPTION_SIDE_BAND_64K);
 
-		String line;
+		String line = consumeCapabilities(pckIn,
+				serverOption -> reqBuilder.addServerOption(serverOption),
+				agent -> reqBuilder.setAgent(agent));
 
-		// Currently, we do not support any capabilities, so the next
-		// line is DELIM.
-		if ((line = pckIn.readString()) != PacketLineIn.DELIM) {
-			throw new PackProtocolException(MessageFormat
-					.format(JGitText.get().unexpectedPacketLine, line));
+		if (line == PacketLineIn.END) {
+			return reqBuilder.build();
+		}
+
+		if (line != PacketLineIn.DELIM) {
+			throw new PackProtocolException(
+					MessageFormat.format(JGitText.get().unexpectedPacketLine,
+							line));
 		}
 
 		boolean filterReceived = false;
 		while ((line = pckIn.readString()) != PacketLineIn.END) {
 			if (line.startsWith("want ")) { //$NON-NLS-1$
-				reqBuilder.addWantsIds(ObjectId.fromString(line.substring(5)));
+				reqBuilder.addWantId(ObjectId.fromString(line.substring(5)));
 			} else if (transferConfig.isAllowRefInWant()
 					&& line.startsWith(OPTION_WANT_REF + " ")) { //$NON-NLS-1$
 				String refName = line.substring(OPTION_WANT_REF.length() + 1);
@@ -134,19 +173,19 @@ FetchV2Request parseFetchRequest(PacketLineIn pckIn, RefDatabase refdb)
 							.format(JGitText.get().invalidRefName, refName));
 				}
 				reqBuilder.addWantedRef(refName, oid);
-				reqBuilder.addWantsIds(oid);
+				reqBuilder.addWantId(oid);
 			} else if (line.startsWith("have ")) { //$NON-NLS-1$
 				reqBuilder.addPeerHas(ObjectId.fromString(line.substring(5)));
 			} else if (line.equals("done")) { //$NON-NLS-1$
 				reqBuilder.setDoneReceived();
 			} else if (line.equals(OPTION_THIN_PACK)) {
-				reqBuilder.addOption(OPTION_THIN_PACK);
+				reqBuilder.addClientCapability(OPTION_THIN_PACK);
 			} else if (line.equals(OPTION_NO_PROGRESS)) {
-				reqBuilder.addOption(OPTION_NO_PROGRESS);
+				reqBuilder.addClientCapability(OPTION_NO_PROGRESS);
 			} else if (line.equals(OPTION_INCLUDE_TAG)) {
-				reqBuilder.addOption(OPTION_INCLUDE_TAG);
+				reqBuilder.addClientCapability(OPTION_INCLUDE_TAG);
 			} else if (line.equals(OPTION_OFS_DELTA)) {
-				reqBuilder.addOption(OPTION_OFS_DELTA);
+				reqBuilder.addClientCapability(OPTION_OFS_DELTA);
 			} else if (line.startsWith("shallow ")) { //$NON-NLS-1$
 				reqBuilder.addClientShallowCommit(
 						ObjectId.fromString(line.substring(8)));
@@ -173,7 +212,7 @@ FetchV2Request parseFetchRequest(PacketLineIn pckIn, RefDatabase refdb)
 							JGitText.get().deepenNotWithDeepen);
 				}
 			} else if (line.equals(OPTION_DEEPEN_RELATIVE)) {
-				reqBuilder.addOption(OPTION_DEEPEN_RELATIVE);
+				reqBuilder.addClientCapability(OPTION_DEEPEN_RELATIVE);
 			} else if (line.startsWith("deepen-since ")) { //$NON-NLS-1$
 				int ts = Integer.parseInt(line.substring(13));
 				if (ts <= 0) {
@@ -204,6 +243,57 @@ FetchV2Request parseFetchRequest(PacketLineIn pckIn, RefDatabase refdb)
 	}
 
 	/**
+	 * Parse the incoming ls-refs request arguments from the wire. This is meant
+	 * for calling immediately after the caller has consumed a "command=ls-refs"
+	 * line indicating the beginning of a ls-refs request.
+	 *
+	 * The incoming PacketLineIn is consumed until an END line, but the caller
+	 * is responsible for closing it (if needed)
+	 *
+	 * @param pckIn
+	 *            incoming lines. This method will read until an END line.
+	 * @return a LsRefsV2Request object with the data received in the wire.
+	 * @throws PackProtocolException
+	 *             for inconsistencies in the protocol (e.g. unexpected lines)
+	 * @throws IOException
+	 *             reporting problems reading the incoming messages from the
+	 *             wire
+	 */
+	LsRefsV2Request parseLsRefsRequest(PacketLineIn pckIn)
+			throws PackProtocolException, IOException {
+		LsRefsV2Request.Builder builder = LsRefsV2Request.builder();
+		List<String> prefixes = new ArrayList<>();
+
+		String line = consumeCapabilities(pckIn,
+				serverOption -> builder.addServerOption(serverOption),
+				agent -> builder.setAgent(agent));
+
+		if (line == PacketLineIn.END) {
+			return builder.build();
+		}
+
+		if (line != PacketLineIn.DELIM) {
+			throw new PackProtocolException(MessageFormat
+					.format(JGitText.get().unexpectedPacketLine, line));
+		}
+
+		while ((line = pckIn.readString()) != PacketLineIn.END) {
+			if (line.equals("peel")) { //$NON-NLS-1$
+				builder.setPeel(true);
+			} else if (line.equals("symrefs")) { //$NON-NLS-1$
+				builder.setSymrefs(true);
+			} else if (line.startsWith("ref-prefix ")) { //$NON-NLS-1$
+				prefixes.add(line.substring("ref-prefix ".length())); //$NON-NLS-1$
+			} else {
+				throw new PackProtocolException(MessageFormat
+						.format(JGitText.get().unexpectedPacketLine, line));
+			}
+		}
+
+		return builder.setRefPrefixes(prefixes).build();
+	}
+
+	/*
 	 * Process the content of "filter" line from the protocol. It has a shape
 	 * like "blob:none" or "blob:limit=N", with limit a positive number.
 	 *
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefAdvertiser.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefAdvertiser.java
index 4662435..6595cab 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefAdvertiser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefAdvertiser.java
@@ -207,7 +207,8 @@ public void setUseProtocolV2(boolean b) {
 	 * <p>
 	 * This method must be invoked prior to any of the following:
 	 * <ul>
-	 * <li>{@link #send(Map)}
+	 * <li>{@link #send(Map)}</li>
+	 * <li>{@link #send(Collection)}</li>
 	 * </ul>
 	 *
 	 * @param deref
@@ -223,8 +224,9 @@ public void setDerefTags(boolean deref) {
 	 * <p>
 	 * This method must be invoked prior to any of the following:
 	 * <ul>
-	 * <li>{@link #send(Map)}
-	 * <li>{@link #advertiseHave(AnyObjectId)}
+	 * <li>{@link #send(Map)}</li>
+	 * <li>{@link #send(Collection)}</li>
+	 * <li>{@link #advertiseHave(AnyObjectId)}</li>
 	 * </ul>
 	 *
 	 * @param name
@@ -257,8 +259,9 @@ public void advertiseCapability(String name, String value) {
 	 * <p>
 	 * This method must be invoked prior to any of the following:
 	 * <ul>
-	 * <li>{@link #send(Map)}
-	 * <li>{@link #advertiseHave(AnyObjectId)}
+	 * <li>{@link #send(Map)}</li>
+	 * <li>{@link #send(Collection)}</li>
+	 * <li>{@link #advertiseHave(AnyObjectId)}</li>
 	 * </ul>
 	 *
 	 * @param from
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandInputStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandInputStream.java
index 90600cb..fde4401 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandInputStream.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandInputStream.java
@@ -236,7 +236,7 @@ private void doProgressLine(String msg) throws IOException {
 
 		messages.write(msg);
 		if (out != null)
-			out.write(msg.getBytes());
+			out.write(msg.getBytes(UTF_8));
 	}
 
 	private void beginTask(int totalWorkUnits) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransferConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransferConfig.java
index 6b8d5c5..4f2ea64 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransferConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransferConfig.java
@@ -106,7 +106,8 @@ enum ProtocolVersion {
 			this.name = name;
 		}
 
