Merge branch 'master' into stable-5.0

* master:
  DescribeCommand: Refactor to not use deprecated Repository#peel
  Repository: Deprecate #peel method
  Repository: Make #exactRef and #findRef final
  Skip ignored directories in FileTreeIterator
  Repository: Deprecate getTags method
  InfoRefsServlet: Refactor to not use deprecated methods
  RefAdvertiser: Add send(Collection<Ref>) and deprecate send(Map<String, Ref>)
  Remove deprecated Repository#notifyIndexChanged
  Implementors should override Repository#notifyIndexChanged(boolean)
  Revive Repository#notifyIndexChanged()
  Remove further unnecessary 'final' keywords
  Execute AdvertiseRefsHook only for protocol v0 and v1
  Add protocol v2 support in "jgit daemon"
  Teach UploadPack "ofs-delta" in "fetch"
  Teach UploadPack "include-tag" in "fetch"
  Avoid using #refs in UploadPack#sendPack
  FileRepository: Don't use deprecated RefDatabase#getRefs(String)
  BatchRefUpdate: Don't use deprecated RefDatabase#getRefs(String)

Change-Id: I16c5da62d09262d3f4070aa0f466dd6c8352b5ea
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/AsIsFileFilter.java

@@ -66,7 +66,7 @@ import org.eclipse.jgit.transport.resolver.ServiceNotEnabledException;
 class AsIsFileFilter implements Filter {
 	private final AsIsFileService asIs;
 
-	AsIsFileFilter(final AsIsFileService getAnyFile) {
+	AsIsFileFilter(AsIsFileService getAnyFile) {
 		this.asIs = getAnyFile;
 	}
 

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/FileSender.java

@@ -84,7 +84,7 @@ final class FileSender {
 
 	private long end;
 
-	FileSender(final File path) throws FileNotFoundException {
+	FileSender(File path) throws FileNotFoundException {
 		this.path = path;
 		this.source = new RandomAccessFile(path, "r");
 

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/InfoRefsServlet.java

@@ -44,18 +44,15 @@
 package org.eclipse.jgit.http.server;
 
 import static org.eclipse.jgit.http.server.ServletUtils.getRepository;
-import static org.eclipse.jgit.lib.RefDatabase.ALL;
 
 import java.io.IOException;
 import java.io.OutputStreamWriter;
-import java.util.Map;
 
 import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.eclipse.jgit.lib.Constants;
-import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.transport.RefAdvertiser;
 import org.eclipse.jgit.util.HttpSupport;
@@ -94,10 +91,7 @@ class InfoRefsServlet extends HttpServlet {
 			};
 			adv.init(db);
 			adv.setDerefTags(true);
-
-			Map<String, Ref> refs = db.getRefDatabase().getRefs(ALL);
-			refs.remove(Constants.HEAD);
-			adv.send(refs);
+			adv.send(db.getRefDatabase().getRefsByPrefix(Constants.R_REFS));
 		}
 	}
 }

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ObjectFileServlet.java

@@ -75,7 +75,7 @@ abstract class ObjectFileServlet extends HttpServlet {
 		}
 
 		@Override
-		String etag(final FileSender sender) throws IOException {
+		String etag(FileSender sender) throws IOException {
 			return Long.toHexString(sender.getLastModified());
 		}
 	}
@@ -88,7 +88,7 @@ abstract class ObjectFileServlet extends HttpServlet {
 		}
 
 		@Override
-		String etag(final FileSender sender) throws IOException {
+		String etag(FileSender sender) throws IOException {
 			return sender.getTailChecksum();
 		}
 	}
@@ -111,7 +111,7 @@ abstract class ObjectFileServlet extends HttpServlet {
 
 	private final String contentType;
 
-	ObjectFileServlet(final String contentType) {
+	ObjectFileServlet(String contentType) {
 		this.contentType = contentType;
 	}
 

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ServletUtils.java

@@ -238,7 +238,7 @@ public final class ServletUtils {
 		return content;
 	}
 
-	static boolean acceptsGzipEncoding(final HttpServletRequest req) {
+	static boolean acceptsGzipEncoding(HttpServletRequest req) {
 		return acceptsGzipEncoding(req.getHeader(HDR_ACCEPT_ENCODING));
 	}
 

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/SmartServiceInfoRefs.java

@@ -75,7 +75,7 @@ abstract class SmartServiceInfoRefs implements Filter {
 
 	private final Filter[] filters;
 
-	SmartServiceInfoRefs(final String service, final List<Filter> filters) {
+	SmartServiceInfoRefs(String service, List<Filter> filters) {
 		this.svc = service;
 		this.filters = filters.toArray(new Filter[filters.size()]);
 	}

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/TextFileServlet.java

@@ -64,7 +64,7 @@ class TextFileServlet extends HttpServlet {
 
 	private final String fileName;
 
-	TextFileServlet(final String name) {
+	TextFileServlet(String name) {
 		this.fileName = name;
 	}
 

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/glue/RegexPipeline.java

@@ -87,11 +87,11 @@ class RegexPipeline extends UrlPipeline {
 	static class Binder extends ServletBinderImpl {
 		private final Pattern pattern;
 
-		Binder(final String p) {
+		Binder(String p) {
 			pattern = Pattern.compile(p);
 		}
 
-		Binder(final Pattern p) {
+		Binder(Pattern p) {
 			pattern = p;
 		}
 
@@ -110,7 +110,7 @@ class RegexPipeline extends UrlPipeline {
 	}
 
 	@Override
-	boolean match(final HttpServletRequest req) {
+	boolean match(HttpServletRequest req) {
 		final String pathInfo = req.getPathInfo();
 		return pathInfo != null && pattern.matcher(pathInfo).matches();
 	}

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/glue/SuffixPipeline.java

@@ -67,7 +67,7 @@ class SuffixPipeline extends UrlPipeline {
 	static class Binder extends ServletBinderImpl {
 		private final String suffix;
 
-		Binder(final String suffix) {
+		Binder(String suffix) {
 			this.suffix = suffix;
 		}
 
@@ -89,7 +89,7 @@ class SuffixPipeline extends UrlPipeline {
 	}
 
 	@Override
-	boolean match(final HttpServletRequest req) {
+	boolean match(HttpServletRequest req) {
 		final String pathInfo = req.getPathInfo();
 		return pathInfo != null && pathInfo.endsWith(suffix);
 	}

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/glue/UrlPipeline.java

@@ -79,7 +79,7 @@ abstract class UrlPipeline {
 	/** Instance that must generate the response; never null. */
 	private final HttpServlet servlet;
 
-	UrlPipeline(final Filter[] filters, final HttpServlet servlet) {
+	UrlPipeline(Filter[] filters, HttpServlet servlet) {
 		this.filters = filters;
 		this.servlet = servlet;
 	}
@@ -99,7 +99,7 @@ abstract class UrlPipeline {
 	 * @throws ServletException
 	 *             a filter or servlet is unable to initialize.
 	 */
-	void init(final ServletContext context, final Set<Object> inited)
+	void init(ServletContext context, Set<Object> inited)
 			throws ServletException {
 		for (Filter ref : filters)
 			initFilter(ref, context, inited);
@@ -165,7 +165,7 @@ abstract class UrlPipeline {
 	 *            destroyed a second time. Filters and servlets that are first
 	 *            destroyed by this pipeline will be added to this set.
 	 */
-	void destroy(final Set<Object> destroyed) {
+	void destroy(Set<Object> destroyed) {
 		for (Filter ref : filters)
 			destroyFilter(ref, destroyed);
 		destroyServlet(servlet, destroyed);
@@ -230,7 +230,7 @@ abstract class UrlPipeline {
 
 		private int filterIdx;
 
-		Chain(final Filter[] filters, final HttpServlet servlet) {
+		Chain(Filter[] filters, HttpServlet servlet) {
 			this.filters = filters;
 			this.servlet = servlet;
 		}

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/AsIsFileService.java

@@ -73,7 +73,7 @@ public class AsIsFileService {
 	private static class ServiceConfig {
 		final boolean enabled;
 
-		ServiceConfig(final Config cfg) {
+		ServiceConfig(Config cfg) {
 			enabled = cfg.getBoolean("http", "getanyfile", true);
 		}
 	}

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/DefaultReceivePackFactory.java

@@ -74,7 +74,7 @@ public class DefaultReceivePackFactory implements
 
 		final boolean enabled;
 
-		ServiceConfig(final Config cfg) {
+		ServiceConfig(Config cfg) {
 			set = cfg.getString("http", null, "receivepack") != null;
 			enabled = cfg.getBoolean("http", "receivepack", false);
 		}

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/resolver/DefaultUploadPackFactory.java

@@ -64,7 +64,7 @@ public class DefaultUploadPackFactory implements
 	private static class ServiceConfig {
 		final boolean enabled;
 
-		ServiceConfig(final Config cfg) {
+		ServiceConfig(Config cfg) {
 			enabled = cfg.getBoolean("http", "uploadpack", true);
 		}
 	}

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

@@ -133,7 +133,7 @@ public class AsIsServiceTest extends LocalDiskRepositoryTestCase {
 
 		private final String host;
 
-		R(final String user, final String host) {
+		R(String user, String host) {
 			super(new Request(null, null) /* can't pass null, sigh */);
 			this.user = user;
 			this.host = host;

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

@@ -205,7 +205,7 @@ public class DefaultReceivePackFactoryTest extends LocalDiskRepositoryTestCase {
 
 		private final String host;
 
-		R(final String user, final String host) {
+		R(String user, String host) {
 			super(new Request(null, null) /* can't pass null, sigh */);
 			this.user = user;
 			this.host = host;

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

@@ -161,7 +161,7 @@ public class DefaultUploadPackFactoryTest extends LocalDiskRepositoryTestCase {
 
 		private final String host;
 
-		R(final String user, final String host) {
+		R(String user, String host) {
 			super(new Request(null, null) /* can't pass null, sigh */);
 			this.user = user;
 			this.host = host;

org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/AccessEvent.java

@@ -67,7 +67,7 @@ public class AccessEvent {
 
 	private final Map<String, String> responseHeaders;
 
-	AccessEvent(final Request req, final Response rsp) {
+	AccessEvent(Request req, Response rsp) {
 		method = req.getMethod();
 		uri = req.getRequestURI();
 		requestHeaders = cloneHeaders(req);

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

@@ -318,7 +318,7 @@ public class TestRepository<R extends Repository> {
 	public RevTree tree(DirCacheEntry... entries) throws Exception {
 		final DirCache dc = DirCache.newInCore();
 		final DirCacheBuilder b = dc.builder();
-		for (final DirCacheEntry e : entries)
+		for (DirCacheEntry e : entries)
 			b.add(e);
 		b.finish();
 		ObjectId root;
@@ -962,7 +962,7 @@ public class TestRepository<R extends Repository> {
 	public class BranchBuilder {
 		private final String ref;
 
