diff --git a/org.eclipse.jgit.iplog/src/org/eclipse/jgit/iplog/IpLogMeta.java b/org.eclipse.jgit.iplog/src/org/eclipse/jgit/iplog/IpLogMeta.java
index 2799a4a..372469d 100644
--- a/org.eclipse.jgit.iplog/src/org/eclipse/jgit/iplog/IpLogMeta.java
+++ b/org.eclipse.jgit.iplog/src/org/eclipse/jgit/iplog/IpLogMeta.java
@@ -61,6 +61,7 @@
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.storage.file.LockFile;
+import org.eclipse.jgit.util.FS;
 
 /**
  * Manages the {@code .eclipse_iplog} file in a project.
@@ -167,6 +168,9 @@ private List<Project> parseProjects(final Config cfg,
 	 *
 	 * @param file
 	 *            local file to update with current CQ records.
+	 * @param fs
+	 *            the file system abstraction which will be necessary to perform
+	 *            certain file system operations.
 	 * @param base
 	 *            base https:// URL of the IPzilla server.
 	 * @param username
@@ -181,16 +185,16 @@ private List<Project> parseProjects(final Config cfg,
 	 *             the local file cannot be read, as it is not a valid
 	 *             configuration file format.
 	 */
-	public void syncCQs(File file, URL base, String username, String password)
-			throws IOException, ConfigInvalidException {
+	public void syncCQs(File file, FS fs, URL base, String username,
+			String password) throws IOException, ConfigInvalidException {
 		if (!file.getParentFile().exists())
 			file.getParentFile().mkdirs();
 
-		LockFile lf = new LockFile(file);
+		LockFile lf = new LockFile(file, fs);
 		if (!lf.lock())
 			throw new IOException(MessageFormat.format(IpLogText.get().cannotLock, file));
 		try {
-			FileBasedConfig cfg = new FileBasedConfig(file);
+			FileBasedConfig cfg = new FileBasedConfig(file, fs);
 			cfg.load();
 			loadFrom(cfg);
 
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java
index 2b82d82..47956e5 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java
@@ -69,6 +69,7 @@
 import org.eclipse.jgit.storage.file.FileRepository;
 import org.eclipse.jgit.storage.file.WindowCache;
 import org.eclipse.jgit.storage.file.WindowCacheConfig;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.IO;
 import org.eclipse.jgit.util.SystemReader;
 
@@ -128,7 +129,7 @@ public void run() {
 
 		mockSystemReader = new MockSystemReader();
 		mockSystemReader.userGitConfig = new FileBasedConfig(new File(trash,
-				"usergitconfig"));
+				"usergitconfig"), FS.DETECTED);
 		ceilTestDirectories(getCeilings());
 		SystemReader.setInstance(mockSystemReader);
 
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/MockSystemReader.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/MockSystemReader.java
index eb08417..5c2e77f 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/MockSystemReader.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/MockSystemReader.java
@@ -67,7 +67,7 @@ public MockSystemReader() {
 		init(Constants.GIT_AUTHOR_EMAIL_KEY);
 		init(Constants.GIT_COMMITTER_NAME_KEY);
 		init(Constants.GIT_COMMITTER_EMAIL_KEY);
-		userGitConfig = new FileBasedConfig(null) {
+		userGitConfig = new FileBasedConfig(null, null) {
 			@Override
 			public void load() throws IOException, ConfigInvalidException {
 				// Do nothing
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java
index 3c58271..afe1c0b 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java
@@ -654,7 +654,7 @@ private static File nameFor(ObjectDirectory odb, ObjectId name, String t) {
 