-		static @Nullable ProtocolVersion parse(@Nullable String name) {
+		@Nullable
+		static ProtocolVersion parse(@Nullable String name) {
 			if (name == null) {
 				return null;
 			}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java
index 026fd81..70fb1f0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java
@@ -48,10 +48,11 @@
 
 package org.eclipse.jgit.transport;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
+
 import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.Serializable;
-import java.io.UnsupportedEncodingException;
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.util.BitSet;
@@ -282,12 +283,7 @@ private static String unescape(String s) throws URISyntaxException {
 		if (s.indexOf('%') < 0)
 			return s;
 
-		byte[] bytes;
-		try {
-			bytes = s.getBytes(Constants.CHARACTER_ENCODING);
-		} catch (UnsupportedEncodingException e) {
-			throw new RuntimeException(e); // can't happen
-		}
+		byte[] bytes = s.getBytes(UTF_8);
 
 		byte[] os = new byte[bytes.length];
 		int j = 0;
@@ -335,12 +331,7 @@ private static String escape(String s, boolean escapeReservedChars,
 		if (s == null)
 			return null;
 		ByteArrayOutputStream os = new ByteArrayOutputStream(s.length());
-		byte[] bytes;
-		try {
-			bytes = s.getBytes(Constants.CHARACTER_ENCODING);
-		} catch (UnsupportedEncodingException e) {
-			throw new RuntimeException(e); // cannot happen
-		}
+		byte[] bytes = s.getBytes(UTF_8);
 		for (int i = 0; i < bytes.length; ++i) {
 			int b = bytes[i] & 0xFF;
 			if (b <= 32 || (encodeNonAscii && b > 127) || b == '%'
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 cd7290e..535c914 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java
@@ -48,6 +48,7 @@
 import static org.eclipse.jgit.transport.GitProtocolConstants.CAPABILITY_REF_IN_WANT;
 import static org.eclipse.jgit.transport.GitProtocolConstants.COMMAND_FETCH;
 import static org.eclipse.jgit.transport.GitProtocolConstants.COMMAND_LS_REFS;
+import static org.eclipse.jgit.transport.GitProtocolConstants.CAPABILITY_SERVER_OPTION;
 import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_AGENT;
 import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_ALLOW_REACHABLE_SHA1_IN_WANT;
 import static org.eclipse.jgit.transport.GitProtocolConstants.OPTION_ALLOW_TIP_SHA1_IN_WANT;
@@ -69,6 +70,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
+import java.io.UncheckedIOException;
 import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -86,6 +88,7 @@
 import org.eclipse.jgit.errors.PackProtocolException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.internal.storage.pack.PackWriter;
+import org.eclipse.jgit.internal.transport.parser.FirstWant;
 import org.eclipse.jgit.lib.BitmapIndex;
 import org.eclipse.jgit.lib.BitmapIndex.BitmapBuilder;
 import org.eclipse.jgit.lib.Constants;
@@ -177,44 +180,48 @@ void checkWants(UploadPack up, List<ObjectId> wants)
 				throws PackProtocolException, IOException;
 	}
 
-	/** Data in the first line of a request, the line itself plus options. */
+	/**
+	 * Data in the first line of a want-list, the line itself plus options.
+	 *
+	 * @deprecated Use {@link FirstWant} instead
+	 */
+	@Deprecated
 	public static class FirstLine {
-		private final String line;
-		private final Set<String> options;
+
+		private final FirstWant firstWant;
 
 		/**
-		 * Parse the first line of a receive-pack request.
-		 *
 		 * @param line
 		 *            line from the client.
 		 */
 		public FirstLine(String line) {
-			if (line.length() > 45) {
-				final HashSet<String> opts = new HashSet<>();
-				String opt = line.substring(45);
-				if (opt.startsWith(" ")) //$NON-NLS-1$
-					opt = opt.substring(1);
-				for (String c : opt.split(" ")) //$NON-NLS-1$
-					opts.add(c);
-				this.line = line.substring(0, 45);
-				this.options = Collections.unmodifiableSet(opts);
-			} else {
-				this.line = line;
-				this.options = Collections.emptySet();
+			try {
+				firstWant = FirstWant.fromLine(line);
+			} catch (PackProtocolException e) {
+				throw new UncheckedIOException(e);
 			}
 		}
 
 		/** @return non-capabilities part of the line. */
 		public String getLine() {
-			return line;
+			return firstWant.getLine();
 		}
 
-		/** @return options parsed from the line. */
+		/** @return capabilities parsed from the line. */
 		public Set<String> getOptions() {
-			return options;
+			return firstWant.getCapabilities();
 		}
 	}
 
+	/*
+	 * {@link java.util.function.Consumer} doesn't allow throwing checked
+	 * exceptions. Define our own to propagate IOExceptions.
+	 */
+	@FunctionalInterface
+	private static interface IOConsumer<R> {
+		void accept(R t) throws IOException;
+	}
+
 	/** Database we read the objects from. */
 	private final Repository db;
 
@@ -280,12 +287,11 @@ public Set<String> getOptions() {
 	/** Hook for taking post upload actions. */
 	private PostUploadHook postUploadHook = PostUploadHook.NULL;
 
-	/** Capabilities requested by the client. */
-	private Set<String> options;
+	/** Caller user agent */
 	String userAgent;
 
 	/** Raw ObjectIds the client has asked for, before validating them. */
-	private final Set<ObjectId> wantIds = new HashSet<>();
+	private Set<ObjectId> wantIds = new HashSet<>();
 
 	/** Objects the client wants to obtain. */
 	private final Set<RevObject> wantAll = new HashSet<>();
@@ -293,25 +299,6 @@ public Set<String> getOptions() {
 	/** Objects on both sides, these don't have to be sent. */
 	private final Set<RevObject> commonBase = new HashSet<>();
 
-	/** Shallow commits the client already has. */
-	private Set<ObjectId> clientShallowCommits = new HashSet<>();
-
-	/** Desired depth from the client on a shallow request. */
-	private int depth;
-
-	/**
-	 * Commit time of the newest objects the client has asked us using
-	 * --shallow-since not to send. Cannot be nonzero if depth is nonzero.
-	 */
-	private int shallowSince;
-
-	/**
-	 * (Possibly short) ref names, ancestors of which the client has asked us
-	 * not to send using --shallow-exclude. Cannot be non-empty if depth is
-	 * nonzero.
-	 */
-	private List<String> deepenNotRefs = new ArrayList<>();
-
 	/** Commit time of the oldest common commit, in seconds. */
 	private int oldestTime;
 
