Merge branch 'master' into stable-4.4

* master:
  JGit CLI: allow to call git init with specific directory
  Redirect all Show output to outs
  Support git config [include] section with absolute path(s)
  Added filter for merge and non-merges commits.
  [findBugs] Prevent potential NPE in FS_POSIX.readUmask()
  [findBugs] Fix calculation of host header in SignerV4
  Update Orbit repository to S20160518051658 for Neon RC2
  Fix StashApply regarding handling of untracked files
  GC should not pack objects only referenced by ORIG_HEAD,...
  Make sure to overwrite files when "reset --hard" detects conflicts
  Allow setting FileMode to executable when applying patches in 
    ApplyCommand
  Fix config value get to return last instead of 1st just like git
  Remove UTF-8 checking duplication in Config lib subclasses
  Update Maven plugins
  Fix type parameter in javadoc in TestRepository.delete(String ref)
  TestRepository: Add delete() method
  Make BaseReceivePack.setAtomic public
  ReceivePack: Pass atomic setting from client to BatchRefUpdate

Change-Id: I5c9c5b7ccb23fb48b44b3da10b2c5d876d043d24
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

40 files changed, 672 insertions, 57 deletions

diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java
index 1119e63824..07df56d3f1 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java
@@ -586,6 +586,31 @@ public class TestRepository<R extends Repository> {
 		}
 	}
 
+	/**
+	 * Delete a reference.
+	 *
+	 * @param ref
+	 *	      the name of the reference to delete. This is normalized
+	 *	      in the same way as {@link #update(String, AnyObjectId)}.
+	 * @throws Exception
+	 * @since 4.4
+	 */
+	public void delete(String ref) throws Exception {
+		ref = normalizeRef(ref);
+		RefUpdate u = db.updateRef(ref);
+		switch (u.delete()) {
+		case FAST_FORWARD:
+		case FORCED:
+		case NEW:
+		case NO_CHANGE:
+			updateServerInfo();
+			return;
+
+		default:
+			throw new IOException("Cannot delete " + ref + " " + u.getResult());
+		}
+	}
+
 	private static String normalizeRef(String ref) {
 		if (Constants.HEAD.equals(ref)) {
 			// nothing
@@ -959,6 +984,15 @@ public class TestRepository<R extends Repository> {
 		public RevCommit update(RevCommit to) throws Exception {
 			return TestRepository.this.update(ref, to);
 		}
+
+		/**
+		 * Delete this branch.
+		 * @throws Exception
+		 * @since 4.4
+		 */
+		public void delete() throws Exception {
+			TestRepository.this.delete(ref);
+		}
 	}
 
 	/** Helper to generate a commit. */
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 08bb4b96fd..f95b605c85 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
@@ -229,12 +229,12 @@ class SignerV4 {
 
 	private static void addHostHeader(URL url,
 			Map<String, String> headers) {
-		String hostHeader = url.getHost();
+		StringBuilder hostHeader = new StringBuilder(url.getHost());
 		int port = url.getPort();
 		if (port > -1) {
-			hostHeader.concat(":" + Integer.toString(port)); //$NON-NLS-1$
+			hostHeader.append(":").append(port); //$NON-NLS-1$
 		}
-		headers.put("Host", hostHeader); //$NON-NLS-1$
+		headers.put("Host", hostHeader.toString()); //$NON-NLS-1$
 	}
 
 	private static String canonicalizeHeaderNames(
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target
index d8cacb4c68..f7d5622552 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/mbarbero/fr.obeo.releng.targetplatform -->
-<target name="jgit-4.6" sequenceNumber="1462141948">
+<target name="jgit-4.6" sequenceNumber="1463612069">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.2.13.v20150730"/>
@@ -39,8 +39,8 @@
       <unit id="org.kohsuke.args4j.source" version="2.0.21.v201301150030"/>
       <unit id="org.hamcrest.core" version="1.3.0.v201303031735"/>
       <unit id="org.hamcrest.core.source" version="1.3.0.v201303031735"/>
-      <unit id="javaewah" version="0.7.9.v201401101600"/>
-      <unit id="javaewah.source" version="0.7.9.v201401101600"/>
+      <unit id="javaewah" version="0.7.9.v201605172130"/>
+      <unit id="javaewah.source" version="0.7.9.v201605172130"/>
       <unit id="org.objenesis" version="1.0.0.v201505121915"/>
       <unit id="org.objenesis.source" version="1.0.0.v201505121915"/>
       <unit id="org.mockito" version="1.8.4.v201303031500"/>
@@ -58,7 +58,7 @@
       <unit id="org.slf4j.api.source" version="1.7.2.v20121108-1250"/>
       <unit id="org.slf4j.impl.log4j12" version="1.7.2.v20131105-2200"/>
       <unit id="org.slf4j.impl.log4j12.source" version="1.7.2.v20131105-2200"/>
-      <repository location="http://download.eclipse.org/tools/orbit/downloads/drops/S20160501200945/repository/"/>
+      <repository location="http://download.eclipse.org/tools/orbit/downloads/drops/S20160518051658/repository/"/>
     </location>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.osgi" version="0.0.0"/>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.tpd
index 83a68ddc56..9b5365fc65 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.tpd
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.tpd
@@ -1,7 +1,7 @@
 target "jgit-4.6" with source configurePhase
 
 include "projects/jetty-9.2.13.tpd"
-include "orbit/S20160501200945-Neon.tpd"
+include "orbit/S20160518051658-Neon.tpd"
 
 location "http://download.eclipse.org/releases/neon/" {
 	org.eclipse.osgi lazy
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/S20160501200945-Neon.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/S20160518051658-Neon.tpd
index a5d87e93d5..efb6cbd118 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/S20160501200945-Neon.tpd
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/S20160518051658-Neon.tpd
@@ -1,7 +1,7 @@
-target "S20160501200945-Neon" with source configurePhase
+target "S20160518051658-Neon" with source configurePhase
 // see http://download.eclipse.org/tools/orbit/downloads/
 
