diff --git a/.bazelversion b/.bazelversion
index 3eefcb9..7ec1d6d 100644
--- a/.bazelversion
+++ b/.bazelversion
@@ -1 +1 @@
-1.0.0
+2.1.0
diff --git a/WORKSPACE b/WORKSPACE
index 5fd2ed9..547c439 100644
--- a/WORKSPACE
+++ b/WORKSPACE
@@ -20,7 +20,7 @@
 
 load("//tools:bazlets.bzl", "load_bazlets")
 
-load_bazlets(commit = "09a035e98077dce549d5f6a7472d06c4b8f792d2")
+load_bazlets(commit = "f30a992da9fc855dce819875afb59f9dd6f860cd")
 
 load(
     "@com_googlesource_gerrit_bazlets//tools:maven_jar.bzl",
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
index cee898a..3d0daca 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
@@ -408,6 +408,7 @@
 		Git git2 = command.call();
 		addRepoToClose(git2.getRepository());
 		assertNotNull(git2);
+		assertTrue(git2.getRepository().isBare());
 		assertNotNull(git2.getRepository().resolve("tag-for-blob"));
 		assertNotNull(git2.getRepository().resolve("tag-initial"));
 		assertEquals(git2.getRepository().getFullBranch(), "refs/heads/master");
@@ -448,6 +449,60 @@
 				specs.get(0));
 	}
 
+	@Test
+	public void testCloneRepositoryAllBranchesTakesPreference()
+			throws Exception {
+		File directory = createTempDirectory(
+				"testCloneRepositoryAllBranchesTakesPreference");
+		CloneCommand command = Git.cloneRepository();
+		command.setCloneAllBranches(true);
+		command.setBranchesToClone(
+				Collections.singletonList("refs/heads/test"));
+		command.setDirectory(directory);
+		command.setURI(fileUri());
+		Git git2 = command.call();
+		addRepoToClose(git2.getRepository());
+		assertNotNull(git2);
+		assertEquals(git2.getRepository().getFullBranch(), "refs/heads/test");
+		// Expect both remote branches to exist; setCloneAllBranches(true)
+		// should override any setBranchesToClone().
+		assertNotNull(
+				git2.getRepository().resolve("refs/remotes/origin/master"));
+		assertNotNull(git2.getRepository().resolve("refs/remotes/origin/test"));
+		RemoteConfig cfg = new RemoteConfig(git2.getRepository().getConfig(),
+				Constants.DEFAULT_REMOTE_NAME);
+		List<RefSpec> specs = cfg.getFetchRefSpecs();
+		assertEquals(1, specs.size());
+		assertEquals(new RefSpec("+refs/heads/*:refs/remotes/origin/*"),
+				specs.get(0));
+	}
+
+	@Test
+	public void testCloneRepositoryAllBranchesIndependent() throws Exception {
+		File directory = createTempDirectory(
+				"testCloneRepositoryAllBranchesIndependent");
+		CloneCommand command = Git.cloneRepository();
+		command.setCloneAllBranches(true);
+		command.setBranchesToClone(
+				Collections.singletonList("refs/heads/test"));
+		command.setCloneAllBranches(false);
+		command.setDirectory(directory);
+		command.setURI(fileUri());
+		Git git2 = command.call();
+		addRepoToClose(git2.getRepository());
+		assertNotNull(git2);
+		assertEquals(git2.getRepository().getFullBranch(), "refs/heads/test");
+		// Expect only the test branch; allBranches was re-set to false
+		assertNull(git2.getRepository().resolve("refs/remotes/origin/master"));
+		assertNotNull(git2.getRepository().resolve("refs/remotes/origin/test"));
+		RemoteConfig cfg = new RemoteConfig(git2.getRepository().getConfig(),
+				Constants.DEFAULT_REMOTE_NAME);
+		List<RefSpec> specs = cfg.getFetchRefSpecs();
+		assertEquals(1, specs.size());
+		assertEquals(new RefSpec("+refs/heads/test:refs/remotes/origin/test"),
+				specs.get(0));
+	}
+
 	public static String allRefNames(List<Ref> refs) {
 		StringBuilder sb = new StringBuilder();
 		for (Ref f : refs) {
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 9da3507..b13cdb9 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
@@ -26,6 +26,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.security.SecureRandom;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -510,6 +511,43 @@
 	}
 