@@ -345,7 +332,14 @@ public Set<String> getOptions() {
 
 	private PackStatistics statistics;
 
-	private long filterBlobLimit = -1;
+	/**
+	 * Request this instance is handling.
+	 *
+	 * We need to keep a reference to it for {@link PreUploadHook pre upload
+	 * hooks}. They receive a reference this instance and invoke methods like
+	 * getDepth() to get information about the request.
+	 */
+	private FetchRequest currentRequest;
 
 	/**
 	 * Create a new pack upload for an open repository.
@@ -687,10 +681,12 @@ public void setTransferConfig(TransferConfig tc) {
 	 *             read.
 	 */
 	public boolean isSideBand() throws RequestNotYetReadException {
-		if (options == null)
+		if (currentRequest == null) {
 			throw new RequestNotYetReadException();
-		return (options.contains(OPTION_SIDE_BAND)
-				|| options.contains(OPTION_SIDE_BAND_64K));
+		}
+		Set<String> caps = currentRequest.getClientCapabilities();
+		return caps.contains(OPTION_SIDE_BAND)
+				|| caps.contains(OPTION_SIDE_BAND_64K);
 	}
 
 	/**
@@ -804,6 +800,7 @@ private void service() throws IOException {
 		// writing a response. Buffer the response until then.
 		PackStatistics.Accumulator accumulator = new PackStatistics.Accumulator();
 		List<ObjectId> unshallowCommits = new ArrayList<>();
+		FetchRequest req;
 		try {
 			if (biDirectionalPipe)
 				sendAdvertisedRefs(new PacketLineOutRefAdvertiser(pckOut));
@@ -814,29 +811,46 @@ else if (requestValidator instanceof AnyRequestValidator)
 
 			long negotiateStart = System.currentTimeMillis();
 			accumulator.advertised = advertised.size();
-			recvWants();
-			if (wantIds.isEmpty()) {
-				preUploadHook.onBeginNegotiateRound(this, wantIds, 0);
-				preUploadHook.onEndNegotiateRound(this, wantIds, 0, 0, false);
+
+			ProtocolV0Parser parser = new ProtocolV0Parser(transferConfig);
+			req = parser.recvWants(pckIn);
+			currentRequest = req;
+
+			wantIds = req.getWantIds();
+
+			if (req.getWantIds().isEmpty()) {
+				preUploadHook.onBeginNegotiateRound(this, req.getWantIds(), 0);
+				preUploadHook.onEndNegotiateRound(this, req.getWantIds(), 0, 0,
+						false);
 				return;
 			}
-			accumulator.wants = wantIds.size();
+			accumulator.wants = req.getWantIds().size();
 
-			if (options.contains(OPTION_MULTI_ACK_DETAILED)) {
+			if (req.getClientCapabilities().contains(OPTION_MULTI_ACK_DETAILED)) {
 				multiAck = MultiAck.DETAILED;
-				noDone = options.contains(OPTION_NO_DONE);
-			} else if (options.contains(OPTION_MULTI_ACK))
+				noDone = req.getClientCapabilities().contains(OPTION_NO_DONE);
+			} else if (req.getClientCapabilities().contains(OPTION_MULTI_ACK))
 				multiAck = MultiAck.CONTINUE;
 			else
 				multiAck = MultiAck.OFF;
 
-			if (!clientShallowCommits.isEmpty())
-				verifyClientShallow(clientShallowCommits);
-			if (depth != 0)
-				processShallow(null, unshallowCommits, true);
-			if (!clientShallowCommits.isEmpty())
-				walk.assumeShallow(clientShallowCommits);
-			sendPack = negotiate(accumulator);
+			if (!req.getClientShallowCommits().isEmpty()) {
+				verifyClientShallow(req.getClientShallowCommits());
+			}
+
+			if (req.getDepth() != 0 || req.getDeepenSince() != 0) {
+				computeShallowsAndUnshallows(req, shallow -> {
+					pckOut.writeString("shallow " + shallow.name() + '\n'); //$NON-NLS-1$
+				}, unshallow -> {
+					pckOut.writeString("unshallow " + unshallow.name() + '\n'); //$NON-NLS-1$
+					unshallowCommits.add(unshallow);
+				});
+				pckOut.end();
+			}
+
+			if (!req.getClientShallowCommits().isEmpty())
+				walk.assumeShallow(req.getClientShallowCommits());
+			sendPack = negotiate(req, accumulator);
 			accumulator.timeNegotiating += System.currentTimeMillis()
 					- negotiateStart;
 
@@ -886,35 +900,14 @@ else if (requestValidator instanceof AnyRequestValidator)
 		}
 
 		if (sendPack) {
-			sendPack(accumulator, refs == null ? null : refs.values(), unshallowCommits);
+			sendPack(accumulator, req, refs == null ? null : refs.values(),
+					unshallowCommits);
 		}
 	}
 
 	private void lsRefsV2() throws IOException {
-		LsRefsV2Request.Builder builder = LsRefsV2Request.builder();
-		List<String> prefixes = new ArrayList<>();
-		String line = pckIn.readString();
-		// Currently, we do not support any capabilities, so the next
-		// line is DELIM if there are arguments or END if not.
-		if (line == PacketLineIn.DELIM) {
-			while ((line = pckIn.readString()) != PacketLineIn.END) {
-				if (line.equals("peel")) { //$NON-NLS-1$
-					builder.setPeel(true);
-				} else if (line.equals("symrefs")) { //$NON-NLS-1$
-					builder.setSymrefs(true);
-				} else if (line.startsWith("ref-prefix ")) { //$NON-NLS-1$
-					prefixes.add(line.substring("ref-prefix ".length())); //$NON-NLS-1$
-				} else {
-					throw new PackProtocolException(MessageFormat
-							.format(JGitText.get().unexpectedPacketLine, line));
-				}
-			}
-		} else if (line != PacketLineIn.END) {
-			throw new PackProtocolException(MessageFormat
-					.format(JGitText.get().unexpectedPacketLine, line));
-		}
-		LsRefsV2Request req = builder.setRefPrefixes(prefixes).build();
-
+		ProtocolV2Parser parser = new ProtocolV2Parser(transferConfig);
+		LsRefsV2Request req = parser.parseLsRefsRequest(pckIn);
 		protocolV2Hook.onLsRefs(req);
 
 		rawOut.stopBuffering();
@@ -928,10 +921,9 @@ private void lsRefsV2() throws IOException {
 			refsToSend = getAdvertisedOrDefaultRefs();
 		} else {
 			refsToSend = new HashMap<>();
-			for (String refPrefix : req.getRefPrefixes()) {
-				for (Ref ref : db.getRefDatabase().getRefsByPrefix(refPrefix)) {
-					refsToSend.put(ref.getName(), ref);
-				}
+			String[] prefixes = req.getRefPrefixes().toArray(new String[0]);
+			for (Ref ref : db.getRefDatabase().getRefsByPrefix(prefixes)) {
+				refsToSend.put(ref.getName(), ref);
 			}
 		}
 		if (req.getSymrefs()) {
@@ -958,31 +950,29 @@ private void fetchV2() throws IOException {
 		ProtocolV2Parser parser = new ProtocolV2Parser(transferConfig);
 		FetchV2Request req = parser.parseFetchRequest(pckIn,
 				db.getRefDatabase());
+		currentRequest = req;
 		rawOut.stopBuffering();
 
 		protocolV2Hook.onFetch(req);
 
