Merge branch 'master' into stable-4.0

* master:
  Add more reports to maven site
  Update project meta-data in pom.xml used for site generation
  Update dependencies to the versions used in target platform
  Update 4.5 target platform to use final Mars Orbit repository
  Compare API changes in clirr report against 3.7.0
  Fix CommitCommand.setOnly()
  Add "src" folder to source folders of org.eclipse.jgit.test
  Improve exception thrown when pull can't find advertised ref
  Silence unchecked conversion warning in TransportSftp
  Silence deprecation warning in WindowCacheConfig
  Silence deprecation warning in DirCacheCheckout
  Fix unchecked conversion warning in MergeFormatter
  Fix hidden field warnings in bundle org.eclipse.jgit
  Close WindowCursor using try-with-resources in UnpackedObject
  Fix WindowCursor memory leak.
  archive: Drop unnecessary empty comments and 'final' qualifiers on locals
  Close 'out' consistently in ArchiveCommand.call
  Fix that exceptions in ReceivePack cause Invalid Channel 101 exceptions
  Better report too large pack-files from PushCommand
  FS: Extract GobblerThread into a private static class
  Add bitmap index misses to PackWriter.Statistics
  Enable public access to SimilarityIndex scoring function
  Add getters to RepoProject.
  Silence unused object warning in MyersDiff
  Silence resource leak warnings where caller is responsible to close
  Silence false potential null pointer access warnings
  Fix potential null pointer access in IndexDiffFilter
  Add tests for ObjectFilter
  Expose Sets helper to tests outside org.eclipse.jgit.api

Change-Id: I34b2bb45f51ed6f52a6bb1215de654ebb2ffde10
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

org.eclipse.jgit.http.server/pom.xml

@@ -75,7 +75,7 @@
 
     <dependency>
       <groupId>javax.servlet</groupId>
-      <artifactId>servlet-api</artifactId>
+      <artifactId>javax.servlet-api</artifactId>
       <scope>provided</scope>
     </dependency>
   </dependencies>

org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/GitServletResponseTests.java

@@ -0,0 +1,295 @@
+/*
+ * Copyright (C) 2015, christian.Halstrick <christian.halstrick@sap.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.http.test;
+
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.Collection;
+import java.util.Collections;
+
+import javax.servlet.http.HttpServletRequest;
+
+import org.eclipse.jetty.servlet.ServletContextHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.eclipse.jgit.errors.CorruptObjectException;
+import org.eclipse.jgit.errors.RepositoryNotFoundException;
+import org.eclipse.jgit.errors.TooLargePackException;
+import org.eclipse.jgit.errors.TransportException;
+import org.eclipse.jgit.http.server.GitServlet;
+import org.eclipse.jgit.http.server.resolver.DefaultReceivePackFactory;
+import org.eclipse.jgit.junit.TestRepository;
+import org.eclipse.jgit.junit.http.HttpTestCase;
+import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.NullProgressMonitor;
+import org.eclipse.jgit.lib.ObjectChecker;
+import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.StoredConfig;
+import org.eclipse.jgit.revwalk.RevBlob;
+import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.transport.PostReceiveHook;
+import org.eclipse.jgit.transport.PreReceiveHook;
+import org.eclipse.jgit.transport.ReceiveCommand;
+import org.eclipse.jgit.transport.ReceivePack;
+import org.eclipse.jgit.transport.RemoteRefUpdate;
+import org.eclipse.jgit.transport.Transport;
+import org.eclipse.jgit.transport.URIish;
+import org.eclipse.jgit.transport.resolver.RepositoryResolver;
+import org.eclipse.jgit.transport.resolver.ServiceNotAuthorizedException;
+import org.eclipse.jgit.transport.resolver.ServiceNotEnabledException;
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Tests for correct responses of {@link GitServlet}. Especially error
+ * situations where the {@link GitServlet} faces exceptions during request
+ * processing are tested
+ */
+public class GitServletResponseTests extends HttpTestCase {
+	private Repository srvRepo;
+
+	private URIish srvURI;
+
+	private GitServlet gs;
+
+	private long maxPackSize = 0; // the maximum pack file size used by
+									// the server
+
+	private PostReceiveHook postHook = null;
+
+	private PreReceiveHook preHook = null;
+
+	private ObjectChecker oc = null;
+
+	/**
+	 * Setup a http server using {@link GitServlet}. Tests should be able to
+	 * configure the maximum pack file size, the object checker and custom hooks
+	 * just before they talk to the server.
+	 */
+	@Before
+	public void setUp() throws Exception {
+		super.setUp();
+
+		final TestRepository<Repository> srv = createTestRepository();
+		final String repoName = srv.getRepository().getDirectory().getName();
+
+		ServletContextHandler app = server.addContext("/git");
+		gs = new GitServlet();
+		gs.setRepositoryResolver(new RepositoryResolver<HttpServletRequest>() {
+			public Repository open(HttpServletRequest req, String name)
+					throws RepositoryNotFoundException,
+					ServiceNotEnabledException {
+				if (!name.equals(repoName))
+					throw new RepositoryNotFoundException(name);
+
+				final Repository db = srv.getRepository();
+				db.incrementOpen();
+				return db;
+			}
+		});
+		gs.setReceivePackFactory(new DefaultReceivePackFactory() {
+			public ReceivePack create(HttpServletRequest req, Repository db)
+					throws ServiceNotEnabledException,
+					ServiceNotAuthorizedException {
+				ReceivePack recv = super.create(req, db);
+				if (maxPackSize > 0)
+					recv.setMaxPackSizeLimit(maxPackSize);
+				if (postHook != null)
+					recv.setPostReceiveHook(postHook);
+				if (preHook != null)
+					recv.setPreReceiveHook(preHook);
+				if (oc != null)
+					recv.setObjectChecker(oc);
+				return recv;
+			}
+
+		});
+		app.addServlet(new ServletHolder(gs), "/*");
+
+		server.setUp();
+
+		srvRepo = srv.getRepository();
+		srvURI = toURIish(app, repoName);
+
+		StoredConfig cfg = srvRepo.getConfig();
+		cfg.setBoolean("http", null, "receivepack", true);
+		cfg.save();
+	}
+
+	/**
+	 * Configure a {@link GitServlet} that faces a {@link IllegalStateException}
+	 * during executing preReceiveHooks. This used to lead to exceptions with a
+	 * description of "invalid channel 101" on the client side. Make sure
+	 * clients receive the correct response on the correct sideband.
+	 *
+	 * @throws Exception
+	 */
+	@Test
+	public void testRuntimeExceptionInPreReceiveHook() throws Exception {
+		final TestRepository client = createTestRepository();
+		final RevBlob Q_txt = client
+				.blob("some blob content to measure pack size");
+		final RevCommit Q = client.commit().add("Q", Q_txt).create();
+		final Repository clientRepo = client.getRepository();
+		final String srvBranchName = Constants.R_HEADS + "new.branch";
+		Transport t;
+
+		maxPackSize = 0;
+		postHook = null;
+		preHook = new PreReceiveHook() {
+			@Override
+			public void onPreReceive(ReceivePack rp,
+					Collection<ReceiveCommand> commands) {
+				throw new IllegalStateException();
+			}
+		};
+
+		t = Transport.open(clientRepo, srvURI);
+		try {
+			RemoteRefUpdate update = new RemoteRefUpdate(clientRepo, Q.name(),
+					srvBranchName, false, null, null);
+			try {
+				t.push(NullProgressMonitor.INSTANCE,
+						Collections.singleton(update));
+				fail("should not reach this line");
+			} catch (Exception e) {
+				assertTrue(e instanceof TransportException);
+			}
+		} finally {
+			t.close();
+		}
+	}
+
+	/**
+	 * Configure a {@link GitServlet} that faces a {@link IllegalStateException}
+	 * during executing objectChecking.
+	 *
+	 * @throws Exception
+	 */
+	@Test
+	public void testObjectCheckerException() throws Exception {
+		final TestRepository client = createTestRepository();
+		final RevBlob Q_txt = client
+				.blob("some blob content to measure pack size");
+		final RevCommit Q = client.commit().add("Q", Q_txt).create();
+		final Repository clientRepo = client.getRepository();
+		final String srvBranchName = Constants.R_HEADS + "new.branch";
+		Transport t;
+
+		maxPackSize = 0;
+		postHook = null;
+		preHook = null;
+		oc = new ObjectChecker() {
+			@Override
+			public void checkCommit(byte[] raw) throws CorruptObjectException {
+				throw new IllegalStateException();
+			}
+		};
+
+		t = Transport.open(clientRepo, srvURI);
+		try {
+			RemoteRefUpdate update = new RemoteRefUpdate(clientRepo, Q.name(),
+					srvBranchName, false, null, null);
+			try {
+				t.push(NullProgressMonitor.INSTANCE,
+						Collections.singleton(update));
+				fail("should not reach this line");
+			} catch (Exception e) {
+				assertTrue(e instanceof TransportException);
+			}
+		} finally {
+			t.close();
+		}
+	}
+
+	/**
+	 * Configure a {@link GitServlet} that faces a {@link TooLargePackException}
+	 * during persisting the pack and a {@link IllegalStateException} during
+	 * executing postReceiveHooks. This used to lead to exceptions with a
+	 * description of "invalid channel 101" on the client side. Make sure
+	 * clients receive the correct response about the too large pack on the
+	 * correct sideband.
+	 *
+	 * @throws Exception
+	 */
+	@Test
+	public void testUnpackErrorWithSubsequentExceptionInPostReceiveHook()
+			throws Exception {
+		final TestRepository client = createTestRepository();
+		final RevBlob Q_txt = client
+				.blob("some blob content to measure pack size");
+		final RevCommit Q = client.commit().add("Q", Q_txt).create();
+		final Repository clientRepo = client.getRepository();
+		final String srvBranchName = Constants.R_HEADS + "new.branch";
+		Transport t;
+
+		// this maxPackSize leads to an unPackError
+		maxPackSize = 400;
+		// this PostReceiveHook when called after an unsuccesfull unpack will
+		// lead to an IllegalStateException
+		postHook = new PostReceiveHook() {
+			public void onPostReceive(ReceivePack rp,
+					Collection<ReceiveCommand> commands) {
+				// the maxPackSize setting caused that the packfile couldn't be
+				// saved to disk. Calling getPackSize() now will lead to a
+				// IllegalStateException.
+				rp.getPackSize();
+			}
+		};
+
+		t = Transport.open(clientRepo, srvURI);
+		try {
+			RemoteRefUpdate update = new RemoteRefUpdate(clientRepo, Q.name(),
+					srvBranchName, false, null, null);
+			try {
+				t.push(NullProgressMonitor.INSTANCE,
+						Collections.singleton(update));
+				fail("should not reach this line");
+			} catch (Exception e) {
+				assertTrue(e instanceof TooLargePackException);
+			}
+		} finally {
+			t.close();
+		}
+	}
+}