-		BranchBuilder(final String ref) {
+		BranchBuilder(String ref) {
 			this.ref = ref;
 		}
 

org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/UploadTest.java

@@ -122,7 +122,7 @@ public class UploadTest extends LfsServerTest {
 
 		ExecutorService e = Executors.newFixedThreadPool(count);
 		try {
-			for (final Path p : paths) {
+			for (Path p : paths) {
 				e.submit(new Callable<Void>() {
 					@Override
 					public Void call() throws Exception {

org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/AbbreviatedLongObjectId.java

@@ -173,7 +173,7 @@ public final class AbbreviatedLongObjectId implements Serializable {
 		return r << (16 - n) * 4;
 	}
 
-	static long mask(final int nibbles, final long word, final long v) {
+	static long mask(int nibbles, long word, long v) {
 		final long b = (word - 1) * 16;
 		if (b + 16 <= nibbles) {
 			// We have all of the bits required for this word.

org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/AnyLongObjectId.java

@@ -476,7 +476,7 @@ public abstract class AnyLongObjectId implements Comparable<AnyLongObjectId> {
 	private static final char[] hexchar = { '0', '1', '2', '3', '4', '5', '6',
 			'7', '8', '9', 'a', 'b', 'c', 'd', 'e', 'f' };
 
-	static void formatHexChar(final char[] dst, final int p, long w) {
+	static void formatHexChar(char[] dst, int p, long w) {
 		int o = p + 15;
 		while (o >= p && w != 0) {
 			dst[o--] = hexchar[(int) (w & 0xf)];

org.eclipse.jgit.pgm.test/src/org/eclipse/jgit/pgm/CLIGitCommand.java

@@ -157,7 +157,7 @@ public class CLIGitCommand extends Main {
 	}
 
 	@Override
-	void init(final TextBuiltin cmd) throws IOException {
+	void init(TextBuiltin cmd) throws IOException {
 		cmd.outs = result.out;
 		cmd.errs = result.err;
 		super.init(cmd);

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

@@ -43,10 +43,11 @@
 package org.eclipse.jgit.pgm;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.lib.CLIRepositoryTestCase;
-import org.eclipse.jgit.lib.Ref;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -75,13 +76,9 @@ public class TagTest extends CLIRepositoryTestCase {
 	@Test
 	public void testTagDelete() throws Exception {
 		git.tag().setName("test").call();
-
-		Ref ref = git.getRepository().getTags().get("test");
-		assertEquals("refs/tags/test", ref.getName());
-
+		assertNotNull(git.getRepository().exactRef("refs/tags/test"));
 		assertEquals("", executeUnchecked("git tag -d test")[0]);
-		Ref deletedRef = git.getRepository().getTags().get("test");
-		assertEquals(null, deletedRef);
+		assertNull(git.getRepository().exactRef("refs/tags/test"));
 	}
 
 	@Test

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

@@ -77,7 +77,7 @@ abstract class AbstractFetchCommand extends TextBuiltin {
 	protected void showFetchResult(FetchResult r) throws IOException {
 		try (ObjectReader reader = db.newObjectReader()) {
 			boolean shownURI = false;
-			for (final TrackingRefUpdate u : r.getTrackingRefUpdates()) {
+			for (TrackingRefUpdate u : r.getTrackingRefUpdates()) {
 				if (!verbose && u.getResult() == RefUpdate.Result.NO_CHANGE)
 					continue;
 

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/AmazonS3Client.java

@@ -105,7 +105,7 @@ class AmazonS3Client extends TextBuiltin {
 			}
 
 		} else if ("ls".equals(op) || "list".equals(op)) { //$NON-NLS-1$//$NON-NLS-2$
-			for (final String k : s3.list(bucket, key))
+			for (String k : s3.list(bucket, key))
 				outw.println(k);
 
 		} else if ("rm".equals(op) || "delete".equals(op)) { //$NON-NLS-1$ //$NON-NLS-2$

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

@@ -292,7 +292,7 @@ class Branch extends TextBuiltin {
 				addRefs(refs, Constants.R_REMOTES);
 
 				try (ObjectReader reader = db.newObjectReader()) {
-					for (final Entry<String, Ref> e : printRefs.entrySet()) {
+					for (Entry<String, Ref> e : printRefs.entrySet()) {
 						final Ref ref = e.getValue();
 						printHead(reader, e.getKey(),
 								current.equals(ref.getName()), ref);
@@ -303,7 +303,7 @@ class Branch extends TextBuiltin {
 	}
 
 	private void addRefs(Collection<Ref> refs, String prefix) {
-		for (final Ref ref : RefComparator.sort(refs)) {
+		for (Ref ref : RefComparator.sort(refs)) {
 			final String name = ref.getName();
 			if (name.startsWith(prefix))
 				addRef(name.substring(name.indexOf('/', 5) + 1), ref);

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

@@ -107,7 +107,7 @@ public class CommandCatalog {
 	 */
 	public static CommandRef[] common() {
 		final ArrayList<CommandRef> common = new ArrayList<>();
-		for (final CommandRef c : INSTANCE.commands.values())
+		for (CommandRef c : INSTANCE.commands.values())
 			if (c.isCommon())
 				common.add(c);
 		return toSortedArray(common);

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

@@ -66,11 +66,11 @@ public class CommandRef {
 
 	boolean common;
 
-	CommandRef(final Class<? extends TextBuiltin> clazz) {
+	CommandRef(Class<? extends TextBuiltin> clazz) {
 		this(clazz, guessName(clazz));
 	}
 
-	CommandRef(final Class<? extends TextBuiltin> clazz, final Command cmd) {
+	CommandRef(Class<? extends TextBuiltin> clazz, Command cmd) {
 		this(clazz, cmd.name().length() > 0 ? cmd.name() : guessName(clazz));
 		usage = cmd.usage();
 		common = cmd.common();
@@ -88,7 +88,7 @@ public class CommandRef {
 			s.append("debug-"); //$NON-NLS-1$
 
 		boolean lastWasDash = true;
-		for (final char c : clazz.getSimpleName().toCharArray()) {
+		for (char c : clazz.getSimpleName().toCharArray()) {
 			if (Character.isUpperCase(c)) {
 				if (!lastWasDash)
 					s.append('-');

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

@@ -142,7 +142,7 @@ class Daemon extends TextBuiltin {
 			packConfig.setExecutor(Executors.newFixedThreadPool(threads));
 
 		final FileResolver<DaemonClient> resolver = new FileResolver<>();
-		for (final File f : directory) {
+		for (File f : directory) {
 			outw.println(MessageFormat.format(CLIText.get().exporting, f.getAbsolutePath()));
 			resolver.exportDirectory(f);
 		}
@@ -157,14 +157,14 @@ class Daemon extends TextBuiltin {
 		if (0 <= timeout)
 			d.setTimeout(timeout);
 
-		for (final String n : enable)
+		for (String n : enable)
 			service(d, n).setEnabled(true);
-		for (final String n : disable)
+		for (String n : disable)
 			service(d, n).setEnabled(false);
 
-		for (final String n : canOverride)
+		for (String n : canOverride)
 			service(d, n).setOverridable(true);
-		for (final String n : forbidOverride)
+		for (String n : forbidOverride)
 			service(d, n).setOverridable(false);
 		if (ketchServerType == KetchServerType.LEADER) {
 			startKetchLeader(d);

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

@@ -75,9 +75,9 @@ class DiffTree extends TextBuiltin {
 	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
-		try (final TreeWalk walk = new TreeWalk(db)) {
+		try (TreeWalk walk = new TreeWalk(db)) {
 			walk.setRecursive(recursive);
-			for (final AbstractTreeIterator i : trees)
+			for (AbstractTreeIterator i : trees)
 				walk.addTree(i);
 			walk.setFilter(AndTreeFilter.create(TreeFilter.ANY_DIFF, pathFilter));
 

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

@@ -266,7 +266,7 @@ class Log extends RevWalkTextBuiltin {
 
 		outw.println();
 		final String[] lines = c.getFullMessage().split("\n"); //$NON-NLS-1$
-		for (final String s : lines) {
+		for (String s : lines) {
 			outw.print("    "); //$NON-NLS-1$
 			outw.print(s);
 			outw.println();

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

@@ -83,7 +83,7 @@ class LsRemote extends TextBuiltin {
 			}
 		});
 		refs.addAll(command.call());
-		for (final Ref r : refs) {
+		for (Ref r : refs) {
 			show(r.getObjectId(), r.getName());
 			if (r.getPeeledObjectId() != null)
 				show(r.getPeeledObjectId(), r.getName() + "^{}"); //$NON-NLS-1$

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

@@ -73,7 +73,7 @@ class LsTree extends TextBuiltin {
 	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
-		try (final TreeWalk walk = new TreeWalk(db)) {
+		try (TreeWalk walk = new TreeWalk(db)) {
 			walk.reset(); // drop the first empty tree, which we do not need here
 			if (paths.size() > 0)
 				walk.setFilter(PathFilterGroup.createFromStrings(paths));

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

@@ -256,12 +256,12 @@ public class Main {
 				writer.println(CLIText.get().mostCommonlyUsedCommandsAre);
 				final CommandRef[] common = CommandCatalog.common();
 				int width = 0;
-				for (final CommandRef c : common) {
+				for (CommandRef c : common) {
 					width = Math.max(width, c.getName().length());
 				}
 				width += 2;
 
-				for (final CommandRef c : common) {
+				for (CommandRef c : common) {
 					writer.print(' ');
 					writer.print(c.getName());
 					for (int i = c.getName().length(); i < width; i++) {
@@ -296,7 +296,7 @@ public class Main {
 		}
 	}
 
-	void init(final TextBuiltin cmd) throws IOException {
+	void init(TextBuiltin cmd) throws IOException {
 		if (cmd.requiresRepository()) {
 			cmd.init(openGitDir(gitdir), null);
 		} else {

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

@@ -68,7 +68,7 @@ class MergeBase extends TextBuiltin {
 	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
-		for (final RevCommit c : commits)
+		for (RevCommit c : commits)
 			argWalk.markStart(c);
 		argWalk.setRevFilter(RevFilter.MERGE_BASE);
 		int max = all ? Integer.MAX_VALUE : 1;

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

@@ -149,7 +149,7 @@ class Push extends TextBuiltin {
 		boolean everythingUpToDate = true;
 
