Repository can be configured with FS

On Windows, FS_Win32_Cygwin has been used if a Cygwin Git installation
is present in the PATH. Assuming that the user works with the Cygwin
Git installation may result in unnecessary overhead if he actually
does not.

Applications built on top of jgit may have more knowledge on the
actually used Git client (Cygwin or not) and hence should be able to
configure which FS to use accordingly.

Change-Id: Ifc4278078b298781d55cf5421e9647a21fa5db24

18 files changed, 217 insertions, 140 deletions

diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/GitIndex.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/GitIndex.java
index 0203d5d44a..d5cab0e4c6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/GitIndex.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/GitIndex.java
@@ -71,7 +71,6 @@ import org.eclipse.jgit.JGitText;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.errors.CorruptObjectException;
 import org.eclipse.jgit.errors.NotSupportedException;
-import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.RawParseUtils;
 
 /**
@@ -328,16 +327,16 @@ public class GitIndex {
 		}
 	}
 
-	static boolean File_canExecute( File f){
-		return FS.INSTANCE.canExecute(f);
+	private boolean File_canExecute(File f){
+		return db.getFS().canExecute(f);
 	}
 
-	static boolean File_setExecute(File f, boolean value) {
-		return FS.INSTANCE.setExecute(f, value);
+	private boolean File_setExecute(File f, boolean value) {
+		return db.getFS().setExecute(f, value);
 	}
 
-	static boolean File_hasExecute() {
-		return FS.INSTANCE.supportsExecute();
+	private boolean File_hasExecute() {
+		return db.getFS().supportsExecute();
 	}
 
 	static byte[] makeKey(File wd, File f) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectDirectory.java
index 06700ebe1d..9a5bcdb68c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectDirectory.java
@@ -88,6 +88,8 @@ public class ObjectDirectory extends ObjectDatabase {
 
 	private final File[] alternateObjectDir;
 
+	private final FS fs;
+
 	/**
 	 * Initialize a reference to an on-disk object directory.
 	 *
@@ -95,14 +97,18 @@ public class ObjectDirectory extends ObjectDatabase {
 	 *            the location of the <code>objects</code> directory.
 	 * @param alternateObjectDir
 	 *            a list of alternate object directories
+	 * @param fs
+	 *            the file system abstraction which will be necessary to
+	 *            perform certain file system operations.
 	 */
-	public ObjectDirectory(final File dir, File[] alternateObjectDir) {
+	public ObjectDirectory(final File dir, File[] alternateObjectDir, FS fs) {
 		objects = dir;
 		this.alternateObjectDir = alternateObjectDir;
 		infoDirectory = new File(objects, "info");
 		packDirectory = new File(objects, "pack");
 		alternatesFile = new File(infoDirectory, "alternates");
 		packList = new AtomicReference<PackList>(NO_PACKS);
+		this.fs = fs;
 	}
 
 	/**
@@ -485,17 +491,17 @@ public class ObjectDirectory extends ObjectDatabase {
 
 	private ObjectDatabase openAlternate(final String location)
 			throws IOException {
-		final File objdir = FS.resolve(objects, location);
+		final File objdir = fs.resolve(objects, location);
 		return openAlternate(objdir);
 	}
 
 	private ObjectDatabase openAlternate(File objdir) throws IOException {
 		final File parent = objdir.getParentFile();
-		if (FileKey.isGitRepository(parent)) {
-			final Repository db = RepositoryCache.open(FileKey.exact(parent));
+		if (FileKey.isGitRepository(parent, fs)) {
+			final Repository db = RepositoryCache.open(FileKey.exact(parent, fs));
 			return new AlternateRepositoryDatabase(db);
 		}
-		return new ObjectDirectory(objdir, null);
+		return new ObjectDirectory(objdir, null, fs);
 	}
 
 	private static final class PackList {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefDirectory.java
index 5ba186955f..302b63b486 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefDirectory.java
@@ -151,12 +151,13 @@ public class RefDirectory extends RefDatabase {
 	private final AtomicInteger lastNotifiedModCnt = new AtomicInteger();
 