-location "http://download.eclipse.org/tools/orbit/downloads/drops/S20160501200945/repository/" {
+location "http://download.eclipse.org/tools/orbit/downloads/drops/S20160518051658/repository/" {
 	org.apache.ant [1.9.6.v201510161327,1.9.6.v201510161327]
 	org.apache.ant.source [1.9.6.v201510161327,1.9.6.v201510161327]
 	org.apache.commons.compress [1.6.0.v201310281400,1.6.0.v201310281400]
@@ -18,8 +18,8 @@ location "http://download.eclipse.org/tools/orbit/downloads/drops/S2016050120094
 	org.kohsuke.args4j.source [2.0.21.v201301150030,2.0.21.v201301150030]
 	org.hamcrest.core [1.3.0.v201303031735,1.3.0.v201303031735]
 	org.hamcrest.core.source [1.3.0.v201303031735,1.3.0.v201303031735]
-	javaewah [0.7.9.v201401101600,0.7.9.v201401101600]
-	javaewah.source [0.7.9.v201401101600,0.7.9.v201401101600]
+	javaewah [0.7.9.v201605172130,0.7.9.v201605172130]
+	javaewah.source [0.7.9.v201605172130,0.7.9.v201605172130]
 	org.objenesis [1.0.0.v201505121915,1.0.0.v201505121915]
 	org.objenesis.source [1.0.0.v201505121915,1.0.0.v201505121915]
 	org.mockito [1.8.4.v201303031500,1.8.4.v201303031500]
diff --git a/org.eclipse.jgit.packaging/pom.xml b/org.eclipse.jgit.packaging/pom.xml
index 21d79dd668..a3d7d7352e 100644
--- a/org.eclipse.jgit.packaging/pom.xml
+++ b/org.eclipse.jgit.packaging/pom.xml
@@ -59,7 +59,7 @@
   <name>JGit Tycho Parent</name>
 
   <properties>
-    <tycho-version>0.23.0</tycho-version>
+    <tycho-version>0.25.0</tycho-version>
     <tycho-extras-version>${tycho-version}</tycho-extras-version>
     <target-platform>jgit-4.6</target-platform>
   </properties>
@@ -149,7 +149,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-resources-plugin</artifactId>
-          <version>2.5</version>
+          <version>2.7</version>
           <configuration>
             <encoding>ISO-8859-1</encoding>
           </configuration>
@@ -216,12 +216,12 @@
         <plugin>
           <groupId>org.eclipse.cbi.maven.plugins</groupId>
           <artifactId>eclipse-jarsigner-plugin</artifactId>
-          <version>1.1.2</version>
+          <version>1.1.3</version>
         </plugin>
         <plugin>
           <groupId>org.codehaus.mojo</groupId>
           <artifactId>build-helper-maven-plugin</artifactId>
-          <version>1.9</version>
+          <version>1.10</version>
         </plugin>
       </plugins>
     </pluginManagement>
diff --git a/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF
index 1f70e98438..286c6d9ecf 100644
--- a/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.pgm.test/META-INF/MANIFEST.MF
@@ -25,6 +25,7 @@ Import-Package: org.eclipse.jgit.api;version="[4.4.0,4.5.0)",
  org.eclipse.jgit.util;version="[4.4.0,4.5.0)",
  org.eclipse.jgit.util.io;version="[4.4.0,4.5.0)",
  org.hamcrest.core;bundle-version="[1.1.0,2.0.0)",
- org.junit;version="[4.4.0,5.0.0)",
+ org.junit;version="[4.11.0,5.0.0)",
+ org.junit.rules;version="[4.11.0,5.0.0)",
  org.kohsuke.args4j;version="[2.0.12,2.1.0)"
 Require-Bundle: org.tukaani.xz;bundle-version="[1.3.0,2.0.0)"
diff --git a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/InitTest.java b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/InitTest.java
new file mode 100644
index 0000000000..c7dbc244dd
--- /dev/null
+++ b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/InitTest.java
@@ -0,0 +1,90 @@
+/*
+ * Copyright (C) 2016, Rüdiger Herrmann <ruediger.herrmann@gmx.de>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.pgm;
+
+import static org.junit.Assert.assertArrayEquals;
+
+import java.io.File;
+
+import org.eclipse.jgit.lib.CLIRepositoryTestCase;
+import org.eclipse.jgit.lib.Constants;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+
+public class InitTest extends CLIRepositoryTestCase {
+
+	@Rule
+	public final TemporaryFolder tempFolder = new TemporaryFolder();
+
+	@Test
+	public void testInitBare() throws Exception {
+		File directory = tempFolder.getRoot();
+
+		String[] result = execute(
+				"git init '" + directory.getCanonicalPath() + "' --bare");
+
+		String[] expecteds = new String[] {
+				"Initialized empty Git repository in "
+						+ directory.getCanonicalPath(),
+				"" };
+		assertArrayEquals(expecteds, result);
+	}
+
+	@Test
+	public void testInitDirectory() throws Exception {
+		File workDirectory = tempFolder.getRoot();
+		File gitDirectory = new File(workDirectory, Constants.DOT_GIT);
+
+		String[] result = execute(
+				"git init '" + workDirectory.getCanonicalPath() + "'");
+
+		String[] expecteds = new String[] {
+				"Initialized empty Git repository in "
+						+ gitDirectory.getCanonicalPath(),
+				"" };
+		assertArrayEquals(expecteds, result);
+	}
+
+}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java
index b3e73b5d99..a7bee7f7b9 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java
@@ -4,6 +4,7 @@
  * Copyright (C) 2010, Robin Rosenberg <robin.rosenberg@dewire.com>
  * Copyright (C) 2010, Sasa Zivkov <sasa.zivkov@sap.com>
  * Copyright (C) 2010, Chris Aniszczyk <caniszczyk@gmail.com>
+ * Copyright (C) 2016, Rüdiger Herrmann <ruediger.herrmann@gmx.de>
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -54,6 +55,7 @@ import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.InitCommand;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.pgm.internal.CLIText;
+import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.Option;
 
 @Command(common = true, usage = "usage_CreateAnEmptyGitRepository")
@@ -61,6 +63,9 @@ class Init extends TextBuiltin {
 	@Option(name = "--bare", usage = "usage_CreateABareRepository")
 	private boolean bare;
 
+	@Argument(index = 0, metaVar = "metaVar_directory")
+	private String directory;
+
 	@Override
 	protected final boolean requiresRepository() {
 		return false;
@@ -70,8 +75,12 @@ class Init extends TextBuiltin {
 	protected void run() throws Exception {
 		InitCommand command = Git.init();
 		command.setBare(bare);
-		if (gitdir != null)
+		if (gitdir != null) {
 			command.setDirectory(new File(gitdir));
+		}
+		if (directory != null) {
+			command.setDirectory(new File(directory));
+		}
 		Repository repository = command.call().getRepository();
 		outw.println(MessageFormat.format(
 				CLIText.get().initializedEmptyGitRepositoryIn, repository
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java
index c5986b01aa..6892c9973f 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java
@@ -63,6 +63,7 @@ import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.PersonIdent;
+import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.pgm.opt.PathTreeFilterHandler;
 import org.eclipse.jgit.revwalk.RevCommit;
@@ -81,8 +82,7 @@ class Show extends TextBuiltin {
 
 	private final DateFormat fmt;
 