 	private void writeFile(final File p, final byte[] bin) throws IOException,
 			ObjectWritingException {
-		final LockFile lck = new LockFile(p);
+		final LockFile lck = new LockFile(p, db.getFS());
 		if (!lck.lock())
 			throw new ObjectWritingException("Can't write " + p);
 		try {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java
index 5b75c1b..b8e2a8f 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java
@@ -227,7 +227,7 @@ private void detachHead() throws IOException {
 		final ObjectId id = db.resolve(Constants.HEAD);
 		if (!ObjectId.isId(head) && id != null) {
 			final LockFile lf;
-			lf = new LockFile(new File(db.getDirectory(), Constants.HEAD));
+			lf = new LockFile(new File(db.getDirectory(), Constants.HEAD), db.getFS());
 			if (!lf.lock())
 				throw new IOException(MessageFormat.format(CLIText.get().cannotLock, Constants.HEAD));
 			lf.write(id);
@@ -254,7 +254,7 @@ private void recreateRefs() throws Exception {
 			protected void writeFile(final String name, final byte[] content)
 					throws IOException {
 				final File file = new File(db.getDirectory(), name);
-				final LockFile lck = new LockFile(file);
+				final LockFile lck = new LockFile(file, db.getFS());
 				if (!lck.lock())
 					throw new ObjectWritingException(MessageFormat.format(CLIText.get().cantWrite, file));
 				try {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/eclipse/Iplog.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/eclipse/Iplog.java
index a99e0ab..84859a8 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/eclipse/Iplog.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/eclipse/Iplog.java
@@ -98,7 +98,7 @@ else if (version == null)
 		if (output != null) {
 			if (!output.getParentFile().exists())
 				output.getParentFile().mkdirs();
-			LockFile lf = new LockFile(output);
+			LockFile lf = new LockFile(output, db.getFS());
 			if (!lf.lock())
 				throw die(MessageFormat.format(CLIText.get().cannotLock, output));
 			try {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/eclipse/Ipzilla.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/eclipse/Ipzilla.java
index b563f07..6653209 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/eclipse/Ipzilla.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/eclipse/Ipzilla.java
@@ -94,6 +94,6 @@ protected void run() throws Exception {
 			output = new File(db.getWorkTree(), IpLogMeta.IPLOG_CONFIG_FILE);
 
 		IpLogMeta meta = new IpLogMeta();
-		meta.syncCQs(output, ipzilla, username, password);
+		meta.syncCQs(output, db.getFS(), ipzilla, username, password);
 	}
 }
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/AbstractTreeIteratorHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/AbstractTreeIteratorHandler.java
index 0198160..7126982 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/AbstractTreeIteratorHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/AbstractTreeIteratorHandler.java
@@ -103,7 +103,7 @@ public int parseArguments(final Parameters params) throws CmdLineException {
 		if (new File(name).isFile()) {
 			final DirCache dirc;
 			try {
-				dirc = DirCache.read(new File(name));
+				dirc = DirCache.read(new File(name), FS.DETECTED);
 			} catch (IOException e) {
 				throw new CmdLineException(MessageFormat.format(CLIText.get().notAnIndexFile, name), e);
 			}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBasicTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBasicTest.java
index c3ac952..b6e4e42 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBasicTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBasicTest.java
@@ -63,7 +63,7 @@ public void testReadMissing_TempIndex() throws Exception {
 		final File idx = new File(db.getDirectory(), "tmp_index");
 		assertFalse(idx.exists());
 
-		final DirCache dc = DirCache.read(idx);
+		final DirCache dc = DirCache.read(idx, db.getFS());
 		assertNotNull(dc);
 		assertEquals(0, dc.getEntryCount());
 	}
@@ -91,7 +91,7 @@ public void testLockMissing_TempIndex() throws Exception {
 		assertFalse(idx.exists());
 		assertFalse(lck.exists());
 
-		final DirCache dc = DirCache.lock(idx);
+		final DirCache dc = DirCache.lock(idx, db.getFS());
 		assertNotNull(dc);
 		assertFalse(idx.exists());
 		assertTrue(lck.exists());
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheCGitCompatabilityTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheCGitCompatabilityTest.java
index fa5fea8..f37d040 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheCGitCompatabilityTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheCGitCompatabilityTest.java
@@ -58,6 +58,7 @@
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.treewalk.TreeWalk;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.JGitTestUtil;
 
 public class DirCacheCGitCompatabilityTest extends LocalDiskRepositoryTestCase {
@@ -65,7 +66,7 @@ public class DirCacheCGitCompatabilityTest extends LocalDiskRepositoryTestCase {
 
