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>

org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java

@@ -586,6 +586,31 @@ public <T extends AnyObjectId> T update(String ref, T obj) throws Exception {
 		}
 	}
 
+	/**
+	 * 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 RevCommit update(CommitBuilder to) throws Exception {
 		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. */

org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/s3/SignerV4.java

@@ -229,12 +229,12 @@ private static String formatAuthorizationHeader(
 
 	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(

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" version="0.7.9.v201605172130"/>
-      <unit id="javaewah.source" version="0.7.9.v201401101600"/>
+      <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"/>

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

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 [0.7.9.v201605172130,0.7.9.v201605172130]
-	javaewah.source [0.7.9.v201401101600,0.7.9.v201401101600]
+	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]

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>

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)"

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);
+	}
+
+}

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.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 @@ protected final boolean requiresRepository() {
 	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

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java

@@ -63,6 +63,7 @@
 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( //
+	private DiffFormatter diffFmt;
-			new BufferedOutputStream(System.out));
 
 	@Argument(index = 0, metaVar = "metaVar_object")
 	private String objectName;
@@ -165,6 +165,12 @@ void noPrefix(@SuppressWarnings("unused") boolean on) {
 		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 {

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)"

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java

@@ -44,6 +44,7 @@
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
 import java.io.ByteArrayOutputStream;
@@ -156,6 +157,33 @@ public void testModifyW() throws Exception {
 				b.getString(0, b.size(), false));
 	}
 
+	@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");

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/LogCommandTest.java

@@ -53,7 +53,9 @@
 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 void logAllCommitsWithSkipAndMaxCount() throws Exception {
 		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();
+	}
+
 }

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PullCommandTest.java

@@ -58,6 +58,7 @@
 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;
@@ -184,6 +185,40 @@ public void testPullConflict() throws Exception {
 				.getRepositoryState());
 	}
 
+	@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(

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java

@@ -156,6 +156,34 @@ public void testHardReset() throws JGitInternalException,
 		assertEquals(prevHead, db.readOrigHead());
 	}
 
+	@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 {

org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java

@@ -56,6 +56,9 @@
 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 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 void testEmptyValueAtEof() throws Exception {
 				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));
 	}

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}

org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java

@@ -58,6 +58,7 @@
 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 @@ private void apply(File f, FileHeader fh)
 		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) {

org.eclipse.jgit/src/org/eclipse/jgit/api/LogCommand.java

@@ -65,6 +65,7 @@
 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 @@ else if (maxCount > -1)
 						e);
 			}
 		}
+
+		if (this.revFilter != null) {
+			walk.setRevFilter(this.revFilter);
+		}
+
 		setCallable(false);
 		return walk;
 	}
@@ -342,4 +350,21 @@ private LogCommand add(boolean include, AnyObjectId start)
 					, 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;
+	}
 }

org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java

@@ -223,8 +223,13 @@ public ObjectId call() throws GitAPIException,
 					ResolveMerger untrackedMerger = (ResolveMerger) strategy
 							.newMerger(repo, true);
 					untrackedMerger.setCommitNames(new String[] {
-							"stashed HEAD", "HEAD", "untracked files" }); //$NON-NLS-1$//$NON-NLS-2$//$NON-NLS-3$
+							"null", "HEAD", "untracked files" }); //$NON-NLS-1$//$NON-NLS-2$//$NON-NLS-3$
-					untrackedMerger.setBase(stashHeadCommit);
+					// 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)

org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java

@@ -354,8 +354,16 @@ void processEntry(CanonicalTreeParser m, DirCacheBuildIterator i,
 				// The index entry is missing
 				if (f != null && !FileMode.TREE.equals(f.getEntryFileMode())
 						&& !f.isEntryIgnored()) {
+					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 @@ void processEntry(CanonicalTreeParser m, DirCacheBuildIterator i,
 			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

org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java

@@ -396,6 +396,7 @@ public static JGitText get() {
 	/***/ 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 static JGitText get() {
 	/***/ public String transactionAborted;
 	/***/ public String theFactoryMustNotBeNull;
 	/***/ public String timerAlreadyTerminated;
+	/***/ public String tooManyIncludeRecursions;
 	/***/ public String topologicalSortRequired;
 	/***/ public String transportExceptionBadRef;
 	/***/ public String transportExceptionEmptyRef;