 		// TODO(ifrade): Refactor to pass around the Request object, instead of
 		// copying data back to class fields
-		options = req.getOptions();
-		wantIds.addAll(req.getWantsIds());
-		clientShallowCommits = req.getClientShallowCommits();
-		depth = req.getDepth();
-		shallowSince = req.getDeepenSince();
-		filterBlobLimit = req.getFilterBlobLimit();
-		deepenNotRefs = req.getDeepenNotRefs();
+		wantIds = req.getWantIds();
 
 		boolean sectionSent = false;
-		@Nullable List<ObjectId> shallowCommits = null;
+		boolean mayHaveShallow = req.getDepth() != 0
+				|| req.getDeepenSince() != 0
+				|| !req.getDeepenNotRefs().isEmpty();
+		List<ObjectId> shallowCommits = new ArrayList<>();
 		List<ObjectId> unshallowCommits = new ArrayList<>();
 
 		if (!req.getClientShallowCommits().isEmpty()) {
 			verifyClientShallow(req.getClientShallowCommits());
 		}
-		if (req.getDepth() != 0 || req.getDeepenSince() != 0
-				|| !req.getDeepenNotRefs().isEmpty()) {
-			shallowCommits = new ArrayList<>();
-			processShallow(shallowCommits, unshallowCommits, false);
+		if (mayHaveShallow) {
+			computeShallowsAndUnshallows(req,
+					shallowCommit -> shallowCommits.add(shallowCommit),
+					unshallowCommit -> unshallowCommits.add(unshallowCommit));
 		}
 		if (!req.getClientShallowCommits().isEmpty())
 			walk.assumeShallow(req.getClientShallowCommits());
@@ -1008,7 +998,7 @@ private void fetchV2() throws IOException {
 		}
 
 		if (req.wasDoneReceived() || okToGiveUp()) {
-			if (shallowCommits != null) {
+			if (mayHaveShallow) {
 				if (sectionSent)
 					pckOut.writeDelim();
 				pckOut.writeString("shallow-info\n"); //$NON-NLS-1$
@@ -1038,7 +1028,8 @@ private void fetchV2() throws IOException {
 				pckOut.writeDelim();
 			pckOut.writeString("packfile\n"); //$NON-NLS-1$
 			sendPack(new PackStatistics.Accumulator(),
-					req.getOptions().contains(OPTION_INCLUDE_TAG)
+					req,
+					req.getClientCapabilities().contains(OPTION_INCLUDE_TAG)
 						? db.getRefDatabase().getRefsByPrefix(R_TAGS)
 						: null,
 					unshallowCommits);
@@ -1092,6 +1083,7 @@ private List<String> getV2CapabilityAdvertisement() {
 				(transferConfig.isAllowFilter() ? OPTION_FILTER + ' ' : "") + //$NON-NLS-1$
 				(advertiseRefInWant ? CAPABILITY_REF_IN_WANT + ' ' : "") + //$NON-NLS-1$
 				OPTION_SHALLOW);
+		caps.add(CAPABILITY_SERVER_OPTION);
 		return caps;
 	}
 
@@ -1140,28 +1132,29 @@ private static Set<ObjectId> refIdSet(Collection<Ref> refs) {
 	}
 
 	/*
-	 * Determines what "shallow" and "unshallow" lines to send to the user.
-	 * The information is written to shallowCommits (if not null) and
-	 * unshallowCommits, and also written to #pckOut (if writeToPckOut is
-	 * true).
+	 * Determines what object ids must be marked as shallow or unshallow for the
+	 * client.
 	 */
-	private void processShallow(@Nullable List<ObjectId> shallowCommits,
-			List<ObjectId> unshallowCommits,
-			boolean writeToPckOut) throws IOException {
-		if (options.contains(OPTION_DEEPEN_RELATIVE) ||
-				shallowSince != 0 ||
-				!deepenNotRefs.isEmpty()) {
-			// TODO(jonathantanmy): Implement deepen-relative, deepen-since,
+	private void computeShallowsAndUnshallows(FetchRequest req,
+			IOConsumer<ObjectId> shallowFunc,
+			IOConsumer<ObjectId> unshallowFunc)
+			throws IOException {
+		if (req.getClientCapabilities().contains(OPTION_DEEPEN_RELATIVE)
+				|| !req.getDeepenNotRefs().isEmpty()) {
+			// TODO(jonathantanmy): Implement deepen-relative
 			// and deepen-not.
 			throw new UnsupportedOperationException();
 		}
 
-		int walkDepth = depth - 1;
+		int walkDepth = req.getDepth() == 0 ? Integer.MAX_VALUE
+				: req.getDepth() - 1;
 		try (DepthWalk.RevWalk depthWalk = new DepthWalk.RevWalk(
 				walk.getObjectReader(), walkDepth)) {
 
+			depthWalk.setDeepenSince(req.getDeepenSince());
+
 			// Find all the commits which will be shallow
-			for (ObjectId o : wantIds) {
+			for (ObjectId o : req.getWantIds()) {
 				try {
 					depthWalk.markRoot(depthWalk.parseCommit(o));
 				} catch (IncorrectObjectTypeException notCommit) {
@@ -1173,32 +1166,21 @@ private void processShallow(@Nullable List<ObjectId> shallowCommits,
 			while ((o = depthWalk.next()) != null) {
 				DepthWalk.Commit c = (DepthWalk.Commit) o;
 
+				boolean isBoundary = (c.getDepth() == walkDepth) || c.isBoundary();
+
 				// Commits at the boundary which aren't already shallow in
 				// the client need to be marked as such
-				if (c.getDepth() == walkDepth
-						&& !clientShallowCommits.contains(c)) {
-					if (shallowCommits != null) {
-						shallowCommits.add(c.copy());
-					}
-					if (writeToPckOut) {
-						pckOut.writeString("shallow " + o.name()); //$NON-NLS-1$
-					}
+				if (isBoundary && !req.getClientShallowCommits().contains(c)) {
+					shallowFunc.accept(c.copy());
 				}
 
 				// Commits not on the boundary which are shallow in the client
 				// need to become unshallowed
-				if (c.getDepth() < walkDepth
-						&& clientShallowCommits.remove(c)) {
-					unshallowCommits.add(c.copy());
-					if (writeToPckOut) {
-						pckOut.writeString("unshallow " + c.name()); //$NON-NLS-1$
-					}
+				if (!isBoundary && req.getClientShallowCommits().remove(c)) {
+					unshallowFunc.accept(c.copy());
 				}
 			}
 		}
-		if (writeToPckOut) {
-			pckOut.end();
-		}
 	}
 
 	/*
@@ -1358,67 +1340,6 @@ public OutputStream getMessageOutputStream() {
 		return msgOut;
 	}
 