 	public void testReadIndex_LsFiles() throws Exception {
 		final Map<String, CGitIndexRecord> ls = readLsFiles();
-		final DirCache dc = new DirCache(index);
+		final DirCache dc = new DirCache(index, FS.DETECTED);
 		assertEquals(0, dc.getEntryCount());
 		dc.read();
 		assertEquals(ls.size(), dc.getEntryCount());
@@ -79,7 +80,7 @@ public void testReadIndex_LsFiles() throws Exception {
 	public void testTreeWalk_LsFiles() throws Exception {
 		final Repository db = createBareRepository();
 		final Map<String, CGitIndexRecord> ls = readLsFiles();
-		final DirCache dc = new DirCache(index);
+		final DirCache dc = new DirCache(index, db.getFS());
 		assertEquals(0, dc.getEntryCount());
 		dc.read();
 		assertEquals(ls.size(), dc.getEntryCount());
@@ -102,14 +103,16 @@ public void testTreeWalk_LsFiles() throws Exception {
 	}
 
 	public void testUnsupportedOptionalExtension() throws Exception {
-		final DirCache dc = new DirCache(pathOf("gitgit.index.ZZZZ"));
+		final DirCache dc = new DirCache(pathOf("gitgit.index.ZZZZ"),
+				FS.DETECTED);
 		dc.read();
 		assertEquals(1, dc.getEntryCount());
 		assertEquals("A", dc.getEntry(0).getPathString());
 	}
 
 	public void testUnsupportedRequiredExtension() throws Exception {
-		final DirCache dc = new DirCache(pathOf("gitgit.index.aaaa"));
+		final DirCache dc = new DirCache(pathOf("gitgit.index.aaaa"),
+				FS.DETECTED);
 		try {
 			dc.read();
 			fail("Cache loaded an unsupported extension");
@@ -120,7 +123,8 @@ public void testUnsupportedRequiredExtension() throws Exception {
 	}
 
 	public void testCorruptChecksumAtFooter() throws Exception {
-		final DirCache dc = new DirCache(pathOf("gitgit.index.badchecksum"));
+		final DirCache dc = new DirCache(pathOf("gitgit.index.badchecksum"),
+				FS.DETECTED);
 		try {
 			dc.read();
 			fail("Cache loaded despite corrupt checksum");
@@ -143,7 +147,7 @@ private static void assertEqual(final CGitIndexRecord c,
 	public void testReadIndex_DirCacheTree() throws Exception {
 		final Map<String, CGitIndexRecord> cList = readLsFiles();
 		final Map<String, CGitLsTreeRecord> cTree = readLsTree();
-		final DirCache dc = new DirCache(index);
+		final DirCache dc = new DirCache(index, FS.DETECTED);
 		assertEquals(0, dc.getEntryCount());
 		dc.read();
 		assertEquals(cList.size(), dc.getEntryCount());
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/RefUpdateTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/RefUpdateTest.java
index 875c2e9..8717008 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/RefUpdateTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/RefUpdateTest.java
@@ -555,13 +555,15 @@ public void testUpdateRefLockFailureLocked() throws IOException {
 		ObjectId pid = db.resolve("refs/heads/master^");
 		RefUpdate updateRef = db.updateRef("refs/heads/master");
 		updateRef.setNewObjectId(pid);
-		LockFile lockFile1 = new LockFile(new File(db.getDirectory(),"refs/heads/master"));
+		LockFile lockFile1 = new LockFile(new File(db.getDirectory(),
+				"refs/heads/master"), db.getFS());
 		try {
 			assertTrue(lockFile1.lock()); // precondition to test
 			Result update = updateRef.update();
 			assertEquals(Result.LOCK_FAILURE, update);
 			assertEquals(opid, db.resolve("refs/heads/master"));
-			LockFile lockFile2 = new LockFile(new File(db.getDirectory(),"refs/heads/master"));
+			LockFile lockFile2 = new LockFile(new File(db.getDirectory(),"refs/heads/master"),
+					db.getFS());
 			assertFalse(lockFile2.lock()); // was locked, still is
 		} finally {
 			lockFile1.unlock();
@@ -699,7 +701,8 @@ public void tryRenameWhenLocked(String toLock, String fromName,
 				"logs/" + fromName).exists());
 