-	private final DiffFormatter diffFmt = new DiffFormatter( //
-			new BufferedOutputStream(System.out));
+	private DiffFormatter diffFmt;
 
 	@Argument(index = 0, metaVar = "metaVar_object")
 	private String objectName;
@@ -165,6 +165,12 @@ class Show extends TextBuiltin {
 		fmt = new SimpleDateFormat("EEE MMM dd HH:mm:ss yyyy ZZZZZ", Locale.US); //$NON-NLS-1$
 	}
 
+	@Override
+	protected void init(final Repository repository, final String gitDir) {
+		super.init(repository, gitDir);
+		diffFmt = new DiffFormatter(new BufferedOutputStream(outs));
+	}
+
 	@SuppressWarnings("boxing")
 	@Override
 	protected void run() throws Exception {
diff --git a/org.eclipse.jgit.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
index af357740cd..0dc6b61586 100644
--- a/org.eclipse.jgit.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
@@ -51,6 +51,7 @@ Import-Package: com.googlecode.javaewah;version="[0.7.9,0.8.0)",
  org.hamcrest;version="[1.1.0,2.0.0)",
  org.junit;version="[4.4.0,5.0.0)",
  org.junit.experimental.theories;version="[4.4.0,5.0.0)",
+ org.junit.rules;version="[4.11.0,5.0.0)",
  org.junit.runner;version="[4.4.0,5.0.0)",
  org.junit.runners;version="[4.11.0,5.0.0)",
  org.slf4j;version="[1.7.2,2.0.0)"
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M1.patch b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M1.patch
new file mode 100644
index 0000000000..395bd4c503
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M1.patch
@@ -0,0 +1,9 @@
+diff --git a/M1 b/M1
+new file mode 100755
+index 0000000..de98044
+--- /dev/null
++++ b/M1
+@@ -0,0 +1,3 @@
++a
++b
++c
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M1_PostImage b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M1_PostImage
new file mode 100644
index 0000000000..de980441c3
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M1_PostImage
@@ -0,0 +1,3 @@
+a
+b
+c
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M2.patch b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M2.patch
new file mode 100644
index 0000000000..b56ca0828e
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M2.patch
@@ -0,0 +1,10 @@
+diff --git a/M2 b/M2
+old mode 100644
+new mode 100755
+index 0000000..de98044
+--- a/M2
++++ b/M2
+@@ -1,3 +1,1 @@
+ a
+-b
+-c
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M2_PostImage b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M2_PostImage
new file mode 100644
index 0000000000..7898192261
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M2_PostImage
@@ -0,0 +1 @@
+a
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M2_PreImage b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M2_PreImage
new file mode 100644
index 0000000000..de980441c3
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M2_PreImage
@@ -0,0 +1,3 @@
+a
+b
+c
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M3.patch b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M3.patch
new file mode 100644
index 0000000000..ee536058ab
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M3.patch
@@ -0,0 +1,10 @@
+diff --git a/M3 b/M3
+old mode 100755
+new mode 100644
+index 0000000..de98044
+--- a/M3
++++ b/M3
+@@ -1,1 +1,3 @@
+ a
++b
++c
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M3_PostImage b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M3_PostImage
new file mode 100644
index 0000000000..de980441c3
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M3_PostImage
@@ -0,0 +1,3 @@
+a
+b
+c
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M3_PreImage b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M3_PreImage
new file mode 100755
index 0000000000..7898192261
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M3_PreImage
@@ -0,0 +1 @@
+a
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java
index f2b5b3ba95..172807c43d 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java
@@ -44,6 +44,7 @@ package org.eclipse.jgit.api;
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
 import java.io.ByteArrayOutputStream;
@@ -157,6 +158,33 @@ public class ApplyCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
+	public void testAddM1() throws Exception {
+		ApplyResult result = init("M1", false, true);
+		assertEquals(1, result.getUpdatedFiles().size());
+		assertTrue(result.getUpdatedFiles().get(0).canExecute());
+		checkFile(new File(db.getWorkTree(), "M1"),
+				b.getString(0, b.size(), false));
+	}
+
+	@Test
+	public void testModifyM2() throws Exception {
+		ApplyResult result = init("M2", true, true);
+		assertEquals(1, result.getUpdatedFiles().size());
+		assertTrue(result.getUpdatedFiles().get(0).canExecute());
+		checkFile(new File(db.getWorkTree(), "M2"),
+				b.getString(0, b.size(), false));
+	}
+
+	@Test
+	public void testModifyM3() throws Exception {
+		ApplyResult result = init("M3", true, true);
+		assertEquals(1, result.getUpdatedFiles().size());
+		assertFalse(result.getUpdatedFiles().get(0).canExecute());
+		checkFile(new File(db.getWorkTree(), "M3"),
+				b.getString(0, b.size(), false));
+	}
+
+	@Test
 	public void testModifyX() throws Exception {
 		ApplyResult result = init("X");
 		assertEquals(1, result.getUpdatedFiles().size());
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/LogCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/LogCommandTest.java
index 34432c588b..1310625a9b 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/LogCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/LogCommandTest.java
@@ -53,7 +53,9 @@ import java.util.List;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.merge.MergeStrategy;
 import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.revwalk.filter.RevFilter;
 import org.junit.Test;
 