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.target

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/mbarbero/fr.obeo.releng.targetplatform -->
-<target name="jgit-4.5" sequenceNumber="1432590632">
+<target name="jgit-4.5" sequenceNumber="1433163825">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.2.10.v20150310"/>
@@ -57,7 +57,7 @@
       <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/S20150519210750/repository/"/>
+      <repository location="http://download.eclipse.org/tools/orbit/downloads/drops/R20150519210750/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-4.5.tpd

@@ -1,7 +1,7 @@
 target "jgit-4.5" with source configurePhase
 
 include "projects/jetty-9.2.10.tpd"
-include "orbit/S20150519210750-Mars-RC2.tpd"
+include "orbit/R20150519210750-Mars.tpd"
 
 location "http://download.eclipse.org/releases/mars/" {
 	org.eclipse.osgi lazy

org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20150519210750-Mars.tpd

@@ -1,7 +1,7 @@
-target "S20141023165154-Mars-M3" with source configurePhase
+target "R20150519210750-Mars" with source configurePhase
 // see http://download.eclipse.org/tools/orbit/downloads/
 
-location "http://download.eclipse.org/tools/orbit/downloads/drops/S20150519210750/repository/" {
+location "http://download.eclipse.org/tools/orbit/downloads/drops/R20150519210750/repository/" {
 	org.apache.ant [1.9.4.v201504302020,1.9.4.v201504302020]
 	org.apache.ant.source [1.9.4.v201504302020,1.9.4.v201504302020]
 	org.apache.commons.compress [1.6.0.v201310281400,1.6.0.v201310281400]

org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ArchiveTest.java

@@ -92,22 +92,22 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	@Ignore("Some versions of java.util.zip refuse to write an empty ZIP")
 	@Test
 	public void testEmptyArchive() throws Exception {
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive --format=zip " + emptyTree, db);
 		assertArrayEquals(new String[0], listZipEntries(result));
 	}
 
 	@Test
 	public void testEmptyTar() throws Exception {
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive --format=tar " + emptyTree, db);
 		assertArrayEquals(new String[0], listTarEntries(result));
 	}
 
 	@Test
 	public void testUnrecognizedFormat() throws Exception {
-		final String[] expect = new String[] { "fatal: Unknown archive format 'nonsense'" };
-		final String[] actual = execute("git archive --format=nonsense " + emptyTree);
+		String[] expect = new String[] { "fatal: Unknown archive format 'nonsense'" };
+		String[] actual = execute("git archive --format=nonsense " + emptyTree);
 		assertArrayEquals(expect, actual);
 	}
 
@@ -120,9 +120,9 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern("c").call();
 		git.commit().setMessage("populate toplevel").call();
 
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive --format=zip HEAD", db);
-		assertArrayEquals(new String[] { "a", "c" }, //
+		assertArrayEquals(new String[] { "a", "c" },
 				listZipEntries(result));
 	}
 
@@ -135,9 +135,9 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	@Test
 	public void testDefaultFormatIsTar() throws Exception {
 		commitGreeting();
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive HEAD", db);
-		assertArrayEquals(new String[] { "greeting" }, //
+		assertArrayEquals(new String[] { "greeting" },
 				listTarEntries(result));
 	}
 
@@ -147,8 +147,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 
 	@Test
 	public void testFormatOverridesFilename() throws Exception {
-		final File archive = new File(db.getWorkTree(), "format-overrides-name.tar");
-		final String path = archive.getAbsolutePath();
+		File archive = new File(db.getWorkTree(), "format-overrides-name.tar");
+		String path = archive.getAbsolutePath();
 
 		commitGreeting();
 		assertArrayEquals(new String[] { "" },
@@ -162,8 +162,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 
 	@Test
 	public void testUnrecognizedExtensionMeansTar() throws Exception {
-		final File archive = new File(db.getWorkTree(), "example.txt");
-		final String path = archive.getAbsolutePath();
+		File archive = new File(db.getWorkTree(), "example.txt");
+		String path = archive.getAbsolutePath();
 
 		commitGreeting();
 		assertArrayEquals(new String[] { "" },
@@ -176,8 +176,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 
 	@Test
 	public void testNoExtensionMeansTar() throws Exception {
-		final File archive = new File(db.getWorkTree(), "example");
-		final String path = archive.getAbsolutePath();
+		File archive = new File(db.getWorkTree(), "example");
+		String path = archive.getAbsolutePath();
 
 		commitGreeting();
 		assertArrayEquals(new String[] { "" },
@@ -189,8 +189,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 
 	@Test
 	public void testExtensionMatchIsAnchored() throws Exception {
-		final File archive = new File(db.getWorkTree(), "two-extensions.zip.bak");
-		final String path = archive.getAbsolutePath();
+		File archive = new File(db.getWorkTree(), "two-extensions.zip.bak");
+		String path = archive.getAbsolutePath();
 
 		commitGreeting();
 		assertArrayEquals(new String[] { "" },
@@ -202,8 +202,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 
 	@Test
 	public void testZipExtension() throws Exception {
-		final File archiveWithDot = new File(db.getWorkTree(), "greeting.zip");
-		final File archiveNoDot = new File(db.getWorkTree(), "greetingzip");
+		File archiveWithDot = new File(db.getWorkTree(), "greeting.zip");
+		File archiveNoDot = new File(db.getWorkTree(), "greetingzip");
 
 		commitGreeting();
 		execute("git archive " +
@@ -218,8 +218,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 
 	@Test
 	public void testTarExtension() throws Exception {
-		final File archive = new File(db.getWorkTree(), "tarball.tar");
-		final String path = archive.getAbsolutePath();
+		File archive = new File(db.getWorkTree(), "tarball.tar");
+		String path = archive.getAbsolutePath();
 
 		commitGreeting();
 		assertArrayEquals(new String[] { "" },
@@ -234,8 +234,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		commitGreeting();
 
 		for (String ext : Arrays.asList("tar.gz", "tgz")) {
-			final File archiveWithDot = new File(db.getWorkTree(), "tarball." + ext);
-			final File archiveNoDot = new File(db.getWorkTree(), "tarball" + ext);
+			File archiveWithDot = new File(db.getWorkTree(), "tarball." + ext);
+			File archiveNoDot = new File(db.getWorkTree(), "tarball" + ext);
 
 			execute("git archive " +
 				shellQuote("--output=" + archiveWithDot.getAbsolutePath()) + " " +
@@ -253,8 +253,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		commitGreeting();
 
 		for (String ext : Arrays.asList("tar.bz2", "tbz", "tbz2")) {
-			final File archiveWithDot = new File(db.getWorkTree(), "tarball." + ext);
-			final File archiveNoDot = new File(db.getWorkTree(), "tarball" + ext);
+			File archiveWithDot = new File(db.getWorkTree(), "tarball." + ext);
+			File archiveNoDot = new File(db.getWorkTree(), "tarball" + ext);
 
 			execute("git archive " +
 				shellQuote("--output=" + archiveWithDot.getAbsolutePath()) + " " +
@@ -272,8 +272,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		commitGreeting();
 
 		for (String ext : Arrays.asList("tar.xz", "txz")) {
-			final File archiveWithDot = new File(db.getWorkTree(), "tarball." + ext);
-			final File archiveNoDot = new File(db.getWorkTree(), "tarball" + ext);
+			File archiveWithDot = new File(db.getWorkTree(), "tarball." + ext);
+			File archiveNoDot = new File(db.getWorkTree(), "tarball" + ext);
 
 			execute("git archive " +
 				shellQuote("--output=" + archiveWithDot.getAbsolutePath()) + " " +
@@ -302,7 +302,7 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern("b").call();
 		git.commit().setMessage("add subdir").call();
 
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive --format=zip master", db);
 		String[] expect = { "a", "b.c", "b0c", "b/", "b/a", "b/b", "c" };
 		String[] actual = listZipEntries(result);
@@ -328,7 +328,7 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern("b").call();
 		git.commit().setMessage("add subdir").call();
 
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive --format=tar master", db);
 		String[] expect = { "a", "b.c", "b0c", "b/", "b/a", "b/b", "c" };
 		String[] actual = listTarEntries(result);
@@ -390,7 +390,7 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	@Test
 	public void testPrefixDoesNotNormalizeDoubleSlashInTar() throws Exception {
 		commitFoo();
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive --prefix=x// --format=tar master", db);
 		String[] expect = { "x//foo" };
 		assertArrayEquals(expect, listTarEntries(result));
@@ -421,7 +421,7 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	@Test
 	public void testTarPrefixWithoutTrailingSlash() throws Exception {
 		commitBazAndFooSlashBar();
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive --prefix=my- --format=tar master", db);
 		String[] expect = { "my-baz", "my-foo/", "my-foo/bar" };
 		String[] actual = listTarEntries(result);
@@ -441,7 +441,7 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.submoduleAdd().setURI("./.").setPath("b").call().close();
 		git.commit().setMessage("add submodule").call();
 
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive --format=zip master", db);
 		String[] expect = { ".gitmodules", "a", "b/", "c" };
 		String[] actual = listZipEntries(result);
@@ -461,7 +461,7 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.submoduleAdd().setURI("./.").setPath("b").call().close();
 		git.commit().setMessage("add submodule").call();
 
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive --format=tar master", db);
 		String[] expect = { ".gitmodules", "a", "b/", "c" };
 		String[] actual = listTarEntries(result);
@@ -491,7 +491,7 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 
 		git.commit().setMessage("three files with different modes").call();
 
-		final byte[] zipData = CLIGitCommand.rawExecute( //
+		byte[] zipData = CLIGitCommand.rawExecute(
 				"git archive --format=zip master", db);
 		writeRaw("zip-with-modes.zip", zipData);
 		assertContainsEntryWithMode("zip-with-modes.zip", "-rw-", "plain");
@@ -520,7 +520,7 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 
 		git.commit().setMessage("three files with different modes").call();
 