 		// "someone" has branch X locked
-		LockFile lockFile = new LockFile(new File(db.getDirectory(), toLock));
+		LockFile lockFile = new LockFile(new File(db.getDirectory(), toLock),
+				db.getFS());
 		try {
 			assertTrue(lockFile.lock());
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/RepositorySetupWorkDirTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/RepositorySetupWorkDirTest.java
index 4f6d5b3..d28dd39 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/RepositorySetupWorkDirTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/RepositorySetupWorkDirTest.java
@@ -53,6 +53,7 @@
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.util.FS;
 
 /**
  * Tests for setting up the working directory when creating a Repository
@@ -191,7 +192,8 @@ private void setWorkTree(File gitDir, File workTree) throws IOException,
 
 	private FileBasedConfig configFor(File gitDir) throws IOException,
 			ConfigInvalidException {
-		FileBasedConfig cfg = new FileBasedConfig(new File(gitDir, "config"));
+		File configPath = new File(gitDir, "config");
+		FileBasedConfig cfg = new FileBasedConfig(configPath, FS.DETECTED);
 		cfg.load();
 		return cfg;
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/T0003_Basic.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/T0003_Basic.java
index 477b0df..ecabedd 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/T0003_Basic.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/T0003_Basic.java
@@ -315,7 +315,7 @@ public void test005_ReadSimpleConfig() {
 	public void test006_ReadUglyConfig() throws IOException,
 			ConfigInvalidException {
 		final File cfg = new File(db.getDirectory(), "config");
-		final FileBasedConfig c = new FileBasedConfig(cfg);
+		final FileBasedConfig c = new FileBasedConfig(cfg, db.getFS());
 		final FileWriter pw = new FileWriter(cfg);
 		final String configStr = "  [core];comment\n\tfilemode = yes\n"
 				+ "[user]\n"
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCache.java b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCache.java
index cc10fad..60238c3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCache.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCache.java
@@ -67,6 +67,7 @@
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectInserter;
 import org.eclipse.jgit.storage.file.LockFile;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.IO;
 import org.eclipse.jgit.util.MutableInteger;
 import org.eclipse.jgit.util.NB;
@@ -129,7 +130,7 @@ static int cmp(final byte[] aPath, final int aLen, final byte[] bPath,
 	 *         memory).
 	 */
 	public static DirCache newInCore() {
-		return new DirCache(null);
+		return new DirCache(null, null);
 	}
 
 	/**
@@ -141,6 +142,9 @@ public static DirCache newInCore() {
 	 *
 	 * @param indexLocation
 	 *            location of the index file on disk.
+	 * @param fs
+	 *            the file system abstraction which will be necessary to perform
+	 *            certain file system operations.
 	 * @return a cache representing the contents of the specified index file (if
 	 *         it exists) or an empty cache if the file does not exist.
 	 * @throws IOException
@@ -149,9 +153,9 @@ public static DirCache newInCore() {
 	 *             the index file is using a format or extension that this
 	 *             library does not support.
 	 */
-	public static DirCache read(final File indexLocation)
+	public static DirCache read(final File indexLocation, final FS fs)
 			throws CorruptObjectException, IOException {
-		final DirCache c = new DirCache(indexLocation);
+		final DirCache c = new DirCache(indexLocation, fs);
 		c.read();
 		return c;
 	}
@@ -161,11 +165,14 @@ public static DirCache read(final File indexLocation)
 	 * <p>
 	 * The new index will be locked and then read before it is returned to the
 	 * caller. Read failures are reported as exceptions and therefore prevent
-	 * the method from returning a partially populated index.  On read failure,
+	 * the method from returning a partially populated index. On read failure,
 	 * the lock is released.
 	 *
 	 * @param indexLocation
 	 *            location of the index file on disk.
+	 * @param fs
+	 *            the file system abstraction which will be necessary to perform
+	 *            certain file system operations.
 	 * @return a cache representing the contents of the specified index file (if
 	 *         it exists) or an empty cache if the file does not exist.
 	 * @throws IOException
@@ -175,9 +182,9 @@ public static DirCache read(final File indexLocation)
 	 *             the index file is using a format or extension that this
 	 *             library does not support.
 	 */
-	public static DirCache lock(final File indexLocation)
+	public static DirCache lock(final File indexLocation, final FS fs)
 			throws CorruptObjectException, IOException {
-		final DirCache c = new DirCache(indexLocation);
+		final DirCache c = new DirCache(indexLocation, fs);
 		if (!c.lock())
 			throw new IOException(MessageFormat.format(JGitText.get().cannotLock, indexLocation));
 