 		// at first, print up-to-date ones...
-		for (final RemoteRefUpdate rru : result.getRemoteUpdates()) {
+		for (RemoteRefUpdate rru : result.getRemoteUpdates()) {
 			if (rru.getStatus() == Status.UP_TO_DATE) {
 				if (verbose)
 					printRefUpdateResult(reader, uri, result, rru);
@@ -157,13 +157,13 @@ class Push extends TextBuiltin {
 				everythingUpToDate = false;
 		}
 
-		for (final RemoteRefUpdate rru : result.getRemoteUpdates()) {
+		for (RemoteRefUpdate rru : result.getRemoteUpdates()) {
 			// ...then successful updates...
 			if (rru.getStatus() == Status.OK)
 				printRefUpdateResult(reader, uri, result, rru);
 		}
 
-		for (final RemoteRefUpdate rru : result.getRemoteUpdates()) {
+		for (RemoteRefUpdate rru : result.getRemoteUpdates()) {
 			// ...finally, others (problematic)
 			if (rru.getStatus() != Status.OK
 					&& rru.getStatus() != Status.UP_TO_DATE)

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

@@ -87,7 +87,7 @@ class RevParse extends TextBuiltin {
 						CLIText.format(CLIText.get().needSingleRevision));
 			}
 
-			for (final ObjectId o : commits) {
+			for (ObjectId o : commits) {
 				outw.println(o.name());
 			}
 		}

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

@@ -99,22 +99,22 @@ abstract class RevWalkTextBuiltin extends TextBuiltin {
 	}
 
 	@Option(name = "--date-order")
-	void enableDateOrder(final boolean on) {
+	void enableDateOrder(boolean on) {
 		enableRevSort(RevSort.COMMIT_TIME_DESC, on);
 	}
 
 	@Option(name = "--topo-order")
-	void enableTopoOrder(final boolean on) {
+	void enableTopoOrder(boolean on) {
 		enableRevSort(RevSort.TOPO, on);
 	}
 
 	@Option(name = "--reverse")
-	void enableReverse(final boolean on) {
+	void enableReverse(boolean on) {
 		enableRevSort(RevSort.REVERSE, on);
 	}
 
 	@Option(name = "--boundary")
-	void enableBoundary(final boolean on) {
+	void enableBoundary(boolean on) {
 		enableRevSort(RevSort.BOUNDARY, on);
 	}
 
@@ -130,17 +130,17 @@ abstract class RevWalkTextBuiltin extends TextBuiltin {
 	private final List<RevFilter> revLimiter = new ArrayList<>();
 
 	@Option(name = "--author")
-	void addAuthorRevFilter(final String who) {
+	void addAuthorRevFilter(String who) {
 		revLimiter.add(AuthorRevFilter.create(who));
 	}
 
 	@Option(name = "--committer")
-	void addCommitterRevFilter(final String who) {
+	void addCommitterRevFilter(String who) {
 		revLimiter.add(CommitterRevFilter.create(who));
 	}
 
 	@Option(name = "--grep")
-	void addCMessageRevFilter(final String msg) {
+	void addCMessageRevFilter(String msg) {
 		revLimiter.add(MessageRevFilter.create(msg));
 	}
 
@@ -151,7 +151,7 @@ abstract class RevWalkTextBuiltin extends TextBuiltin {
 	@Override
 	protected void run() throws Exception {
 		walk = createWalk();
-		for (final RevSort s : sorting)
+		for (RevSort s : sorting)
 			walk.sort(s, true);
 
 		if (pathFilter == TreeFilter.ALL) {
@@ -187,7 +187,7 @@ abstract class RevWalkTextBuiltin extends TextBuiltin {
 				throw die(MessageFormat.format(CLIText.get().cannotResolve, Constants.HEAD));
 			commits.add(walk.parseCommit(head));
 		}
-		for (final RevCommit c : commits) {
+		for (RevCommit c : commits) {
 			final RevCommit real = argWalk == walk ? c : walk.parseCommit(c);
 			if (c.has(RevFlag.UNINTERESTING))
 				walk.markUninteresting(real);
@@ -233,7 +233,7 @@ abstract class RevWalkTextBuiltin extends TextBuiltin {
 	 */
 	protected int walkLoop() throws Exception {
 		int n = 0;
-		for (final RevCommit c : walk) {
+		for (RevCommit c : walk) {
 			if (++n > maxCount && maxCount >= 0)
 				break;
 			show(c);

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

@@ -248,7 +248,7 @@ class Show extends TextBuiltin {
 
 		outw.println();
 		final String[] lines = tag.getFullMessage().split("\n"); //$NON-NLS-1$
-		for (final String s : lines) {
+		for (String s : lines) {
 			outw.print("    "); //$NON-NLS-1$
 			outw.print(s);
 			outw.println();
@@ -259,7 +259,7 @@ class Show extends TextBuiltin {
 
 	private void show(RevTree obj) throws MissingObjectException,
 			IncorrectObjectTypeException, CorruptObjectException, IOException {
-		try (final TreeWalk walk = new TreeWalk(db)) {
+		try (TreeWalk walk = new TreeWalk(db)) {
 			walk.reset();
 			walk.addTree(obj);
 
@@ -292,7 +292,7 @@ class Show extends TextBuiltin {
 
 		outw.println();
 		final String[] lines = c.getFullMessage().split("\n"); //$NON-NLS-1$
-		for (final String s : lines) {
+		for (String s : lines) {
 			outw.print("    "); //$NON-NLS-1$
 			outw.print(s);
 			outw.println();

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

@@ -57,7 +57,7 @@ class ShowRef extends TextBuiltin {
 	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
-		for (final Ref r : getSortedRefs()) {
+		for (Ref r : getSortedRefs()) {
 			show(r.getObjectId(), r.getName());
 			if (r.getPeeledObjectId() != null)
 				show(r.getPeeledObjectId(), r.getName() + "^{}"); //$NON-NLS-1$

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

@@ -129,7 +129,7 @@ public abstract class TextBuiltin {
 	/** RevWalk used during command line parsing, if it was required. */
 	protected RevWalk argWalk;
 
-	final void setCommandName(final String name) {
+	final void setCommandName(String name) {
 		commandName = name;
 	}
 
@@ -361,7 +361,7 @@ public abstract class TextBuiltin {
 		return db;
 	}
 
-	ObjectId resolve(final String s) throws IOException {
+	ObjectId resolve(String s) throws IOException {
 		final ObjectId r = db.resolve(s);
 		if (r == null)
 			throw die(MessageFormat.format(CLIText.get().notARevision, s));

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java

@@ -222,7 +222,7 @@ class RebuildCommitGraph extends TextBuiltin {
 
 		ObjectId newId;
 
-		ToRewrite(final ObjectId o, final long t, final ObjectId[] p) {
+		ToRewrite(ObjectId o, long t, ObjectId[] p) {
 			oldId = o;
 			commitTime = t;
 			oldParents = p;

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java

@@ -161,7 +161,7 @@ class RebuildRefTree extends TextBuiltin {
 			}
 			cmds.add(new org.eclipse.jgit.internal.storage.reftree.Command(
 					null,
-					db.peel(r)));
+					db.getRefDatabase().peel(r)));
 		}
 		tree.apply(cmds);
 		return tree;

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowCommands.java

@@ -65,11 +65,11 @@ class ShowCommands extends TextBuiltin {
 		final CommandRef[] list = CommandCatalog.all();
 
 		int width = 0;
-		for (final CommandRef c : list)
+		for (CommandRef c : list)
 			width = Math.max(width, c.getName().length());
 		width += 2;
 
-		for (final CommandRef c : list) {
+		for (CommandRef c : list) {
 			errw.print(c.isCommon() ? '*' : ' ');
 			errw.print(' ');
 
@@ -87,7 +87,7 @@ class ShowCommands extends TextBuiltin {
 		/** */
 		USAGE {
 			@Override
-			void print(ThrowingPrintWriter err, final CommandRef c) throws IOException {
+			void print(ThrowingPrintWriter err, CommandRef c) throws IOException {
 				String usage = c.getUsage();
 				if (usage != null && usage.length() > 0)
 					err.print(CLIText.get().resourceBundle().getString(usage));
@@ -97,7 +97,7 @@ class ShowCommands extends TextBuiltin {
 		/** */
 		CLASSES {
 			@Override
-			void print(ThrowingPrintWriter err, final CommandRef c) throws IOException {
+			void print(ThrowingPrintWriter err, CommandRef c) throws IOException {
 				err.print(c.getImplementationClassName());
 			}
 		},
@@ -105,7 +105,7 @@ class ShowCommands extends TextBuiltin {
 		/** */
 		URLS {
 			@Override
-			void print(ThrowingPrintWriter err, final CommandRef c) throws IOException {
+			void print(ThrowingPrintWriter err, CommandRef c) throws IOException {
 				final ClassLoader ldr = c.getImplementationClassLoader();
 
 				String cn = c.getImplementationClassName();

org.eclipse.jgit.test/exttst/org/eclipse/jgit/patch/EGitPatchHistoryTest.java

@@ -85,7 +85,7 @@ public class EGitPatchHistoryTest {
 
 		int errors;
 
-		PatchReader(final HashMap<String, HashMap<String, StatInfo>> s)
+		PatchReader(HashMap<String, HashMap<String, StatInfo>> s)
 				throws IOException {
 			super(new String[] { "-p" });
 			stats = s;
@@ -103,7 +103,7 @@ public class EGitPatchHistoryTest {
 			p.parse(buf, 0, buf.length - 1);
 			assertEquals("File count " + cid, files.size(), p.getFiles().size());
 			if (!p.getErrors().isEmpty()) {
-				for (final FormatError e : p.getErrors()) {
+				for (FormatError e : p.getErrors()) {
 					System.out.println("error " + e.getMessage());
 					System.out.println("  at " + e.getLineText());
 				}
@@ -111,7 +111,7 @@ public class EGitPatchHistoryTest {
 				fail("Unexpected error in " + cid);
 			}
 
-			for (final FileHeader fh : p.getFiles()) {
+			for (FileHeader fh : p.getFiles()) {
 				final String fileName;
 				if (fh.getChangeType() != FileHeader.ChangeType.DELETE)
 					fileName = fh.getNewPath();
@@ -121,7 +121,7 @@ public class EGitPatchHistoryTest {
 				final String nid = fileName + " in " + cid;
 				assertNotNull("No " + nid, s);
 				int added = 0, deleted = 0;
-				for (final HunkHeader h : fh.getHunks()) {
+				for (HunkHeader h : fh.getHunks()) {
 					added += h.getOldImage().getLinesAdded();
 					deleted += h.getOldImage().getLinesDeleted();
 				}
@@ -188,7 +188,7 @@ public class EGitPatchHistoryTest {
 	static abstract class CommitReader {
 		private Process proc;
 
