diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java
index 045f3571e..bf6ee3a94 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java
@@ -310,24 +310,24 @@ class Branch extends TextBuiltin {
 			throws IOException {
 		String current = db.getBranch();
 		ObjectId head = db.resolve(Constants.HEAD);
-		for (String branch : branches) {
-			if (branch.equals(current)) {
-				throw die(MessageFormat.format(CLIText.get().cannotDeleteTheBranchWhichYouAreCurrentlyOn, branch));
+		for (String b : branches) {
+			if (b.equals(current)) {
+				throw die(MessageFormat.format(CLIText.get().cannotDeleteTheBranchWhichYouAreCurrentlyOn, b));
 			}
 			RefUpdate update = db.updateRef((remote ? Constants.R_REMOTES
 					: Constants.R_HEADS)
-					+ branch);
+					+ b);
 			update.setNewObjectId(head);
 			update.setForceUpdate(force || remote);
 			Result result = update.delete();
 			if (result == Result.REJECTED) {
-				throw die(MessageFormat.format(CLIText.get().branchIsNotAnAncestorOfYourCurrentHEAD, branch));
+				throw die(MessageFormat.format(CLIText.get().branchIsNotAnAncestorOfYourCurrentHEAD, b));
 			} else if (result == Result.NEW)
-				throw die(MessageFormat.format(CLIText.get().branchNotFound, branch));
+				throw die(MessageFormat.format(CLIText.get().branchNotFound, b));
 			if (remote)
-				outw.println(MessageFormat.format(CLIText.get().deletedRemoteBranch, branch));
+				outw.println(MessageFormat.format(CLIText.get().deletedRemoteBranch, b));
 			else if (verbose)
-				outw.println(MessageFormat.format(CLIText.get().deletedBranch, branch));
+				outw.println(MessageFormat.format(CLIText.get().deletedBranch, b));
 		}
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java
index ad3ff60a0..d842046bb 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java
@@ -69,23 +69,24 @@ public class ApplyCommandTest extends RepositoryTestCase {
 
 	private ApplyResult init(final String name, final boolean preExists,
 			final boolean postExists) throws Exception {
-		Git git = new Git(db);
-
-		if (preExists) {
-			a = new RawText(readFile(name + "_PreImage"));
-			write(new File(db.getDirectory().getParent(), name),
-					a.getString(0, a.size(), false));
-
-			git.add().addFilepattern(name).call();
-			git.commit().setMessage("PreImage").call();
+		try (Git git = new Git(db)) {
+			if (preExists) {
+				a = new RawText(readFile(name + "_PreImage"));
+				write(new File(db.getDirectory().getParent(), name),
+						a.getString(0, a.size(), false));
+
+				git.add().addFilepattern(name).call();
+				git.commit().setMessage("PreImage").call();
+			}
+
+			if (postExists) {
+				b = new RawText(readFile(name + "_PostImage"));
+			}
+
+			return git
+					.apply()
+					.setPatch(getTestResource(name + ".patch")).call();
 		}
-
-		if (postExists)
-			b = new RawText(readFile(name + "_PostImage"));
-
-		return git
-				.apply()
-				.setPatch(getTestResource(name + ".patch")).call();
 	}
 
 	@Test
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackFileTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackFileTest.java
index cb80768e5..ba07d6842 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackFileTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackFileTest.java
@@ -191,119 +191,122 @@ public class PackFileTest extends LocalDiskRepositoryTestCase {
 
 	@Test
 	public void testDelta_SmallObjectChain() throws Exception {
-		ObjectInserter.Formatter fmt = new ObjectInserter.Formatter();