 	RefDirectory(final Repository db) {
+		final FS fs = db.getFS();
 		parent = db;
 		gitDir = db.getDirectory();
-		refsDir = FS.resolve(gitDir, R_REFS);
-		logsDir = FS.resolve(gitDir, LOGS);
-		logsRefsDir = FS.resolve(gitDir, LOGS + '/' + R_REFS);
-		packedRefsFile = FS.resolve(gitDir, PACKED_REFS);
+		refsDir = fs.resolve(gitDir, R_REFS);
+		logsDir = fs.resolve(gitDir, LOGS);
+		logsRefsDir = fs.resolve(gitDir, LOGS + '/' + R_REFS);
+		packedRefsFile = fs.resolve(gitDir, PACKED_REFS);
 
 		looseRefs.set(RefList.<LooseRef> emptyList());
 		packedRefs.set(PackedRefList.NO_PACKED_REFS);
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 233cecf310..98362af987 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
@@ -102,6 +102,8 @@ public class Repository {
 
 	private final File gitDir;
 
+	private final FS fs;
+
 	private final FileBasedConfig userConfig;
 
 	private final RepositoryConfig config;
@@ -185,6 +187,41 @@ public class Repository {
 	 */
 	public Repository(final File d, final File workTree, final File objectDir,
 			final File[] alternateObjectDir, final File indexFile) throws IOException {
+		this(d, workTree, objectDir, alternateObjectDir, indexFile, FS.DETECTED);
+	}
+
+	/**
+	 * Construct a representation of a Git repository using the given parameters
+	 * possibly overriding default conventions.
+	 *
+	 * @param d
+	 *            GIT_DIR (the location of the repository metadata). May be null
+	 *            for default value in which case it depends on GIT_WORK_TREE.
+	 * @param workTree
+	 *            GIT_WORK_TREE (the root of the checkout). May be null for
+	 *            default value if GIT_DIR is
+	 * @param objectDir
+	 *            GIT_OBJECT_DIRECTORY (where objects and are stored). May be
+	 *            null for default value. Relative names ares resolved against
+	 *            GIT_WORK_TREE
+	 * @param alternateObjectDir
+	 *            GIT_ALTERNATE_OBJECT_DIRECTORIES (where more objects are read
+	 *            from). May be null for default value. Relative names ares
+	 *            resolved against GIT_WORK_TREE
+	 * @param indexFile
+	 *            GIT_INDEX_FILE (the location of the index file). May be null
+	 *            for default value. Relative names ares resolved against
+	 *            GIT_WORK_TREE.
+	 * @param fs
+	 *            the file system abstraction which will be necessary to
+	 *            perform certain file system operations.
+	 * @throws IOException
+	 *             the repository appears to already exist but cannot be
+	 *             accessed.
+	 */
+	public Repository(final File d, final File workTree, final File objectDir,
+			final File[] alternateObjectDir, final File indexFile,
+			FS fs) throws IOException {
 
 		if (workTree != null) {
 			workDir = workTree;
@@ -199,8 +236,10 @@ public class Repository {
 				throw new IllegalArgumentException(JGitText.get().eitherGIT_DIRorGIT_WORK_TREEmustBePassed);
 		}
 
-		userConfig = SystemReader.getInstance().openUserConfig();
-		config = new RepositoryConfig(userConfig, FS.resolve(gitDir, "config"));
+		this.fs = fs;
+
+		userConfig = SystemReader.getInstance().openUserConfig(fs);
+		config = new RepositoryConfig(userConfig, fs.resolve(gitDir, "config"));
 
 		loadUserConfig();
 		loadConfig();
@@ -208,7 +247,7 @@ public class Repository {
 		if (workDir == null) {
 			String workTreeConfig = getConfig().getString("core", null, "worktree");
 			if (workTreeConfig != null) {
-				workDir = FS.resolve(d, workTreeConfig);
+				workDir = fs.resolve(d, workTreeConfig);
 			} else {
 				workDir = gitDir.getParentFile();
 			}
@@ -216,11 +255,11 @@ public class Repository {
 
 		refs = new RefDirectory(this);
 		if (objectDir != null)
-			objectDatabase = new ObjectDirectory(FS.resolve(objectDir, ""),
-					alternateObjectDir);
+			objectDatabase = new ObjectDirectory(fs.resolve(objectDir, ""),
+					alternateObjectDir, fs);
 		else
-			objectDatabase = new ObjectDirectory(FS.resolve(gitDir, "objects"),
-					alternateObjectDir);
+			objectDatabase = new ObjectDirectory(fs.resolve(gitDir, "objects"),
+					alternateObjectDir, fs);
 
 		if (indexFile != null)
 			this.indexFile = indexFile;
@@ -352,6 +391,13 @@ public class Repository {
 	}
 