-		final byte[] archive = CLIGitCommand.rawExecute( //
+		byte[] archive = CLIGitCommand.rawExecute(
 				"git archive --format=tar master", db);
 		writeRaw("with-modes.tar", archive);
 		assertTarContainsEntry("with-modes.tar", "-rw-r--r--", "plain");
@@ -532,7 +532,7 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	@Test
 	public void testArchiveWithLongFilename() throws Exception {
 		String filename = "";
-		final List<String> l = new ArrayList<String>();
+		List<String> l = new ArrayList<String>();
 		for (int i = 0; i < 20; i++) {
 			filename = filename + "1234567890/";
 			l.add(filename);
@@ -543,7 +543,7 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern("1234567890").call();
 		git.commit().setMessage("file with long name").call();
 
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive --format=zip HEAD", db);
 		assertArrayEquals(l.toArray(new String[l.size()]),
 				listZipEntries(result));
@@ -552,7 +552,7 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	@Test
 	public void testTarWithLongFilename() throws Exception {
 		String filename = "";
-		final List<String> l = new ArrayList<String>();
+		List<String> l = new ArrayList<String>();
 		for (int i = 0; i < 20; i++) {
 			filename = filename + "1234567890/";
 			l.add(filename);
@@ -563,7 +563,7 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern("1234567890").call();
 		git.commit().setMessage("file with long name").call();
 
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive --format=tar HEAD", db);
 		assertArrayEquals(l.toArray(new String[l.size()]),
 				listTarEntries(result));
@@ -571,34 +571,34 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 
 	@Test
 	public void testArchivePreservesContent() throws Exception {
-		final String payload = "“The quick brown fox jumps over the lazy dog!”";
+		String payload = "“The quick brown fox jumps over the lazy dog!”";
 		writeTrashFile("xyzzy", payload);
 		git.add().addFilepattern("xyzzy").call();
 		git.commit().setMessage("add file with content").call();
 
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive --format=zip HEAD", db);
-		assertArrayEquals(new String[] { payload }, //
+		assertArrayEquals(new String[] { payload },
 				zipEntryContent(result, "xyzzy"));
 	}
 
 	@Test
 	public void testTarPreservesContent() throws Exception {
-		final String payload = "“The quick brown fox jumps over the lazy dog!”";
+		String payload = "“The quick brown fox jumps over the lazy dog!”";
 		writeTrashFile("xyzzy", payload);
 		git.add().addFilepattern("xyzzy").call();
 		git.commit().setMessage("add file with content").call();
 
-		final byte[] result = CLIGitCommand.rawExecute( //
+		byte[] result = CLIGitCommand.rawExecute(
 				"git archive --format=tar HEAD", db);
-		assertArrayEquals(new String[] { payload }, //
+		assertArrayEquals(new String[] { payload },
 				tarEntryContent(result, "xyzzy"));
 	}
 
 	private Process spawnAssumingCommandPresent(String... cmdline) {
-		final File cwd = db.getWorkTree();
-		final ProcessBuilder procBuilder = new ProcessBuilder(cmdline) //
-				.directory(cwd) //
+		File cwd = db.getWorkTree();
+		ProcessBuilder procBuilder = new ProcessBuilder(cmdline)
+				.directory(cwd)
 				.redirectErrorStream(true);
 		Process proc = null;
 		try {
@@ -612,15 +612,15 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	}
 
 	private BufferedReader readFromProcess(Process proc) throws Exception {
-		return new BufferedReader( //
+		return new BufferedReader(
 				new InputStreamReader(proc.getInputStream(), "UTF-8"));
 	}
 
-	private void grepForEntry(String name, String mode, String... cmdline) //
+	private void grepForEntry(String name, String mode, String... cmdline)
 			throws Exception {
-		final Process proc = spawnAssumingCommandPresent(cmdline);
+		Process proc = spawnAssumingCommandPresent(cmdline);
 		proc.getOutputStream().close();
-		final BufferedReader reader = readFromProcess(proc);
+		BufferedReader reader = readFromProcess(proc);
 		try {
 			String line;
 			while ((line = reader.readLine()) != null)
@@ -672,20 +672,20 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		assertMagic(new byte[] { (byte) 0xfd, '7', 'z', 'X', 'Z', 0 }, file);
 	}
 
-	private void assertContainsEntryWithMode(String zipFilename, String mode, String name) //
+	private void assertContainsEntryWithMode(String zipFilename, String mode, String name)
 			throws Exception {
 		grepForEntry(name, mode, "zipinfo", zipFilename);
 	}
 
-	private void assertTarContainsEntry(String tarfile, String mode, String name) //
+	private void assertTarContainsEntry(String tarfile, String mode, String name)
 			throws Exception {
 		grepForEntry(name, mode, "tar", "tvf", tarfile);
 	}
 
-	private void writeRaw(String filename, byte[] data) //
+	private void writeRaw(String filename, byte[] data)
 			throws IOException {
-		final File path = new File(db.getWorkTree(), filename);
-		final OutputStream out = new FileOutputStream(path);
+		File path = new File(db.getWorkTree(), filename);
+		OutputStream out = new FileOutputStream(path);
 		try {
 			out.write(data);
 		} finally {
@@ -694,8 +694,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	}
 
 	private static String[] listZipEntries(byte[] zipData) throws IOException {
-		final List<String> l = new ArrayList<String>();
-		final ZipInputStream in = new ZipInputStream( //
+		List<String> l = new ArrayList<String>();
+		ZipInputStream in = new ZipInputStream(
 				new ByteArrayInputStream(zipData));
 
 		ZipEntry e;
@@ -706,9 +706,9 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	}
 
 	private static Future<Object> writeAsync(final OutputStream stream, final byte[] data) {
-		final ExecutorService executor = Executors.newSingleThreadExecutor();
+		ExecutorService executor = Executors.newSingleThreadExecutor();
 
-		return executor.submit(new Callable<Object>() { //
+		return executor.submit(new Callable<Object>() {
 			public Object call() throws IOException {
 				try {
 					stream.write(data);
@@ -721,13 +721,13 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	}
 
 	private String[] listTarEntries(byte[] tarData) throws Exception {
-		final List<String> l = new ArrayList<String>();
-		final Process proc = spawnAssumingCommandPresent("tar", "tf", "-");
-		final BufferedReader reader = readFromProcess(proc);
-		final OutputStream out = proc.getOutputStream();
+		List<String> l = new ArrayList<String>();
+		Process proc = spawnAssumingCommandPresent("tar", "tf", "-");
+		BufferedReader reader = readFromProcess(proc);
+		OutputStream out = proc.getOutputStream();
 
 		// Dump tarball to tar stdin in background
-		final Future<?> writing = writeAsync(out, tarData);
+		Future<?> writing = writeAsync(out, tarData);
 
 		try {
 			String line;
@@ -742,9 +742,9 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		}
 	}
 
-	private static String[] zipEntryContent(byte[] zipData, String path) //
+	private static String[] zipEntryContent(byte[] zipData, String path)
 			throws IOException {
-		final ZipInputStream in = new ZipInputStream( //
+		ZipInputStream in = new ZipInputStream(
 				new ByteArrayInputStream(zipData));
 		ZipEntry e;
 		while ((e = in.getNextEntry()) != null) {
@@ -752,8 +752,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 				continue;
 
 			// found!
-			final List<String> l = new ArrayList<String>();
-			final BufferedReader reader = new BufferedReader( //
+			List<String> l = new ArrayList<String>();
+			BufferedReader reader = new BufferedReader(
 					new InputStreamReader(in, "UTF-8"));
 			String line;
 			while ((line = reader.readLine()) != null)
@@ -765,13 +765,13 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		return null;
 	}
 
-	private String[] tarEntryContent(byte[] tarData, String path) //
+	private String[] tarEntryContent(byte[] tarData, String path)
 			throws Exception {
-		final List<String> l = new ArrayList<String>();
-		final Process proc = spawnAssumingCommandPresent("tar", "Oxf", "-", path);
-		final BufferedReader reader = readFromProcess(proc);
-		final OutputStream out = proc.getOutputStream();
-		final Future<?> writing = writeAsync(out, tarData);
+		List<String> l = new ArrayList<String>();
+		Process proc = spawnAssumingCommandPresent("tar", "Oxf", "-", path);
+		BufferedReader reader = readFromProcess(proc);
+		OutputStream out = proc.getOutputStream();
+		Future<?> writing = writeAsync(out, tarData);
 
 		try {
 			String line;

org.eclipse.jgit.test/.classpath

@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry excluding="**/*.idx|**/*.pack" kind="src" path="tst"/>
+	<classpathentry kind="src" path="src"/>
 	<classpathentry kind="src" path="tst-rsrc"/>
 	<classpathentry kind="src" path="exttst"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>

org.eclipse.jgit.test/pom.xml

@@ -102,6 +102,7 @@
   </dependencies>
 
   <build>
+    <sourceDirectory>src/</sourceDirectory>
     <testSourceDirectory>tst/</testSourceDirectory>
 
     <testResources>

org.eclipse.jgit.test/src/org/eclipse/jgit/lib/Sets.java

@@ -41,13 +41,13 @@
  * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-package org.eclipse.jgit.api;
+package org.eclipse.jgit.lib;
 
 import java.util.HashSet;
 import java.util.Set;
 
-class Sets {
-	static <T> Set<T> of(T... elements) {
+public class Sets {
+	public static <T> Set<T> of(T... elements) {
 		Set<T> ret = new HashSet<T>();
 		for (T element : elements)
 			ret.add(element);

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

@@ -514,6 +514,17 @@ public class CommitCommandTest extends RepositoryTestCase {
 		}
 	}
 
+	@Test
+	public void commitOnlyShouldHandleIgnored() throws Exception {
+		try (Git git = new Git(db)) {
+			writeTrashFile("subdir/foo", "Hello World");
+			writeTrashFile("subdir/bar", "Hello World");
+			writeTrashFile(".gitignore", "bar");
+			git.add().addFilepattern("subdir").call();
+			git.commit().setOnly("subdir").setMessage("first commit").call();
+		}
+	}
+
 	private static void addUnmergedEntry(String file, DirCacheBuilder builder) {
 		DirCacheEntry stage1 = new DirCacheEntry(file, DirCacheEntry.STAGE_1);
 		DirCacheEntry stage2 = new DirCacheEntry(file, DirCacheEntry.STAGE_2);

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

@@ -62,6 +62,7 @@ import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.RepositoryState;
+import org.eclipse.jgit.lib.Sets;
 import org.eclipse.jgit.merge.MergeStrategy;
 import org.eclipse.jgit.merge.ResolveMerger.MergeFailureReason;
 import org.eclipse.jgit.revwalk.RevCommit;