-		byte[] data0 = new byte[512];
-		Arrays.fill(data0, (byte) 0xf3);
-		ObjectId id0 = fmt.idFor(Constants.OBJ_BLOB, data0);
-
-		TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(64 * 1024);
-		packHeader(pack, 4);
-		objectHeader(pack, Constants.OBJ_BLOB, data0.length);
-		deflate(pack, data0);
-
-		byte[] data1 = clone(0x01, data0);
-		byte[] delta1 = delta(data0, data1);
-		ObjectId id1 = fmt.idFor(Constants.OBJ_BLOB, data1);
-		objectHeader(pack, Constants.OBJ_REF_DELTA, delta1.length);
-		id0.copyRawTo(pack);
-		deflate(pack, delta1);
-
-		byte[] data2 = clone(0x02, data1);
-		byte[] delta2 = delta(data1, data2);
-		ObjectId id2 = fmt.idFor(Constants.OBJ_BLOB, data2);
-		objectHeader(pack, Constants.OBJ_REF_DELTA, delta2.length);
-		id1.copyRawTo(pack);
-		deflate(pack, delta2);
-
-		byte[] data3 = clone(0x03, data2);
-		byte[] delta3 = delta(data2, data3);
-		ObjectId id3 = fmt.idFor(Constants.OBJ_BLOB, data3);
-		objectHeader(pack, Constants.OBJ_REF_DELTA, delta3.length);
-		id2.copyRawTo(pack);
-		deflate(pack, delta3);
-
-		digest(pack);
-		PackParser ip = index(pack.toByteArray());
-		ip.setAllowThin(true);
-		ip.parse(NullProgressMonitor.INSTANCE);
-
-		assertTrue("has blob", wc.has(id3));
-
-		ObjectLoader ol = wc.open(id3);
-		assertNotNull("created loader", ol);
-		assertEquals(Constants.OBJ_BLOB, ol.getType());
-		assertEquals(data3.length, ol.getSize());
-		assertFalse("is large", ol.isLarge());
-		assertNotNull(ol.getCachedBytes());
-		assertArrayEquals(data3, ol.getCachedBytes());
-
-		ObjectStream in = ol.openStream();
-		assertNotNull("have stream", in);
-		assertEquals(Constants.OBJ_BLOB, in.getType());
-		assertEquals(data3.length, in.getSize());
-		byte[] act = new byte[data3.length];
-		IO.readFully(in, act, 0, data3.length);
-		assertTrue("same content", Arrays.equals(act, data3));
-		assertEquals("stream at EOF", -1, in.read());
-		in.close();
+		try (ObjectInserter.Formatter fmt = new ObjectInserter.Formatter()) {
+			byte[] data0 = new byte[512];
+			Arrays.fill(data0, (byte) 0xf3);
+			ObjectId id0 = fmt.idFor(Constants.OBJ_BLOB, data0);
+
+			TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(64 * 1024);
+			packHeader(pack, 4);
+			objectHeader(pack, Constants.OBJ_BLOB, data0.length);
+			deflate(pack, data0);
+
+			byte[] data1 = clone(0x01, data0);
+			byte[] delta1 = delta(data0, data1);
+			ObjectId id1 = fmt.idFor(Constants.OBJ_BLOB, data1);
+			objectHeader(pack, Constants.OBJ_REF_DELTA, delta1.length);
+			id0.copyRawTo(pack);
+			deflate(pack, delta1);
+
+			byte[] data2 = clone(0x02, data1);
+			byte[] delta2 = delta(data1, data2);
+			ObjectId id2 = fmt.idFor(Constants.OBJ_BLOB, data2);
+			objectHeader(pack, Constants.OBJ_REF_DELTA, delta2.length);
+			id1.copyRawTo(pack);
+			deflate(pack, delta2);
+
+			byte[] data3 = clone(0x03, data2);
+			byte[] delta3 = delta(data2, data3);
+			ObjectId id3 = fmt.idFor(Constants.OBJ_BLOB, data3);
+			objectHeader(pack, Constants.OBJ_REF_DELTA, delta3.length);
+			id2.copyRawTo(pack);
+			deflate(pack, delta3);
+
+			digest(pack);
+			PackParser ip = index(pack.toByteArray());
+			ip.setAllowThin(true);
+			ip.parse(NullProgressMonitor.INSTANCE);
+
+			assertTrue("has blob", wc.has(id3));
+
+			ObjectLoader ol = wc.open(id3);
+			assertNotNull("created loader", ol);
+			assertEquals(Constants.OBJ_BLOB, ol.getType());
+			assertEquals(data3.length, ol.getSize());
+			assertFalse("is large", ol.isLarge());