 	@Test
+	public void compactFully() throws Exception {
+		FileReftableDatabase refDb = (FileReftableDatabase) db.getRefDatabase();
+		PersonIdent person = new PersonIdent("jane", "jane@invalid");
+
+		ObjectId aId  = db.exactRef("refs/heads/a").getObjectId();
+		ObjectId bId  = db.exactRef("refs/heads/b").getObjectId();
+
+		SecureRandom random = new SecureRandom();
+		List<String> strs = new ArrayList<>();
+		for (int i = 0; i < 1024; i++) {
+			strs.add(String.format("%02x",
+					Integer.valueOf(random.nextInt(256))));
+		}
+
+		String randomStr = String.join("", strs);
+		String refName = "branch";
+		for (long i = 0; i < 2; i++) {
+			RefUpdate ru = refDb.newUpdate(refName, false);
+			ru.setNewObjectId(i % 2 == 0 ? aId : bId);
+			ru.setForceUpdate(true);
+			// Only write a large string in the first table, so it becomes much larger
+			// than the second, and the result is not autocompacted.
+			ru.setRefLogMessage(i == 0 ? randomStr : "short", false);
+			ru.setRefLogIdent(person);
+
+			RefUpdate.Result res = ru.update();
+			assertTrue(res == Result.NEW || res == FORCED);
+		}
+
+		assertEquals(refDb.exactRef(refName).getObjectId(), bId);
+		assertTrue(randomStr.equals(refDb.getReflogReader(refName).getReverseEntry(1).getComment()));
+		refDb.compactFully();
+		assertEquals(refDb.exactRef(refName).getObjectId(), bId);
+		assertTrue(randomStr.equals(refDb.getReflogReader(refName).getReverseEntry(1).getComment()));
+	}
+
+	@Test
 	public void reftableRefsStorageClass() throws IOException {
 		Ref b = db.exactRef("refs/heads/b");
 		assertEquals(Ref.Storage.PACKED, b.getStorage());
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
index 5232223..2525cbb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
@@ -71,7 +71,9 @@
 
 	private ProgressMonitor monitor = NullProgressMonitor.INSTANCE;
 
-	private FETCH_TYPE fetchType = FETCH_TYPE.ALL_BRANCHES;
+	private boolean cloneAllBranches;
+
+	private boolean mirror;
 
 	private boolean cloneSubmodules;
 
@@ -85,6 +87,8 @@
 
 	private boolean gitDirExistsInitially;
 
+	private FETCH_TYPE fetchType;
+
 	private enum FETCH_TYPE {
 		MULTIPLE_BRANCHES, ALL_BRANCHES, MIRROR
 	}
@@ -162,6 +166,7 @@
 			throw new InvalidRemoteException(
 					MessageFormat.format(JGitText.get().invalidURL, uri));
 		}
+		setFetchType();
 		@SuppressWarnings("resource") // Closed by caller
 		Repository repository = init();
 		FetchResult fetchResult = null;
@@ -205,6 +210,20 @@
 		return new Git(repository, true);
 	}
 
+	private void setFetchType() {
+		if (mirror) {
+			fetchType = FETCH_TYPE.MIRROR;
+			setBare(true);
+		} else if (cloneAllBranches) {
+			fetchType = FETCH_TYPE.ALL_BRANCHES;
+		} else if (branchesToClone != null && !branchesToClone.isEmpty()) {
+			fetchType = FETCH_TYPE.MULTIPLE_BRANCHES;
+		} else {
+			// Default: neither mirror nor all nor specific refs given
+			fetchType = FETCH_TYPE.ALL_BRANCHES;
+		}
+	}
+
 	private static boolean isNonEmptyDirectory(File dir) {
 		if (dir != null && dir.exists()) {
 			File[] files = dir.listFiles();
@@ -586,8 +605,7 @@
 	 * @return {@code this}
 	 */
 	public CloneCommand setCloneAllBranches(boolean cloneAllBranches) {
-		this.fetchType = cloneAllBranches ? FETCH_TYPE.ALL_BRANCHES
-				: this.fetchType;
+		this.cloneAllBranches = cloneAllBranches;
 		return this;
 	}
 