 	/**
+	 * @return the used file system abstraction
+	 */
+	public FS getFS() {
+		return fs;
+	}
+
+	/**
 	 * Construct a filename where the loose object having a specified SHA-1
 	 * should be stored. If the object is stored in a shared repository the path
 	 * to the alternative repo will be returned. If the object is not yet store
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCache.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCache.java
index b086968c6c..0b0260a4cc 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCache.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCache.java
@@ -120,7 +120,7 @@ public class RepositoryCache {
 	 *            repository to register.
 	 */
 	public static void register(final Repository db) {
-		cache.registerRepository(FileKey.exact(db.getDirectory()), db);
+		cache.registerRepository(FileKey.exact(db.getDirectory(), db.getFS()), db);
 	}
 
 	/**
@@ -133,7 +133,7 @@ public class RepositoryCache {
 	 *            repository to unregister.
 	 */
 	public static void close(final Repository db) {
-		cache.unregisterRepository(FileKey.exact(db.getDirectory()));
+		cache.unregisterRepository(FileKey.exact(db.getDirectory(), db.getFS()));
 	}
 
 	/** Unregister all repositories from the cache. */
@@ -248,11 +248,14 @@ public class RepositoryCache {
 		 *
 		 * @param directory
 		 *            location where the repository database is.
+		 * @param fs
+		 *            the file system abstraction which will be necessary to
+		 *            perform certain file system operations.
 		 * @return a key for the given directory.
-		 * @see #lenient(File)
+		 * @see #lenient(File, FS)
 		 */
-		public static FileKey exact(final File directory) {
-			return new FileKey(directory);
+		public static FileKey exact(final File directory, FS fs) {
+			return new FileKey(directory, fs);
 		}
 
 		/**
@@ -268,22 +271,30 @@ public class RepositoryCache {
 		 *
 		 * @param directory
 		 *            location where the repository database might be.
+		 * @param fs
+		 *            the file system abstraction which will be necessary to
+		 *            perform certain file system operations.
 		 * @return a key for the given directory.
-		 * @see #exact(File)
+		 * @see #exact(File, FS)
 		 */
-		public static FileKey lenient(final File directory) {
-			final File gitdir = resolve(directory);
-			return new FileKey(gitdir != null ? gitdir : directory);
+		public static FileKey lenient(final File directory, FS fs) {
+			final File gitdir = resolve(directory, fs);
+			return new FileKey(gitdir != null ? gitdir : directory, fs);
 		}
 
 		private final File path;
+		private final FS fs;
 
 		/**
 		 * @param directory
 		 *            exact location of the repository.
+		 * @param fs
+		 *            the file system abstraction which will be necessary to
+		 *            perform certain file system operations.
 		 */
-		protected FileKey(final File directory) {
+		protected FileKey(final File directory, FS fs) {
 			path = canonical(directory);
+			this.fs = fs;
 		}
 
 		private static File canonical(final File path) {
@@ -300,7 +311,7 @@ public class RepositoryCache {
 		}
 
 		public Repository open(final boolean mustExist) throws IOException {
-			if (mustExist && !isGitRepository(path))
+			if (mustExist && !isGitRepository(path, fs))
 				throw new RepositoryNotFoundException(path);
 			return new Repository(path);
 		}
@@ -328,13 +339,16 @@ public class RepositoryCache {
 		 *
 		 * @param dir
 		 *            the location of the directory to examine.
+		 * @param fs
+		 *            the file system abstraction which will be necessary to
+		 *            perform certain file system operations.
 		 * @return true if the directory "looks like" a Git repository; false if
 		 *         it doesn't look enough like a Git directory to really be a
 		 *         Git directory.
 		 */
-		public static boolean isGitRepository(final File dir) {
-			return FS.resolve(dir, "objects").exists()
-					&& FS.resolve(dir, "refs").exists()
+		public static boolean isGitRepository(final File dir, FS fs) {
+			return fs.resolve(dir, "objects").exists()
+					&& fs.resolve(dir, "refs").exists()
 					&& isValidHead(new File(dir, Constants.HEAD));
 		}
 
