diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java
index 903f2e889..73530efca 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java
@@ -106,7 +106,7 @@ class Clone extends AbstractFetchCommand {
 			}
 		}
 		if (gitdir == null)
-			gitdir = new File(localName, Constants.DOT_GIT);
+			gitdir = new File(localName, Constants.DOT_GIT).getAbsolutePath();
 
 		dst = new FileRepository(gitdir);
 		dst.create();
@@ -116,8 +116,7 @@ class Clone extends AbstractFetchCommand {
 		db = dst;
 
 		out.print(MessageFormat.format(
-				CLIText.get().initializedEmptyGitRepositoryIn, gitdir
-						.getAbsolutePath()));
+				CLIText.get().initializedEmptyGitRepositoryIn, gitdir));
 		out.println();
 		out.flush();
 
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java
index c56540a76..98f086d46 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java
@@ -47,6 +47,7 @@
 
 package org.eclipse.jgit.pgm;
 
+import java.io.File;
 import java.text.MessageFormat;
 
 import org.eclipse.jgit.api.Git;
@@ -68,7 +69,7 @@ class Init extends TextBuiltin {
 	protected void run() throws Exception {
 		InitCommand command = Git.init();
 		command.setBare(bare);
-		command.setDirectory(gitdir);
+		command.setDirectory(new File(gitdir));
 		Repository repository = command.call().getRepository();
 		out.println(MessageFormat.format(
 				CLIText.get().initializedEmptyGitRepositoryIn, repository
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java
index 62ffd8d9c..654eed2cd 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java
@@ -186,7 +186,7 @@ public class Main {
 		if (cmd.requiresRepository())
 			cmd.init(openGitDir(gitdir), null);
 		else
-			cmd.init(null, gitdir != null ? new File(gitdir) : null);
+			cmd.init(null, gitdir);
 		try {
 			cmd.execute(arguments.toArray(new String[arguments.size()]));
 		} finally {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java
index b6f12a1ab..2988dfc54 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java
@@ -49,19 +49,18 @@ import static org.eclipse.jgit.lib.Constants.R_REMOTES;
 import static org.eclipse.jgit.lib.Constants.R_TAGS;
 
 import java.io.BufferedWriter;
-import java.io.File;
 import java.io.IOException;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.text.MessageFormat;
 import java.util.ResourceBundle;
 
-import org.kohsuke.args4j.CmdLineException;
-import org.kohsuke.args4j.Option;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.pgm.opt.CmdLineParser;
 import org.eclipse.jgit.revwalk.RevWalk;
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.Option;
 
 /**
  * Abstract command which can be invoked from the command line.
@@ -87,7 +86,7 @@ public abstract class TextBuiltin {
 	protected Repository db;
 
 	/** Directory supplied via --git-dir command line option. */
-	protected File gitdir;
+	protected String gitdir;
 
 	/** RevWalk used during command line parsing, if it was required. */
 	protected RevWalk argWalk;
@@ -101,9 +100,19 @@ public abstract class TextBuiltin {
 		return true;
 	}
 
-	void init(final Repository repo, final File gd) {
+	/**
+	 * Initialize the command to work with a repository.
+	 *
+	 * @param repository
+	 *            the opened repository that the command should work on.
+	 * @param gitDir
+	 *            value of the {@code --git-dir} command line option, if
+	 *            {@code repository} is null.
+	 */
+	protected void init(final Repository repository, final String gitDir) {
 		try {
-			final String outputEncoding = repo != null ? repo.getConfig()
+			final String outputEncoding = repository != null ? repository
+					.getConfig()
 					.getString("i18n", null, "logOutputEncoding") : null;
 			if (outputEncoding != null)
 				out = new PrintWriter(new BufferedWriter(
@@ -115,12 +124,12 @@ public abstract class TextBuiltin {
 			throw die(CLIText.get().cannotCreateOutputStream);
 		}
 
-		if (repo != null) {
-			db = repo;
-			gitdir = repo.getDirectory();
+		if (repository != null && repository.getDirectory() != null) {
+			db = repository;
+			gitdir = repository.getDirectory().getAbsolutePath();
 		} else {
-			db = null;
-			gitdir = gd;
+			db = repository;
+			gitdir = gitDir;
 		}
 	}
 
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/DiffAlgorithms.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/DiffAlgorithms.java
index 552d70450..60d92d6be 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/DiffAlgorithms.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/DiffAlgorithms.java
@@ -135,7 +135,7 @@ class DiffAlgorithms extends TextBuiltin {
 
 		if (gitDirs.isEmpty()) {
 			RepositoryBuilder rb = new RepositoryBuilder() //
-					.setGitDir(gitdir) //
+					.setGitDir(new File(gitdir)) //
 					.readEnvironment() //
 					.findGitDir();
 			if (rb.getGitDir() == null)
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java
index 5ce9d808c..61a8ecc38 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java
@@ -266,7 +266,7 @@ class TextHashFunctions extends TextBuiltin {
 	protected void run() throws Exception {
 		if (gitDirs.isEmpty()) {
 			RepositoryBuilder rb = new RepositoryBuilder() //
-					.setGitDir(gitdir) //
+					.setGitDir(new File(gitdir)) //
 					.readEnvironment() //
 					.findGitDir();
 			if (rb.getGitDir() == null)