diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
index 6af4ce1dd..78ca1a712 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
@@ -48,6 +48,7 @@ import java.util.List;
 import java.util.Map;
 
 import org.eclipse.jgit.internal.storage.reftree.RefTree;
+import org.eclipse.jgit.internal.storage.reftree.RefTreeDatabase;
 import org.eclipse.jgit.lib.CommitBuilder;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectInserter;
@@ -59,12 +60,11 @@ import org.eclipse.jgit.lib.RefUpdate;
 import org.eclipse.jgit.pgm.Command;
 import org.eclipse.jgit.pgm.TextBuiltin;
 import org.eclipse.jgit.revwalk.RevWalk;
-import org.kohsuke.args4j.Argument;
 
 @Command(usage = "usage_RebuildRefTree")
 class RebuildRefTree extends TextBuiltin {
-	@Argument(index = 0, required = true, metaVar = "metaVar_ref", usage = "usage_updateRef")
-	String refName;
+	private String txnNamespace;
+	private String txnCommitted;
 
 	@Override
 	protected void run() throws Exception {
@@ -72,10 +72,25 @@ class RebuildRefTree extends TextBuiltin {
 				RevWalk rw = new RevWalk(reader);
 				ObjectInserter inserter = db.newObjectInserter()) {
 			RefDatabase refDb = db.getRefDatabase();
+			if (refDb instanceof RefTreeDatabase) {
+				RefTreeDatabase d = (RefTreeDatabase) refDb;
+				refDb = d.getBootstrap();
+				txnNamespace = d.getTxnNamespace();
+				txnCommitted = d.getTxnCommitted();
+			} else {
+				RefTreeDatabase d = new RefTreeDatabase(db, refDb);
+				txnNamespace = d.getTxnNamespace();
+				txnCommitted = d.getTxnCommitted();
+			}
+
+			errw.format("Rebuilding %s from %s", //$NON-NLS-1$
+					txnCommitted, refDb.getClass().getSimpleName());
+			errw.println();
+			errw.flush();
 
 			CommitBuilder b = new CommitBuilder();
-			Ref ref = db.getRefDatabase().exactRef(refName);
-			RefUpdate update = db.updateRef(refName);
+			Ref ref = refDb.exactRef(txnCommitted);
+			RefUpdate update = refDb.newUpdate(txnCommitted, true);
 			ObjectId oldTreeId;
 
 			if (ref != null && ref.getObjectId() != null) {
@@ -116,10 +131,10 @@ class RebuildRefTree extends TextBuiltin {
 			= new ArrayList<>();
 
 		for (Ref r : refMap.values()) {
-			if (refName.equals(r.getName())) {
+			if (r.getName().equals(txnCommitted)
+					|| r.getName().startsWith(txnNamespace)) {
 				continue;
 			}
-
 			cmds.add(new org.eclipse.jgit.internal.storage.reftree.Command(
 					null,
 					db.peel(r)));
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileRepositoryBuilderTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileRepositoryBuilderTest.java
index 280d6040c..6c8ee737d 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileRepositoryBuilderTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileRepositoryBuilderTest.java
@@ -104,7 +104,7 @@ public class FileRepositoryBuilderTest extends LocalDiskRepositoryTestCase {
 		Repository r = createWorkRepository();
 		StoredConfig config = r.getConfig();
 		config.setLong(ConfigConstants.CONFIG_CORE_SECTION, null,
-				ConfigConstants.CONFIG_KEY_REPO_FORMAT_VERSION, 1);
+				ConfigConstants.CONFIG_KEY_REPO_FORMAT_VERSION, 999999);
 		config.save();
 
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
index 490cbcaa8..4f45cbee5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
@@ -63,6 +63,7 @@ import org.eclipse.jgit.events.ConfigChangedEvent;
 import org.eclipse.jgit.events.ConfigChangedListener;
 import org.eclipse.jgit.events.IndexChangedEvent;
 import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.internal.storage.reftree.RefTreeDatabase;
 import org.eclipse.jgit.internal.storage.file.ObjectDirectory.AlternateHandle;
 import org.eclipse.jgit.internal.storage.file.ObjectDirectory.AlternateRepository;
 import org.eclipse.jgit.lib.BaseRepositoryBuilder;
@@ -201,7 +202,22 @@ public class FileRepository extends Repository {
 			}
 		});
 
-		refs = new RefDirectory(this);
+		final long repositoryFormatVersion = getConfig().getLong(
+				ConfigConstants.CONFIG_CORE_SECTION, null,
+				ConfigConstants.CONFIG_KEY_REPO_FORMAT_VERSION, 0);
+
+		String reftype = repoConfig.getString(
+				"extensions", null, "refsBackendType"); //$NON-NLS-1$ //$NON-NLS-2$
+		if (repositoryFormatVersion >= 1 && reftype != null) {
+			if (StringUtils.equalsIgnoreCase(reftype, "reftree")) { //$NON-NLS-1$
+				refs = new RefTreeDatabase(this, new RefDirectory(this));
+			} else {
+				throw new IOException(JGitText.get().unknownRepositoryFormat);
+			}
+		} else {
+			refs = new RefDirectory(this);
+		}
+
 		objectDatabase = new ObjectDirectory(repoConfig, //
 				options.getObjectDirectory(), //
 				options.getAlternateObjectDirectories(), //
@@ -209,10 +225,7 @@ public class FileRepository extends Repository {
 				new File(getDirectory(), Constants.SHALLOW));
 
 		if (objectDatabase.exists()) {
-			final long repositoryFormatVersion = getConfig().getLong(
-					ConfigConstants.CONFIG_CORE_SECTION, null,
-					ConfigConstants.CONFIG_KEY_REPO_FORMAT_VERSION, 0);
-			if (repositoryFormatVersion > 0)
+			if (repositoryFormatVersion > 1)
 				throw new IOException(MessageFormat.format(
 						JGitText.get().unknownRepositoryFormat2,
 						Long.valueOf(repositoryFormatVersion)));
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftree/RefTreeDatabase.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftree/RefTreeDatabase.java
index 983216e30..dc6031110 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftree/RefTreeDatabase.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftree/RefTreeDatabase.java
@@ -54,6 +54,7 @@ import java.util.Map;
 
 import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.lib.BatchRefUpdate;
+import org.eclipse.jgit.lib.Config;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectIdRef;
 import org.eclipse.jgit.lib.Ref;
@@ -88,6 +89,28 @@ public class RefTreeDatabase extends RefDatabase {
 	private final String txnNamespace;
 	private volatile Scanner.Result refs;
 
+	/**
+	 * Create a RefTreeDb for a repository.
+	 *
+	 * @param repo
+	 *            the repository using references in this database.
+	 * @param bootstrap
+	 *            bootstrap reference database storing the references that
+	 *            anchor the {@link RefTree}.
+	 */
+	public RefTreeDatabase(Repository repo, RefDatabase bootstrap) {
+		Config cfg = repo.getConfig();
+		String committed = cfg.getString("reftree", null, "committedRef"); //$NON-NLS-1$ //$NON-NLS-2$
+		if (committed == null || committed.isEmpty()) {
+			committed = "refs/txn/committed"; //$NON-NLS-1$
+		}
+
+		this.repo = repo;
+		this.bootstrap = bootstrap;
+		this.txnNamespace = initNamespace(committed);
+		this.txnCommitted = committed;
+	}
+
 	/**
 	 * Create a RefTreeDb for a repository.
 	 *