+			assertNotNull(ol.getCachedBytes());
+			assertArrayEquals(data3, ol.getCachedBytes());
+
+			ObjectStream in = ol.openStream();
+			assertNotNull("have stream", in);
+			assertEquals(Constants.OBJ_BLOB, in.getType());
+			assertEquals(data3.length, in.getSize());
+			byte[] act = new byte[data3.length];
+			IO.readFully(in, act, 0, data3.length);
+			assertTrue("same content", Arrays.equals(act, data3));
+			assertEquals("stream at EOF", -1, in.read());
+			in.close();
+		}
 	}
 
 	@Test
 	public void testDelta_FailsOver2GiB() throws Exception {
-		ObjectInserter.Formatter fmt = new ObjectInserter.Formatter();
-		byte[] base = new byte[] { 'a' };
-		ObjectId idA = fmt.idFor(Constants.OBJ_BLOB, base);
-		ObjectId idB = fmt.idFor(Constants.OBJ_BLOB, new byte[] { 'b' });
-
-		PackedObjectInfo a = new PackedObjectInfo(idA);
-		PackedObjectInfo b = new PackedObjectInfo(idB);
-
-		TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(64 * 1024);
-		packHeader(pack, 2);
-		a.setOffset(pack.length());
-		objectHeader(pack, Constants.OBJ_BLOB, base.length);
-		deflate(pack, base);
-
-		ByteArrayOutputStream tmp = new ByteArrayOutputStream();
-		DeltaEncoder de = new DeltaEncoder(tmp, base.length, 3L << 30);
-		de.copy(0, 1);
-		byte[] delta = tmp.toByteArray();
-		b.setOffset(pack.length());
-		objectHeader(pack, Constants.OBJ_REF_DELTA, delta.length);
-		idA.copyRawTo(pack);
-		deflate(pack, delta);
-		byte[] footer = digest(pack);
-
-		File dir = new File(repo.getObjectDatabase().getDirectory(), "pack");
-		File packName = new File(dir, idA.name() + ".pack");
-		File idxName = new File(dir, idA.name() + ".idx");
-
-		FileOutputStream f = new FileOutputStream(packName);
-		try {
-			f.write(pack.toByteArray());
-		} finally {
-			f.close();
-		}
-
-		f = new FileOutputStream(idxName);
-		try {
-			List<PackedObjectInfo> list = new ArrayList<PackedObjectInfo>();
-			list.add(a);
-			list.add(b);
-			Collections.sort(list);
-			new PackIndexWriterV1(f).write(list, footer);
-		} finally {
-			f.close();
-		}
-
-		PackFile packFile = new PackFile(packName, PackExt.INDEX.getBit());
-		try {
-			packFile.get(wc, b);
-			fail("expected LargeObjectException.ExceedsByteArrayLimit");
-		} catch (LargeObjectException.ExceedsByteArrayLimit bad) {
-			assertNull(bad.getObjectId());
-		} finally {
-			packFile.close();
+		try (ObjectInserter.Formatter fmt = new ObjectInserter.Formatter()) {
+			byte[] base = new byte[] { 'a' };
+			ObjectId idA = fmt.idFor(Constants.OBJ_BLOB, base);
+			ObjectId idB = fmt.idFor(Constants.OBJ_BLOB, new byte[] { 'b' });
+
+			PackedObjectInfo a = new PackedObjectInfo(idA);
+			PackedObjectInfo b = new PackedObjectInfo(idB);
+
+			TemporaryBuffer.Heap pack = new TemporaryBuffer.Heap(64 * 1024);
+			packHeader(pack, 2);
+			a.setOffset(pack.length());
+			objectHeader(pack, Constants.OBJ_BLOB, base.length);
+			deflate(pack, base);
+
+			ByteArrayOutputStream tmp = new ByteArrayOutputStream();
+			DeltaEncoder de = new DeltaEncoder(tmp, base.length, 3L << 30);
+			de.copy(0, 1);
+			byte[] delta = tmp.toByteArray();
+			b.setOffset(pack.length());
+			objectHeader(pack, Constants.OBJ_REF_DELTA, delta.length);
+			idA.copyRawTo(pack);
+			deflate(pack, delta);
+			byte[] footer = digest(pack);
+
+			File dir = new File(repo.getObjectDatabase().getDirectory(),
+					"pack");
+			File packName = new File(dir, idA.name() + ".pack");
+			File idxName = new File(dir, idA.name() + ".idx");
+