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

@@ -53,6 +53,7 @@ import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.NoFilepatternException;
 import org.eclipse.jgit.errors.NoWorkTreeException;
 import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.lib.Sets;
 import org.junit.Test;
 
 public class StatusCommandTest extends RepositoryTestCase {

org.eclipse.jgit.test/tst/org/eclipse/jgit/gitrepo/ManifestParserTest.java

@@ -87,9 +87,9 @@ public class ManifestParserTest {
 		for (RepoProject proj : parser.getProjects()) {
 			String msg = String.format(
 					"project \"%s\" should be included in unfiltered projects",
-					proj.path);
-			assertTrue(msg, results.contains(proj.path));
-			results.remove(proj.path);
+					proj.getPath());
+			assertTrue(msg, results.contains(proj.getPath()));
+			results.remove(proj.getPath());
 		}
 		assertTrue(
 				"Unfiltered projects shouldn't contain any unexpected results",
@@ -101,9 +101,9 @@ public class ManifestParserTest {
 		for (RepoProject proj : parser.getFilteredProjects()) {
 			String msg = String.format(
 					"project \"%s\" should be included in filtered projects",
-					proj.path);
-			assertTrue(msg, results.contains(proj.path));
-			results.remove(proj.path);
+					proj.getPath());
+			assertTrue(msg, results.contains(proj.getPath()));
+			results.remove(proj.getPath());
 		}
 		assertTrue(
 				"Filtered projects shouldn't contain any unexpected results",

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackFileTest.java

@@ -123,7 +123,7 @@ public class PackFileTest extends LocalDiskRepositoryTestCase {
 	@After
 	public void tearDown() throws Exception {
 		if (wc != null)
-			wc.release();
+			wc.close();
 		new WindowCacheConfig().install();
 		super.tearDown();
 	}

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/UnpackedObjectTest.java

@@ -108,7 +108,7 @@ public class UnpackedObjectTest extends LocalDiskRepositoryTestCase {
 	@After
 	public void tearDown() throws Exception {
 		if (wc != null)
-			wc.release();
+			wc.close();
 		new WindowCacheConfig().install();
 		super.tearDown();
 	}

org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/ObjectWalkFilterTest.java

@@ -0,0 +1,186 @@
+/*
+ * Copyright (C) 2015, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.revwalk;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import org.eclipse.jgit.internal.storage.dfs.DfsRepositoryDescription;
+import org.eclipse.jgit.internal.storage.dfs.InMemoryRepository;
+import org.eclipse.jgit.junit.TestRepository;
+import org.eclipse.jgit.lib.AnyObjectId;
+import org.eclipse.jgit.lib.Sets;
+import org.eclipse.jgit.revwalk.ObjectWalk;
+import org.eclipse.jgit.revwalk.filter.MessageRevFilter;
+import org.eclipse.jgit.revwalk.filter.NotRevFilter;
+import org.eclipse.jgit.revwalk.filter.ObjectFilter;
+
+import java.io.IOException;
+import java.util.Set;
+
+public class ObjectWalkFilterTest {
+	private TestRepository<InMemoryRepository> tr;
+	private ObjectWalk rw;
+
+	// 3 commits, 2 top-level trees, 4 subtrees, 3 blobs
+	private static final int OBJECT_COUNT = 12;
+
+	@Before
+	public void setUp() throws Exception {
+		tr = new TestRepository<>(new InMemoryRepository(
+				new DfsRepositoryDescription("test")));
+		rw = new ObjectWalk(tr.getRepository());
+
+		rw.markStart(tr.branch("master").commit()
+			.add("a/a", "1")
+			.add("b/b", "2")
+			.add("c/c", "3")
+			.message("initial commit")
+
+			.child()
+			.rm("a/a")
+			.add("a/A", "1")
+			.message("capitalize a/a")
+
+			.child()
+			.rm("a/A")
+			.add("a/a", "1")
+			.message("make a/A lowercase again")
+			.create());
+	}
+
+	@After
+	public void tearDown() {
+		rw.close();
+		tr.getRepository().close();
+	}
+
+	private static class BlacklistObjectFilter extends ObjectFilter {
+		final Set<AnyObjectId> badObjects;
+
+		BlacklistObjectFilter(Set<AnyObjectId> badObjects) {
+			this.badObjects = badObjects;
+		}
+
+		@Override
+		public boolean include(ObjectWalk walker, AnyObjectId o) {
+			return !badObjects.contains(o);
+		}
+	}
+
+	private AnyObjectId resolve(String revstr) throws Exception {
+		return tr.getRepository().resolve(revstr);
+	}
+
+	private int countObjects() throws IOException {
+		int n = 0;
+		while (rw.next() != null) {
+			n++;
+		}
+		while (rw.nextObject() != null) {
+			n++;
+		}
+		return n;
+	}
+
+	@Test
+	public void testDefaultFilter() throws Exception {
+		assertTrue("filter is ALL",
+				rw.getObjectFilter() == ObjectFilter.ALL);
+		assertEquals(OBJECT_COUNT, countObjects());
+	}
+
+	@Test
+	public void testObjectFilterCanFilterOutBlob() throws Exception {
+		AnyObjectId one = rw.parseAny(resolve("master:a/a"));
+		AnyObjectId two = rw.parseAny(resolve("master:b/b"));
+		rw.setObjectFilter(new BlacklistObjectFilter(Sets.of(one, two)));
+
+		// 2 blobs filtered out
+		assertEquals(OBJECT_COUNT - 2, countObjects());
+	}
+
+	@Test
+	public void testFilteringCommitsHasNoEffect() throws Exception {
+		AnyObjectId initial = rw.parseCommit(resolve("master^^"));
+		rw.setObjectFilter(new BlacklistObjectFilter(Sets.of(initial)));
+		assertEquals(OBJECT_COUNT, countObjects());
+	}
+
+	@Test
+	public void testRevFilterAndObjectFilterCanCombine() throws Exception {
+		AnyObjectId one = rw.parseAny(resolve("master:a/a"));
+		AnyObjectId two = rw.parseAny(resolve("master:b/b"));
+		rw.setObjectFilter(new BlacklistObjectFilter(Sets.of(one, two)));
+		rw.setRevFilter(NotRevFilter.create(
+				MessageRevFilter.create("capitalize")));
+
+		// 2 blobs, one commit, two trees filtered out
+		assertEquals(OBJECT_COUNT - 5, countObjects());
+	}
+
+	@Test
+	public void testFilteringTreeFiltersSubtrees() throws Exception {
+		AnyObjectId capitalizeTree = rw.parseAny(resolve("master^:"));
+		rw.setObjectFilter(new BlacklistObjectFilter(
+				Sets.of(capitalizeTree)));
+
+		// trees "master^:" and "master^:a" filtered out
+		assertEquals(OBJECT_COUNT - 2, countObjects());
+	}
+
+	@Test
+	public void testFilteringTreeFiltersReferencedBlobs() throws Exception {
+		AnyObjectId a1 = rw.parseAny(resolve("master:a"));
+		AnyObjectId a2 = rw.parseAny(resolve("master^:a"));
+		rw.setObjectFilter(new BlacklistObjectFilter(Sets.of(a1, a2)));
+
+		// 2 trees, one blob filtered out
+		assertEquals(OBJECT_COUNT - 3, countObjects());
+	}
+}

org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties

@@ -181,7 +181,7 @@ corruptObjectTruncatedInObjectId=truncated in object id
 couldNotCheckOutBecauseOfConflicts=Could not check out because of conflicts
 couldNotDeleteLockFileShouldNotHappen=Could not delete lock file. Should not happen
 couldNotDeleteTemporaryIndexFileShouldNotHappen=Could not delete temporary index file. Should not happen
-couldNotGetAdvertisedRef=Could not get advertised Ref for branch {0}
+couldNotGetAdvertisedRef=Remote {0} did not advertise Ref for branch {1}. This Ref may not exist in the remote or may be hidden by permission settings.
 couldNotGetRepoStatistics=Could not get repository statistics
 couldNotLockHEAD=Could not lock HEAD
 couldNotReadIndexInOneGo=Could not read index in one go, only {0} out of {1} read
@@ -257,6 +257,7 @@ exceptionCaughtDuringExecutionOfResetCommand=Exception caught during execution o
 exceptionCaughtDuringExecutionOfRevertCommand=Exception caught during execution of revert command. {0}
 exceptionCaughtDuringExecutionOfRmCommand=Exception caught during execution of rm command
 exceptionCaughtDuringExecutionOfTagCommand=Exception caught during execution of tag command
+exceptionCaughtDuringExcecutionOfCommand=Exception caught during execution of command {0} in {1}
 exceptionHookExecutionInterrupted=Execution of "{0}" hook interrupted.
 exceptionOccurredDuringAddingOfOptionToALogCommand=Exception occurred during adding of {0} as option to a Log command
 exceptionOccurredDuringReadingOfGIT_DIR=Exception occurred during reading of $GIT_DIR/{0}. {1}

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

@@ -364,19 +364,20 @@ public class ArchiveCommand extends GitCommand<OutputStream> {
 	}
 
 	private <T extends Closeable> OutputStream writeArchive(Format<T> fmt) {
-		final String pfx = prefix == null ? "" : prefix; //$NON-NLS-1$
-		try (final TreeWalk walk = new TreeWalk(repo)) {
-			final T outa = fmt.createArchiveOutputStream(out, formatOptions);
-			try (final RevWalk rw = new RevWalk(walk.getObjectReader())) {
-				final MutableObjectId idBuf = new MutableObjectId();
-				final ObjectReader reader = walk.getObjectReader();
+		try {
+			try (TreeWalk walk = new TreeWalk(repo);
+					RevWalk rw = new RevWalk(walk.getObjectReader())) {
+				String pfx = prefix == null ? "" : prefix; //$NON-NLS-1$
+				T outa = fmt.createArchiveOutputStream(out, formatOptions);
+				MutableObjectId idBuf = new MutableObjectId();
+				ObjectReader reader = walk.getObjectReader();
 
 				walk.reset(rw.parseTree(tree));
 				if (!paths.isEmpty())
 					walk.setFilter(PathFilterGroup.createFromStrings(paths));
 
 				while (walk.next()) {
-					final String name = pfx + walk.getPathString();
+					String name = pfx + walk.getPathString();
 					FileMode mode = walk.getFileMode(0);
 
 					if (walk.isSubtree())
@@ -395,10 +396,10 @@ public class ArchiveCommand extends GitCommand<OutputStream> {
 					fmt.putEntry(outa, name, mode, reader.open(idBuf));
 				}
 				outa.close();
+				return out;
 			} finally {
 				out.close();
 			}
-			return out;
 		} catch (IOException e) {
 			// TODO(jrn): Throw finer-grained errors.
 			throw new JGitInternalException(
@@ -413,7 +414,7 @@ public class ArchiveCommand extends GitCommand<OutputStream> {
 	public OutputStream call() throws GitAPIException {
 		checkCallable();
 