-	private void recvWants() throws IOException {
-		boolean isFirst = true;
-		boolean filterReceived = false;
-		for (;;) {
-			String line;
-			try {
-				line = pckIn.readString();
-			} catch (EOFException eof) {
-				if (isFirst)
-					break;
-				throw eof;
-			}
-
-			if (line == PacketLineIn.END)
-				break;
-
-			if (line.startsWith("deepen ")) { //$NON-NLS-1$
-				depth = Integer.parseInt(line.substring(7));
-				if (depth <= 0) {
-					throw new PackProtocolException(
-							MessageFormat.format(JGitText.get().invalidDepth,
-									Integer.valueOf(depth)));
-				}
-				continue;
-			}
-
-			if (line.startsWith("shallow ")) { //$NON-NLS-1$
-				clientShallowCommits.add(ObjectId.fromString(line.substring(8)));
-				continue;
-			}
-
-			if (transferConfig.isAllowFilter()
-					&& line.startsWith(OPTION_FILTER + " ")) { //$NON-NLS-1$
-				String arg = line.substring(OPTION_FILTER.length() + 1);
-
-				if (filterReceived) {
-					throw new PackProtocolException(JGitText.get().tooManyFilters);
-				}
-				filterReceived = true;
-
-				filterBlobLimit = ProtocolV2Parser.filterLine(arg);
-				continue;
-			}
-
-			if (!line.startsWith("want ") || line.length() < 45) //$NON-NLS-1$
-				throw new PackProtocolException(MessageFormat.format(JGitText.get().expectedGot, "want", line)); //$NON-NLS-1$
-
-			if (isFirst) {
-				if (line.length() > 45) {
-					FirstLine firstLine = new FirstLine(line);
-					options = firstLine.getOptions();
-					line = firstLine.getLine();
-				} else
-					options = Collections.emptySet();
-			}
-
-			wantIds.add(ObjectId.fromString(line.substring(5)));
-			isFirst = false;
-		}
-	}
-
 	/**
 	 * Returns the clone/fetch depth. Valid only after calling recvWants(). A
 	 * depth of 1 means return only the wants.
@@ -1427,9 +1348,9 @@ private void recvWants() throws IOException {
 	 * @since 4.0
 	 */
 	public int getDepth() {
-		if (options == null)
+		if (currentRequest == null)
 			throw new RequestNotYetReadException();
-		return depth;
+		return currentRequest.getDepth();
 	}
 
 	/**
@@ -1448,10 +1369,16 @@ public int getDepth() {
 	 * @since 4.0
 	 */
 	public String getPeerUserAgent() {
-		return UserAgent.getAgent(options, userAgent);
+		if (currentRequest == null) {
+			return userAgent;
+		}
+
+		return UserAgent.getAgent(currentRequest.getClientCapabilities(),
+				userAgent);
 	}
 
-	private boolean negotiate(PackStatistics.Accumulator accumulator)
+	private boolean negotiate(FetchRequest req,
+			PackStatistics.Accumulator accumulator)
 			throws IOException {
 		okToGiveUp = Boolean.FALSE;
 
@@ -1467,7 +1394,7 @@ private boolean negotiate(PackStatistics.Accumulator accumulator)
 				// disconnected, and will try another request with actual want/have.
 				// Don't report the EOF here, its a bug in the protocol that the client
 				// just disconnects without sending an END.
-				if (!biDirectionalPipe && depth > 0)
+				if (!biDirectionalPipe && req.getDepth() > 0)
 					return false;
 				throw eof;
 			}
@@ -1848,25 +1775,27 @@ private boolean wantSatisfied(RevObject want) throws IOException {
 	 * Send the requested objects to the client.
 	 *
 	 * @param accumulator
-	 *                where to write statistics about the content of the pack.
+	 *            where to write statistics about the content of the pack.
+	 * @param req
+	 *            request in process
 	 * @param allTags
-	 *                refs to search for annotated tags to include in the pack
-	 *                if the {@link #OPTION_INCLUDE_TAG} capability was
-	 *                requested.
+	 *            refs to search for annotated tags to include in the pack if
+	 *            the {@link #OPTION_INCLUDE_TAG} capability was requested.
 	 * @param unshallowCommits
-	 *                shallow commits on the client that are now becoming
-	 *                unshallow
+	 *            shallow commits on the client that are now becoming unshallow
 	 * @throws IOException
-	 *                if an error occured while generating or writing the pack.
+	 *             if an error occured while generating or writing the pack.
 	 */
 	private void sendPack(PackStatistics.Accumulator accumulator,
+			FetchRequest req,
 			@Nullable Collection<Ref> allTags,
 			List<ObjectId> unshallowCommits) throws IOException {
-		final boolean sideband = options.contains(OPTION_SIDE_BAND)
-				|| options.contains(OPTION_SIDE_BAND_64K);
+		Set<String> caps = req.getClientCapabilities();
+		boolean sideband = caps.contains(OPTION_SIDE_BAND)
+				|| caps.contains(OPTION_SIDE_BAND_64K);
 		if (sideband) {
 			try {
-				sendPack(true, accumulator, allTags, unshallowCommits);
+				sendPack(true, req, accumulator, allTags, unshallowCommits);
 			} catch (ServiceMayNotContinueException noPack) {
 				// This was already reported on (below).
 				throw noPack;
@@ -1887,7 +1816,7 @@ private void sendPack(PackStatistics.Accumulator accumulator,
 					throw err;
 			}
 		} else {
-			sendPack(false, accumulator, allTags, unshallowCommits);
+			sendPack(false, req, accumulator, allTags, unshallowCommits);
 		}
 	}
 
@@ -1911,21 +1840,22 @@ private boolean reportInternalServerErrorOverSideband() {
 	 * Send the requested objects to the client.
 	 *
 	 * @param sideband
-	 *                whether to wrap the pack in side-band pkt-lines,
-	 *                interleaved with progress messages and errors.
+	 *            whether to wrap the pack in side-band pkt-lines, interleaved
+	 *            with progress messages and errors.
+	 * @param req
+	 *            request being processed
 	 * @param accumulator
-	 *                where to write statistics about the content of the pack.
+	 *            where to write statistics about the content of the pack.
 	 * @param allTags
-	 *                refs to search for annotated tags to include in the pack
-	 *                if the {@link #OPTION_INCLUDE_TAG} capability was
-	 *                requested.
+	 *            refs to search for annotated tags to include in the pack if
+	 *            the {@link #OPTION_INCLUDE_TAG} capability was requested.
 	 * @param unshallowCommits
-	 *                shallow commits on the client that are now becoming
-	 *                unshallow
+	 *            shallow commits on the client that are now becoming unshallow
 	 * @throws IOException
-	 *                if an error occured while generating or writing the pack.
+	 *             if an error occured while generating or writing the pack.
 	 */
 	private void sendPack(final boolean sideband,
+			FetchRequest req,
 			PackStatistics.Accumulator accumulator,
 			@Nullable Collection<Ref> allTags,
 			List<ObjectId> unshallowCommits) throws IOException {
@@ -1934,12 +1864,12 @@ private void sendPack(final boolean sideband,
 
 		if (sideband) {
 			int bufsz = SideBandOutputStream.SMALL_BUF;
-			if (options.contains(OPTION_SIDE_BAND_64K))
+			if (req.getClientCapabilities().contains(OPTION_SIDE_BAND_64K))
 				bufsz = SideBandOutputStream.MAX_BUF;
 
