diff --git a/org.eclipse.jgit.benchmarks/src/org/eclipse/jgit/benchmarks/CreateFileSnapshotBenchmark.java b/org.eclipse.jgit.benchmarks/src/org/eclipse/jgit/benchmarks/CreateFileSnapshotBenchmark.java
index ffe4a26..21c54c5 100644
--- a/org.eclipse.jgit.benchmarks/src/org/eclipse/jgit/benchmarks/CreateFileSnapshotBenchmark.java
+++ b/org.eclipse.jgit.benchmarks/src/org/eclipse/jgit/benchmarks/CreateFileSnapshotBenchmark.java
@@ -45,7 +45,6 @@
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.util.UUID;
 import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.internal.storage.file.FileSnapshot;
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileReftableTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileReftableTest.java
index bb68ef1..0e06d45 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileReftableTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileReftableTest.java
@@ -73,6 +73,7 @@
 import org.eclipse.jgit.lib.RefUpdate.Result;
 import org.eclipse.jgit.lib.ReflogEntry;
 import org.eclipse.jgit.lib.ReflogReader;
+import org.eclipse.jgit.lib.RepositoryCache;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.test.resources.SampleDataRepositoryTestCase;
 import org.eclipse.jgit.transport.ReceiveCommand;
@@ -123,6 +124,11 @@ public void testRacyReload() throws Exception {
 	}
 
 	@Test
+	public void additionalRefsAreRemoved() {
+	 	assertFalse(new File(db.getDirectory(), Constants.HEAD).exists());
+	}
+
+	@Test
 	public void testCompactFully() throws Exception {
 		ObjectId c1 = db.resolve("master^^");
 		ObjectId c2 = db.resolve("master^");
@@ -503,6 +509,11 @@ public void testRenameCurrentBranch() throws IOException {
 	}
 
 	@Test
+	public void isGitRepository() {
+		assertTrue(RepositoryCache.FileKey.isGitRepository(db.getDirectory(), db.getFS()));
+	}
+
+	@Test
 	public void testRenameDestExists() throws IOException {
 		ObjectId rb = db.resolve("refs/heads/b");
 		writeSymref(Constants.HEAD, "refs/heads/b");
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java
index 89a2fc4..c9a3393 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java
@@ -254,7 +254,9 @@ public void testFsTimestampResolution() throws Exception {
 						formatter.format(t1.toInstant()),
 						Long.valueOf(resolutionNs)), t2.compareTo(t1) > 0);
 			} finally {
-				Files.delete(f);
+				if (f != null) {
+					Files.delete(f);
+				}
 			}
 		}
 	}
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 cb00fc4..2f6ef51 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
@@ -46,6 +46,8 @@
 
 package org.eclipse.jgit.internal.storage.file;
 
+import static java.util.stream.Collectors.toList;
+
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -740,6 +742,10 @@ void convertToReftable(boolean writeLogs, boolean backup)
 		File packedRefs = new File(getDirectory(), Constants.PACKED_REFS);
 		File logsDir = new File(getDirectory(), Constants.LOGS);
 
+
+		List<String> additional = getRefDatabase().getAdditionalRefs().stream()
+				.map(Ref::getName).collect(toList());
+		additional.add(Constants.HEAD);
 		if (backup) {
 			FileUtils.rename(refsFile, new File(getDirectory(), "refs.old"));
 			if (packedRefs.exists()) {
@@ -750,10 +756,17 @@ void convertToReftable(boolean writeLogs, boolean backup)
 				FileUtils.rename(logsDir,
 						new File(getDirectory(), Constants.LOGS + ".old"));
 			}
+			for (String r : additional) {
+				FileUtils.rename(new File(getDirectory(), r),
+					new File(getDirectory(), r + ".old"));
+			}
 		} else {
 			packedRefs.delete(); // ignore return value.
 			FileUtils.delete(logsDir, FileUtils.RECURSIVE);
 			FileUtils.delete(refsFile, FileUtils.RECURSIVE);
+			for (String r : additional) {
+				new File(getDirectory(), r).delete();
+			}
 		}
 
 		// Put new data.
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 fa113bf..fc74f53 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCache.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RepositoryCache.java
@@ -476,7 +476,8 @@ public String toString() {
 		public static boolean isGitRepository(File dir, FS fs) {
 			return fs.resolve(dir, Constants.OBJECTS).exists()
 					&& fs.resolve(dir, "refs").exists() //$NON-NLS-1$
-					&& isValidHead(new File(dir, Constants.HEAD));
+					&& (fs.resolve(dir, Constants.REFTABLE).exists()
+							|| isValidHead(new File(dir, Constants.HEAD)));
 		}
 
 		private static boolean isValidHead(File head) {