+			FileOutputStream f = new FileOutputStream(packName);
+			try {
+				f.write(pack.toByteArray());
+			} finally {
+				f.close();
+			}
+
+			f = new FileOutputStream(idxName);
+			try {
+				List<PackedObjectInfo> list = new ArrayList<PackedObjectInfo>();
+				list.add(a);
+				list.add(b);
+				Collections.sort(list);
+				new PackIndexWriterV1(f).write(list, footer);
+			} finally {
+				f.close();
+			}
+
+			PackFile packFile = new PackFile(packName, PackExt.INDEX.getBit());
+			try {
+				packFile.get(wc, b);
+				fail("expected LargeObjectException.ExceedsByteArrayLimit");
+			} catch (LargeObjectException.ExceedsByteArrayLimit bad) {
+				assertNull(bad.getObjectId());
+			} finally {
+				packFile.close();
+			}
 		}
 	}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutTest.java
index 92901f826..c1b882a65 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutTest.java
@@ -140,52 +140,53 @@ public class DirCacheCheckoutTest extends RepositoryTestCase {
 	@Test
 	public void testResetHard() throws IOException, NoFilepatternException,
 			GitAPIException {
-		Git git = new Git(db);
-		writeTrashFile("f", "f()");
-		writeTrashFile("D/g", "g()");
-		git.add().addFilepattern(".").call();
-		git.commit().setMessage("inital").call();
-		assertIndex(mkmap("f", "f()", "D/g", "g()"));
-
-		git.branchCreate().setName("topic").call();
-
-		writeTrashFile("f", "f()\nmaster");
-		writeTrashFile("D/g", "g()\ng2()");
-		writeTrashFile("E/h", "h()");
-		git.add().addFilepattern(".").call();
-		RevCommit master = git.commit().setMessage("master-1").call();
-		assertIndex(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h", "h()"));
-
-		checkoutBranch("refs/heads/topic");
-		assertIndex(mkmap("f", "f()", "D/g", "g()"));
-
-		writeTrashFile("f", "f()\nside");
-		assertTrue(new File(db.getWorkTree(), "D/g").delete());
-		writeTrashFile("G/i", "i()");
-		git.add().addFilepattern(".").call();
-		git.add().addFilepattern(".").setUpdate(true).call();
-		RevCommit topic = git.commit().setMessage("topic-1").call();
-		assertIndex(mkmap("f", "f()\nside", "G/i", "i()"));
-
-		writeTrashFile("untracked", "untracked");
-
-		resetHard(master);
-		assertIndex(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h", "h()"));
-		resetHard(topic);
-		assertIndex(mkmap("f", "f()\nside", "G/i", "i()"));
-		assertWorkDir(mkmap("f", "f()\nside", "G/i", "i()", "untracked",
-				"untracked"));
-
-		assertEquals(MergeStatus.CONFLICTING, git.merge().include(master)
-				.call().getMergeStatus());
-		assertEquals(
-				"[D/g, mode:100644, stage:1][D/g, mode:100644, stage:3][E/h, mode:100644][G/i, mode:100644][f, mode:100644, stage:1][f, mode:100644, stage:2][f, mode:100644, stage:3]",
-				indexState(0));
-
-		resetHard(master);
-		assertIndex(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h", "h()"));
-		assertWorkDir(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h",
-				"h()", "untracked", "untracked"));
+		try (Git git = new Git(db)) {
+			writeTrashFile("f", "f()");
+			writeTrashFile("D/g", "g()");
+			git.add().addFilepattern(".").call();
+			git.commit().setMessage("inital").call();
+			assertIndex(mkmap("f", "f()", "D/g", "g()"));
+
+			git.branchCreate().setName("topic").call();
+
+			writeTrashFile("f", "f()\nmaster");
+			writeTrashFile("D/g", "g()\ng2()");
+			writeTrashFile("E/h", "h()");
+			git.add().addFilepattern(".").call();
+			RevCommit master = git.commit().setMessage("master-1").call();