-		CommitReader(final String[] args) throws IOException {
+		CommitReader(String[] args) throws IOException {
 			final String[] realArgs = new String[3 + args.length + 1];
 			realArgs[0] = "git";
 			realArgs[1] = "log";

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

@@ -1289,7 +1289,7 @@ public class CommitOnlyTest extends RepositoryTestCase {
 		return null;
 	}
 
-	static private String getHead(final Git git, final String path)
+	static private String getHead(Git git, String path)
 			throws Exception {
 		try {
 			final Repository repo = git.getRepository();

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

@@ -116,7 +116,7 @@ public class LogCommandTest extends RepositoryTestCase {
 		Iterator<RevCommit> log = git.log().all().call().iterator();
 		assertTrue(log.hasNext());
 		RevCommit commit = log.next();
-		tag = db.peel(tag);
+		tag = db.getRefDatabase().peel(tag);
 
 		assertEquals(commit.getName(), tag.getPeeledObjectId().getName());
 		assertTrue(commits.contains(commit));

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

@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.api;
 
+import static org.eclipse.jgit.lib.Constants.R_TAGS;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.fail;
 
@@ -66,19 +67,22 @@ public class TagCommandTest extends RepositoryTestCase {
 				RevWalk walk = new RevWalk(db)) {
 			RevCommit commit = git.commit().setMessage("initial commit").call();
 			Ref tagRef = git.tag().setName("tag").call();
-			assertEquals(commit.getId(), db.peel(tagRef).getPeeledObjectId());
+			assertEquals(commit.getId(),
+					db.getRefDatabase().peel(tagRef).getPeeledObjectId());
 			assertEquals("tag", walk.parseTag(tagRef.getObjectId()).getTagName());
 		}
 	}
 
 	@Test
-	public void testTagging() throws GitAPIException, JGitInternalException {
+	public void testTagging()
+			throws GitAPIException, JGitInternalException, IOException {
 		try (Git git = new Git(db)) {
 			git.commit().setMessage("initial commit").call();
 			RevCommit commit = git.commit().setMessage("second commit").call();
 			git.commit().setMessage("third commit").call();
 			Ref tagRef = git.tag().setObjectId(commit).setName("tag").call();
-			assertEquals(commit.getId(), db.peel(tagRef).getPeeledObjectId());
+			assertEquals(commit.getId(),
+					db.getRefDatabase().peel(tagRef).getPeeledObjectId());
 		}
 	}
 
@@ -135,26 +139,30 @@ public class TagCommandTest extends RepositoryTestCase {
 		}
 	}
 
+	private List<Ref> getTags() throws Exception {
+		return db.getRefDatabase().getRefsByPrefix(R_TAGS);
+	}
+
 	@Test
 	public void testDelete() throws Exception {
 		try (Git git = new Git(db)) {
 			git.commit().setMessage("initial commit").call();
 			Ref tagRef = git.tag().setName("tag").call();
-			assertEquals(1, db.getTags().size());
+			assertEquals(1, getTags().size());
 
 			List<String> deleted = git.tagDelete().setTags(tagRef.getName())
 					.call();
 			assertEquals(1, deleted.size());
 			assertEquals(tagRef.getName(), deleted.get(0));
-			assertEquals(0, db.getTags().size());
+			assertEquals(0, getTags().size());
 
 			Ref tagRef1 = git.tag().setName("tag1").call();
 			Ref tagRef2 = git.tag().setName("tag2").call();
-			assertEquals(2, db.getTags().size());
+			assertEquals(2, getTags().size());
 			deleted = git.tagDelete().setTags(tagRef1.getName(), tagRef2.getName())
 					.call();
 			assertEquals(2, deleted.size());
-			assertEquals(0, db.getTags().size());
+			assertEquals(0, getTags().size());
 		}
 	}
 
@@ -163,13 +171,13 @@ public class TagCommandTest extends RepositoryTestCase {
 		try (Git git = new Git(db)) {
 			git.commit().setMessage("initial commit").call();
 			Ref tagRef = git.tag().setName("tag").call();
-			assertEquals(1, db.getTags().size());
+			assertEquals(1, getTags().size());
 
 			List<String> deleted = git.tagDelete()
 					.setTags(Repository.shortenRefName(tagRef.getName())).call();
 			assertEquals(1, deleted.size());
 			assertEquals(tagRef.getName(), deleted.get(0));
-			assertEquals(0, db.getTags().size());
+			assertEquals(0, getTags().size());
 		}
 	}
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBuilderIteratorTest.java

@@ -78,7 +78,7 @@ public class DirCacheBuilderIteratorTest extends RepositoryTestCase {
 
 		final int expIdx = 2;
 		final DirCacheBuilder b = dc.builder();
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.addTree(new DirCacheBuildIterator(b));
 			tw.setRecursive(true);
 			tw.setFilter(PathFilterGroup.createFromStrings(Collections

org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheCGitCompatabilityTest.java

@@ -99,7 +99,7 @@ public class DirCacheCGitCompatabilityTest extends LocalDiskRepositoryTestCase {
 		assertEquals(ls.size(), dc.getEntryCount());
 		{
 			final Iterator<CGitIndexRecord> rItr = ls.values().iterator();
-			try (final TreeWalk tw = new TreeWalk(db)) {
+			try (TreeWalk tw = new TreeWalk(db)) {
 				tw.setRecursive(true);
 				tw.addTree(new DirCacheIterator(dc));
 				while (rItr.hasNext()) {
@@ -180,7 +180,7 @@ public class DirCacheCGitCompatabilityTest extends LocalDiskRepositoryTestCase {
 		assertEquals(cList.size(), jTree.getEntrySpan());
 
 		final ArrayList<CGitLsTreeRecord> subtrees = new ArrayList<>();
-		for (final CGitLsTreeRecord r : cTree.values()) {
+		for (CGitLsTreeRecord r : cTree.values()) {
 			if (FileMode.TREE.equals(r.mode))
 				subtrees.add(r);
 		}
@@ -268,7 +268,7 @@ public class DirCacheCGitCompatabilityTest extends LocalDiskRepositoryTestCase {
 
 		final String path;
 
-		CGitIndexRecord(final String line) {
+		CGitIndexRecord(String line) {
 			final int tab = line.indexOf('\t');
 			final int sp1 = line.indexOf(' ');
 			final int sp2 = line.indexOf(' ', sp1 + 1);
@@ -286,7 +286,7 @@ public class DirCacheCGitCompatabilityTest extends LocalDiskRepositoryTestCase {
 
 		final String path;
 
-		CGitLsTreeRecord(final String line) {
+		CGitLsTreeRecord(String line) {
 			final int tab = line.indexOf('\t');
 			final int sp1 = line.indexOf(' ');
 			final int sp2 = line.indexOf(' ', sp1 + 1);

org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheIteratorTest.java

@@ -76,7 +76,7 @@ public class DirCacheIteratorTest extends RepositoryTestCase {
 		final DirCache dc = DirCache.newInCore();
 		assertEquals(0, dc.getEntryCount());
 
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.addTree(new DirCacheIterator(dc));
 			assertFalse(tw.next());
 		}
@@ -126,7 +126,7 @@ public class DirCacheIteratorTest extends RepositoryTestCase {
 		b.finish();
 
 		final DirCacheIterator i = new DirCacheIterator(dc);
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.addTree(i);
 			int pathIdx = 0;
 			while (tw.next()) {
@@ -164,7 +164,7 @@ public class DirCacheIteratorTest extends RepositoryTestCase {
 		final int expPos[] = { 0, -1, 4 };
 
 		final DirCacheIterator i = new DirCacheIterator(dc);
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.addTree(i);
 			tw.setRecursive(false);
 			int pathIdx = 0;
@@ -205,7 +205,7 @@ public class DirCacheIteratorTest extends RepositoryTestCase {
 		b.finish();
 
 		final DirCacheIterator i = new DirCacheIterator(dc);
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.addTree(i);
 			tw.setRecursive(true);
 			int pathIdx = 0;
@@ -240,7 +240,7 @@ public class DirCacheIteratorTest extends RepositoryTestCase {
 			b.add(ents[i]);
 		b.finish();
 
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.addTree(new DirCacheIterator(dc));
 			tw.setRecursive(true);
 			int pathIdx = 0;
@@ -402,7 +402,7 @@ public class DirCacheIteratorTest extends RepositoryTestCase {
 			b.add(ents[i]);
 		b.finish();
 
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			for (int victimIdx = 0; victimIdx < paths.length; victimIdx++) {
 				tw.reset();
 				tw.addTree(new DirCacheIterator(dc));
@@ -430,7 +430,7 @@ public class DirCacheIteratorTest extends RepositoryTestCase {
 		final DirCache dc = DirCache.read(path, FS.DETECTED);
 		assertEquals(2, dc.getEntryCount());
 
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.setRecursive(true);
 			tw.addTree(new DirCacheIterator(dc));
 

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

@@ -160,7 +160,7 @@ public class RepoCommandTest extends RepositoryTestCase {
 				Ref ref = r.findRef(refname);
 				if (ref == null) return null;
 
-				ref = r.peel(ref);
+				ref = r.getRefDatabase().peel(ref);
 				ObjectId id = ref.getObjectId();
 				return id;
 			} catch (IOException e) {

org.eclipse.jgit.test/tst/org/eclipse/jgit/ignore/CGitIgnoreTest.java

@@ -141,7 +141,9 @@ public class CGitIgnoreTest extends RepositoryTestCase {
 		// Do a tree walk that does descend into ignored directories and return
 		// a list of all ignored files
 		try (TreeWalk walk = new TreeWalk(db)) {
-			walk.addTree(new FileTreeIterator(db));
+			FileTreeIterator iter = new FileTreeIterator(db);
+			iter.setWalkIgnoredDirectories(true);
+			walk.addTree(iter);
 			walk.setRecursive(true);
 			while (walk.next()) {
 				if (walk.getTree(WorkingTreeIterator.class).isEntryIgnored()) {

org.eclipse.jgit.test/tst/org/eclipse/jgit/ignore/IgnoreNodeTest.java

@@ -732,7 +732,9 @@ public class IgnoreNodeTest extends RepositoryTestCase {
 
 	private void beginWalk() {
 		walk = new TreeWalk(db);
-		walk.addTree(new FileTreeIterator(db));
+		FileTreeIterator iter = new FileTreeIterator(db);
+		iter.setWalkIgnoredDirectories(true);
+		walk.addTree(iter);
 	}
 
 	private void endWalk() throws IOException {

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

@@ -220,7 +220,7 @@ public class ConcurrentRepackTest extends RepositoryTestCase {
 	private File[] pack(Repository src, RevObject... list)
 			throws IOException {
 		try (PackWriter pw = new PackWriter(src)) {
-			for (final RevObject o : list) {
+			for (RevObject o : list) {
 				pw.addObject(o);
 			}
 