 public class LogCommandTest extends RepositoryTestCase {
@@ -210,4 +212,81 @@ public class LogCommandTest extends RepositoryTestCase {
 		assertEquals("commit#2", commit.getShortMessage());
 		assertFalse(log.hasNext());
 	}
+
+	@Test
+	public void logOnlyMergeCommits() throws Exception {
+		setCommitsAndMerge();
+		Git git = Git.wrap(db);
+
+		Iterable<RevCommit> commits = git.log().all().call();
+		Iterator<RevCommit> i = commits.iterator();
+		RevCommit commit = i.next();
+		assertEquals("merge s0 with m1", commit.getFullMessage());
+		commit = i.next();
+		assertEquals("s0", commit.getFullMessage());
+		commit = i.next();
+		assertEquals("m1", commit.getFullMessage());
+		commit = i.next();
+		assertEquals("m0", commit.getFullMessage());
+		assertFalse(i.hasNext());
+
+		commits = git.log().setRevFilter(RevFilter.ONLY_MERGES).call();
+		i = commits.iterator();
+		commit = i.next();
+		assertEquals("merge s0 with m1", commit.getFullMessage());
+		assertFalse(i.hasNext());
+	}
+
+	@Test
+	public void logNoMergeCommits() throws Exception {
+		setCommitsAndMerge();
+		Git git = Git.wrap(db);
+
+		Iterable<RevCommit> commits = git.log().all().call();
+		Iterator<RevCommit> i = commits.iterator();
+		RevCommit commit = i.next();
+		assertEquals("merge s0 with m1", commit.getFullMessage());
+		commit = i.next();
+		assertEquals("s0", commit.getFullMessage());
+		commit = i.next();
+		assertEquals("m1", commit.getFullMessage());
+		commit = i.next();
+		assertEquals("m0", commit.getFullMessage());
+		assertFalse(i.hasNext());
+
+		commits = git.log().setRevFilter(RevFilter.NO_MERGES).call();
+		i = commits.iterator();
+		commit = i.next();
+		assertEquals("m1", commit.getFullMessage());
+		commit = i.next();
+		assertEquals("s0", commit.getFullMessage());
+		commit = i.next();
+		assertEquals("m0", commit.getFullMessage());
+		assertFalse(i.hasNext());
+	}
+
+	private void setCommitsAndMerge() throws Exception {
+		Git git = Git.wrap(db);
+		writeTrashFile("file1", "1\n2\n3\n4\n");
+		git.add().addFilepattern("file1").call();
+		RevCommit masterCommit0 = git.commit().setMessage("m0").call();
+
+		createBranch(masterCommit0, "refs/heads/side");
+		checkoutBranch("refs/heads/side");
+
+		writeTrashFile("file2", "1\n2\n3\n4\n5\n6\n7\n8\n");
+		git.add().addFilepattern("file2").call();
+		RevCommit c = git.commit().setMessage("s0").call();
+
+		checkoutBranch("refs/heads/master");
+
+		writeTrashFile("file3", "1\n2\n");
+		git.add().addFilepattern("file3").call();
+		git.commit().setMessage("m1").call();
+
+		git.merge().include(c.getId())
+				.setStrategy(MergeStrategy.RESOLVE)
+				.setMessage("merge s0 with m1").call();
+	}
+
 }
\ No newline at end of file
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PullCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PullCommandTest.java
index ff7066e8bf..a526fdaa7e 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PullCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PullCommandTest.java
@@ -58,6 +58,7 @@ import java.util.concurrent.Callable;
 import org.eclipse.jgit.api.CreateBranchCommand.SetupUpstreamMode;
 import org.eclipse.jgit.api.MergeResult.MergeStatus;
 import org.eclipse.jgit.api.errors.NoHeadException;
+import org.eclipse.jgit.junit.JGitTestUtil;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
@@ -185,6 +186,40 @@ public class PullCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
+	public void testPullWithUntrackedStash() throws Exception {
+		target.pull().call();
+
+		// change the source file
+		writeToFile(sourceFile, "Source change");
+		source.add().addFilepattern("SomeFile.txt").call();
+		source.commit().setMessage("Source change in remote").call();
+
+		// write untracked file
+		writeToFile(new File(dbTarget.getWorkTree(), "untracked.txt"),
+				"untracked");
+		RevCommit stash = target.stashCreate().setIndexMessage("message here")
+				.setIncludeUntracked(true).call();
+		assertNotNull(stash);
+		assertTrue(target.status().call().isClean());
+
+		// pull from source
+		assertTrue(target.pull().call().isSuccessful());
+		assertEquals("[SomeFile.txt, mode:100644, content:Source change]",
+				indexState(dbTarget, CONTENT));
+		assertFalse(JGitTestUtil.check(dbTarget, "untracked.txt"));
+		assertEquals("Source change",
+				JGitTestUtil.read(dbTarget, "SomeFile.txt"));
+
+		// apply the stash
+		target.stashApply().setStashRef(stash.getName()).call();
+		assertEquals("[SomeFile.txt, mode:100644, content:Source change]",
+				indexState(dbTarget, CONTENT));
+		assertEquals("untracked", JGitTestUtil.read(dbTarget, "untracked.txt"));
+		assertEquals("Source change",
+				JGitTestUtil.read(dbTarget, "SomeFile.txt"));
+	}
+
+	@Test
 	public void testPullLocalConflict() throws Exception {
 		target.branchCreate().setName("basedOnMaster").setStartPoint(
 				"refs/heads/master").setUpstreamMode(SetupUpstreamMode.TRACK)
@@ -576,4 +611,4 @@ public class PullCommandTest extends RepositoryTestCase {
 				fis.close();
 		}
 	}
-}
+}
\ No newline at end of file
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 40d8458efd..725ebc0d23 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
@@ -157,6 +157,34 @@ public class ResetCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
+	public void testHardResetWithConflicts_DoOverWriteUntrackedFile()
+			throws JGitInternalException,
+			AmbiguousObjectException, IOException, GitAPIException {
+		setupRepository();
+		git.rm().setCached(true).addFilepattern("a.txt").call();
+		assertTrue(new File(db.getWorkTree(), "a.txt").exists());
+		git.reset().setMode(ResetType.HARD).setRef(Constants.HEAD)
+				.call();
+		assertTrue(new File(db.getWorkTree(), "a.txt").exists());
+		assertEquals("content", read(new File(db.getWorkTree(), "a.txt")));
+	}
+
+	@Test
+	public void testHardResetWithConflicts_DoDeleteFileFolderConflicts()
+			throws JGitInternalException,
+			AmbiguousObjectException, IOException, GitAPIException {
+		setupRepository();
+		writeTrashFile("d/c.txt", "x");
+		git.add().addFilepattern("d/c.txt").call();
+		FileUtils.delete(new File(db.getWorkTree(), "d"), FileUtils.RECURSIVE);
+		writeTrashFile("d", "y");
+
+		git.reset().setMode(ResetType.HARD).setRef(Constants.HEAD)
+				.call();
+		assertFalse(new File(db.getWorkTree(), "d").exists());
+	}
+
+	@Test
 	public void testResetToNonexistingHEAD() throws JGitInternalException,
 			AmbiguousObjectException, IOException, GitAPIException {
 
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 6238a354d8..6d07d34d3a 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
@@ -56,6 +56,9 @@ import static org.junit.Assert.assertSame;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
 import java.text.MessageFormat;
 import java.util.Arrays;
 import java.util.Iterator;
@@ -64,18 +67,29 @@ import java.util.Set;
 
 import org.eclipse.jgit.api.MergeCommand.FastForwardMode;
 import org.eclipse.jgit.errors.ConfigInvalidException;
+import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.junit.MockSystemReader;
 import org.eclipse.jgit.merge.MergeConfig;
+import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.SystemReader;
 import org.junit.After;
+import org.junit.Rule;
 import org.junit.Test;
+import org.junit.rules.ExpectedException;
+import org.junit.rules.TemporaryFolder;
 