-		final Format<?> fmt;
+		Format<?> fmt;
 		if (format == null)
 			fmt = formatBySuffix(suffix);
 		else

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

@@ -358,7 +358,7 @@ public class CommitCommand extends GitCommand<RevCommit> {
 					// check if entry refers to a tracked file
 					boolean tracked = dcTree != null || hTree != null;
 					if (!tracked)
-						break;
+						continue;
 
 					// for an unmerged path, DirCacheBuildIterator will yield 3
 					// entries, we only want to add one

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

@@ -54,6 +54,7 @@ import org.eclipse.jgit.api.errors.InvalidConfigurationException;
 import org.eclipse.jgit.api.errors.InvalidRemoteException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.NoHeadException;
+import org.eclipse.jgit.api.errors.RefNotAdvertisedException;
 import org.eclipse.jgit.api.errors.RefNotFoundException;
 import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
 import org.eclipse.jgit.internal.JGitText;
@@ -171,6 +172,7 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	 * @throws InvalidRemoteException
 	 * @throws CanceledException
 	 * @throws RefNotFoundException
+	 * @throws RefNotAdvertisedException
 	 * @throws NoHeadException
 	 * @throws org.eclipse.jgit.api.errors.TransportException
 	 * @throws GitAPIException
@@ -178,7 +180,7 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	public PullResult call() throws GitAPIException,
 			WrongRepositoryStateException, InvalidConfigurationException,
 			DetachedHeadException, InvalidRemoteException, CanceledException,
-			RefNotFoundException, NoHeadException,
+			RefNotFoundException, RefNotAdvertisedException, NoHeadException,
 			org.eclipse.jgit.api.errors.TransportException {
 		checkCallable();
 
@@ -284,11 +286,13 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 					r = fetchRes.getAdvertisedRef(Constants.R_HEADS
 							+ remoteBranchName);
 			}
-			if (r == null)
-				throw new JGitInternalException(MessageFormat.format(JGitText
-						.get().couldNotGetAdvertisedRef, remoteBranchName));
-			else
+			if (r == null) {
+				throw new RefNotAdvertisedException(MessageFormat.format(
+						JGitText.get().couldNotGetAdvertisedRef, remote,
+						remoteBranchName));
+			} else {
 				commitToMerge = r.getObjectId();
+			}
 		} else {
 			try {
 				commitToMerge = repo.resolve(remoteBranchName);

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

@@ -55,6 +55,7 @@ import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRemoteException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.errors.NotSupportedException;
+import org.eclipse.jgit.errors.TooLargePackException;
 import org.eclipse.jgit.errors.TransportException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
@@ -156,6 +157,9 @@ public class PushCommand extends
 					PushResult result = transport.push(monitor, toPush, out);
 					pushResults.add(result);
 
+				} catch (TooLargePackException e) {
+					throw new org.eclipse.jgit.api.errors.TooLargePackException(
+							e.getMessage(), e);
 				} catch (TransportException e) {
 					throw new org.eclipse.jgit.api.errors.TransportException(
 							e.getMessage(), e);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/RefNotAdvertisedException.java

@@ -0,0 +1,54 @@
+/*
+ * Copyright (C) 2015,Matthias Sohn <matthias.sohn@sap.com> and
+ * other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Distribution License v1.0 which accompanies this
+ * distribution, is reproduced below, and is available at
+ * http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the names of its
+ * contributors may be used to endorse or promote products derived from this
+ * software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.api.errors;
+
+/**
+ * Thrown when a ref is not found in advertised refs
+ *
+ * @since 4.0
+ */
+public class RefNotAdvertisedException extends GitAPIException {
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * @param message
+	 */
+	public RefNotAdvertisedException(String message) {
+		super(message);
+	}
+}

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/TooLargePackException.java

@@ -0,0 +1,65 @@
+/*
+ * Copyright (C) 2015, Christian Halstrick <christian.halstrick@sap.com> and
+ * other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Distribution License v1.0 which accompanies this
+ * distribution, is reproduced below, and is available at
+ * http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the names of its
+ * contributors may be used to endorse or promote products derived from this
+ * software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.api.errors;
+
+/**
+ * Exception thrown when the server rejected a too large pack
+ *
+ * @since 4.0
+ */
+public class TooLargePackException extends TransportException {
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * @param msg
+	 *            message describing the transport failure.
+	 */
+	public TooLargePackException(String msg) {
+		super(msg);
+	}
+
+	/**
+	 * @param msg
+	 *            message describing the transport exception.
+	 * @param cause
+	 *            why the transport failed.
+	 */
+	public TooLargePackException(String msg, Throwable cause) {
+		super(msg, cause);
+	}
+}

org.eclipse.jgit/src/org/eclipse/jgit/diff/MyersDiff.java

@@ -114,6 +114,7 @@ import org.eclipse.jgit.util.LongList;
 public class MyersDiff<S extends Sequence> {
 	/** Singleton instance of MyersDiff. */
 	public static final DiffAlgorithm INSTANCE = new LowLevelDiffAlgorithm() {
+		@SuppressWarnings("unused")
 		@Override
 		public <S extends Sequence> void diffNonCommon(EditList edits,
 				HashedSequenceComparator<S> cmp, HashedSequence<S> a,

org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java

@@ -63,10 +63,13 @@ import org.eclipse.jgit.lib.ObjectStream;
  * will not exceed 1 MiB per instance. The index starts out at a smaller size
  * (closer to 2 KiB), but may grow as more distinct blocks within the scanned
  * file are discovered.
+ *
+ * @since 4.0
  */
-class SimilarityIndex {
+public class SimilarityIndex {
 	/** A special {@link TableFullException} used in place of OutOfMemoryError. */
-	private static final TableFullException TABLE_FULL_OUT_OF_MEMORY = new TableFullException();
+	public static final TableFullException
+			TABLE_FULL_OUT_OF_MEMORY = new TableFullException();
 
 	/**
 	 * Shift to apply before storing a key.
@@ -105,6 +108,26 @@ class SimilarityIndex {
 	/** {@code idHash.length == 1 << idHashBits}. */
 	private int idHashBits;
 
+	/**
+	 * Create a new similarity index for the given object
+	 *
+	 * @param obj
+	 *            the object to hash
+	 * @return similarity index for this object
+	 * @throws IOException
+	 *             file contents cannot be read from the repository.
+	 * @throws TableFullException
+	 *             object hashing overflowed the storage capacity of the
+	 *             SimilarityIndex.
+	 */
+	public static SimilarityIndex create(ObjectLoader obj) throws IOException,
+			TableFullException {
+		SimilarityIndex idx = new SimilarityIndex();
+		idx.hash(obj);
+		idx.sort();
+		return idx;
+	}
+
 	SimilarityIndex() {
 		idHashBits = 8;
 		idHash = new long[1 << idHashBits];
@@ -212,7 +235,27 @@ class SimilarityIndex {
 		Arrays.sort(idHash);
 	}
 
-	int score(SimilarityIndex dst, int maxScore) {
+	/**
+	 * Compute the similarity score between this index and another.
+	 * <p>
+	 * A region of a file is defined as a line in a text file or a fixed-size
+	 * block in a binary file. To prepare an index, each region in the file is
+	 * hashed; the values and counts of hashes are retained in a sorted table.
+	 * Define the similarity fraction F as the the count of matching regions
+	 * between the two files divided between the maximum count of regions in
+	 * either file. The similarity score is F multiplied by the maxScore
+	 * constant, yielding a range [0, maxScore]. It is defined as maxScore for
+	 * the degenerate case of two empty files.
+	 * <p>
+	 * The similarity score is symmetrical; i.e. a.score(b) == b.score(a).
+	 *
+	 * @param dst
+	 *            the other index
+	 * @param maxScore
+	 *            the score representing a 100% match
+	 * @return the similarity score
+	 */
+	public int score(SimilarityIndex dst, int maxScore) {
 		long max = Math.max(hashedCnt, dst.hashedCnt);
 		if (max == 0)
 			return maxScore;
@@ -381,7 +424,8 @@ class SimilarityIndex {
 		return v & MAX_COUNT;
 	}
 
-	static class TableFullException extends Exception {
+	/** Thrown by {@code create()} when file is too large. */
+	public static class TableFullException extends Exception {
 		private static final long serialVersionUID = 1L;
 	}
 }

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

@@ -1192,6 +1192,7 @@ public class DirCacheCheckout {
 		entry.setLastModified(f.lastModified());
 	}
 
+	@SuppressWarnings("deprecation")
 	private static void checkValidPath(CanonicalTreeParser t)
 			throws InvalidPathException {
 		ObjectChecker chk = new ObjectChecker()

org.eclipse.jgit/src/org/eclipse/jgit/errors/TooLargePackException.java

@@ -43,17 +43,17 @@
 
 package org.eclipse.jgit.errors;
 
-import java.io.IOException;
 import java.text.MessageFormat;
 
 import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.transport.URIish;
 
 /**
  * Thrown when a pack exceeds a given size limit
  *
  * @since 3.3
  */
-public class TooLargePackException extends IOException {
+public class TooLargePackException extends TransportException {
 	private static final long serialVersionUID = 1L;
 