@@ -215,6 +222,9 @@ public static DirCache lock(final File indexLocation)
 	/** Our active lock (if we hold it); null if we don't have it locked. */
 	private LockFile myLock;
 
+	/** file system abstraction **/
+	private final FS fs;
+
 	/**
 	 * Create a new in-core index representation.
 	 * <p>
@@ -223,9 +233,13 @@ public static DirCache lock(final File indexLocation)
 	 *
 	 * @param indexLocation
 	 *            location of the index file on disk.
+	 * @param fs
+	 *            the file system abstraction which will be necessary to perform
+	 *            certain file system operations.
 	 */
-	public DirCache(final File indexLocation) {
+	public DirCache(final File indexLocation, final FS fs) {
 		liveFile = indexLocation;
+		this.fs = fs;
 		clear();
 	}
 
@@ -429,7 +443,7 @@ private static boolean is_DIRC(final byte[] hdr) {
 	public boolean lock() throws IOException {
 		if (liveFile == null)
 			throw new IOException(JGitText.get().dirCacheDoesNotHaveABackingFile);
-		final LockFile tmp = new LockFile(liveFile);
+		final LockFile tmp = new LockFile(liveFile, fs);
 		if (tmp.lock()) {
 			tmp.setNeedStatInformation(true);
 			myLock = tmp;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BaseRepositoryBuilder.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BaseRepositoryBuilder.java
index 92edb03..410c85f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BaseRepositoryBuilder.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BaseRepositoryBuilder.java
@@ -555,7 +555,7 @@ protected Config loadConfig() throws IOException {
 			// repository and not inherited from other files.
 			//
 			File path = safeFS().resolve(getGitDir(), "config");
-			FileBasedConfig cfg = new FileBasedConfig(path);
+			FileBasedConfig cfg = new FileBasedConfig(path, safeFS());
 			try {
 				cfg.load();
 			} catch (ConfigInvalidException err) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
index a39af86..4be1e69 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
@@ -930,7 +930,7 @@ public File getIndexFile() throws NoWorkTreeException {
 	 */
 	public DirCache readDirCache() throws NoWorkTreeException,
 			CorruptObjectException, IOException {
-		return DirCache.read(getIndexFile());
+		return DirCache.read(getIndexFile(), getFS());
 	}
 
 	/**
@@ -954,7 +954,7 @@ public DirCache readDirCache() throws NoWorkTreeException,
 	 */
 	public DirCache lockDirCache() throws NoWorkTreeException,
 			CorruptObjectException, IOException {
-		return DirCache.lock(getIndexFile());
+		return DirCache.lock(getIndexFile(), getFS());
 	}
 
 	static byte[] gitInternalSlash(byte[] bytes) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java
index 4cbb848..8ffbe80 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java
@@ -59,6 +59,7 @@
 import org.eclipse.jgit.lib.Config;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.StoredConfig;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.IO;
 import org.eclipse.jgit.util.RawParseUtils;
 
@@ -68,15 +69,19 @@
 public class FileBasedConfig extends StoredConfig {
 	private final File configFile;
 	private volatile long lastModified;
+	private final FS fs;
 