+			assertIndex(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h", "h()"));
+
+			checkoutBranch("refs/heads/topic");
+			assertIndex(mkmap("f", "f()", "D/g", "g()"));
+
+			writeTrashFile("f", "f()\nside");
+			assertTrue(new File(db.getWorkTree(), "D/g").delete());
+			writeTrashFile("G/i", "i()");
+			git.add().addFilepattern(".").call();
+			git.add().addFilepattern(".").setUpdate(true).call();
+			RevCommit topic = git.commit().setMessage("topic-1").call();
+			assertIndex(mkmap("f", "f()\nside", "G/i", "i()"));
+
+			writeTrashFile("untracked", "untracked");
+
+			resetHard(master);
+			assertIndex(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h", "h()"));
+			resetHard(topic);
+			assertIndex(mkmap("f", "f()\nside", "G/i", "i()"));
+			assertWorkDir(mkmap("f", "f()\nside", "G/i", "i()", "untracked",
+					"untracked"));
+
+			assertEquals(MergeStatus.CONFLICTING, git.merge().include(master)
+					.call().getMergeStatus());
+			assertEquals(
+					"[D/g, mode:100644, stage:1][D/g, mode:100644, stage:3][E/h, mode:100644][G/i, mode:100644][f, mode:100644, stage:1][f, mode:100644, stage:2][f, mode:100644, stage:3]",
+					indexState(0));
+
+			resetHard(master);
+			assertIndex(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h", "h()"));
+			assertWorkDir(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h",
+					"h()", "untracked", "untracked"));
+		}
 	}
 
 	/**
@@ -200,21 +201,22 @@ public class DirCacheCheckoutTest extends RepositoryTestCase {
 	@Test
 	public void testResetHardFromIndexEntryWithoutFileToTreeWithoutFile()
 			throws Exception {
-		Git git = new Git(db);
-		writeTrashFile("x", "x");
-		git.add().addFilepattern("x").call();
-		RevCommit id1 = git.commit().setMessage("c1").call();
-
-		writeTrashFile("f/g", "f/g");
-		git.rm().addFilepattern("x").call();
-		git.add().addFilepattern("f/g").call();
-		git.commit().setMessage("c2").call();
-		deleteTrashFile("f/g");
-		deleteTrashFile("f");
-
-		// The actual test
-		git.reset().setMode(ResetType.HARD).setRef(id1.getName()).call();
-		assertIndex(mkmap("x", "x"));
+		try (Git git = new Git(db)) {
+			writeTrashFile("x", "x");
+			git.add().addFilepattern("x").call();
+			RevCommit id1 = git.commit().setMessage("c1").call();
+
+			writeTrashFile("f/g", "f/g");
+			git.rm().addFilepattern("x").call();
+			git.add().addFilepattern("f/g").call();
+			git.commit().setMessage("c2").call();
+			deleteTrashFile("f/g");
+			deleteTrashFile("f");
+
+			// The actual test
+			git.reset().setMode(ResetType.HARD).setRef(id1.getName()).call();
+			assertIndex(mkmap("x", "x"));
+		}
 	}
 
 	/**
@@ -224,14 +226,14 @@ public class DirCacheCheckoutTest extends RepositoryTestCase {
 	 */
 	@Test
 	public void testInitialCheckout() throws Exception {
-		Git git = new Git(db);
-
-		TestRepository<Repository> db_t = new TestRepository<Repository>(db);
-		BranchBuilder master = db_t.branch("master");
-		master.commit().add("f", "1").message("m0").create();
-		assertFalse(new File(db.getWorkTree(), "f").exists());
-		git.checkout().setName("master").call();
-		assertTrue(new File(db.getWorkTree(), "f").exists());
+		try (Git git = new Git(db)) {
+			TestRepository<Repository> db_t = new TestRepository<Repository>(db);
+			BranchBuilder master = db_t.branch("master");
+			master.commit().add("f", "1").message("m0").create();
+			assertFalse(new File(db.getWorkTree(), "f").exists());
+			git.checkout().setName("master").call();