 	/**
@@ -66,4 +66,17 @@ public class TooLargePackException extends IOException {
 		super(MessageFormat.format(JGitText.get().receivePackTooLarge,
 				Long.valueOf(packSizeLimit)));
 	}
+
+	/**
+	 * Construct a too large pack exception.
+	 *
+	 * @param uri
+	 *            URI used for transport
+	 * @param s
+	 *            message
+	 * @since 4.0
+	 */
+	public TooLargePackException(URIish uri, String s) {
+		super(uri.setPass(null) + ": " + s); //$NON-NLS-1$
+	}
 }

org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/ManifestParser.java

@@ -205,7 +205,7 @@ public class ManifestParser extends DefaultHandler {
 				throw new SAXException(RepoText.get().invalidManifest);
 			currentProject.addCopyFile(new CopyFile(
 						rootRepo,
-						currentProject.path,
+						currentProject.getPath(),
 						attributes.getValue("src"), //$NON-NLS-1$
 						attributes.getValue("dest"))); //$NON-NLS-1$
 		} else if ("include".equals(qName)) { //$NON-NLS-1$
@@ -266,7 +266,7 @@ public class ManifestParser extends DefaultHandler {
 			throw new SAXException(e);
 		}
 		for (RepoProject proj : projects) {
-			String remote = proj.remote;
+			String remote = proj.getRemote();
 			if (remote == null) {
 				if (defaultRemote == null) {
 					if (filename != null)
@@ -286,7 +286,7 @@ public class ManifestParser extends DefaultHandler {
 					remoteUrl = remoteUrl + "/"; //$NON-NLS-1$
 				remoteUrls.put(remote, remoteUrl);
 			}
-			proj.setUrl(remoteUrl + proj.name)
+			proj.setUrl(remoteUrl + proj.getName())
 					.setDefaultRevision(defaultRevision);
 		}
 
@@ -339,7 +339,7 @@ public class ManifestParser extends DefaultHandler {
 
 	boolean inGroups(RepoProject proj) {
 		for (String group : minusGroups) {
-			if (proj.groups.contains(group)) {
+			if (proj.inGroup(group)) {
 				// minus groups have highest priority.
 				return false;
 			}
@@ -349,7 +349,7 @@ public class ManifestParser extends DefaultHandler {
 			return true;
 		}
 		for (String group : plusGroups) {
-			if (proj.groups.contains(group))
+			if (proj.inGroup(group))
 				return true;
 		}
 		return false;

org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java

@@ -379,10 +379,10 @@ public class RepoCommand extends GitCommand<RevCommit> {
 			try {
 				parser.read(inputStream);
 				for (RepoProject proj : parser.getFilteredProjects()) {
-					addSubmodule(proj.url,
-							proj.path,
+					addSubmodule(proj.getUrl(),
+							proj.getPath(),
 							proj.getRevision(),
-							proj.copyfiles);
+							proj.getCopyFiles());
 				}
 			} catch (GitAPIException | IOException e) {
 				throw new ManifestErrorException(e);
@@ -403,17 +403,17 @@ public class RepoCommand extends GitCommand<RevCommit> {
 			try (RevWalk rw = new RevWalk(repo)) {
 				Config cfg = new Config();
 				for (RepoProject proj : bareProjects) {
-					String name = proj.path;
-					String nameUri = proj.name;
+					String name = proj.getPath();
+					String nameUri = proj.getName();
 					cfg.setString("submodule", name, "path", name); //$NON-NLS-1$ //$NON-NLS-2$
 					cfg.setString("submodule", name, "url", nameUri); //$NON-NLS-1$ //$NON-NLS-2$
 					// create gitlink
 					DirCacheEntry dcEntry = new DirCacheEntry(name);
 					ObjectId objectId;
-					if (ObjectId.isId(proj.revision))
-						objectId = ObjectId.fromString(proj.revision);
+					if (ObjectId.isId(proj.getRevision()))
+						objectId = ObjectId.fromString(proj.getRevision());
 					else {
-						objectId = callback.sha1(nameUri, proj.revision);
+						objectId = callback.sha1(nameUri, proj.getRevision());
 					}
 					if (objectId == null)
 						throw new RemoteUnavailableException(nameUri);
@@ -421,9 +421,9 @@ public class RepoCommand extends GitCommand<RevCommit> {
 					dcEntry.setFileMode(FileMode.GITLINK);
 					builder.add(dcEntry);
 
-					for (CopyFile copyfile : proj.copyfiles) {
+					for (CopyFile copyfile : proj.getCopyFiles()) {
 						byte[] src = callback.readFile(
-								nameUri, proj.revision, copyfile.src);
+								nameUri, proj.getRevision(), copyfile.src);
 						objectId = inserter.insert(Constants.OBJ_BLOB, src);
 						dcEntry = new DirCacheEntry(copyfile.dest);
 						dcEntry.setObjectId(objectId);
@@ -495,7 +495,7 @@ public class RepoCommand extends GitCommand<RevCommit> {
 			List<CopyFile> copyfiles) throws GitAPIException, IOException {
 		if (repo.isBare()) {
 			RepoProject proj = new RepoProject(url, name, revision, null, null);
-			proj.copyfiles.addAll(copyfiles);
+			proj.addCopyFiles(copyfiles);
 			bareProjects.add(proj);
 		} else {
 			SubmoduleAddCommand add = git

org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoProject.java

@@ -49,6 +49,8 @@ import java.io.IOException;
 import java.nio.channels.FileChannel;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -62,14 +64,14 @@ import org.eclipse.jgit.lib.Repository;
  * @since 4.0
  */
 public class RepoProject implements Comparable<RepoProject> {
-	final String name;
-	final String path;
-	final String revision;
-	final String remote;
-	final Set<String> groups;
-	final List<CopyFile> copyfiles;
-	String url;
-	String defaultRevision;
+	private final String name;
+	private final String path;
+	private final String revision;
+	private final String remote;
+	private final Set<String> groups;
+	private final List<CopyFile> copyfiles;
+	private String url;
+	private String defaultRevision;
 
 	/**
 	 * The representation of a copy file configuration.
@@ -82,10 +84,13 @@ public class RepoProject implements Comparable<RepoProject> {
 
 		/**
 		 * @param repo
+		 *            the super project.
 		 * @param path
 		 *            the path of the project containing this copyfile config.
 		 * @param src
+		 *            the source path relative to the sub repo.
 		 * @param dest
+		 *            the destination path relative to the super project.
 		 */
 		public CopyFile(Repository repo, String path, String src, String dest) {
 			this.repo = repo;
@@ -108,7 +113,8 @@ public class RepoProject implements Comparable<RepoProject> {
 				FileOutputStream output = new FileOutputStream(destFile);
 				try {
 					FileChannel channel = input.getChannel();
-					output.getChannel().transferFrom(channel, 0, channel.size());
+					output.getChannel().transferFrom(
+							channel, 0, channel.size());
 				} finally {
 					output.close();
 				}
@@ -120,10 +126,15 @@ public class RepoProject implements Comparable<RepoProject> {
 
 	/**
 	 * @param name
+	 *            the relative path to the {@code remote}
 	 * @param path
+	 *            the relative path to the super project
 	 * @param revision
+	 *            a SHA-1 or branch name or tag name
 	 * @param remote
+	 *            name of the remote definition
 	 * @param groups
+	 *            comma separated group list
 	 */
 	public RepoProject(String name, String path, String revision,
 			String remote, String groups) {
@@ -162,15 +173,70 @@ public class RepoProject implements Comparable<RepoProject> {
 		return this;
 	}
 
+	/**
+	 * Get the name (relative path to the {@code remote}) of this sub repo.
+	 *
+	 * @return {@code name}
+	 */
+	public String getName() {
+		return name;
+	}
+
+	/**
+	 * Get the path (relative path to the super project) of this sub repo.
+	 *
+	 * @return {@code path}
+	 */
+	public String getPath() {
+		return path;
+	}
+
 	/**
 	 * Get the revision of the sub repo.
 	 *
-	 * @return revision if set, or default revision.
+	 * @return {@code revision} if set, or {@code defaultRevision}.
 	 */
 	public String getRevision() {
 		return revision == null ? defaultRevision : revision;
 	}
 
+	/**
+	 * Getter for the copyfile configurations.
+	 *
+	 * @return Immutable copy of {@code copyfiles}
+	 */
+	public List<CopyFile> getCopyFiles() {
+		return Collections.unmodifiableList(copyfiles);
+	}
+
+	/**
+	 * Get the url of the sub repo.
+	 *
+	 * @return {@code url}
+	 */
+	public String getUrl() {
+		return url;
+	}
+
+	/**
+	 * Get the name of the remote definition of the sub repo.
+	 *
+	 * @return {@remote}
+	 */
+	public String getRemote() {
+		return remote;
+	}
+
+	/**
+	 * Test whether this sub repo belongs to a specified group.
+	 *
+	 * @param group
+	 * @return true if {@code group} is present.
+	 */
+	public boolean inGroup(String group) {
+		return groups.contains(group);
+	}
+
 	/**
 	 * Add a copy file configuration.
 	 *
@@ -180,7 +246,16 @@ public class RepoProject implements Comparable<RepoProject> {
 		copyfiles.add(copyfile);
 	}
 
-	String getPathWithSlash() {
+	/**
+	 * Add a bunch of copyfile configurations.
+	 *
+	 * @param copyfiles
+	 */
+	public void addCopyFiles(Collection<CopyFile> copyfiles) {
+		this.copyfiles.addAll(copyfiles);
+	}
+
+	private String getPathWithSlash() {
 		if (path.endsWith("/")) //$NON-NLS-1$
 			return path;
 		else

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

@@ -316,6 +316,7 @@ public class JGitText extends TranslationBundle {
 	/***/ public String exceptionCaughtDuringExecutionOfRevertCommand;
 	/***/ public String exceptionCaughtDuringExecutionOfRmCommand;
 	/***/ public String exceptionCaughtDuringExecutionOfTagCommand;
+	/***/ public String exceptionCaughtDuringExcecutionOfCommand;
 	/***/ public String exceptionHookExecutionInterrupted;
 	/***/ public String exceptionOccurredDuringAddingOfOptionToALogCommand;
 	/***/ public String exceptionOccurredDuringReadingOfGIT_DIR;

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

@@ -533,6 +533,7 @@ public final class DfsPackFile {
 		return ByteBuffer.wrap(copyBuf, 0, bs);
 	}
 
+	@SuppressWarnings("null")
 	void copyAsIs(PackOutputStream out, DfsObjectToPack src,
 			boolean validate, DfsReader ctx) throws IOException,
 			StoredObjectRepresentationNotAvailableException {
@@ -836,6 +837,7 @@ public final class DfsPackFile {
 		return buf.position();
 	}
 
+	@SuppressWarnings("null")
 	ObjectLoader load(DfsReader ctx, long pos)
 			throws IOException {
 		try {

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

@@ -366,11 +366,10 @@ public class ObjectDirectoryPackParser extends PackParser {
 