 	/**
 	 * Create a configuration with no default fallback.
 	 *
 	 * @param cfgLocation
 	 *            the location of the configuration file on the file system
+	 * @param fs
+	 *            the file system abstraction which will be necessary to perform
+	 *            certain file system operations.
 	 */
-	public FileBasedConfig(File cfgLocation) {
-		this(null, cfgLocation);
+	public FileBasedConfig(File cfgLocation, FS fs) {
+		this(null, cfgLocation, fs);
 	}
 
 	/**
@@ -86,10 +91,14 @@ public FileBasedConfig(File cfgLocation) {
 	 *            the base configuration file
 	 * @param cfgLocation
 	 *            the location of the configuration file on the file system
+	 * @param fs
+	 *            the file system abstraction which will be necessary to perform
+	 *            certain file system operations.
 	 */
-	public FileBasedConfig(Config base, File cfgLocation) {
+	public FileBasedConfig(Config base, File cfgLocation, FS fs) {
 		super(base);
 		configFile = cfgLocation;
+		this.fs = fs;
 	}
 
 	/** @return location of the configuration file on disk */
@@ -138,7 +147,7 @@ public void load() throws IOException, ConfigInvalidException {
 	 */
 	public void save() throws IOException {
 		final byte[] out = Constants.encode(toText());
-		final LockFile lf = new LockFile(getFile());
+		final LockFile lf = new LockFile(getFile(), fs);
 		if (!lf.lock())
 			throw new IOException(MessageFormat.format(JGitText.get().cannotLockFile, getFile()));
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileRepository.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileRepository.java
index 15aafbd..69cce71 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileRepository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileRepository.java
@@ -136,7 +136,9 @@ public FileRepository(final BaseRepositoryBuilder options) throws IOException {
 		super(options);
 
 		userConfig = SystemReader.getInstance().openUserConfig(getFS());
-		repoConfig = new FileBasedConfig(userConfig, getFS().resolve(getDirectory(), "config"));
+		repoConfig = new FileBasedConfig(userConfig, //
+				getFS().resolve(getDirectory(), "config"), //
+				getFS());
 
 		loadUserConfig();
 		loadRepoConfig();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/LockFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/LockFile.java
index ad89a24..e8bc3e2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/LockFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/LockFile.java
@@ -59,6 +59,7 @@
 import org.eclipse.jgit.JGitText;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.util.FS;
 
 /**
  * Git style file locking and replacement.
@@ -94,15 +95,21 @@ public boolean accept(File dir, String name) {
 
 	private long commitLastModified;
 
+	private final FS fs;
+
 	/**
 	 * Create a new lock for any file.
 	 *
 	 * @param f
 	 *            the file that will be locked.
+	 * @param fs
+	 *            the file system abstraction which will be necessary to perform
+	 *            certain file system operations.
 	 */
-	public LockFile(final File f) {
+	public LockFile(final File f, FS fs) {
 		ref = f;
 		lck = new File(ref.getParentFile(), ref.getName() + SUFFIX);
+		this.fs = fs;
 	}
 
 	/**
@@ -393,13 +400,32 @@ public boolean commit() {
 		saveStatInformation();
 		if (lck.renameTo(ref))
 			return true;
-		if (!ref.exists() || ref.delete())
+		if (!ref.exists() || deleteRef())
 			if (lck.renameTo(ref))
 				return true;
 		unlock();
 		return false;
 	}
 
+	private boolean deleteRef() {
+		if (!fs.retryFailedLockFileCommit())
+			return ref.delete();
+
+		// File deletion fails on windows if another thread is
+		// concurrently reading the same file. So try a few times.
+		//
+		for (int attempts = 0; attempts < 10; attempts++) {
+			if (ref.delete())
+				return true;
+			try {
+				Thread.sleep(100);
+			} catch (InterruptedException e) {
+				return false;
+			}
+		}
+		return false;
+	}
+
 	private void saveStatInformation() {
 		if (needStatInformation)
 			commitLastModified = lck.lastModified();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/PackLock.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/PackLock.java
index be25011..dd08dfb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/PackLock.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/PackLock.java
@@ -47,21 +47,26 @@
 import java.io.IOException;
 
 import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.util.FS;
 