 /**
  * Test reading of git config
  */
 public class ConfigTest {
 
+	@Rule
+	public ExpectedException expectedEx = ExpectedException.none();
+
+	@Rule
+	public TemporaryFolder tmp = new TemporaryFolder();
+
 	@After
 	public void tearDown() {
 		SystemReader.setInstance(null);
@@ -739,6 +753,81 @@ public class ConfigTest {
 				c.getStringList("a", null, "x"));
 	}
 
+	@Test
+	public void testReadMultipleValuesForName() throws ConfigInvalidException {
+		Config c = parse("[foo]\nbar=false\nbar=true\n");
+		assertTrue(c.getBoolean("foo", "bar", false));
+	}
+
+	@Test
+	public void testIncludeInvalidName() throws ConfigInvalidException {
+		expectedEx.expect(ConfigInvalidException.class);
+		expectedEx.expectMessage(JGitText.get().invalidLineInConfigFile);
+		parse("[include]\nbar\n");
+	}
+
+	@Test
+	public void testIncludeNoValue() throws ConfigInvalidException {
+		expectedEx.expect(ConfigInvalidException.class);
+		expectedEx.expectMessage(JGitText.get().invalidLineInConfigFile);
+		parse("[include]\npath\n");
+	}
+
+	@Test
+	public void testIncludeEmptyValue() throws ConfigInvalidException {
+		expectedEx.expect(ConfigInvalidException.class);
+		expectedEx.expectMessage(JGitText.get().invalidLineInConfigFile);
+		parse("[include]\npath=\n");
+	}
+
+	@Test
+	public void testIncludeValuePathNotFound() throws ConfigInvalidException {
+		String notFound = "/not/found";
+		expectedEx.expect(ConfigInvalidException.class);
+		expectedEx.expectMessage(notFound);
+		parse("[include]\npath=" + notFound + "\n");
+	}
+
+	@Test
+	public void testIncludeTooManyRecursions() throws IOException {
+		File config = tmp.newFile("config");
+		String include = "[include]\npath=" + config.toPath() + "\n";
+		Files.write(config.toPath(), include.getBytes());
+		FileBasedConfig fbConfig = new FileBasedConfig(null, config,
+				FS.DETECTED);
+		try {
+			fbConfig.load();
+			fail();
+		} catch (ConfigInvalidException cie) {
+			assertEquals(JGitText.get().tooManyIncludeRecursions,
+					cie.getCause().getMessage());
+		}
+	}
+
+	@Test
+	public void testInclude() throws IOException, ConfigInvalidException {
+		File config = tmp.newFile("config");
+		File more = tmp.newFile("config.more");
+		File other = tmp.newFile("config.other");
+
+		String fooBar = "[foo]\nbar=true\n";
+		String includeMore = "[include]\npath=" + more.toPath() + "\n";
+		String includeOther = "path=" + other.toPath() + "\n";
+		String fooPlus = fooBar + includeMore + includeOther;
+		Files.write(config.toPath(), fooPlus.getBytes());
+
+		String fooMore = "[foo]\nmore=bar\n";
+		Files.write(more.toPath(), fooMore.getBytes());
+
+		String otherMore = "[other]\nmore=bar\n";
+		Files.write(other.toPath(), otherMore.getBytes());
+
+		Config parsed = parse("[include]\npath=" + config.toPath() + "\n");
+		assertTrue(parsed.getBoolean("foo", "bar", false));
+		assertEquals("bar", parsed.getString("foo", null, "more"));
+		assertEquals("bar", parsed.getString("other", null, "more"));
+	}
+
 	private static void assertReadLong(long exp) throws ConfigInvalidException {
 		assertReadLong(exp, String.valueOf(exp));
 	}
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 a99bd7e911..f7d9374bd7 100644
--- a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
+++ b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
@@ -337,6 +337,7 @@ invalidId0=Invalid id
 invalidIdLength=Invalid id length {0}; should be {1}
 invalidIgnoreParamSubmodule=Found invalid ignore param for submodule {0}.
 invalidIgnoreRule=Exception caught while parsing ignore rule ''{0}''.
+invalidIncludedPathInConfigFile=Invalid included path in config file: {0}
 invalidIntegerValue=Invalid integer value: {0}.{1}={2}
 invalidKey=Invalid key: {0}
 invalidLineInConfigFile=Invalid line in config file
@@ -592,6 +593,7 @@ tagNameInvalid=tag name {0} is invalid
 tagOnRepoWithoutHEADCurrentlyNotSupported=Tag on repository without HEAD currently not supported
 theFactoryMustNotBeNull=The factory must not be null
 timerAlreadyTerminated=Timer already terminated
+tooManyIncludeRecursions=Too many recursions; circular includes in config file(s)?
 topologicalSortRequired=Topological sort required.
 transactionAborted=transaction aborted
 transportExceptionBadRef=Empty ref: {0}: {1}
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 8fbf83954c..d74e991395 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java
@@ -58,6 +58,7 @@ import org.eclipse.jgit.api.errors.PatchFormatException;
 import org.eclipse.jgit.diff.DiffEntry.ChangeType;
 import org.eclipse.jgit.diff.RawText;
 import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.patch.FileHeader;
 import org.eclipse.jgit.patch.HunkHeader;
@@ -260,6 +261,8 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 		FileWriter fw = new FileWriter(f);
 		fw.write(sb.toString());
 		fw.close();
+
+		getRepository().getFS().setExecute(f, fh.getNewMode() == FileMode.EXECUTABLE_FILE);
 	}
 
 	private static boolean isChanged(List<String> ol, List<String> nl) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/LogCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/LogCommand.java
index 9690f799c1..bb1a738149 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/LogCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/LogCommand.java
@@ -65,6 +65,7 @@ import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.revwalk.filter.AndRevFilter;
 import org.eclipse.jgit.revwalk.filter.MaxCountRevFilter;
+import org.eclipse.jgit.revwalk.filter.RevFilter;
 import org.eclipse.jgit.revwalk.filter.SkipRevFilter;
 import org.eclipse.jgit.treewalk.filter.AndTreeFilter;
 import org.eclipse.jgit.treewalk.filter.PathFilter;
@@ -104,6 +105,8 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 
 	private boolean startSpecified = false;
 