@@ -253,7 +253,7 @@ public class ConcurrentRepackTest extends RepositoryTestCase {
 
 	private static void delete(File[] list) throws IOException {
 		final long begin = list[0].getParentFile().lastModified();
-		for (final File f : list) {
+		for (File f : list) {
 			FileUtils.delete(f);
 			assertFalse(f + " was removed", f.exists());
 		}

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

@@ -368,7 +368,7 @@ public class PackWriterTest extends SampleDataRepositoryTestCase {
 				ObjectId.fromString("902d5476fa249b7abc9d84c611577a81381f0327"),
 				ObjectId.fromString("6ff87c4664981e4397625791c8ea3bbb5f2279a3") ,
 				ObjectId.fromString("5b6e7c66c276e7610d4a73c70ec1a1f7c1003259") };
-		try (final RevWalk parser = new RevWalk(db)) {
+		try (RevWalk parser = new RevWalk(db)) {
 			final RevObject forcedOrderRevs[] = new RevObject[forcedOrder.length];
 			for (int i = 0; i < forcedOrder.length; i++)
 				forcedOrderRevs[i] = parser.parseAny(forcedOrder[i]);

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/T0003_BasicTest.java

@@ -305,7 +305,7 @@ public class T0003_BasicTest extends SampleDataRepositoryTestCase {
 		// object (as it already exists in the pack).
 		//
 		final Repository newdb = createBareRepository();
-		try (final ObjectInserter oi = newdb.newObjectInserter()) {
+		try (ObjectInserter oi = newdb.newObjectInserter()) {
 			final ObjectId treeId = oi.insert(new TreeFormatter());
 			assertEquals("4b825dc642cb6eb9a060e54bf8d69288fbee4904",
 					treeId.name());
@@ -373,7 +373,7 @@ public class T0003_BasicTest extends SampleDataRepositoryTestCase {
 
 	@Test
 	public void test007_Open() throws IOException {
-		try (final FileRepository db2 = new FileRepository(db.getDirectory())) {
+		try (FileRepository db2 = new FileRepository(db.getDirectory())) {
 			assertEquals(db.getDirectory(), db2.getDirectory());
 			assertEquals(db.getObjectDatabase().getDirectory(), db2
 					.getObjectDatabase().getDirectory());
@@ -557,7 +557,7 @@ public class T0003_BasicTest extends SampleDataRepositoryTestCase {
 	@Test
 	public void test026_CreateCommitMultipleparents() throws IOException {
 		final ObjectId treeId;
-		try (final ObjectInserter oi = db.newObjectInserter()) {
+		try (ObjectInserter oi = db.newObjectInserter()) {
 			final ObjectId blobId = oi.insert(Constants.OBJ_BLOB,
 					"and this is the data in me\n".getBytes(Constants.CHARSET
 							.name()));

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

@@ -133,7 +133,7 @@ public class WindowCacheGetTest extends SampleDataRepositoryTestCase {
 	}
 
 	private void doCacheTests() throws IOException {
-		for (final TestObject o : toLoad) {
+		for (TestObject o : toLoad) {
 			final ObjectLoader or = db.open(o.id, o.type);
 			assertNotNull(or);
 			assertEquals(o.type, or.getType());
@@ -145,7 +145,7 @@ public class WindowCacheGetTest extends SampleDataRepositoryTestCase {
 
 		int type;
 
-		void setType(final String typeStr) throws CorruptObjectException {
+		void setType(String typeStr) throws CorruptObjectException {
 			final byte[] typeRaw = Constants.encode(typeStr + " ");
 			final MutableInteger ptr = new MutableInteger();
 			type = Constants.decodeTypeString(id, typeRaw, (byte) ' ', ptr);

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

@@ -53,7 +53,7 @@ import org.eclipse.jgit.util.NB;
 class XInputStream extends BufferedInputStream {
 	private final byte[] intbuf = new byte[8];
 
-	XInputStream(final InputStream s) {
+	XInputStream(InputStream s) {
 		super(s);
 	}
 
@@ -63,7 +63,7 @@ class XInputStream extends BufferedInputStream {
 		return b;
 	}
 
-	synchronized void readFully(final byte[] b, int o, int len)
+	synchronized void readFully(byte[] b, int o, int len)
 			throws IOException {
 		int r;
 		while (len > 0 && (r = read(b, o, len)) > 0) {

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

@@ -78,8 +78,10 @@ import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.junit.TestRepository.BranchBuilder;
 import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.treewalk.AbstractTreeIterator;
 import org.eclipse.jgit.treewalk.FileTreeIterator;
 import org.eclipse.jgit.treewalk.TreeWalk;
+import org.eclipse.jgit.treewalk.WorkingTreeIterator;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
 import org.junit.Assume;
@@ -1904,6 +1906,117 @@ public class DirCacheCheckoutTest extends RepositoryTestCase {
 		assertUpdated(longFileName);
 	}
 
+	@Test
+	public void testIgnoredDirectory() throws Exception {
+		writeTrashFile(".gitignore", "src/ignored");
+		writeTrashFile("src/ignored/sub/foo.txt", "1");
+		try (Git git = new Git(db)) {
+			git.add().addFilepattern(".").call();
+			RevCommit commit = git.commit().setMessage("adding .gitignore")
+					.call();
+			writeTrashFile("foo.txt", "2");
+			writeTrashFile("zzz.txt", "3");
+			git.add().addFilepattern("foo.txt").call();
+			git.commit().setMessage("add file").call();
+			assertEquals("Should not have entered ignored directory", 1,
+					resetHardAndCount(commit));
+		}
+	}
+
+	@Test
+	public void testIgnoredDirectoryWithTrackedContent() throws Exception {
+		writeTrashFile("src/ignored/sub/foo.txt", "1");
+		try (Git git = new Git(db)) {
+			git.add().addFilepattern(".").call();
+			git.commit().setMessage("adding foo.txt").call();
+			writeTrashFile(".gitignore", "src/ignored");
+			writeTrashFile("src/ignored/sub/foo.txt", "2");
+			writeTrashFile("src/ignored/other/bar.txt", "3");
+			git.add().addFilepattern(".").call();
+			RevCommit commit = git.commit().setMessage("adding .gitignore")
+					.call();
+			writeTrashFile("foo.txt", "2");
+			writeTrashFile("zzz.txt", "3");
+			git.add().addFilepattern("foo.txt").call();
+			git.commit().setMessage("add file").call();
+			File file = writeTrashFile("src/ignored/sub/foo.txt", "3");
+			assertEquals("Should have entered ignored directory", 3,
+					resetHardAndCount(commit));
+			checkFile(file, "2");
+		}
+	}
+
+	@Test
+	public void testResetWithChangeInGitignore() throws Exception {
+		writeTrashFile(".gitignore", "src/ignored");
+		writeTrashFile("src/ignored/sub/foo.txt", "1");
+		try (Git git = new Git(db)) {
+			git.add().addFilepattern(".").call();
+			RevCommit initial = git.commit().setMessage("initial").call();
+			writeTrashFile("src/newignored/foo.txt", "2");
+			writeTrashFile("src/.gitignore", "newignored");
+			git.add().addFilepattern(".").call();
+			RevCommit commit = git.commit().setMessage("newignored").call();
+			assertEquals("Should not have entered src/newignored directory", 1,
+					resetHardAndCount(initial));
+			assertEquals("Should have entered src/newignored directory", 2,
+					resetHardAndCount(commit));
+			deleteTrashFile("src/.gitignore");
+			git.rm().addFilepattern("src/.gitignore").call();
+			RevCommit top = git.commit().setMessage("Unignore newignore")
+					.call();
+			assertEquals("Should have entered src/newignored directory", 2,
+					resetHardAndCount(initial));
+			assertEquals("Should have entered src/newignored directory", 2,
+					resetHardAndCount(commit));
+			assertEquals("Should not have entered src/newignored directory", 1,
+					resetHardAndCount(top));
+
+		}
+	}
+
+	private static class TestFileTreeIterator extends FileTreeIterator {
+
+		// For assertions only
+		private final int[] count;
+
+		public TestFileTreeIterator(Repository repo, int[] count) {
+			super(repo);
+			this.count = count;
+		}
+
+		protected TestFileTreeIterator(final WorkingTreeIterator p,
+				final File root, FS fs, FileModeStrategy fileModeStrategy,
+				int[] count) {
+			super(p, root, fs, fileModeStrategy);
+			this.count = count;
+		}
+
+		@Override
+		protected AbstractTreeIterator enterSubtree() {
+			count[0] += 1;
+			return new TestFileTreeIterator(this,
+					((FileEntry) current()).getFile(), fs, fileModeStrategy,
+					count);
+		}
+	}
+
+	private int resetHardAndCount(RevCommit commit) throws Exception {
+		int[] callCount = { 0 };
+		DirCache cache = db.lockDirCache();
+		FileTreeIterator workingTreeIterator = new TestFileTreeIterator(db,
+				callCount);
+		try {
+			DirCacheCheckout checkout = new DirCacheCheckout(db, null, cache,
+					commit.getTree().getId(), workingTreeIterator);
+			checkout.setFailOnConflict(false);
+			checkout.checkout();
+		} finally {
+			cache.unlock();
+		}
+		return callCount[0];
+	}
+
 	public void assertWorkDir(Map<String, String> i)
 			throws CorruptObjectException,
 			IOException {

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

@@ -470,7 +470,8 @@ public class IndexDiffTest extends RepositoryTestCase {
 	}
 
 	/**
-	 * Test that ignored folders aren't listed as untracked
+	 * Test that ignored folders aren't listed as untracked, but are listed as
+	 * ignored.
 	 *
 	 * @throws Exception
 	 */
@@ -499,6 +500,8 @@ public class IndexDiffTest extends RepositoryTestCase {
 			diff.diff();
 			assertEquals(new HashSet<>(Arrays.asList("src")),
 					diff.getUntrackedFolders());
+			assertEquals(new HashSet<>(Arrays.asList("sr", "target")),
+					diff.getIgnoredNotInIndex());
 
 			git.add().addFilepattern("src").call();
 			writeTrashFile("sr/com/X1.java", "");