@@ -371,18 +385,21 @@ public class RepositoryCache {
 		 *
 		 * @param directory
 		 *            location to guess from. Several permutations are tried.
+		 * @param fs
+		 *            the file system abstraction which will be necessary to
+		 *            perform certain file system operations.
 		 * @return the actual directory location if a better match is found;
 		 *         null if there is no suitable match.
 		 */
-		public static File resolve(final File directory) {
-			if (isGitRepository(directory))
+		public static File resolve(final File directory, FS fs) {
+			if (isGitRepository(directory, fs))
 				return directory;
-			if (isGitRepository(new File(directory, Constants.DOT_GIT)))
+			if (isGitRepository(new File(directory, Constants.DOT_GIT), fs))
 				return new File(directory, Constants.DOT_GIT);
 
 			final String name = directory.getName();
 			final File parent = directory.getParentFile();
-			if (isGitRepository(new File(parent, name + Constants.DOT_GIT_EXT)))
+			if (isGitRepository(new File(parent, name + Constants.DOT_GIT_EXT), fs))
 				return new File(parent, name + Constants.DOT_GIT_EXT);
 			return null;
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/Daemon.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/Daemon.java
index 39c7ae8f01..aa2e2521c2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/Daemon.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/Daemon.java
@@ -63,6 +63,7 @@ import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.RepositoryCache;
 import org.eclipse.jgit.lib.RepositoryCache.FileKey;
+import org.eclipse.jgit.util.FS;
 
 /** Basic daemon for the anonymous <code>git://</code> transport protocol. */
 public class Daemon {
@@ -368,7 +369,7 @@ public class Daemon {
 		}
 
 		for (final File baseDir : exportBase) {
-			final File gitdir = FileKey.resolve(new File(baseDir, name));
+			final File gitdir = FileKey.resolve(new File(baseDir, name), FS.DETECTED);
 			if (gitdir != null && canExport(gitdir))
 				return openRepository(gitdir);
 		}
@@ -377,7 +378,7 @@ public class Daemon {
 
 	private static Repository openRepository(final File gitdir) {
 		try {
-			return RepositoryCache.open(FileKey.exact(gitdir));
+			return RepositoryCache.open(FileKey.exact(gitdir, FS.DETECTED));
 		} catch (IOException err) {
 			// null signals it "wasn't found", which is all that is suitable
 			// for the remote client to know.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java
index e7a307f809..20f3174b2e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java
@@ -82,10 +82,13 @@ public class OpenSshConfig {
 	 * requests are cached and are automatically updated if the user modifies
 	 * the configuration file since the last time it was cached.
 	 *
+	 * @param fs
+	 *            the file system abstraction which will be necessary to
+	 *            perform certain file system operations.
 	 * @return a caching reader of the user's configuration file.
 	 */
-	public static OpenSshConfig get() {
-		File home = FS.userHome();
+	public static OpenSshConfig get(FS fs) {
+		File home = fs.userHome();
 		if (home == null)
 			home = new File(".").getAbsoluteFile();
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshConfigSessionFactory.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshConfigSessionFactory.java
index c30d32d9f9..daa6f4ca2f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshConfigSessionFactory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshConfigSessionFactory.java
@@ -83,15 +83,18 @@ public abstract class SshConfigSessionFactory extends SshSessionFactory {
 
 	@Override
 	public synchronized Session getSession(String user, String pass,
-			String host, int port) throws JSchException {
-		final OpenSshConfig.Host hc = getConfig().lookup(host);
+			String host, int port, FS fs) throws JSchException {
+		if (config == null)
+			config = OpenSshConfig.get(fs);
+
+		final OpenSshConfig.Host hc = config.lookup(host);
 		host = hc.getHostName();
 		if (port <= 0)
 			port = hc.getPort();
 		if (user == null)
 			user = hc.getUser();
 
-		final Session session = createSession(hc, user, host, port);
+		final Session session = createSession(hc, user, host, port, fs);
 		if (pass != null)
 			session.setPassword(pass);
 		final String strictHostKeyCheckingPolicy = hc
@@ -117,14 +120,17 @@ public abstract class SshConfigSessionFactory extends SshSessionFactory {
 	 *            server name to connect to.
 	 * @param port
 	 *            port number of the SSH daemon (typically 22).
+	 * @param fs
+	 *            the file system abstraction which will be necessary to
+	 *            perform certain file system operations.
 	 * @return new session instance, but otherwise unconfigured.
 	 * @throws JSchException
 	 *             the session could not be created.
 	 */
 	protected Session createSession(final OpenSshConfig.Host hc,
-			final String user, final String host, final int port)
+			final String user, final String host, final int port, FS fs)
 			throws JSchException {
-		return getJSch(hc).getSession(user, host, port);
+		return getJSch(hc, fs).getSession(user, host, port);
 	}
 