 			packOut = new SideBandOutputStream(SideBandOutputStream.CH_DATA,
 					bufsz, rawOut);
-			if (!options.contains(OPTION_NO_PROGRESS)) {
+			if (!req.getClientCapabilities().contains(OPTION_NO_PROGRESS)) {
 				msgOut = new SideBandOutputStream(
 						SideBandOutputStream.CH_PROGRESS, bufsz, rawOut);
 				pm = new SideBandProgressMonitor(msgOut);
@@ -1975,17 +1905,20 @@ private void sendPack(final boolean sideband,
 				accumulator);
 		try {
 			pw.setIndexDisabled(true);
-			if (filterBlobLimit >= 0) {
-				pw.setFilterBlobLimit(filterBlobLimit);
+			if (req.getFilterBlobLimit() >= 0) {
+				pw.setFilterBlobLimit(req.getFilterBlobLimit());
 				pw.setUseCachedPacks(false);
 			} else {
 				pw.setUseCachedPacks(true);
 			}
-			pw.setUseBitmaps(depth == 0 && clientShallowCommits.isEmpty());
-			pw.setClientShallowCommits(clientShallowCommits);
+			pw.setUseBitmaps(
+					req.getDepth() == 0
+							&& req.getClientShallowCommits().isEmpty());
+			pw.setClientShallowCommits(req.getClientShallowCommits());
 			pw.setReuseDeltaCommits(true);
-			pw.setDeltaBaseAsOffset(options.contains(OPTION_OFS_DELTA));
-			pw.setThin(options.contains(OPTION_THIN_PACK));
+			pw.setDeltaBaseAsOffset(
+					req.getClientCapabilities().contains(OPTION_OFS_DELTA));
+			pw.setThin(req.getClientCapabilities().contains(OPTION_THIN_PACK));
 			pw.setReuseValidatingObjects(false);
 
 			// Objects named directly by references go at the beginning
@@ -2004,14 +1937,18 @@ else if (ref.getName().startsWith(Constants.R_HEADS))
 			}
 
 			RevWalk rw = walk;
-			if (depth > 0) {
-				pw.setShallowPack(depth, unshallowCommits);
-				rw = new DepthWalk.RevWalk(walk.getObjectReader(), depth - 1);
-				rw.assumeShallow(clientShallowCommits);
+			if (req.getDepth() > 0 || req.getDeepenSince() != 0) {
+				int walkDepth = req.getDepth() == 0 ? Integer.MAX_VALUE
+						: req.getDepth() - 1;
+				pw.setShallowPack(req.getDepth(), unshallowCommits);
+				rw = new DepthWalk.RevWalk(walk.getObjectReader(), walkDepth);
+				((DepthWalk.RevWalk) rw).setDeepenSince(req.getDeepenSince());
+				rw.assumeShallow(req.getClientShallowCommits());
 			}
 
 			if (wantAll.isEmpty()) {
-				pw.preparePack(pm, wantIds, commonBase, clientShallowCommits);
+				pw.preparePack(pm, wantIds, commonBase,
+						req.getClientShallowCommits());
 			} else {
 				walk.reset();
 
@@ -2020,7 +1957,8 @@ else if (ref.getName().startsWith(Constants.R_HEADS))
 				rw = ow;
 			}
 
-			if (options.contains(OPTION_INCLUDE_TAG) && allTags != null) {
+			if (req.getClientCapabilities().contains(OPTION_INCLUDE_TAG)
+					&& allTags != null) {
 				for (Ref ref : allTags) {
 					ObjectId objectId = ref.getObjectId();
 					if (objectId == null) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java
index 24b9ac0..3d25c23 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java
@@ -46,6 +46,8 @@
 
 package org.eclipse.jgit.treewalk;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
+
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.FileInputStream;
@@ -412,7 +414,7 @@ public long getLastModified() {
 		public InputStream openInputStream() throws IOException {
 			if (attributes.isSymbolicLink()) {
 				return new ByteArrayInputStream(fs.readSymLink(getFile())
-						.getBytes(Constants.CHARACTER_ENCODING));
+						.getBytes(UTF_8));
 			} else {
 				return new FileInputStream(getFile());
 			}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
index e5c2922..7f0308f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
@@ -43,6 +43,8 @@
 
 package org.eclipse.jgit.util;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
+
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.Closeable;
@@ -1172,7 +1174,7 @@ public int runProcess(ProcessBuilder processBuilder,
 			OutputStream outRedirect, OutputStream errRedirect, String stdinArgs)
 			throws IOException, InterruptedException {
 		InputStream in = (stdinArgs == null) ? null : new ByteArrayInputStream(
-				stdinArgs.getBytes(Constants.CHARACTER_ENCODING));
+						stdinArgs.getBytes(UTF_8));
 		return runProcess(processBuilder, outRedirect, errRedirect, in);
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/HttpSupport.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/HttpSupport.java
index 6f92b37..9190a59 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/HttpSupport.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/HttpSupport.java
@@ -44,7 +44,7 @@
 
 package org.eclipse.jgit.util;
 
-import static org.eclipse.jgit.lib.Constants.CHARACTER_ENCODING;
+import static java.nio.charset.StandardCharsets.UTF_8;
 
 import java.io.IOException;
 import java.io.UnsupportedEncodingException;
@@ -181,7 +181,7 @@ public static void encode(StringBuilder urlstr, String key) {
 		if (key == null || key.length() == 0)
 			return;
 		try {
-			urlstr.append(URLEncoder.encode(key, CHARACTER_ENCODING));
+			urlstr.append(URLEncoder.encode(key, UTF_8.name()));
 		} catch (UnsupportedEncodingException e) {
 			throw new RuntimeException(JGitText.get().couldNotURLEncodeToUTF8, e);
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/LfsFactory.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/LfsFactory.java
index 6d60ef3..96636b7 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/LfsFactory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/LfsFactory.java
@@ -152,7 +152,8 @@ public ObjectLoader applySmudgeFilter(Repository db,
 	 * @param outputStream
 	 * @return a {@link PrePushHook} implementation or <code>null</code>
 	 */
-	public @Nullable PrePushHook getPrePushHook(Repository repo,
+	@Nullable
+	public PrePushHook getPrePushHook(Repository repo,
 			PrintStream outputStream) {
 		return null;
 	}
@@ -163,7 +164,8 @@ public ObjectLoader applySmudgeFilter(Repository db,
 	 *
 	 * @return a command to install LFS support.
 	 */
-	public @Nullable LfsInstallCommand getInstallCommand() {
+	@Nullable
+	public LfsInstallCommand getInstallCommand() {
 		return null;
 	}
 
@@ -294,6 +296,11 @@ public int read() throws IOException {
 			return stream.read();
 		}
 
+		@Override
+		public int read(byte b[], int off, int len) throws IOException {
+			return stream.read(b, off, len);
+		}
+
 		/**
 		 * @return the length of the stream
 		 */
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 28f406a..bbb1645 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/RawParseUtils.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/RawParseUtils.java
@@ -729,7 +729,8 @@ public static final IntList lineMapOrBinary(byte[] buf, int ptr, int end)
 		return map;
 	}
 
-	private static @Nullable IntList lineMapOrNull(byte[] buf, int ptr, int end) {
+	@Nullable
+	private static IntList lineMapOrNull(byte[] buf, int ptr, int end) {
 		// Experimentally derived from multiple source repositories
 		// the average number of bytes/line is 36. Its a rough guess
 		// to initially size our map close to the target.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolStreamTypeUtil.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolStreamTypeUtil.java
index 822961f..d7c6bec 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolStreamTypeUtil.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolStreamTypeUtil.java
@@ -1,5 +1,6 @@
 /*
  * Copyright (C) 2015, Ivan Motsch <ivan.motsch@bsiag.com>
+ * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
  * under the terms of the Eclipse Distribution License v1.0 which
@@ -49,6 +50,7 @@
 import org.eclipse.jgit.lib.CoreConfig.EolStreamType;
 import org.eclipse.jgit.treewalk.TreeWalk.OperationType;
 import org.eclipse.jgit.treewalk.WorkingTreeOptions;
+import org.eclipse.jgit.util.SystemReader;
 