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java

@@ -241,7 +241,12 @@ private Collection<Ref> getAllRefs() throws IOException {
 		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;

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java

@@ -655,8 +655,12 @@ private Set<ObjectId> listRefLogObjects(Ref ref, long minTime) throws IOExceptio
 	}
 
 	/**
-	 * Returns a collection of all refs and additional refs (e.g. FETCH_HEAD,
+	 * Returns a collection of all refs and additional refs.
-	 * MERGE_HEAD, ...)
+	 *
+	 * 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 @@ private Collection<Ref> getAllRefs() throws IOException {
 		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;

org.eclipse.jgit/src/org/eclipse/jgit/lib/BlobBasedConfig.java

@@ -80,8 +80,7 @@ public BlobBasedConfig(Config base, final byte[] blob)
 			throws ConfigInvalidException {
 		super(base);
 		final String decoded;
-		if (blob.length >= 3 && blob[0] == (byte) 0xEF
+		if (isUtf8(blob)) {
-				&& blob[1] == (byte) 0xBB && blob[2] == (byte) 0xBF) {
 			decoded = RawParseUtils.decode(RawParseUtils.UTF8_CHARSET,
 					blob, 3, blob.length);
 		} else {

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.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();
@@ -633,13 +638,14 @@ protected void fireConfigChangedEvent() {
 	private String getRawString(final String section, final String subsection,
 			final String name) {
 		String[] lst = getRawStringList(section, subsection, name);
-		if (lst != null)
+		if (lst != null) {
-			return lst[0];
+			return lst[lst.length - 1];
-		else if (baseConfig != null)
+		} else if (baseConfig != null) {
 			return baseConfig.getRawString(section, subsection, name);
-		else
+		} else {
 			return null;
 		}
+	}
 
 	private String[] getRawStringList(String section, String subsection,
 			String name) {
@@ -1026,6 +1032,15 @@ public String toText() {
 	 *             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 void fromText(final String text) throws ConfigInvalidException {
 				} 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 @@ protected void clear() {
 		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();

org.eclipse.jgit/src/org/eclipse/jgit/revwalk/filter/RevFilter.java

@@ -82,6 +82,7 @@
  * <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 String toString() {
 		}
 	}
 
+	/**
+	 * 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();
 

org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java

@@ -147,8 +147,7 @@ public void load() throws IOException, ConfigInvalidException {
 					snapshot = newSnapshot;
 			} else {
 				final String decoded;
-				if (in.length >= 3 && in[0] == (byte) 0xEF
+				if (isUtf8(in)) {
-						&& in[1] == (byte) 0xBB && in[2] == (byte) 0xBF) {
 					decoded = RawParseUtils.decode(RawParseUtils.UTF8_CHARSET,
 							in, 3, in.length);
 					utf8Bom = true;

org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java

@@ -176,6 +176,12 @@ public Set<String> getCapabilities() {
 	/** 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 void setAllowNonFastForwards(final boolean canRewind) {
 		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 @@ protected void executeCommands() {
 
 		BatchRefUpdate batch = db.getRefDatabase().newBatchUpdate();
 		batch.setAllowNonFastForwards(isAllowNonFastForwards());
+		batch.setAtomic(isAtomic());
 		batch.setRefLogIdent(getRefLogIdent());
 		batch.setRefLogMessage("push", true); //$NON-NLS-1$
 		batch.addCommand(toApply);

org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java

@@ -201,6 +201,8 @@ private void service() throws IOException {
 
 			if (unpackError == null) {
 				boolean atomic = isCapabilityEnabled(CAPABILITY_ATOMIC);
+				setAtomic(atomic);
+
 				validateCommands();
 				if (atomic && anyRejects())
 					failPendingCommands();

org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java

@@ -122,7 +122,7 @@ private static int readUmask() {
 							.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);
 					}
 				}

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>
+    <maven-javadoc-plugin-version>2.10.3</maven-javadoc-plugin-version>
-    <tycho-extras-version>0.23.0</tycho-extras-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>