 	/**
@@ -143,58 +149,54 @@ public abstract class SshConfigSessionFactory extends SshSessionFactory {
 	 *
 	 * @param hc
 	 *            host configuration
+	 * @param fs
+	 *            the file system abstraction which will be necessary to
+	 *            perform certain file system operations.
 	 * @return the JSch instance to use.
 	 * @throws JSchException
 	 *             the user configuration could not be created.
 	 */
-	protected JSch getJSch(final OpenSshConfig.Host hc) throws JSchException {
-		final JSch def = getDefaultJSch();
+	protected JSch getJSch(final OpenSshConfig.Host hc, FS fs) throws JSchException {
+		if (defaultJSch == null) {
+			defaultJSch = createDefaultJSch(fs);
+			for (Object name : defaultJSch.getIdentityNames()) {
+				byIdentityFile.put((String) name, defaultJSch);
+			}
+		}
+
 		final File identityFile = hc.getIdentityFile();
 		if (identityFile == null) {
-			return def;
+			return defaultJSch;
 		}
 
 		final String identityKey = identityFile.getAbsolutePath();
 		JSch jsch = byIdentityFile.get(identityKey);
 		if (jsch == null) {
 			jsch = new JSch();
-			jsch.setHostKeyRepository(def.getHostKeyRepository());
+			jsch.setHostKeyRepository(defaultJSch.getHostKeyRepository());
 			jsch.addIdentity(identityKey);
 			byIdentityFile.put(identityKey, jsch);
 		}
 		return jsch;
 	}
 
-	private JSch getDefaultJSch() throws JSchException {
-		if (defaultJSch == null) {
-			defaultJSch = createDefaultJSch();
-			for (Object name : defaultJSch.getIdentityNames()) {
-				byIdentityFile.put((String) name, defaultJSch);
-			}
-		}
-		return defaultJSch;
-	}
-
 	/**
+	 * @param fs
+	 *            the file system abstraction which will be necessary to
+	 *            perform certain file system operations.
 	 * @return the new default JSch implementation.
 	 * @throws JSchException
 	 *             known host keys cannot be loaded.
 	 */
-	protected JSch createDefaultJSch() throws JSchException {
+	protected JSch createDefaultJSch(FS fs) throws JSchException {
 		final JSch jsch = new JSch();
-		knownHosts(jsch);
-		identities(jsch);
+		knownHosts(jsch, fs);
+		identities(jsch, fs);
 		return jsch;
 	}
 
-	private OpenSshConfig getConfig() {
-		if (config == null)
-			config = OpenSshConfig.get();
-		return config;
-	}
-
-	private static void knownHosts(final JSch sch) throws JSchException {
-		final File home = FS.userHome();
+	private static void knownHosts(final JSch sch, FS fs) throws JSchException {
+		final File home = fs.userHome();
 		if (home == null)
 			return;
 		final File known_hosts = new File(new File(home, ".ssh"), "known_hosts");
@@ -212,8 +214,8 @@ public abstract class SshConfigSessionFactory extends SshSessionFactory {
 		}
 	}
 
-	private static void identities(final JSch sch) {
-		final File home = FS.userHome();
+	private static void identities(final JSch sch, FS fs) {
+		final File home = fs.userHome();
 		if (home == null)
 			return;
 		final File sshdir = new File(home, ".ssh");
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshSessionFactory.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshSessionFactory.java
index 810b04ce40..d10010fcf6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshSessionFactory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshSessionFactory.java
@@ -44,6 +44,8 @@
 
 package org.eclipse.jgit.transport;
 
+import org.eclipse.jgit.util.FS;
+
 import com.jcraft.jsch.JSchException;
 import com.jcraft.jsch.Session;
 
@@ -109,19 +111,22 @@ public abstract class SshSessionFactory {
 	 * @param port
 	 *            port number the server is listening for connections on. May be <=
 	 *            0 to indicate the IANA registered port of 22 should be used.
+	 * @param fs
+	 *            the file system abstraction which will be necessary to
+	 *            perform certain file system operations.
 	 * @return a session that can contact the remote host.
 	 * @throws JSchException
 	 *             the session could not be created.
 	 */
 	public abstract Session getSession(String user, String pass, String host,
-			int port) throws JSchException;
+			int port, FS fs) throws JSchException;
 