+	private RevFilter revFilter;
+
 	private final List<PathFilter> pathFilters = new ArrayList<PathFilter>();
 
 	private int maxCount = -1;
@@ -156,6 +159,11 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 						e);
 			}
 		}
+
+		if (this.revFilter != null) {
+			walk.setRevFilter(this.revFilter);
+		}
+
 		setCallable(false);
 		return walk;
 	}
@@ -342,4 +350,21 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 					, start), e);
 		}
 	}
+
+
+	/**
+	 * Sets a filter for the <code>LogCommand</code>.
+	 *
+	 *
+	 * @param aFilter
+	 *            the filter that this instance of <code>LogCommand</code>
+	 *            should use
+	 * @return {@code this}
+	 * @since 4.4
+	 */
+	public LogCommand setRevFilter(RevFilter aFilter) {
+		checkCallable();
+		this.revFilter = aFilter;
+		return this;
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
index 1699b9f3d7..b8ee1ec0b3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
@@ -223,8 +223,13 @@ public class StashApplyCommand extends GitCommand<ObjectId> {
 					ResolveMerger untrackedMerger = (ResolveMerger) strategy
 							.newMerger(repo, true);
 					untrackedMerger.setCommitNames(new String[] {
-							"stashed HEAD", "HEAD", "untracked files" }); //$NON-NLS-1$//$NON-NLS-2$//$NON-NLS-3$
-					untrackedMerger.setBase(stashHeadCommit);
+							"null", "HEAD", "untracked files" }); //$NON-NLS-1$//$NON-NLS-2$//$NON-NLS-3$
+					// There is no common base for HEAD & untracked files
+					// because the commit for untracked files has no parent. If
+					// we use stashHeadCommit as common base (as in the other
+					// merges) we potentially report conflicts for files
+					// which are not even member of untracked files commit
+					untrackedMerger.setBase(null);
 					boolean ok = untrackedMerger.merge(headCommit,
 							untrackedCommit);
 					if (ok)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
index fc4cc90937..12ceb74abb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
@@ -354,8 +354,16 @@ public class DirCacheCheckout {
 				// The index entry is missing
 				if (f != null && !FileMode.TREE.equals(f.getEntryFileMode())
 						&& !f.isEntryIgnored()) {
-					// don't overwrite an untracked and not ignored file
-					conflicts.add(walk.getPathString());
+					if (failOnConflict) {
+						// don't overwrite an untracked and not ignored file
+						conflicts.add(walk.getPathString());
+					} else {
+						// failOnConflict is false. Putting something to conflicts
+						// would mean we delete it. Instead we want the mergeCommit
+						// content to be checked out.
+						update(m.getEntryPathString(), m.getEntryObjectId(),
+								m.getEntryFileMode());
+					}
 				} else
 					update(m.getEntryPathString(), m.getEntryObjectId(),
 						m.getEntryFileMode());
@@ -390,6 +398,9 @@ public class DirCacheCheckout {
 			if (f != null) {
 				// There is a file/folder for that path in the working tree
 				if (walk.isDirectoryFileConflict()) {
+					// We put it in conflicts. Even if failOnConflict is false
+					// this would cause the path to be deleted. Thats exactly what
+					// we want in this situation
 					conflicts.add(walk.getPathString());
 				} else {
 					// No file/folder conflict exists. All entries are files or
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 dc640fe314..d07c001b60 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
@@ -396,6 +396,7 @@ public class JGitText extends TranslationBundle {
 	/***/ public String invalidIdLength;
 	/***/ public String invalidIgnoreParamSubmodule;
 	/***/ public String invalidIgnoreRule;
+	/***/ public String invalidIncludedPathInConfigFile;
 	/***/ public String invalidIntegerValue;
 	/***/ public String invalidKey;
 	/***/ public String invalidLineInConfigFile;
@@ -652,6 +653,7 @@ public class JGitText extends TranslationBundle {
 	/***/ public String transactionAborted;
 	/***/ public String theFactoryMustNotBeNull;
 	/***/ public String timerAlreadyTerminated;
+	/***/ public String tooManyIncludeRecursions;
 	/***/ public String topologicalSortRequired;
 	/***/ public String transportExceptionBadRef;
 	/***/ public String transportExceptionEmptyRef;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java
index 33be3b15a8..dc91a70866 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java
@@ -241,7 +241,12 @@ public class DfsGarbageCollector {
 		if (!addl.isEmpty()) {
 			List<Ref> all = new ArrayList<>(refs.size() + addl.size());
 			all.addAll(refs);
-			all.addAll(addl);
+			// add additional refs which start with refs/
+			for (Ref r : addl) {
+				if (r.getName().startsWith(Constants.R_REFS)) {
+					all.add(r);
+				}
+			}
 			return all;
 		}
 		return refs;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
index 9cdb753221..c998ebe960 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
@@ -655,8 +655,12 @@ public class GC {
 	}
 
 	/**
-	 * Returns a collection of all refs and additional refs (e.g. FETCH_HEAD,
-	 * MERGE_HEAD, ...)
+	 * Returns a collection of all refs and additional refs.
+	 *
+	 * Additional refs which don't start with "refs/" are not returned because
+	 * they should not save objects from being garbage collected. Examples for
+	 * such references are ORIG_HEAD, MERGE_HEAD, FETCH_HEAD and
+	 * CHERRY_PICK_HEAD.
 	 *
 	 * @return a collection of refs pointing to live objects.
 	 * @throws IOException
@@ -668,7 +672,12 @@ public class GC {
 		if (!addl.isEmpty()) {
 			List<Ref> all = new ArrayList<>(refs.size() + addl.size());
 			all.addAll(refs);
-			all.addAll(addl);
+			// add additional refs which start with refs/
+			for (Ref r : addl) {
+				if (r.getName().startsWith(Constants.R_REFS)) {
+					all.add(r);
+				}
+			}
 			return all;
 		}
 		return refs;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BlobBasedConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BlobBasedConfig.java
index 7d52991df0..8958ce7e85 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BlobBasedConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BlobBasedConfig.java
@@ -80,8 +80,7 @@ public class BlobBasedConfig extends Config {
 			throws ConfigInvalidException {
 		super(base);
 		final String decoded;
-		if (blob.length >= 3 && blob[0] == (byte) 0xEF
-				&& blob[1] == (byte) 0xBB && blob[2] == (byte) 0xBF) {
+		if (isUtf8(blob)) {
 			decoded = RawParseUtils.decode(RawParseUtils.UTF8_CHARSET,
 					blob, 3, blob.length);
 		} else {
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 088dcdfd04..b8eba3acc2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
@@ -51,6 +51,8 @@
 
 package org.eclipse.jgit.lib;
 