 	@Override
 	protected void onEndThinPack() throws IOException {
-		final byte[] tailHash = this.tailDigest.digest();
 		final byte[] buf = buffer();
 
 		final MessageDigest origDigest = Constants.newMessageDigest();
-		final MessageDigest tailDigest = Constants.newMessageDigest();
+		final MessageDigest tailDigest2 = Constants.newMessageDigest();
 		final MessageDigest packDigest = Constants.newMessageDigest();
 
 		long origRemaining = origEnd;
@@ -393,15 +392,15 @@ public class ObjectDirectoryPackParser extends PackParser {
 				origDigest.update(buf, 0, origCnt);
 				origRemaining -= origCnt;
 				if (origRemaining == 0)
-					tailDigest.update(buf, origCnt, n - origCnt);
+					tailDigest2.update(buf, origCnt, n - origCnt);
 			} else
-				tailDigest.update(buf, 0, n);
+				tailDigest2.update(buf, 0, n);
 
 			packDigest.update(buf, 0, n);
 		}
 
-		if (!Arrays.equals(origDigest.digest(), origHash)
-				|| !Arrays.equals(tailDigest.digest(), tailHash))
+		if (!Arrays.equals(origDigest.digest(), origHash) || !Arrays
+				.equals(tailDigest2.digest(), this.tailDigest.digest()))
 			throw new IOException(
 					JGitText.get().packCorruptedWhileWritingToFilesystem);
 

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

@@ -80,6 +80,6 @@ class PackInputStream extends InputStream {
 
 	@Override
 	public void close() {
-		wc.release();
+		wc.close();
 	}
 }

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

@@ -91,11 +91,8 @@ public class UnpackedObject {
 	 */
 	public static ObjectLoader parse(byte[] raw, AnyObjectId id)
 			throws IOException {
-		WindowCursor wc = new WindowCursor(null);
-		try {
+		try (WindowCursor wc = new WindowCursor(null)) {
 			return open(new ByteArrayInputStream(raw), null, id, wc);
-		} finally {
-			wc.release();
 		}
 	}
 

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

@@ -330,7 +330,8 @@ final class WindowCursor extends ObjectReader implements ObjectReuseAsIs {
 	}
 
 	/** Release the current window cursor. */
-	public void release() {
+	@Override
+	public void close() {
 		window = null;
 		baseCache = null;
 		try {

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java

@@ -1591,6 +1591,7 @@ public class PackWriter implements AutoCloseable {
 				findObjectsToPackUsingBitmaps(bitmapWalker, want, have);
 				endPhase(countingMonitor);
 				stats.timeCounting = System.currentTimeMillis() - countingStart;
+				stats.bitmapIndexMisses = bitmapWalker.getCountOfBitmapIndexMisses();
 				return;
 			}
 		}
@@ -2084,6 +2085,8 @@ public class PackWriter implements AutoCloseable {
 
 		long totalObjects;
 
+		long bitmapIndexMisses;
+
 		long totalDeltas;
 
 		long reusedObjects;
@@ -2165,6 +2168,16 @@ public class PackWriter implements AutoCloseable {
 			return totalObjects;
 		}
 
+		/**
+		 * @return the count of objects that needed to be discovered through an
+		 *         object walk because they were not found in bitmap indices.
+		 *
+		 * @since 4.0
+		 */
+		public long getBitmapIndexMisses() {
+			return bitmapIndexMisses;
+		}
+
 		/**
 		 * @return total number of deltas output. This may be lower than the
 		 *         actual number of deltas if a cached pack was reused.

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriterBitmapWalker.java

@@ -71,6 +71,8 @@ final class PackWriterBitmapWalker {
 
 	private final ProgressMonitor pm;
 
+	private long countOfBitmapIndexMisses;
+
 	PackWriterBitmapWalker(
 			ObjectWalk walker, BitmapIndex bitmapIndex, ProgressMonitor pm) {
 		this.walker = walker;
@@ -78,6 +80,10 @@ final class PackWriterBitmapWalker {
 		this.pm = (pm == null) ? NullProgressMonitor.INSTANCE : pm;
 	}
 
+	long getCountOfBitmapIndexMisses() {
+		return countOfBitmapIndexMisses;
+	}
+
 	BitmapBuilder findObjects(Set<? extends ObjectId> start, BitmapBuilder seen, boolean ignoreMissingStart)
 			throws MissingObjectException, IncorrectObjectTypeException,
 			IOException {
@@ -104,7 +110,8 @@ final class PackWriterBitmapWalker {
 		}
 
 		if (marked) {
-			walker.setRevFilter(newRevFilter(seen, bitmapResult));
+			BitmapRevFilter filter = newRevFilter(seen, bitmapResult);
+			walker.setRevFilter(filter);
 
 			while (walker.next() != null) {
 				// Iterate through all of the commits. The BitmapRevFilter does
@@ -117,6 +124,7 @@ final class PackWriterBitmapWalker {
 				bitmapResult.add(ro, ro.getType());
 				pm.update(1);
 			}
+			countOfBitmapIndexMisses += filter.getCountOfLoadedCommits();
 		}
 
 		return bitmapResult;
@@ -126,7 +134,7 @@ final class PackWriterBitmapWalker {
 		walker.reset();
 	}
 
-	static RevFilter newRevFilter(
+	static BitmapRevFilter newRevFilter(
 			final BitmapBuilder seen, final BitmapBuilder bitmapResult) {
 		if (seen != null) {
 			return new BitmapRevFilter() {
@@ -146,12 +154,16 @@ final class PackWriterBitmapWalker {
 	}
 
 	static abstract class BitmapRevFilter extends RevFilter {
+		private long countOfLoadedCommits;
+
 		protected abstract boolean load(RevCommit cmit);
 
 		@Override
 		public final boolean include(RevWalk walker, RevCommit cmit) {
-			if (load(cmit))
+			if (load(cmit)) {
+				countOfLoadedCommits++;
 				return true;
+			}
 			for (RevCommit p : cmit.getParents())
 				p.add(RevFlag.SEEN);
 			return false;
@@ -166,5 +178,9 @@ final class PackWriterBitmapWalker {
 		public final boolean requiresCommitBody() {
 			return false;
 		}
+
+		long getCountOfLoadedCommits() {
+			return countOfLoadedCommits;
+		}
 	}
 }

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

@@ -565,14 +565,16 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 	 * based on other options. If insufficient information is available, an
 	 * exception is thrown to the caller.
 	 *
-	 * @return a repository matching this configuration.
+	 * @return a repository matching this configuration. The caller is
+	 *         responsible to close the repository instance when it is no longer
+	 *         needed.
 	 * @throws IllegalArgumentException
 	 *             insufficient parameters were set.
 	 * @throws IOException
 	 *             the repository could not be accessed to configure the rest of
 	 *             the builder's parameters.
 	 */
-	@SuppressWarnings("unchecked")
+	@SuppressWarnings({ "unchecked", "resource" })
 	public R build() throws IOException {
 		R repo = (R) new FileRepository(setup());
 		if (isMustExist() && !repo.getObjectDatabase().exists())

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

@@ -430,7 +430,5 @@ public abstract class ObjectReader implements AutoCloseable {
 	 * @since 4.0
 	 */
 	@Override
-	public void close() {
-		// Do nothing.
-	}
+	public abstract void close();
 }

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

@@ -159,6 +159,7 @@ public class RepositoryCache {
 			openLocks[i] = new Lock();
 	}
 
+	@SuppressWarnings("resource")
 	private Repository openRepository(final Key location,
 			final boolean mustExist) throws IOException {
 		Reference<Repository> ref = cacheMap.get(location);

org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeFormatter.java

@@ -102,7 +102,7 @@ public class MergeFormatter {
 	 *            metadata
 	 * @throws IOException
 	 */
-	public void formatMerge(OutputStream out, MergeResult res, String baseName,
+	public void formatMerge(OutputStream out, MergeResult<RawText> res, String baseName,
 			String oursName, String theirsName, String charsetName) throws IOException {
 		List<String> names = new ArrayList<String>(3);
 		names.add(baseName);

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

@@ -221,6 +221,7 @@ public class WindowCacheConfig {
 	 *
 	 * @since 3.0
 	 */
+	@SuppressWarnings("deprecation")
 	public void install() {
 		WindowCache.reconfigure(this);
 	}

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

@@ -55,6 +55,7 @@ import java.util.Set;
 import org.eclipse.jgit.errors.NoRemoteRepositoryException;
 import org.eclipse.jgit.errors.NotSupportedException;
 import org.eclipse.jgit.errors.PackProtocolException;
+import org.eclipse.jgit.errors.TooLargePackException;
 import org.eclipse.jgit.errors.TransportException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.internal.storage.pack.PackWriter;
@@ -314,6 +315,9 @@ public abstract class BasePackPushConnection extends BasePackConnection implemen
 		if (!unpackLine.startsWith("unpack ")) //$NON-NLS-1$
 			throw new PackProtocolException(uri, MessageFormat.format(JGitText.get().unexpectedReportLine, unpackLine));
 		final String unpackStatus = unpackLine.substring("unpack ".length()); //$NON-NLS-1$
+		if (unpackStatus.startsWith("error Pack exceeds the limit of")) //$NON-NLS-1$
+			throw new TooLargePackException(uri,
+					unpackStatus.substring("error ".length())); //$NON-NLS-1$
 		if (!unpackStatus.equals("ok")) //$NON-NLS-1$
 			throw new TransportException(uri, MessageFormat.format(
 					JGitText.get().errorOccurredDuringUnpackingOnTheRemoteEnd, unpackStatus));

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

@@ -1583,7 +1583,9 @@ public abstract class BaseReceivePack {
 		pckIn = null;
 		pckOut = null;
 		refs = null;
-		enabledCapabilities = null;
+		// Keep the capabilities. If responses are sent after this release
+		// we need to remember at least whether sideband communication has to be
+		// used
 		commands = null;
 		if (timer != null) {
 			try {

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

@@ -240,10 +240,16 @@ public class ReceivePack extends BaseReceivePack {
 				});
 			}
 
-			postReceive.onPostReceive(this, filterCommands(Result.OK));
-
-			if (unpackError != null)
+			if (unpackError != null) {
+				// we already know which exception to throw. Ignore
+				// potential additional exceptions raised in postReceiveHooks
+				try {
+					postReceive.onPostReceive(this, filterCommands(Result.OK));
+				} catch (Throwable e) {
+				}
 				throw new UnpackException(unpackError);
+			}
+			postReceive.onPostReceive(this, filterCommands(Result.OK));
 		}
 	}
 