+			assertTrue(new File(db.getWorkTree(), "f").exists());
+		}
 	}
 
 	private DirCacheCheckout resetHard(RevCommit commit)
@@ -1612,46 +1614,47 @@ public class DirCacheCheckoutTest extends RepositoryTestCase {
 	public void assertWorkDir(Map<String, String> i)
 			throws CorruptObjectException,
 			IOException {
-		TreeWalk walk = new TreeWalk(db);
-		walk.setRecursive(false);
-		walk.addTree(new FileTreeIterator(db));
-		String expectedValue;
-		String path;
-		int nrFiles = 0;
-		FileTreeIterator ft;
-		while (walk.next()) {
-			ft = walk.getTree(0, FileTreeIterator.class);
-			path = ft.getEntryPathString();
-			expectedValue = i.get(path);
-			File file = new File(db.getWorkTree(), path);
-			assertTrue(file.exists());
-			if (file.isFile()) {
-				assertNotNull("found unexpected file for path " + path
-						+ " in workdir", expectedValue);
-				FileInputStream is = new FileInputStream(file);
-				byte[] buffer = new byte[(int) file.length()];
-				int offset = 0;
-				int numRead = 0;
-				while (offset < buffer.length
-						&& (numRead = is.read(buffer, offset, buffer.length
-								- offset)) >= 0) {
-					offset += numRead;
-				}
-				is.close();
-				assertArrayEquals("unexpected content for path " + path
-						+ " in workDir. ", buffer, i.get(path).getBytes());
-				nrFiles++;
-			} else if (file.isDirectory()) {
-				if (file.list().length == 0) {
-					assertEquals("found unexpected empty folder for path "
-							+ path + " in workDir. ", "/", i.get(path));
+		try (TreeWalk walk = new TreeWalk(db)) {
+			walk.setRecursive(false);
+			walk.addTree(new FileTreeIterator(db));
+			String expectedValue;
+			String path;
+			int nrFiles = 0;
+			FileTreeIterator ft;
+			while (walk.next()) {
+				ft = walk.getTree(0, FileTreeIterator.class);
+				path = ft.getEntryPathString();
+				expectedValue = i.get(path);
+				File file = new File(db.getWorkTree(), path);
+				assertTrue(file.exists());
+				if (file.isFile()) {
+					assertNotNull("found unexpected file for path " + path
+							+ " in workdir", expectedValue);
+					FileInputStream is = new FileInputStream(file);
+					byte[] buffer = new byte[(int) file.length()];
+					int offset = 0;
+					int numRead = 0;
+					while (offset < buffer.length
+							&& (numRead = is.read(buffer, offset, buffer.length
+									- offset)) >= 0) {
+						offset += numRead;
+					}
+					is.close();
+					assertArrayEquals("unexpected content for path " + path
+							+ " in workDir. ", buffer, i.get(path).getBytes());
 					nrFiles++;
+				} else if (file.isDirectory()) {
+					if (file.list().length == 0) {
+						assertEquals("found unexpected empty folder for path "
+								+ path + " in workDir. ", "/", i.get(path));
+						nrFiles++;
+					}
+				}
+				if (walk.isSubtree()) {
+					walk.enterSubtree();
 				}
 			}
-			if (walk.isSubtree()) {
-				walk.enterSubtree();
-			}
+			assertEquals("WorkDir has not the right size.", i.size(), nrFiles);
 		}
-		assertEquals("WorkDir has not the right size.", i.size(), nrFiles);
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
index b5057ad28..0abb8ba4e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
@@ -312,7 +312,7 @@ public class CommitCommand extends GitCommand<RevCommit> {
 		}
 	}
 
-	private void insertChangeId(ObjectId treeId) throws IOException {
+	private void insertChangeId(ObjectId treeId) {
 		ObjectId firstParentId = null;
 		if (!parents.isEmpty())
 			firstParentId = parents.get(0);