+import java.io.File;
+import java.io.IOException;
 import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -64,6 +66,8 @@ import org.eclipse.jgit.events.ConfigChangedListener;
 import org.eclipse.jgit.events.ListenerHandle;
 import org.eclipse.jgit.events.ListenerList;
 import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.util.IO;
+import org.eclipse.jgit.util.RawParseUtils;
 import org.eclipse.jgit.util.StringUtils;
 
 
@@ -75,6 +79,7 @@ public class Config {
 	private static final long KiB = 1024;
 	private static final long MiB = 1024 * KiB;
 	private static final long GiB = 1024 * MiB;
+	private static final int MAX_DEPTH = 999;
 
 	/** the change listeners */
 	private final ListenerList listeners = new ListenerList();
@@ -633,12 +638,13 @@ public class Config {
 	private String getRawString(final String section, final String subsection,
 			final String name) {
 		String[] lst = getRawStringList(section, subsection, name);
-		if (lst != null)
-			return lst[0];
-		else if (baseConfig != null)
+		if (lst != null) {
+			return lst[lst.length - 1];
+		} else if (baseConfig != null) {
 			return baseConfig.getRawString(section, subsection, name);
-		else
+		} else {
 			return null;
+		}
 	}
 
 	private String[] getRawStringList(String section, String subsection,
@@ -1026,6 +1032,15 @@ public class Config {
 	 *             made to {@code this}.
 	 */
 	public void fromText(final String text) throws ConfigInvalidException {
+		state.set(newState(fromTextRecurse(text, 1)));
+	}
+
+	private List<ConfigLine> fromTextRecurse(final String text, int depth)
+			throws ConfigInvalidException {
+		if (depth > MAX_DEPTH) {
+			throw new ConfigInvalidException(
+					JGitText.get().tooManyIncludeRecursions);
+		}
 		final List<ConfigLine> newEntries = new ArrayList<ConfigLine>();
 		final StringReader in = new StringReader(text);
 		ConfigLine last = null;
@@ -1084,11 +1099,38 @@ public class Config {
 				} else
 					e.value = readValue(in, false, -1);
 
+				if (e.section.equals("include")) { //$NON-NLS-1$
+					addIncludedConfig(newEntries, e, depth);
+				}
 			} else
 				throw new ConfigInvalidException(JGitText.get().invalidLineInConfigFile);
 		}
 
-		state.set(newState(newEntries));
+		return newEntries;
+	}
+
+	private void addIncludedConfig(final List<ConfigLine> newEntries,
+			ConfigLine line, int depth) throws ConfigInvalidException {
+		if (!line.name.equals("path") || //$NON-NLS-1$
+				line.value == null || line.value.equals(MAGIC_EMPTY_VALUE)) {
+			throw new ConfigInvalidException(
+					JGitText.get().invalidLineInConfigFile);
+		}
+		File path = new File(line.value);
+		try {
+			byte[] bytes = IO.readFully(path);
+			String decoded;
+			if (isUtf8(bytes)) {
+				decoded = RawParseUtils.decode(RawParseUtils.UTF8_CHARSET,
+						bytes, 3, bytes.length);
+			} else {
+				decoded = RawParseUtils.decode(bytes);
+			}
+			newEntries.addAll(fromTextRecurse(decoded, depth + 1));
+		} catch (IOException ioe) {
+			throw new ConfigInvalidException(MessageFormat.format(
+					JGitText.get().invalidIncludedPathInConfigFile, path));
+		}
 	}
 
 	private ConfigSnapshot newState() {
@@ -1108,6 +1150,19 @@ public class Config {
 		state.set(newState());
 	}
 
+	/**
+	 * Check if bytes should be treated as UTF-8 or not.
+	 *
+	 * @param bytes
+	 *            the bytes to check encoding for.
+	 * @return true if bytes should be treated as UTF-8, false otherwise.
+	 * @since 4.4
+	 */
+	protected boolean isUtf8(final byte[] bytes) {
+		return bytes.length >= 3 && bytes[0] == (byte) 0xEF
+				&& bytes[1] == (byte) 0xBB && bytes[2] == (byte) 0xBF;
+	}
+
 	private static String readSectionName(final StringReader in)
 			throws ConfigInvalidException {
 		final StringBuilder name = new StringBuilder();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/filter/RevFilter.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/filter/RevFilter.java
index 2a5cb2b2ac..14a98a10bf 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/filter/RevFilter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/filter/RevFilter.java
@@ -82,6 +82,7 @@ import org.eclipse.jgit.revwalk.RevWalk;
  * <b>Merge filters:</b>
  * <ul>
  * <li>Skip all merges: {@link #NO_MERGES}.</li>
+ * <li>Skip all non-merges: {@link #ONLY_MERGES}</li>
  * </ul>
  *
  * <p>
@@ -143,6 +144,37 @@ public abstract class RevFilter {
 		}
 	}
 
+	/**
+	 * Filter including only merge commits, excluding all commits with less than
+	 * two parents (thread safe).
+	 *
+	 * @since 4.4
+	 */
+	public static final RevFilter ONLY_MERGES = new OnlyMergesFilter();
+
+	private static final class OnlyMergesFilter extends RevFilter {
+
+		@Override
+		public boolean include(RevWalk walker, RevCommit c) {
+			return c.getParentCount() >= 2;
+		}
+
+		@Override
+		public RevFilter clone() {
+			return this;
+		}
+
+		@Override
+		public boolean requiresCommitBody() {
+			return false;
+		}
+
+		@Override
+		public String toString() {
+			return "ONLY_MERGES"; //$NON-NLS-1$
+		}
+	}
+
 	/** Excludes commits with more than one parent (thread safe). */
 	public static final RevFilter NO_MERGES = new NoMergesFilter();
 
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 702fd70765..4b4822c763 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
@@ -147,8 +147,7 @@ public class FileBasedConfig extends StoredConfig {
 					snapshot = newSnapshot;
 			} else {
 				final String decoded;
-				if (in.length >= 3 && in[0] == (byte) 0xEF
-						&& in[1] == (byte) 0xBB && in[2] == (byte) 0xBF) {
+				if (isUtf8(in)) {
 					decoded = RawParseUtils.decode(RawParseUtils.UTF8_CHARSET,
 							in, 3, in.length);
 					utf8Bom = true;
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 a20e652553..b5f9e2f020 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java
@@ -176,6 +176,12 @@ public abstract class BaseReceivePack {
 	/** Should an incoming transfer permit non-fast-forward requests? */
 	private boolean allowNonFastForwards;
 
+	/**
+	 * Should the requested ref updates be performed as a single atomic
+	 * transaction?
+	 */
+	private boolean atomic;
+
 	private boolean allowOfsDelta;
 	private boolean allowQuiet = true;
 