 	/**
 	 * Close (or recycle) a session to a host.
 	 *
 	 * @param session
 	 *            a session previously obtained from this factory's
-	 *            {@link #getSession(String,String, String, int)} method.s
+	 *            {@link #getSession(String,String, String, int, FS)} method.s
 	 */
 	public void releaseSession(final Session session) {
 		if (session.isConnected())
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshTransport.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshTransport.java
index d25a7b6180..f642ac1ea8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshTransport.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshTransport.java
@@ -128,7 +128,7 @@ public abstract class SshTransport extends TcpTransport {
 		final String host = uri.getHost();
 		final int port = uri.getPort();
 		try {
-			sock = sch.getSession(user, pass, host, port);
+			sock = sch.getSession(user, pass, host, port, local.getFS());
 			if (!sock.isConnected())
 				sock.connect(tms);
 		} catch (JSchException je) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/Transport.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/Transport.java
index 2fe3cb9326..e1988a6c85 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/Transport.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/Transport.java
@@ -66,6 +66,7 @@ import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.TransferConfig;
+import org.eclipse.jgit.util.FS;
 
 /**
  * Connects two Git repositories together and copies objects between them.
@@ -323,9 +324,11 @@ public abstract class Transport {
 	 *
 	 * @param remote
 	 *            location of the remote repository.
+	 * @param fs
+	 *            type of filesystem the local repository is stored on.
 	 * @return true if the protocol is supported.
 	 */
-	public static boolean canHandleProtocol(final URIish remote) {
+	public static boolean canHandleProtocol(final URIish remote, final FS fs) {
 		if (TransportGitSsh.canHandle(remote))
 			return true;
 
@@ -341,10 +344,10 @@ public abstract class Transport {
 		else if (TransportAmazonS3.canHandle(remote))
 			return true;
 
-		else if (TransportBundleFile.canHandle(remote))
+		else if (TransportBundleFile.canHandle(remote, fs))
 			return true;
 
-		else if (TransportLocal.canHandle(remote))
+		else if (TransportLocal.canHandle(remote, fs))
 			return true;
 
 		return false;
@@ -378,10 +381,10 @@ public abstract class Transport {
 		else if (TransportAmazonS3.canHandle(remote))
 			return new TransportAmazonS3(local, remote);
 
-		else if (TransportBundleFile.canHandle(remote))
+		else if (TransportBundleFile.canHandle(remote, local.getFS()))
 			return new TransportBundleFile(local, remote);
 
-		else if (TransportLocal.canHandle(remote))
+		else if (TransportLocal.canHandle(remote, local.getFS()))
 			return new TransportLocal(local, remote);
 
 		throw new NotSupportedException(MessageFormat.format(JGitText.get().URINotSupported, remote));
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportAmazonS3.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportAmazonS3.java
index bcf6e873fe..56a5c9796d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportAmazonS3.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportAmazonS3.java
@@ -69,7 +69,6 @@ import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.SymbolicRef;
 import org.eclipse.jgit.lib.Ref.Storage;
-import org.eclipse.jgit.util.FS;
 
 /**
  * Transport over the non-Git aware Amazon S3 protocol.
@@ -130,7 +129,7 @@ public class TransportAmazonS3 extends HttpTransport implements WalkTransport {
 		Properties props = null;
 		File propsFile = new File(local.getDirectory(), uri.getUser());
 		if (!propsFile.isFile())
-			propsFile = new File(FS.userHome(), uri.getUser());
+			propsFile = new File(local.getFS().userHome(), uri.getUser());
 		if (propsFile.isFile()) {
 			try {
 				props = AmazonS3.properties(propsFile);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleFile.java
index 0245818fe3..c47833f21c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleFile.java
@@ -58,13 +58,13 @@ import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.util.FS;
 
 class TransportBundleFile extends Transport implements TransportBundle {
-	static boolean canHandle(final URIish uri) {
+	static boolean canHandle(final URIish uri, FS fs) {
 		if (uri.getHost() != null || uri.getPort() > 0 || uri.getUser() != null
 				|| uri.getPass() != null || uri.getPath() == null)
 			return false;
 
 		if ("file".equals(uri.getScheme()) || uri.getScheme() == null) {
-			final File f = FS.resolve(new File("."), uri.getPath());
+			final File f = fs.resolve(new File("."), uri.getPath());
 			return f.isFile() || f.getName().endsWith(".bundle");
 		}
 
@@ -75,7 +75,7 @@ class TransportBundleFile extends Transport implements TransportBundle {
 
 	TransportBundleFile(final Repository local, final URIish uri) {
 		super(local, uri);
-		bundle = FS.resolve(new File("."), uri.getPath()).getAbsoluteFile();
+		bundle = local.getFS().resolve(new File("."), uri.getPath()).getAbsoluteFile();
 	}
 