 /** Keeps track of a {@link PackFile}'s associated <code>.keep</code> file. */
 public class PackLock {
 	private final File keepFile;
+	private final FS fs;
 
 	/**
 	 * Create a new lock for a pack file.
 	 *
 	 * @param packFile
 	 *            location of the <code>pack-*.pack</code> file.
+	 * @param fs
+	 *            the filesystem abstraction used by the repository.
 	 */
-	public PackLock(final File packFile) {
+	public PackLock(final File packFile, final FS fs) {
 		final File p = packFile.getParentFile();
 		final String n = packFile.getName();
 		keepFile = new File(p, n.substring(0, n.length() - 5) + ".keep");
+		this.fs = fs;
 	}
 
 	/**
@@ -78,7 +83,7 @@ public boolean lock(String msg) throws IOException {
 			return false;
 		if (!msg.endsWith("\n"))
 			msg += "\n";
-		final LockFile lf = new LockFile(keepFile);
+		final LockFile lf = new LockFile(keepFile, fs);
 		if (!lf.lock())
 			return false;
 		lf.write(Constants.encode(msg));
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/RefDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/RefDirectory.java
index 68b0270..b22b14a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/RefDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/RefDirectory.java
@@ -512,7 +512,8 @@ void delete(RefDirectoryUpdate update) throws IOException {
 		// we don't miss an edit made externally.
 		final PackedRefList packed = getPackedRefs();
 		if (packed.contains(name)) {
-			LockFile lck = new LockFile(packedRefsFile);
+			LockFile lck = new LockFile(packedRefsFile,
+					update.getRepository().getFS());
 			if (!lck.lock())
 				throw new IOException(MessageFormat.format(
 					JGitText.get().cannotLockFile, packedRefsFile));
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/RefDirectoryUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/RefDirectoryUpdate.java
index 8d35ec3..a9f0548 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/RefDirectoryUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/RefDirectoryUpdate.java
@@ -79,7 +79,7 @@ protected boolean tryLock(boolean deref) throws IOException {
 		if (deref)
 			dst = dst.getLeaf();
 		String name = dst.getName();
-		lock = new LockFile(database.fileFor(name));
+		lock = new LockFile(database.fileFor(name), getRepository().getFS());
 		if (lock.lock()) {
 			dst = database.getRef(name);
 			setOldObjectId(dst != null ? dst.getObjectId() : null);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
index ca68858..f747616 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
@@ -279,7 +279,8 @@ private void updateFETCH_HEAD(final FetchResult result) throws IOException {
 		File meta = transport.local.getDirectory();
 		if (meta == null)
 			return;
-		final LockFile lock = new LockFile(new File(meta, "FETCH_HEAD"));
+		final LockFile lock = new LockFile(new File(meta, "FETCH_HEAD"),
+				transport.local.getFS());
 		try {
 			if (lock.lock()) {
 				final Writer w = new OutputStreamWriter(lock.getOutputStream());
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/IndexPack.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/IndexPack.java
index 25b499b..2daa105 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/IndexPack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/IndexPack.java
@@ -1101,7 +1101,7 @@ public PackLock renameAndOpenPack(final String lockMessage)
 		final File packDir = new File(repo.getObjectsDirectory(), "pack");
 		final File finalPack = new File(packDir, "pack-" + name + ".pack");
 		final File finalIdx = new File(packDir, "pack-" + name + ".idx");
-		final PackLock keep = new PackLock(finalPack);
+		final PackLock keep = new PackLock(finalPack, repo.getFS());
 
 		if (!packDir.exists() && !packDir.mkdir() && !packDir.exists()) {
 			// The objects/pack directory isn't present, and we are unable
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java
index f4382eb..475c871 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java
@@ -74,7 +74,7 @@ public String getProperty(String key) {
 
 		public FileBasedConfig openUserConfig(FS fs) {
 			final File home = fs.userHome();
-			return new FileBasedConfig(new File(home, ".gitconfig"));
+			return new FileBasedConfig(new File(home, ".gitconfig"), fs);
 		}
 
 		public String getHostname() {