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

@@ -76,7 +76,7 @@ public class RevObjectTest extends RevWalkTestCase {
 
 		final RevCommit a2;
 		final RevCommit b2;
-		try (final RevWalk rw2 = new RevWalk(db)) {
+		try (RevWalk rw2 = new RevWalk(db)) {
 			a2 = rw2.parseCommit(a1);
 			b2 = rw2.parseCommit(b1);
 		}

org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkPathFilter6012Test.java

@@ -105,14 +105,14 @@ public class RevWalkPathFilter6012Test extends RevWalkTestCase {
 	protected void check(RevCommit... order) throws Exception {
 		markStart(i);
 		final StringBuilder act = new StringBuilder();
-		for (final RevCommit z : rw) {
+		for (RevCommit z : rw) {
 			final String name = byName.get(z);
 			assertNotNull(name);
 			act.append(name);
 			act.append(' ');
 		}
 		final StringBuilder exp = new StringBuilder();
-		for (final RevCommit z : order) {
+		for (RevCommit z : order) {
 			final String name = byName.get(z);
 			assertNotNull(name);
 			exp.append(name);

org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/PushProcessTest.java

@@ -422,7 +422,7 @@ public class PushProcessTest extends SampleDataRepositoryTestCase {
 			PushConnection {
 		MockPushConnection() {
 			final Map<String, Ref> refsMap = new HashMap<>();
-			for (final Ref r : advertisedRefs)
+			for (Ref r : advertisedRefs)
 				refsMap.put(r.getName(), r);
 			available(refsMap);
 		}
@@ -443,7 +443,7 @@ public class PushProcessTest extends SampleDataRepositoryTestCase {
 		public void push(ProgressMonitor monitor,
 				Map<String, RemoteRefUpdate> refsToUpdate)
 				throws TransportException {
-			for (final RemoteRefUpdate rru : refsToUpdate.values()) {
+			for (RemoteRefUpdate rru : refsToUpdate.values()) {
 				assertEquals(Status.NOT_ATTEMPTED, rru.getStatus());
 				rru.setStatus(connectionUpdateStatus);
 			}

org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/ReceivePackAdvertiseRefsHookTest.java

@@ -136,7 +136,7 @@ public class ReceivePackAdvertiseRefsHookTest extends LocalDiskRepositoryTestCas
 		try (TransportLocal t = new TransportLocal(src, uriOf(dst),
 				dst.getDirectory()) {
 			@Override
-			ReceivePack createReceivePack(final Repository db) {
+			ReceivePack createReceivePack(Repository db) {
 				db.close();
 				dst.incrementOpen();
 
@@ -203,7 +203,7 @@ public class ReceivePackAdvertiseRefsHookTest extends LocalDiskRepositoryTestCas
 			throws Exception {
 		return new TransportLocal(src, uriOf(dst), dst.getDirectory()) {
 			@Override
-			ReceivePack createReceivePack(final Repository db) {
+			ReceivePack createReceivePack(Repository db) {
 				db.close();
 				dst.incrementOpen();
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/TransportTest.java

@@ -142,7 +142,7 @@ public class TransportTest extends SampleDataRepositoryTestCase {
 		assertEquals(12, result.size());
 		boolean foundA = false;
 		boolean foundB = false;
-		for (final RemoteRefUpdate rru : result) {
+		for (RemoteRefUpdate rru : result) {
 			if ("refs/heads/a".equals(rru.getSrcRef())
 					&& "refs/heads/test/a".equals(rru.getRemoteName()))
 				foundA = true;
@@ -174,7 +174,7 @@ public class TransportTest extends SampleDataRepositoryTestCase {
 		assertEquals(2, result.size());
 		boolean foundA = false;
 		boolean foundC = false;
-		for (final RemoteRefUpdate rru : result) {
+		for (RemoteRefUpdate rru : result) {
 			if ("refs/heads/a".equals(rru.getSrcRef())
 					&& "refs/heads/b".equals(rru.getRemoteName()))
 				foundA = true;
@@ -233,7 +233,7 @@ public class TransportTest extends SampleDataRepositoryTestCase {
 		assertEquals(2, result.size());
 		boolean foundA = false;
 		boolean foundC = false;
-		for (final RemoteRefUpdate rru : result) {
+		for (RemoteRefUpdate rru : result) {
 			if ("refs/heads/a".equals(rru.getSrcRef())
 					&& "refs/heads/b".equals(rru.getRemoteName())) {
 				foundA = true;

org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/UploadPackTest.java

@@ -518,15 +518,18 @@ public class UploadPackTest {
 	 * Parse multiplexed packfile output from upload-pack using protocol V2
 	 * into the client repository.
 	 */
-	private void parsePack(ByteArrayInputStream recvStream) throws Exception {
-		parsePack(recvStream, NullProgressMonitor.INSTANCE);
+	private ReceivedPackStatistics parsePack(ByteArrayInputStream recvStream) throws Exception {
+		return parsePack(recvStream, NullProgressMonitor.INSTANCE);
 	}
 
-	private void parsePack(ByteArrayInputStream recvStream, ProgressMonitor pm)
+	private ReceivedPackStatistics parsePack(ByteArrayInputStream recvStream, ProgressMonitor pm)
 			throws Exception {
 		SideBandInputStream sb = new SideBandInputStream(
-				recvStream, pm, new StringWriter(), NullOutputStream.INSTANCE);
-		client.newObjectInserter().newPackParser(sb).parse(NullProgressMonitor.INSTANCE);
+				recvStream, pm,
+				new StringWriter(), NullOutputStream.INSTANCE);
+		PackParser pp = client.newObjectInserter().newPackParser(sb);
+		pp.parse(NullProgressMonitor.INSTANCE);
+		return pp.getReceivedPackStatistics();
 	}
 
 	@Test
@@ -805,6 +808,75 @@ public class UploadPackTest {
 		assertTrue(sw.toString().isEmpty());
 	}
 
+	@Test
+	public void testV2FetchIncludeTag() throws Exception {
+		RevCommit commit = remote.commit().message("x").create();
+		RevTag tag = remote.tag("tag", commit);
+		remote.update("branch1", commit);
+		remote.update("refs/tags/tag", tag);
+
+		// Without include-tag.
+		ByteArrayInputStream recvStream = uploadPackV2(
+			"command=fetch\n",
+			PacketLineIn.DELIM,
+			"want " + commit.toObjectId().getName() + "\n",
+			"done\n",
+			PacketLineIn.END);
+		PacketLineIn pckIn = new PacketLineIn(recvStream);
+		assertThat(pckIn.readString(), is("packfile"));
+		parsePack(recvStream);
+		assertFalse(client.hasObject(tag.toObjectId()));
+
+		// With tag.
+		recvStream = uploadPackV2(
+			"command=fetch\n",
+			PacketLineIn.DELIM,
+			"want " + commit.toObjectId().getName() + "\n",
+			"include-tag\n",
+			"done\n",
+			PacketLineIn.END);
+		pckIn = new PacketLineIn(recvStream);
+		assertThat(pckIn.readString(), is("packfile"));
+		parsePack(recvStream);
+		assertTrue(client.hasObject(tag.toObjectId()));
+	}
+
+	@Test
+	public void testV2FetchOfsDelta() throws Exception {
+		String commonInBlob = "abcdefghijklmnopqrstuvwxyz";
+
+		RevBlob parentBlob = remote.blob(commonInBlob + "a");
+		RevCommit parent = remote.commit(remote.tree(remote.file("foo", parentBlob)));
+		RevBlob childBlob = remote.blob(commonInBlob + "b");
+		RevCommit child = remote.commit(remote.tree(remote.file("foo", childBlob)), parent);
+		remote.update("branch1", child);
+
+		// Without ofs-delta.
+		ByteArrayInputStream recvStream = uploadPackV2(
+			"command=fetch\n",
+			PacketLineIn.DELIM,
+			"want " + child.toObjectId().getName() + "\n",
+			"done\n",
+			PacketLineIn.END);
+		PacketLineIn pckIn = new PacketLineIn(recvStream);
+		assertThat(pckIn.readString(), is("packfile"));
+		ReceivedPackStatistics stats = parsePack(recvStream);
+		assertTrue(stats.getNumOfsDelta() == 0);
+
+		// With ofs-delta.
+		recvStream = uploadPackV2(
+			"command=fetch\n",
+			PacketLineIn.DELIM,
+			"want " + child.toObjectId().getName() + "\n",
+			"ofs-delta\n",
+			"done\n",
+			PacketLineIn.END);
+		pckIn = new PacketLineIn(recvStream);
+		assertThat(pckIn.readString(), is("packfile"));
+		stats = parsePack(recvStream);
+		assertTrue(stats.getNumOfsDelta() != 0);
+	}
+
 	private static class RejectAllRefFilter implements RefFilter {
 		@Override
 		public Map<String, Ref> filter(Map<String, Ref> refs) {

org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/CanonicalTreeParserTest.java

@@ -93,7 +93,7 @@ public class CanonicalTreeParserTest {
 
 	private static byte[] mktree(byte[]... data) throws Exception {
 		final ByteArrayOutputStream out = new ByteArrayOutputStream();
-		for (final byte[] e : data)
+		for (byte[] e : data)
 			out.write(e);
 		return out.toByteArray();
 	}

org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/PostOrderTreeWalkTest.java

@@ -60,14 +60,14 @@ import org.junit.Test;
 public class PostOrderTreeWalkTest extends RepositoryTestCase {
 	@Test
 	public void testInitialize_NoPostOrder() throws Exception {
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			assertFalse(tw.isPostOrderTraversal());
 		}
 	}
 
 	@Test
 	public void testInitialize_TogglePostOrder() throws Exception {
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			assertFalse(tw.isPostOrderTraversal());
 			tw.setPostOrderTraversal(true);
 			assertTrue(tw.isPostOrderTraversal());
@@ -78,7 +78,7 @@ public class PostOrderTreeWalkTest extends RepositoryTestCase {
 
 	@Test
 	public void testResetDoesNotAffectPostOrder() throws Exception {
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.setPostOrderTraversal(true);
 			assertTrue(tw.isPostOrderTraversal());
 			tw.reset();
@@ -104,7 +104,7 @@ public class PostOrderTreeWalkTest extends RepositoryTestCase {
 		b.finish();
 		assertEquals(4, tree.getEntryCount());
 
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.setPostOrderTraversal(false);
 			tw.addTree(new DirCacheIterator(tree));
 
@@ -132,7 +132,7 @@ public class PostOrderTreeWalkTest extends RepositoryTestCase {
 		b.finish();
 		assertEquals(4, tree.getEntryCount());
 
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.setPostOrderTraversal(true);
 			tw.addTree(new DirCacheIterator(tree));
 
@@ -166,7 +166,7 @@ public class PostOrderTreeWalkTest extends RepositoryTestCase {
 		b.finish();
 		assertEquals(4, tree.getEntryCount());
 