 	@Override
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportLocal.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportLocal.java
index cf4dbd5392..08fd8901d8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportLocal.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportLocal.java
@@ -91,13 +91,13 @@ import org.eclipse.jgit.util.io.StreamCopyThread;
 class TransportLocal extends Transport implements PackTransport {
 	private static final String PWD = ".";
 
-	static boolean canHandle(final URIish uri) {
+	static boolean canHandle(final URIish uri, FS fs) {
 		if (uri.getHost() != null || uri.getPort() > 0 || uri.getUser() != null
 				|| uri.getPass() != null || uri.getPath() == null)
 			return false;
 
 		if ("file".equals(uri.getScheme()) || uri.getScheme() == null)
-			return FS.resolve(new File(PWD), uri.getPath()).isDirectory();
+			return fs.resolve(new File(PWD), uri.getPath()).isDirectory();
 		return false;
 	}
 
@@ -106,7 +106,7 @@ class TransportLocal extends Transport implements PackTransport {
 	TransportLocal(final Repository local, final URIish uri) {
 		super(local, uri);
 
-		File d = FS.resolve(new File(PWD), uri.getPath()).getAbsoluteFile();
+		File d = local.getFS().resolve(new File(PWD), uri.getPath()).getAbsoluteFile();
 		if (new File(d, Constants.DOT_GIT).isDirectory())
 			d = new File(d, Constants.DOT_GIT);
 		remoteGitDir = d;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java
index 19db39a8ff..8dfab8aa57 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java
@@ -65,6 +65,7 @@ import org.eclipse.jgit.util.FS;
  */
 public class FileTreeIterator extends WorkingTreeIterator {
 	private final File directory;
+	private final FS fs;
 
 	/**
 	 * Create a new iterator to traverse the given directory and its children.
@@ -72,9 +73,13 @@ public class FileTreeIterator extends WorkingTreeIterator {
 	 * @param root
 	 *            the starting directory. This directory should correspond to
 	 *            the root of the repository.
+	 * @param fs
+	 *            the file system abstraction which will be necessary to
+	 *            perform certain file system operations.
 	 */
-	public FileTreeIterator(final File root) {
+	public FileTreeIterator(final File root, FS fs) {
 		directory = root;
+		this.fs = fs;
 		init(entries());
 	}
 
@@ -83,20 +88,24 @@ public class FileTreeIterator extends WorkingTreeIterator {
 	 *
 	 * @param p
 	 *            the parent iterator we were created from.
+	 * @param fs
+	 *            the file system abstraction which will be necessary to
+	 *            perform certain file system operations.
 	 * @param root
 	 *            the subdirectory. This should be a directory contained within
 	 *            the parent directory.
 	 */
-	protected FileTreeIterator(final FileTreeIterator p, final File root) {
+	protected FileTreeIterator(final FileTreeIterator p, final File root, FS fs) {
 		super(p);
 		directory = root;
+		this.fs = fs;
 		init(entries());
 	}
 
 	@Override
 	public AbstractTreeIterator createSubtreeIterator(final Repository repo)
 			throws IncorrectObjectTypeException, IOException {
-		return new FileTreeIterator(this, ((FileEntry) current()).file);
+		return new FileTreeIterator(this, ((FileEntry) current()).file, fs);
 	}
 
 	private Entry[] entries() {
@@ -105,7 +114,7 @@ public class FileTreeIterator extends WorkingTreeIterator {
 			return EOF;
 		final Entry[] r = new Entry[all.length];
 		for (int i = 0; i < r.length; i++)
-			r[i] = new FileEntry(all[i]);
+			r[i] = new FileEntry(all[i], fs);
 		return r;
 	}
 
@@ -121,7 +130,7 @@ public class FileTreeIterator extends WorkingTreeIterator {
 
 		private long lastModified;
 
-		FileEntry(final File f) {
+		FileEntry(final File f, FS fs) {
 			file = f;
 
 			if (f.isDirectory()) {
@@ -129,7 +138,7 @@ public class FileTreeIterator extends WorkingTreeIterator {
 					mode = FileMode.GITLINK;
 				else
 					mode = FileMode.TREE;
-			} else if (FS.INSTANCE.canExecute(file))
+			} else if (fs.canExecute(file))
 				mode = FileMode.EXECUTABLE_FILE;
 			else
 				mode = FileMode.REGULAR_FILE;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
index c4f4242f90..b8d433762e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
@@ -49,19 +49,28 @@ import java.security.PrivilegedAction;
 