 /**
  * Utility used to create input and output stream wrappers for
@@ -57,7 +59,6 @@
  * @since 4.3
  */
 public final class EolStreamTypeUtil {
-	private static final boolean FORCE_EOL_LF_ON_CHECKOUT = false;
 
 	private EolStreamTypeUtil() {
 	}
@@ -164,11 +165,11 @@ private static EolStreamType checkInStreamType(WorkingTreeOptions options,
 
 		// old git system
 		if (attrs.isSet("crlf")) {//$NON-NLS-1$
-			return EolStreamType.TEXT_LF;
+			return EolStreamType.TEXT_LF; // Same as isSet("text")
 		} else if (attrs.isUnset("crlf")) {//$NON-NLS-1$
-			return EolStreamType.DIRECT;
+			return EolStreamType.DIRECT; // Same as isUnset("text")
 		} else if ("input".equals(attrs.getValue("crlf"))) {//$NON-NLS-1$ //$NON-NLS-2$
-			return EolStreamType.TEXT_LF;
+			return EolStreamType.TEXT_LF; // Same as eol=lf
 		}
 
 		// new git system
@@ -196,6 +197,28 @@ private static EolStreamType checkInStreamType(WorkingTreeOptions options,
 		return EolStreamType.DIRECT;
 	}
 
+	private static EolStreamType getOutputFormat(WorkingTreeOptions options) {
+		switch (options.getAutoCRLF()) {
+		case TRUE:
+			return EolStreamType.TEXT_CRLF;
+		default:
+			// no decision
+		}
+		switch (options.getEOL()) {
+		case CRLF:
+			return EolStreamType.TEXT_CRLF;
+		case NATIVE:
+			if (SystemReader.getInstance().isWindows()) {
+				return EolStreamType.TEXT_CRLF;
+			}
+			return EolStreamType.TEXT_LF;
+		case LF:
+		default:
+			break;
+		}
+		return EolStreamType.DIRECT;
+	}
+
 	private static EolStreamType checkOutStreamType(WorkingTreeOptions options,
 			Attributes attrs) {
 		if (attrs.isUnset("text")) {//$NON-NLS-1$
@@ -205,57 +228,35 @@ private static EolStreamType checkOutStreamType(WorkingTreeOptions options,
 
 		// old git system
 		if (attrs.isSet("crlf")) {//$NON-NLS-1$
-			return FORCE_EOL_LF_ON_CHECKOUT ? EolStreamType.TEXT_LF
-					: EolStreamType.DIRECT;
+			return getOutputFormat(options); // Same as isSet("text")
 		} else if (attrs.isUnset("crlf")) {//$NON-NLS-1$
-			return EolStreamType.DIRECT;
+			return EolStreamType.DIRECT; // Same as isUnset("text")
 		} else if ("input".equals(attrs.getValue("crlf"))) {//$NON-NLS-1$ //$NON-NLS-2$
-			return EolStreamType.DIRECT;
+			return EolStreamType.DIRECT; // Same as eol=lf
 		}
 
 		// new git system
 		String eol = attrs.getValue("eol"); //$NON-NLS-1$
-		if (eol != null && "crlf".equals(eol)) //$NON-NLS-1$
-			return EolStreamType.TEXT_CRLF;
-		if (eol != null && "lf".equals(eol)) //$NON-NLS-1$
-			return FORCE_EOL_LF_ON_CHECKOUT ? EolStreamType.TEXT_LF
-					: EolStreamType.DIRECT;
-
-		if (attrs.isSet("text")) { //$NON-NLS-1$
-			switch (options.getAutoCRLF()) {
-			case TRUE:
+		if (eol != null) {
+			if ("crlf".equals(eol)) {//$NON-NLS-1$
 				return EolStreamType.TEXT_CRLF;
-			default:
-				// no decision
-			}
-			switch (options.getEOL()) {
-			case CRLF:
-				return EolStreamType.TEXT_CRLF;
-			case LF:
-				return FORCE_EOL_LF_ON_CHECKOUT ? EolStreamType.TEXT_LF
-						: EolStreamType.DIRECT;
-			case NATIVE:
-			default:
+			} else if ("lf".equals(eol)) { //$NON-NLS-1$
 				return EolStreamType.DIRECT;
 			}
 		}
+		if (attrs.isSet("text")) { //$NON-NLS-1$
+			return getOutputFormat(options);
+		}
 
 		if ("auto".equals(attrs.getValue("text"))) { //$NON-NLS-1$ //$NON-NLS-2$
-			switch (options.getAutoCRLF()) {
-			case TRUE:
+			EolStreamType basic = getOutputFormat(options);
+			switch (basic) {
+			case TEXT_CRLF:
 				return EolStreamType.AUTO_CRLF;
+			case TEXT_LF:
+				return EolStreamType.AUTO_LF;
 			default:
-				// no decision
-			}
-			switch (options.getEOL()) {
-			case CRLF:
-				return EolStreamType.AUTO_CRLF;
-			case LF:
-				return FORCE_EOL_LF_ON_CHECKOUT ? EolStreamType.TEXT_LF
-						: EolStreamType.DIRECT;
-			case NATIVE:
-			default:
-				return EolStreamType.DIRECT;
+				return basic;
 			}
 		}
 
diff --git a/pom.xml b/pom.xml
index 41bab39..dc90f06 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>5.1.4-SNAPSHOT</version>
+  <version>5.2.0-SNAPSHOT</version>
 
   <name>JGit - Parent</name>
   <url>${jgit-url}</url>
@@ -216,9 +216,11 @@
     <maven-javadoc-plugin-version>3.0.1</maven-javadoc-plugin-version>
     <tycho-extras-version>1.2.0</tycho-extras-version>
     <gson-version>2.8.2</gson-version>
-    <spotbugs-maven-plugin-version>3.1.6</spotbugs-maven-plugin-version>
-    <maven-surefire-report-plugin-version>2.21.0</maven-surefire-report-plugin-version>
+    <spotbugs-maven-plugin-version>3.1.7</spotbugs-maven-plugin-version>
+    <maven-surefire-version>2.22.1</maven-surefire-version>
     <maven-compiler-plugin-version>3.8.0</maven-compiler-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>
 
     <!-- Properties to enable jacoco code coverage analysis -->
     <sonar.core.codeCoveragePlugin>jacoco</sonar.core.codeCoveragePlugin>
@@ -275,7 +277,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-shade-plugin</artifactId>
-          <version>3.1.1</version>
+          <version>3.2.0</version>
         </plugin>
 