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.setPostOrderTraversal(true);
 			tw.addTree(new DirCacheIterator(tree));
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/PathFilterGroupTest.java

@@ -254,7 +254,7 @@ public class PathFilterGroupTest {
 		}
 	}
 
-	TreeWalk fakeWalk(final String path) throws IOException {
+	TreeWalk fakeWalk(String path) throws IOException {
 		DirCache dc = DirCache.newInCore();
 		DirCacheEditor dce = dc.editor();
 		dce.add(new DirCacheEditor.PathEdit(path) {
@@ -274,7 +274,7 @@ public class PathFilterGroupTest {
 		return ret;
 	}
 
-	TreeWalk fakeWalkAtSubtree(final String path) throws IOException {
+	TreeWalk fakeWalkAtSubtree(String path) throws IOException {
 		DirCache dc = DirCache.newInCore();
 		DirCacheEditor dce = dc.editor();
 		dce.add(new DirCacheEditor.PathEdit(path + "/README") {

org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/PathSuffixFilterTest.java

@@ -113,7 +113,7 @@ public class PathSuffixFilterTest extends RepositoryTestCase {
 
 	private List<String> getMatchingPaths(String suffixFilter,
 			final ObjectId treeId, boolean recursiveWalk) throws IOException {
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.setFilter(PathSuffixFilter.create(suffixFilter));
 			tw.setRecursive(recursiveWalk);
 			tw.addTree(treeId);

org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/TreeFilterTest.java

@@ -55,7 +55,7 @@ import org.junit.Test;
 public class TreeFilterTest extends RepositoryTestCase {
 	@Test
 	public void testALL_IncludesAnything() throws Exception {
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.addTree(new EmptyTreeIterator());
 			assertTrue(TreeFilter.ALL.include(tw));
 		}
@@ -73,7 +73,7 @@ public class TreeFilterTest extends RepositoryTestCase {
 
 	@Test
 	public void testNotALL_IncludesNothing() throws Exception {
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.addTree(new EmptyTreeIterator());
 			assertFalse(TreeFilter.ALL.negate().include(tw));
 		}
@@ -81,7 +81,7 @@ public class TreeFilterTest extends RepositoryTestCase {
 
 	@Test
 	public void testANY_DIFF_IncludesSingleTreeCase() throws Exception {
-		try (final TreeWalk tw = new TreeWalk(db)) {
+		try (TreeWalk tw = new TreeWalk(db)) {
 			tw.addTree(new EmptyTreeIterator());
 			assertTrue(TreeFilter.ANY_DIFF.include(tw));
 		}

org.eclipse.jgit.test/tst/org/eclipse/jgit/util/TemporaryBufferTest.java

@@ -248,7 +248,7 @@ public class TemporaryBufferTest {
 	public void testInCoreInputStream() throws IOException {
 		final int cnt = 256;
 		final byte[] test = new TestRng(getName()).nextBytes(cnt);
-		try (final TemporaryBuffer.Heap b = new TemporaryBuffer.Heap(cnt + 4)) {
+		try (TemporaryBuffer.Heap b = new TemporaryBuffer.Heap(cnt + 4)) {
 			b.write(test);
 			InputStream in = b.openInputStream();
 			byte[] act = new byte[cnt];

org.eclipse.jgit.ui/src/org/eclipse/jgit/awtui/AWTPlotRenderer.java

@@ -66,11 +66,11 @@ final class AWTPlotRenderer extends AbstractPlotRenderer<SwingLane, Color>
 
 	transient Graphics2D g;
 
-	AWTPlotRenderer(final GraphCellRender c) {
+	AWTPlotRenderer(GraphCellRender c) {
 		cell = c;
 	}
 
-	void paint(final Graphics in, final PlotCommit<SwingLane> commit) {
+	void paint(Graphics in, PlotCommit<SwingLane> commit) {
 		g = (Graphics2D) in.create();
 		try {
 			final int h = cell.getHeight();
@@ -138,7 +138,7 @@ final class AWTPlotRenderer extends AbstractPlotRenderer<SwingLane, Color>
 		return myLane != null ? myLane.color : Color.black;
 	}
 
-	void paintTriangleDown(final int cx, final int y, final int h) {
+	void paintTriangleDown(int cx, int y, int h) {
 		final int tipX = cx;
 		final int tipY = y + h;
 		final int baseX1 = cx - 10 / 2;

org.eclipse.jgit.ui/src/org/eclipse/jgit/awtui/CommitGraphPane.java

@@ -175,7 +175,7 @@ public class CommitGraphPane extends JTable {
 			}
 		}
 
-		PersonIdent authorFor(final PlotCommit<SwingLane> c) {
+		PersonIdent authorFor(PlotCommit<SwingLane> c) {
 			if (c != lastCommit) {
 				lastCommit = c;
 				lastAuthor = c.getAuthorIdent();
@@ -259,7 +259,7 @@ public class CommitGraphPane extends JTable {
 			strokeCache[i] = new BasicStroke(i);
 	}
 
-	static Stroke stroke(final int width) {
+	static Stroke stroke(int width) {
 		if (width < strokeCache.length)
 			return strokeCache[width];
 		return new BasicStroke(width);

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

@@ -315,7 +315,7 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 			specs.add(wcrs);
 		else if (branchesToClone != null
 				&& branchesToClone.size() > 0) {
-			for (final String selectedRef : branchesToClone)
+			for (String selectedRef : branchesToClone)
 				if (wcrs.matchSource(selectedRef))
 					specs.add(wcrs.expandFromSource(selectedRef));
 		}
@@ -410,7 +410,7 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 		}
 
 		Ref foundBranch = null;
-		for (final Ref r : result.getAdvertisedRefs()) {
+		for (Ref r : result.getAdvertisedRefs()) {
 			final String n = r.getName();
 			if (!n.startsWith(Constants.R_HEADS))
 				continue;
@@ -444,7 +444,7 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 			throws MissingObjectException, IncorrectObjectTypeException,
 			IOException {
 		final RevCommit commit;
-		try (final RevWalk rw = new RevWalk(clonedRepo)) {
+		try (RevWalk rw = new RevWalk(clonedRepo)) {
 			commit = rw.parseCommit(ref.getObjectId());
 		}
 		return commit;

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

@@ -224,12 +224,16 @@ public class DescribeCommand extends GitCommand<String> {
 		}
 	}
 
-	private ObjectId getObjectIdFromRef(Ref r) {
-		ObjectId key = repo.peel(r).getPeeledObjectId();
-		if (key == null) {
-			key = r.getObjectId();
+	private ObjectId getObjectIdFromRef(Ref r) throws JGitInternalException {
+		try {
+			ObjectId key = repo.getRefDatabase().peel(r).getPeeledObjectId();
+			if (key == null) {
+				key = r.getObjectId();
+			}
+			return key;
+		} catch (IOException e) {
+			throw new JGitInternalException(e.getMessage(), e);
 		}
-		return key;
 	}
 
 	/**

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

@@ -274,7 +274,7 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 	public LogCommand all() throws IOException {
 		for (Ref ref : getRepository().getRefDatabase().getRefs()) {
 			if(!ref.isPeeled())
-				ref = getRepository().peel(ref);
+				ref = getRepository().getRefDatabase().peel(ref);
 
 			ObjectId objectId = ref.getPeeledObjectId();
 			if (objectId == null)

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

@@ -255,7 +255,7 @@ public class MergeCommand extends GitCommand<MergeResult> {
 			refLogMessage.append(ref.getName());
 
 			// handle annotated tags
-			ref = repo.peel(ref);
+			ref = repo.getRefDatabase().peel(ref);
 			ObjectId objectId = ref.getPeeledObjectId();
 			if (objectId == null)
 				objectId = ref.getObjectId();

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

@@ -360,7 +360,7 @@ public class ResetCommand extends GitCommand<Ref> {
 
 	private void resetIndexForPaths(ObjectId commitTree) {
 		DirCache dc = null;
-		try (final TreeWalk tw = new TreeWalk(repo)) {
+		try (TreeWalk tw = new TreeWalk(repo)) {
 			dc = repo.lockDirCache();
 			DirCacheBuilder builder = dc.builder();
 

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

@@ -154,7 +154,7 @@ public class RmCommand extends GitCommand<DirCache> {
 		DirCache dc = null;
 
 		List<String> actuallyDeletedFiles = new ArrayList<>();
-		try (final TreeWalk tw = new TreeWalk(repo)) {
+		try (TreeWalk tw = new TreeWalk(repo)) {
 			dc = repo.lockDirCache();
 			DirCacheBuilder builder = dc.builder();
 			tw.reset(); // drop the first empty tree, which we do not need here

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

@@ -195,7 +195,7 @@ public class StashCreateCommand extends GitCommand<RevCommit> {
 
 	private RevCommit parseCommit(final ObjectReader reader,
 			final ObjectId headId) throws IOException {
-		try (final RevWalk walk = new RevWalk(reader)) {
+		try (RevWalk walk = new RevWalk(reader)) {
 			return walk.parseCommit(headId);
 		}
 	}

org.eclipse.jgit/src/org/eclipse/jgit/blame/ReverseWalk.java

@@ -108,7 +108,7 @@ final class ReverseWalk extends RevWalk {
 			return children.length;
 		}
 
-		ReverseCommit getChild(final int nth) {
+		ReverseCommit getChild(int nth) {
 			return children[nth];
 		}
 	}

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

@@ -359,7 +359,7 @@ if (k < beginK || k > endK)
 			abstract int getLeft(int x);
 			abstract int getRight(int x);
 			abstract boolean isBetter(int left, int right);
-			abstract void adjustMinMaxK(final int k, final int x);
+			abstract void adjustMinMaxK(int k, int x);
 			abstract boolean meets(int d, int k, int x, long snake);
 
 			final long newSnake(int k, int x) {
@@ -469,22 +469,22 @@ if (k < beginK || k > endK)
 			}
 
 			@Override
-			final int getLeft(final int x) {
+			final int getLeft(int x) {
 				return x;
 			}
 
 			@Override
-			final int getRight(final int x) {
+			final int getRight(int x) {
 				return x + 1;
 			}
 
 			@Override
-			final boolean isBetter(final int left, final int right) {
+			final boolean isBetter(int left, int right) {
 				return left > right;
 			}
 
 			@Override
-			final void adjustMinMaxK(final int k, final int x) {
+			final void adjustMinMaxK(int k, int x) {
 				if (x >= endA || k + x >= endB) {
 					if (k > backward.middleK)
 						maxK = k;
@@ -517,22 +517,22 @@ if (k < beginK || k > endK)
 			}
 
 			@Override
-			final int getLeft(final int x) {
+			final int getLeft(int x) {
 				return x - 1;
 			}
 