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

@@ -227,6 +227,7 @@ public class TransportSftp extends SshTransport implements WalkTransport {
 		Collection<String> getPackNames() throws IOException {
 			final List<String> packs = new ArrayList<String>();
 			try {
+				@SuppressWarnings("unchecked")
 				final Collection<ChannelSftp.LsEntry> list = ftp.ls("pack"); //$NON-NLS-1$
 				final HashMap<String, ChannelSftp.LsEntry> files;
 				final HashMap<String, Integer> mtimes;

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

@@ -810,9 +810,9 @@ public class UploadPack {
 			adv.advertiseCapability(OPTION_ALLOW_TIP_SHA1_IN_WANT);
 		adv.advertiseCapability(OPTION_AGENT, UserAgent.get());
 		adv.setDerefTags(true);
-		Map<String, Ref> refs = getAdvertisedOrDefaultRefs();
-		findSymrefs(adv, refs);
-		advertised = adv.send(refs);
+		Map<String, Ref> advertisedOrDefaultRefs = getAdvertisedOrDefaultRefs();
+		findSymrefs(adv, advertisedOrDefaultRefs);
+		advertised = adv.send(advertisedOrDefaultRefs);
 		if (adv.isEmpty())
 			adv.advertiseId(ObjectId.zeroId(), "capabilities^{}"); //$NON-NLS-1$
 		adv.end();
@@ -1467,7 +1467,7 @@ public class UploadPack {
 			pckOut.end();
 	}
 
-	private void findSymrefs(
+	private static void findSymrefs(
 			final RefAdvertiser adv, final Map<String, Ref> refs) {
 		Ref head = refs.get(Constants.HEAD);
 		if (head != null && head.isSymbolic()) {

org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/IndexDiffFilter.java

@@ -224,7 +224,8 @@ public class IndexDiffFilter extends TreeFilter {
 		// Only one chance left to detect a diff: between index and working
 		// tree. Make use of the WorkingTreeIterator#isModified() method to
 		// avoid computing SHA1 on filesystem content if not really needed.
-		return wi.isModified(di.getDirCacheEntry(), true, tw.getObjectReader());
+		return wi.isModified(di == null ? null : di.getDirCacheEntry(), true,
+				tw.getObjectReader());
 	}
 
 	/**

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

@@ -440,40 +440,11 @@ public abstract class FS {
 			if (env != null) {
 				pb.environment().putAll(env);
 			}
-			final Process p = pb.start();
-			final BufferedReader lineRead = new BufferedReader(
+			Process p = pb.start();
+			BufferedReader lineRead = new BufferedReader(
 					new InputStreamReader(p.getInputStream(), encoding));
 			p.getOutputStream().close();
-			final AtomicBoolean gooblerFail = new AtomicBoolean(false);
-			Thread gobbler = new Thread() {
-				public void run() {
-					InputStream is = p.getErrorStream();
-					try {
-						int ch;
-						if (debug)
-							while ((ch = is.read()) != -1)
-								System.err.print((char) ch);
-						else
-							while (is.read() != -1) {
-								// ignore
-							}
-					} catch (IOException e) {
-						// Just print on stderr for debugging
-						if (debug)
-							e.printStackTrace(System.err);
-						gooblerFail.set(true);
-					}
-					try {
-						is.close();
-					} catch (IOException e) {
-						// Just print on stderr for debugging
-						if (debug) {
-							LOG.debug("Caught exception in gobbler thread", e); //$NON-NLS-1$
-						}
-						gooblerFail.set(true);
-					}
-				}
-			};
+			GobblerThread gobbler = new GobblerThread(p, command, dir);
 			gobbler.start();
 			String r = null;
 			try {
@@ -498,7 +469,7 @@ public abstract class FS {
 					int rc = p.waitFor();
 					gobbler.join();
 					if (rc == 0 && r != null && r.length() > 0
-							&& !gooblerFail.get())
+							&& !gobbler.fail.get())
 						return r;
 					if (debug) {
 						LOG.debug("readpipe rc=" + rc); //$NON-NLS-1$
@@ -517,6 +488,59 @@ public abstract class FS {
 		return null;
 	}
 
+	private static class GobblerThread extends Thread {
+		private final Process p;
+		private final String desc;
+		private final String dir;
+		private final boolean debug = LOG.isDebugEnabled();
+		private final AtomicBoolean fail = new AtomicBoolean();
+
+		private GobblerThread(Process p, String[] command, File dir) {
+			this.p = p;
+			if (debug) {
+				this.desc = Arrays.asList(command).toString();
+				this.dir = dir.toString();
+			} else {
+				this.desc = null;
+				this.dir = null;
+			}
+		}
+
+		public void run() {
+			InputStream is = p.getErrorStream();
+			try {
+				int ch;
+				if (debug) {
+					while ((ch = is.read()) != -1) {
+						System.err.print((char) ch);
+					}
+				} else {
+					while (is.read() != -1) {
+						// ignore
+					}
+				}
+			} catch (IOException e) {
+				logError(e);
+				fail.set(true);
+			}
+			try {
+				is.close();
+			} catch (IOException e) {
+				logError(e);
+				fail.set(true);
+			}
+		}
+
+		private void logError(Throwable t) {
+			if (!debug) {
+				return;
+			}
+			String msg = MessageFormat.format(
+					JGitText.get().exceptionCaughtDuringExcecutionOfCommand, desc, dir);
+			LOG.debug(msg, t);
+		}
+	}
+
 	/**
 	 * @return the path to the Git executable or {@code null} if it cannot be
 	 *         determined.

pom.xml

@@ -56,15 +56,25 @@
   <name>JGit - Parent</name>
   <url>${jgit-url}</url>
 
+  <organization>
+    <name>Eclipse JGit Project</name>
+    <url>http://www.eclipse.org/jgit</url>
+  </organization>
+
   <description>
     Pure Java implementation of Git
   </description>
 
   <scm>
-    <url>http://egit.eclipse.org/w/?p=jgit.git</url>
-    <connection>scm:git:git://egit.eclipse.org/jgit.git</connection>
+    <url>http://git.eclipse.org/c/jgit/jgit.git/</url>
+    <connection>scm:git:https://git.eclipse.org/r/jgit/jgit</connection>
   </scm>
 
+  <ciManagement>
+    <system>hudson</system>
+    <url>https://hudson.eclipse.org/jgit/</url>
+  </ciManagement>
+
   <developers>
     <developer>
       <name>Chris Aniszczyk</name>
@@ -81,6 +91,9 @@
     <developer>
       <name>Gunnar Wagenknecht</name>
     </developer>
+    <developer>
+      <name>Jonathan Nieder</name>
+    </developer>
     <developer>
       <name>Kevin Sawicki</name>
     </developer>
@@ -93,6 +106,9 @@
     <developer>
       <name>Robin Rosenberg</name>
     </developer>
+    <developer>
+      <name>Robin Stocker</name>
+    </developer>
     <developer>
       <name>Sasa Zivkov</name>
     </developer>
@@ -176,21 +192,22 @@
     <maven.build.timestamp.format>yyyyMMddHHmm</maven.build.timestamp.format>
     <bundle-manifest>${project.build.directory}/META-INF/MANIFEST.MF</bundle-manifest>
 
-    <jgit-last-release-version>3.6.0.201412230720-r</jgit-last-release-version>
-    <jsch-version>0.1.50</jsch-version>
+    <jgit-last-release-version>3.7.0.201502260915-r</jgit-last-release-version>
+    <jsch-version>0.1.51</jsch-version>
     <javaewah-version>0.7.9</javaewah-version>
     <junit-version>4.11</junit-version>
     <test-fork-count>1C</test-fork-count>
     <args4j-version>2.0.15</args4j-version>
     <commons-compress-version>1.6</commons-compress-version>
     <osgi-core-version>4.3.1</osgi-core-version>
-    <servlet-api-version>2.5</servlet-api-version>
+    <servlet-api-version>3.1.0</servlet-api-version>
     <jetty-version>9.2.10.v20150310</jetty-version>
     <clirr-version>2.6.1</clirr-version>
     <httpclient-version>4.1.3</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>0.22.0</tycho-extras-version>
 
     <!-- Properties to enable jacoco code coverage analysis -->
     <sonar.core.codeCoveragePlugin>jacoco</sonar.core.codeCoveragePlugin>
@@ -355,12 +372,12 @@
         <plugin>
           <groupId>org.eclipse.tycho.extras</groupId>
           <artifactId>tycho-pack200a-plugin</artifactId>
-          <version>0.22.0</version>
+          <version>${tycho-extras-version}</version>
         </plugin>
         <plugin>
           <groupId>org.eclipse.tycho.extras</groupId>
           <artifactId>tycho-pack200b-plugin</artifactId>
-          <version>0.22.0</version>
+          <version>${tycho-extras-version}</version>
         </plugin>
         <plugin>
           <groupId>org.jacoco</groupId>
@@ -379,6 +396,21 @@
             </dependency>
           </dependencies>
         </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-surefire-report-plugin</artifactId>
+          <version>2.18.1</version>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-jxr-plugin</artifactId>
+          <version>2.5</version>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-project-info-reports-plugin</artifactId>
+          <version>2.8</version>
+        </plugin>
       </plugins>
     </pluginManagement>
 
@@ -478,6 +510,10 @@
           </execution>
         </executions>
       </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-surefire-report-plugin</artifactId>
+      </plugin>
     </plugins>
   </build>
 
@@ -490,6 +526,29 @@
         <configuration>
         </configuration>
       </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-jxr-plugin</artifactId>
+      </plugin>
+      <plugin>
+        <groupId>org.codehaus.mojo</groupId>
+        <artifactId>clirr-maven-plugin</artifactId>
+      </plugin>
+      <plugin>
+        <groupId>org.codehaus.mojo</groupId>
+        <artifactId>findbugs-maven-plugin</artifactId>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-surefire-report-plugin</artifactId>
+        <configuration>
+          <aggregate>true</aggregate>
+          <alwaysGenerateSurefireReport>false</alwaysGenerateSurefireReport>
+          <reportsDirectories>
+            <reportsDirectories>${project.build.directory}/surefire-reports</reportsDirectories>
+          </reportsDirectories>
+        </configuration>
+      </plugin>
     </plugins>
   </reporting>
 
@@ -521,7 +580,7 @@
 
       <dependency>
         <groupId>javax.servlet</groupId>
-        <artifactId>servlet-api</artifactId>
+        <artifactId>javax.servlet-api</artifactId>
         <version>${servlet-api-version}</version>
       </dependency>