@@ -607,10 +625,7 @@
 	 * @since 5.6
 	 */
 	public CloneCommand setMirror(boolean mirror) {
-		if (mirror) {
-			this.fetchType = FETCH_TYPE.MIRROR;
-			setBare(true);
-		}
+		this.mirror = mirror;
 		return this;
 	}
 
@@ -631,8 +646,9 @@
 	 * Set the branches or tags to clone.
 	 * <p>
 	 * This is ignored if {@link #setCloneAllBranches(boolean)
-	 * setCloneAllBranches(true)} is used. If {@code branchesToClone} is
-	 * {@code null} or empty, it's also ignored and all branches will be cloned.
+	 * setCloneAllBranches(true)} or {@link #setMirror(boolean) setMirror(true)}
+	 * is used. If {@code branchesToClone} is {@code null} or empty, it's also
+	 * ignored.
 	 * </p>
 	 *
 	 * @param branchesToClone
@@ -642,13 +658,7 @@
 	 * @return {@code this}
 	 */
 	public CloneCommand setBranchesToClone(Collection<String> branchesToClone) {
-		if (branchesToClone == null || branchesToClone.isEmpty()) {
-			// fallback to default
-			fetchType = FETCH_TYPE.ALL_BRANCHES;
-		} else {
-			this.fetchType = FETCH_TYPE.MULTIPLE_BRANCHES;
-			this.branchesToClone = branchesToClone;
-		}
+		this.branchesToClone = branchesToClone;
 		return this;
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileReftableDatabase.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileReftableDatabase.java
index dc9c28c..aea14de 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileReftableDatabase.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileReftableDatabase.java
@@ -106,6 +106,7 @@
 		reftableDatabase.getLock().lock();
 		try {
 			reftableStack.compactFully();
+			reftableDatabase.clearCache();
 		} finally {
 			reftableDatabase.getLock().unlock();
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileReftableStack.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileReftableStack.java
index 5b540bd..4cb0bd3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileReftableStack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileReftableStack.java
@@ -237,8 +237,13 @@
 		long max = 1000;
 		long delay = 0;
 		boolean success = false;
-		while (System.currentTimeMillis() < deadline) {
+
+		// Don't check deadline for the first 3 retries, so we can step with a
+		// debugger without worrying about deadlines.
+		int tries = 0;
+		while (tries < 3 || System.currentTimeMillis() < deadline) {
 			List<String> names = readTableNames();
+			tries++;
 			try {
 				reloadOnce(names);
 				success = true;
@@ -260,9 +265,6 @@
 		}
 
 		if (!success) {
-			// TODO: should reexamine the 'refs' file to see if it was the same
-			// if it didn't change, then we must have corruption. If it did,
-			// retry.
 			throw new LockFailedException(stackPath);
 		}
 
@@ -374,7 +376,7 @@
 	 *
 	 * @param w
 	 *            writer to write data to a reftable under construction
-	 * @return true if the transaction.
+	 * @return true if the transaction was successful.
 	 * @throws IOException
 	 *             on I/O problems
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/LogCursor.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/LogCursor.java
index 9d410ae..f78975a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/LogCursor.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/reftable/LogCursor.java
@@ -12,6 +12,7 @@
 
 import java.io.IOException;
 
+import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.lib.ReflogEntry;
 
 /**
@@ -45,8 +46,9 @@
 	/**
 	 * Get current log entry.
 	 *
-	 * @return current log entry.
+	 * @return current log entry. Maybe null if we are producing deletions.
 	 */
+	@Nullable
 	public abstract ReflogEntry getReflogEntry();
 
 	/** {@inheritDoc} */