 /** Abstraction to support various file system operations not in Java. */
 public abstract class FS {
-	/** The implementation selected for this operating system and JRE. */
-	public static final FS INSTANCE;
+	/** The auto-detected implementation selected for this operating system and JRE. */
+	public static final FS DETECTED;
 
 	static {
 		if (FS_Win32.detect()) {
 			if (FS_Win32_Cygwin.detect())
-				INSTANCE = new FS_Win32_Cygwin();
+				DETECTED = new FS_Win32_Cygwin();
 			else
-				INSTANCE = new FS_Win32();
+				DETECTED = new FS_Win32();
 		} else if (FS_POSIX_Java6.detect())
-			INSTANCE = new FS_POSIX_Java6();
+			DETECTED = new FS_POSIX_Java6();
 		else
-			INSTANCE = new FS_POSIX_Java5();
+			DETECTED = new FS_POSIX_Java5();
+	}
+
+	private final File userHome;
+
+	/**
+	 * Constructs a file system abstraction.
+	 */
+	protected FS() {
+		this.userHome = userHomeImpl();
 	}
 
 	/**
@@ -117,29 +126,7 @@ public abstract class FS {
 	 * @return the translated path. <code>new File(dir,name)</code> if this
 	 *         platform does not require path name translation.
 	 */
-	public static File resolve(final File dir, final String name) {
-		return INSTANCE.resolveImpl(dir, name);
-	}
-
-	/**
-	 * Resolve this file to its actual path name that the JRE can use.
-	 * <p>
-	 * This method can be relatively expensive. Computing a translation may
-	 * require forking an external process per path name translated. Callers
-	 * should try to minimize the number of translations necessary by caching
-	 * the results.
-	 * <p>
-	 * Not all platforms and JREs require path name translation. Currently only
-	 * Cygwin on Win32 require translation for Cygwin based paths.
-	 *
-	 * @param dir
-	 *            directory relative to which the path name is.
-	 * @param name
-	 *            path name to translate.
-	 * @return the translated path. <code>new File(dir,name)</code> if this
-	 *         platform does not require path name translation.
-	 */
-	protected File resolveImpl(final File dir, final String name) {
+	public File resolve(final File dir, final String name) {
 		final File abspn = new File(name);
 		if (abspn.isAbsolute())
 			return abspn;
@@ -157,12 +144,8 @@ public abstract class FS {
 	 *
 	 * @return the user's home directory; null if the user does not have one.
 	 */
-	public static File userHome() {
-		return USER_HOME.home;
-	}
-
-	private static class USER_HOME {
-		static final File home = INSTANCE.userHomeImpl();
+	public File userHome() {
+		return userHome;
 	}
 
 	/**
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_Win32_Cygwin.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_Win32_Cygwin.java
index f727084860..39f2c03a06 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_Win32_Cygwin.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_Win32_Cygwin.java
@@ -72,7 +72,7 @@ class FS_Win32_Cygwin extends FS_Win32 {
 		return false;
 	}
 
-	protected File resolveImpl(final File dir, final String pn) {
+	public File resolve(final File dir, final String pn) {
 		try {
 			final Process p;
 
@@ -103,7 +103,7 @@ class FS_Win32_Cygwin extends FS_Win32 {
 			// Fall through and use the default return.
 			//
 		}
-		return super.resolveImpl(dir, pn);
+		return super.resolve(dir, pn);
 	}
 
 	@Override
@@ -116,6 +116,6 @@ class FS_Win32_Cygwin extends FS_Win32 {
 				});
 		if (home == null || home.length() == 0)
 			return super.userHomeImpl();
-		return resolveImpl(new File("."), home);
+		return resolve(new File("."), home);
 	}
 }
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 771e77058a..9d7feb08f2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java
@@ -72,8 +72,8 @@ public abstract class SystemReader {
 			return System.getProperty(key);
 		}
 
-		public FileBasedConfig openUserConfig() {
-			final File home = FS.userHome();
+		public FileBasedConfig openUserConfig(FS fs) {
+			final File home = fs.userHome();
 			return new FileBasedConfig(new File(home, ".gitconfig"));
 		}
 
@@ -136,9 +136,12 @@ public abstract class SystemReader {
 	public abstract String getProperty(String key);
 
 	/**
+	 * @param fs
+	 *            the file system abstraction which will be necessary to
+	 *            perform certain file system operations.
 	 * @return the git configuration found in the user home
 	 */
-	public abstract FileBasedConfig openUserConfig();
+	public abstract FileBasedConfig openUserConfig(FS fs);
 
 	/**
 	 * @return the current system time