 			@Override
-			final int getRight(final int x) {
+			final int getRight(int x) {
 				return x;
 			}
 
 			@Override
-			final boolean isBetter(final int left, final int right) {
+			final boolean isBetter(int left, int right) {
 				return left < right;
 			}
 
 			@Override
-			final void adjustMinMaxK(final int k, final int x) {
+			final void adjustMinMaxK(int k, int x) {
 				if (x <= beginA || k + x <= beginB) {
 					if (k > forward.middleK)
 						maxK = k;

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

@@ -157,7 +157,7 @@ public class SimilarityIndex {
 		}
 	}
 
-	void hash(byte[] raw, int ptr, final int end) throws TableFullException {
+	void hash(byte[] raw, int ptr, int end) throws TableFullException {
 		final boolean text = !RawText.isBinary(raw);
 		hashedCnt = 0;
 		while (ptr < end) {

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

@@ -121,11 +121,11 @@ public class DirCache {
 		}
 	};
 
-	static int cmp(final DirCacheEntry a, final DirCacheEntry b) {
+	static int cmp(DirCacheEntry a, DirCacheEntry b) {
 		return cmp(a.path, a.path.length, b);
 	}
 
-	static int cmp(final byte[] aPath, final int aLen, final DirCacheEntry b) {
+	static int cmp(byte[] aPath, int aLen, DirCacheEntry b) {
 		return cmp(aPath, aLen, b.path, b.path.length);
 	}
 
@@ -404,7 +404,7 @@ public class DirCache {
 		return new DirCacheEditor(this, entryCnt + 16);
 	}
 
-	void replace(final DirCacheEntry[] e, final int cnt) {
+	void replace(DirCacheEntry[] e, int cnt) {
 		sortedEntries = e;
 		entryCnt = cnt;
 		tree = null;
@@ -648,7 +648,7 @@ public class DirCache {
 		}
 	}
 
-	void writeTo(File dir, final OutputStream os) throws IOException {
+	void writeTo(File dir, OutputStream os) throws IOException {
 		final MessageDigest foot = Constants.newMessageDigest();
 		final DigestOutputStream dos = new DigestOutputStream(os, foot);
 
@@ -848,7 +848,7 @@ public class DirCache {
 		return nextIdx;
 	}
 
-	int nextEntry(final byte[] p, final int pLen, int nextIdx) {
+	int nextEntry(byte[] p, int pLen, int nextIdx) {
 		while (nextIdx < entryCnt) {
 			final DirCacheEntry next = sortedEntries[nextIdx];
 			if (!DirCacheTree.peq(p, next.path, pLen))

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

@@ -312,7 +312,7 @@ public class DirCacheEntry {
 		System.arraycopy(src.info, src.infoOffset, info, 0, INFO_LEN);
 	}
 
-	void write(final OutputStream os) throws IOException {
+	void write(OutputStream os) throws IOException {
 		final int len = isExtended() ? INFO_LEN_EXTENDED : INFO_LEN;
 		final int pathLen = path.length;
 		os.write(info, infoOffset, len);
@@ -719,7 +719,7 @@ public class DirCacheEntry {
 	 * @param keepStage
 	 *            if true, the stage attribute will not be copied
 	 */
-	void copyMetaData(final DirCacheEntry src, boolean keepStage) {
+	void copyMetaData(DirCacheEntry src, boolean keepStage) {
 		int origflags = NB.decodeUInt16(info, infoOffset + P_FLAGS);
 		int newflags = NB.decodeUInt16(src.info, src.infoOffset + P_FLAGS);
 		System.arraycopy(src.info, src.infoOffset, info, infoOffset, INFO_LEN);
@@ -771,7 +771,7 @@ public class DirCacheEntry {
 		}
 	}
 
-	static String toString(final byte[] path) {
+	static String toString(byte[] path) {
 		return Constants.CHARSET.decode(ByteBuffer.wrap(path)).toString();
 	}
 

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

@@ -124,7 +124,7 @@ public class DirCacheIterator extends AbstractTreeIterator {
 			parseEntry();
 	}
 
-	DirCacheIterator(final DirCacheIterator p, final DirCacheTree dct) {
+	DirCacheIterator(DirCacheIterator p, DirCacheTree dct) {
 		super(p, p.path, p.pathLen + 1);
 		cache = p.cache;
 		tree = dct;

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

@@ -185,7 +185,7 @@ public class DirCacheTree {
 		childCnt = subcnt;
 	}
 
-	void write(final byte[] tmp, final OutputStream os) throws IOException {
+	void write(byte[] tmp, OutputStream os) throws IOException {
 		int ptr = tmp.length;
 		tmp[--ptr] = '\n';
 		ptr = RawParseUtils.formatBase10(tmp, ptr, childCnt);
@@ -404,7 +404,7 @@ public class DirCacheTree {
 		return encodedName.length;
 	}
 
-	final boolean contains(final byte[] a, int aOff, final int aLen) {
+	final boolean contains(byte[] a, int aOff, int aLen) {
 		final byte[] e = encodedName;
 		final int eLen = e.length;
 		for (int eOff = 0; eOff < eLen && aOff < aLen; eOff++, aOff++)
@@ -531,7 +531,7 @@ public class DirCacheTree {
 		children[n] = null;
 	}
 
-	static boolean peq(final byte[] a, final byte[] b, int aLen) {
+	static boolean peq(byte[] a, byte[] b, int aLen) {
 		if (b.length < aLen)
 			return false;
 		for (aLen--; aLen >= 0; aLen--)

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

@@ -59,7 +59,7 @@ public class CompoundException extends Exception {
 	private static String format(Collection<Throwable> causes) {
 		final StringBuilder msg = new StringBuilder();
 		msg.append(JGitText.get().failureDueToOneOfTheFollowing);
-		for (final Throwable c : causes) {
+		for (Throwable c : causes) {
 			msg.append("  "); //$NON-NLS-1$
 			msg.append(c.getMessage());
 			msg.append("\n"); //$NON-NLS-1$

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

@@ -59,7 +59,7 @@ public class MissingBundlePrerequisiteException extends TransportException {
 	private static String format(Map<ObjectId, String> missingCommits) {
 		final StringBuilder r = new StringBuilder();
 		r.append(JGitText.get().missingPrerequisiteCommits);
-		for (final Map.Entry<ObjectId, String> e : missingCommits.entrySet()) {
+		for (Map.Entry<ObjectId, String> e : missingCommits.entrySet()) {
 			r.append("\n  "); //$NON-NLS-1$
 			r.append(e.getKey().name());
 			if (e.getValue() != null)

org.eclipse.jgit/src/org/eclipse/jgit/fnmatch/GroupHead.java

@@ -61,7 +61,7 @@ final class GroupHead extends AbstractHead {
 
 	private final boolean inverse;
 
-	GroupHead(String pattern, final String wholePattern)
+	GroupHead(String pattern, String wholePattern)
 			throws InvalidPatternException {
 		super(false);
 		this.characterClasses = new ArrayList<>();
@@ -214,7 +214,7 @@ final class GroupHead extends AbstractHead {
 	private static final class OneCharacterPattern implements CharacterPattern {
 		private char expectedCharacter;
 
-		OneCharacterPattern(final char c) {
+		OneCharacterPattern(char c) {
 			this.expectedCharacter = c;
 		}
 

org.eclipse.jgit/src/org/eclipse/jgit/fnmatch/RestrictedWildCardHead.java

@@ -47,7 +47,7 @@ package org.eclipse.jgit.fnmatch;
 final class RestrictedWildCardHead extends AbstractHead {
 	private final char excludedCharacter;
 
-	RestrictedWildCardHead(final char excludedCharacter, final boolean star) {
+	RestrictedWildCardHead(char excludedCharacter, boolean star) {
 		super(star);
 		this.excludedCharacter = excludedCharacter;
 	}

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

@@ -497,7 +497,7 @@ public abstract class DfsObjDatabase extends ObjectDatabase {
 		} while (!packList.compareAndSet(o, n));
 	}
 
-	PackList scanPacks(final PackList original) throws IOException {
+	PackList scanPacks(PackList original) throws IOException {
 		PackList o, n;
 		synchronized (packList) {
 			do {

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

@@ -60,7 +60,7 @@ class DfsObjectToPack extends ObjectToPack {
 	/** Length of the data section of the object. */
 	long length;
 
-	DfsObjectToPack(AnyObjectId src, final int type) {
+	DfsObjectToPack(AnyObjectId src, int type) {
 		super(src, type);
 	}
 

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

@@ -58,7 +58,7 @@ import org.eclipse.jgit.internal.storage.pack.PackOutputStream;
 final class ByteArrayWindow extends ByteWindow {
 	private final byte[] array;
 
-	ByteArrayWindow(final PackFile pack, final long o, final byte[] b) {
+	ByteArrayWindow(PackFile pack, long o, byte[] b) {
 		super(pack, o, b.length);
 		array = b;
 	}

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

@@ -60,7 +60,7 @@ import org.eclipse.jgit.internal.storage.pack.PackOutputStream;
 final class ByteBufferWindow extends ByteWindow {
 	private final ByteBuffer buffer;
 
-	ByteBufferWindow(final PackFile pack, final long o, final ByteBuffer b) {
+	ByteBufferWindow(PackFile pack, long o, ByteBuffer b) {
 		super(pack, o, b.capacity());
 		buffer = b;
 	}

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

@@ -86,7 +86,7 @@ abstract class ByteWindow {
 		return (int) (end - start);
 	}
 
-	final boolean contains(final PackFile neededFile, final long neededPos) {
+	final boolean contains(PackFile neededFile, long neededPos) {
 		return pack == neededFile && start <= neededPos && neededPos < end;
 	}
 

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

@@ -205,7 +205,7 @@ class CachedObjectDirectory extends FileObjectDatabase {
 	}
 
 	@Override
-	ObjectLoader openObject(final WindowCursor curs, final AnyObjectId objectId)
+	ObjectLoader openObject(WindowCursor curs, AnyObjectId objectId)
 			throws IOException {
 		return openObject(curs, objectId, null);
 	}

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

@@ -82,7 +82,7 @@ class DeltaBaseCache {
 		cache = new Slot[CACHE_SZ];
 	}
 
-	Entry get(final PackFile pack, final long position) {
+	Entry get(PackFile pack, long position) {
 		Slot e = cache[hash(position)];
 		if (e == null)
 			return null;
@@ -168,7 +168,7 @@ class DeltaBaseCache {
 
 		final int type;
 
-		Entry(final byte[] aData, final int aType) {
+		Entry(byte[] aData, int aType) {
 			data = aData;
 			type = aType;
 		}