@@ -607,6 +613,25 @@ public abstract class BaseReceivePack {
 		allowNonFastForwards = canRewind;
 	}
 
+	/**
+	 * @return true if the client's commands should be performed as a single
+	 *         atomic transaction.
+	 * @since 4.4
+	 */
+	public boolean isAtomic() {
+		return atomic;
+	}
+
+	/**
+	 * @param atomic
+	 *            true to perform the client's commands as a single atomic
+	 *            transaction.
+	 * @since 4.4
+	 */
+	public void setAtomic(boolean atomic) {
+		this.atomic = atomic;
+	}
+
 	/** @return identity of the user making the changes in the reflog. */
 	public PersonIdent getRefLogIdent() {
 		return refLogIdent;
@@ -1483,6 +1508,7 @@ public abstract class BaseReceivePack {
 
 		BatchRefUpdate batch = db.getRefDatabase().newBatchUpdate();
 		batch.setAllowNonFastForwards(isAllowNonFastForwards());
+		batch.setAtomic(isAtomic());
 		batch.setRefLogIdent(getRefLogIdent());
 		batch.setRefLogMessage("push", true); //$NON-NLS-1$
 		batch.addCommand(toApply);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java
index 6ed9bc8f17..f61e93fff2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java
@@ -201,6 +201,8 @@ public class ReceivePack extends BaseReceivePack {
 
 			if (unpackError == null) {
 				boolean atomic = isCapabilityEnabled(CAPABILITY_ATOMIC);
+				setAtomic(atomic);
+
 				validateCommands();
 				if (atomic && anyRejects())
 					failPendingCommands();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java
index 779b10e1bb..b4f12f4120 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java
@@ -122,7 +122,7 @@ public class FS_POSIX extends FS {
 							.defaultCharset().name()))) {
 				if (p.waitFor() == 0) {
 					String s = lineRead.readLine();
-					if (s.matches("0?\\d{3}")) { //$NON-NLS-1$
+					if (s != null && s.matches("0?\\d{3}")) { //$NON-NLS-1$
 						return Integer.parseInt(s, 8);
 					}
 				}
diff --git a/pom.xml b/pom.xml
index 0b9f4f1c69..9dc6427a35 100644
--- a/pom.xml
+++ b/pom.xml
@@ -206,8 +206,8 @@
     <httpclient-version>4.3.6</httpclient-version>
     <slf4j-version>1.7.2</slf4j-version>
     <log4j-version>1.2.15</log4j-version>
-    <maven-javadoc-plugin-version>2.10.1</maven-javadoc-plugin-version>
-    <tycho-extras-version>0.23.0</tycho-extras-version>
+    <maven-javadoc-plugin-version>2.10.3</maven-javadoc-plugin-version>
+    <tycho-extras-version>0.25.0</tycho-extras-version>
     <gson-version>2.2.4</gson-version>
 
     <!-- Properties to enable jacoco code coverage analysis -->
@@ -259,7 +259,7 @@
 
         <plugin>
           <artifactId>maven-compiler-plugin</artifactId>
-          <version>3.2</version>
+          <version>3.5.1</version>
           <configuration>
             <encoding>UTF-8</encoding>
             <source>1.7</source>
@@ -269,13 +269,13 @@
 
         <plugin>
           <artifactId>maven-clean-plugin</artifactId>
-          <version>2.6.1</version>
+          <version>3.0.0</version>
         </plugin>
 
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-shade-plugin</artifactId>
-          <version>2.3</version>
+          <version>2.4.3</version>
         </plugin>
 
         <plugin>
@@ -293,7 +293,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-source-plugin</artifactId>
-          <version>2.4</version>
+          <version>3.0.0</version>
         </plugin>
 
         <plugin>
@@ -305,7 +305,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-surefire-plugin</artifactId>
-          <version>2.18.1</version>
+          <version>2.19.1</version>
           <configuration>
             <forkCount>${test-fork-count}</forkCount>
             <reuseForks>true</reuseForks>
@@ -315,13 +315,13 @@
         <plugin>
           <groupId>org.codehaus.mojo</groupId>
           <artifactId>build-helper-maven-plugin</artifactId>
-          <version>1.9</version>
+          <version>1.10</version>
         </plugin>
 
         <plugin>
           <groupId>org.codehaus.mojo</groupId>
           <artifactId>findbugs-maven-plugin</artifactId>
-          <version>3.0.0</version>
+          <version>3.0.3</version>
           <configuration>
             <findbugsXmlOutput>true</findbugsXmlOutput>
             <failOnError>false</failOnError>
@@ -338,7 +338,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-pmd-plugin</artifactId>
-          <version>3.4</version>
+          <version>3.6</version>
           <configuration>
             <sourceEncoding>utf-8</sourceEncoding>
             <minimumTokens>100</minimumTokens>
@@ -358,7 +358,7 @@
         <plugin>
           <groupId>org.eclipse.cbi.maven.plugins</groupId>
           <artifactId>eclipse-jarsigner-plugin</artifactId>
-          <version>1.1.2</version>
+          <version>1.1.3</version>
         </plugin>
         <plugin>
           <groupId>org.eclipse.tycho.extras</groupId>
@@ -373,24 +373,24 @@
         <plugin>
           <groupId>org.jacoco</groupId>
           <artifactId>jacoco-maven-plugin</artifactId>
-          <version>0.7.1.201405082137</version>
+          <version>0.7.6.201602180812</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-site-plugin</artifactId>
-          <version>3.4</version>
+          <version>3.5.1</version>
           <dependencies>
             <dependency><!-- add support for ssh/scp -->
               <groupId>org.apache.maven.wagon</groupId>
               <artifactId>wagon-ssh</artifactId>
-              <version>2.7</version>
+              <version>2.10</version>
             </dependency>
           </dependencies>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-surefire-report-plugin</artifactId>
-          <version>2.18.1</version>
+          <version>2.19.1</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
@@ -400,7 +400,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-project-info-reports-plugin</artifactId>
-          <version>2.8</version>
+          <version>2.9</version>
         </plugin>
       </plugins>
     </pluginManagement>
@@ -526,12 +526,12 @@
       <plugin>
         <groupId>org.codehaus.mojo</groupId>
         <artifactId>findbugs-maven-plugin</artifactId>
-        <version>3.0.0</version>
+        <version>3.0.3</version>
       </plugin>
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-surefire-report-plugin</artifactId>
-        <version>2.18.1</version>
+        <version>2.19.1</version>
         <configuration>
           <aggregate>true</aggregate>
           <alwaysGenerateSurefireReport>false</alwaysGenerateSurefireReport>