         <plugin>
@@ -305,7 +307,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-surefire-plugin</artifactId>
-          <version>2.21.0</version>
+          <version>${maven-surefire-version}</version>
           <configuration>
             <forkCount>${test-fork-count}</forkCount>
             <reuseForks>true</reuseForks>
@@ -376,7 +378,7 @@
         <plugin>
           <groupId>org.jacoco</groupId>
           <artifactId>jacoco-maven-plugin</artifactId>
-          <version>0.8.1</version>
+          <version>0.8.2</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
@@ -386,24 +388,24 @@
             <dependency><!-- add support for ssh/scp -->
               <groupId>org.apache.maven.wagon</groupId>
               <artifactId>wagon-ssh</artifactId>
-              <version>3.1.0</version>
+              <version>3.2.0</version>
             </dependency>
           </dependencies>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-surefire-report-plugin</artifactId>
-          <version>${maven-surefire-report-plugin-version}</version>
+          <version>${maven-surefire-version}</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-jxr-plugin</artifactId>
-          <version>2.5</version>
+          <version>${maven-jxr-plugin-version}</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-project-info-reports-plugin</artifactId>
-          <version>2.9</version>
+          <version>${maven-project-info-reports-plugin-version}</version>
         </plugin>
       </plugins>
     </pluginManagement>
@@ -412,7 +414,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-enforcer-plugin</artifactId>
-        <version>3.0.0-M1</version>
+        <version>3.0.0-M2</version>
         <executions>
           <execution>
             <id>enforce-maven</id>
@@ -560,7 +562,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-jxr-plugin</artifactId>
-        <version>2.5</version>
+        <version>${maven-jxr-plugin-version}</version>
       </plugin>
       <plugin>
         <groupId>com.github.spotbugs</groupId>
@@ -570,7 +572,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-surefire-report-plugin</artifactId>
-        <version>${maven-surefire-report-plugin-version}</version>
+        <version>${maven-surefire-version}</version>
         <configuration>
           <aggregate>true</aggregate>
           <alwaysGenerateSurefireReport>false</alwaysGenerateSurefireReport>
@@ -582,7 +584,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-project-info-reports-plugin</artifactId>
-        <version>2.9</version>
+        <version>${maven-project-info-reports-plugin-version}</version>
         <reportSets>
           <reportSet>
             <reports>
@@ -798,7 +800,7 @@
               <dependency>
                 <groupId>com.google.errorprone</groupId>
                 <artifactId>error_prone_core</artifactId>
-                <version>2.3.1</version>
+                <version>2.3.2</version>
               </dependency>
             </dependencies>
           </plugin>
diff --git a/tools/BUILD b/tools/BUILD
index e69de29..b8a621f 100644
--- a/tools/BUILD
+++ b/tools/BUILD
@@ -0,0 +1,107 @@
+load(
+    "@bazel_tools//tools/jdk:default_java_toolchain.bzl",
+    "JDK9_JVM_OPTS",
+    "default_java_toolchain",
+)
+
+default_java_toolchain(
+    name = "error_prone_warnings_toolchain",
+    bootclasspath = ["@bazel_tools//tools/jdk:platformclasspath9.jar"],
+    jvm_opts = JDK9_JVM_OPTS,
+    package_configuration = [
+        ":error_prone",
+    ],
+    visibility = ["//visibility:public"],
+)
+
+# This EP warnings list borrowed from here:
+# https://github.com/bazelbuild/BUILD_file_generator/blob/master/tools/bazel_defs/java.bzl
+java_package_configuration(
+    name = "error_prone",
+    javacopts = [
+        "-XepDisableWarningsInGeneratedCode",
+        "-Xep:MissingCasesInEnumSwitch:ERROR",
+        "-Xep:ReferenceEquality:WARN",
+        "-Xep:StringEquality:WARN",
+        "-Xep:WildcardImport:WARN",
+        "-Xep:AmbiguousMethodReference:WARN",
+        "-Xep:BadAnnotationImplementation:WARN",
+        "-Xep:BadComparable:WARN",
+        "-Xep:BoxedPrimitiveConstructor:ERROR",
+        "-Xep:CannotMockFinalClass:WARN",
+        "-Xep:ClassCanBeStatic:WARN",
+        "-Xep:ClassNewInstance:WARN",
+        "-Xep:DefaultCharset:ERROR",
+        "-Xep:DoubleCheckedLocking:WARN",
+        "-Xep:ElementsCountedInLoop:WARN",
+        "-Xep:EqualsHashCode:WARN",
+        "-Xep:EqualsIncompatibleType:WARN",
+        "-Xep:ExpectedExceptionChecker:ERROR",
+        "-Xep:Finally:WARN",
+        "-Xep:FloatingPointLiteralPrecision:WARN",
+        "-Xep:FragmentInjection:WARN",
+        "-Xep:FragmentNotInstantiable:WARN",
+        "-Xep:FunctionalInterfaceClash:WARN",
+        "-Xep:FutureReturnValueIgnored:WARN",
+        "-Xep:GetClassOnEnum:WARN",
+        "-Xep:ImmutableAnnotationChecker:WARN",
+        "-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:MissingFail:ERROR",
+        "-Xep:MissingOverride:WARN",
+        "-Xep:MutableConstantField:WARN",
+        "-Xep:NarrowingCompoundAssignment:WARN",
+        "-Xep:NonAtomicVolatileUpdate:WARN",
+        "-Xep:NonOverridingEquals:WARN",
+        "-Xep:NullableConstructor:WARN",
+        "-Xep:NullablePrimitive:WARN",
+        "-Xep:NullableVoid:WARN",
+        "-Xep:OperatorPrecedence:WARN",
+        "-Xep:OverridesGuiceInjectableMethod:WARN",
+        "-Xep:PreconditionsInvalidPlaceholder:WARN",
+        "-Xep:ProtoFieldPreconditionsCheckNotNull:WARN",
+        "-Xep:ProtocolBufferOrdinal:WARN",
+        "-Xep:RequiredModifiers:WARN",
+        "-Xep:ShortCircuitBoolean:WARN",
+        "-Xep:SimpleDateFormatConstant:WARN",
+        "-Xep:StaticGuardedByInstance:WARN",
+        "-Xep:SynchronizeOnNonFinalField:WARN",
+        "-Xep:TruthConstantAsserts:WARN",
+        "-Xep:TypeParameterShadowing:WARN",
+        "-Xep:TypeParameterUnusedInFormals:WARN",
+        "-Xep:URLEqualsHashCode:WARN",
+        "-Xep:UnsynchronizedOverridesSynchronized:WARN",
+        "-Xep:WaitNotInLoop:WARN",
+    ],
+    packages = ["error_prone_packages"],
+)
+
+package_group(
+    name = "error_prone_packages",
+    packages = [
+        "//org.eclipse.jgit/...",
+        "//org.eclipse.jgit.ant/...",
+        "//org.eclipse.jgit.ant.test/...",
+        "//org.eclipse.jgit.archive/...",
+        "//org.eclipse.jgit.http.apache/...",
+        "//org.eclipse.jgit.http.server/...",
+        "//org.eclipse.jgit.http.test/...",
+        "//org.eclipse.jgit.junit/...",
+        "//org.eclipse.jgit.junit.http/...",
+        "//org.eclipse.jgit.lfs/...",
+        "//org.eclipse.jgit.lfs.server/...",
+        "//org.eclipse.jgit.lfs.server.test/...",
+        "//org.eclipse.jgit.lfs.test/...",
+        "//org.eclipse.jgit.packaging/...",
+        "//org.eclipse.jgit.pgm/...",
+        "//org.eclipse.jgit.pgm.test/...",
+        "//org.eclipse.jgit.test/...",
+        "//org.eclipse.jgit.ui/...",
+    ],
+)