Merge changes Ifc34e96a,I72be0a0d

* changes:
  Fix javadoc in org.eclipse.jgit rewalk package
  Fix javadoc in org.eclipse.jgit ketch package

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/KetchConstants.java

@@ -45,7 +45,9 @@
 
 import org.eclipse.jgit.revwalk.FooterKey;
 
-/** Frequently used constants in a Ketch system. */
+/**
+ * Frequently used constants in a Ketch system.
+ */
 public class KetchConstants {
 	/**
 	 * Default reference namespace holding {@link #ACCEPTED} and

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/KetchLeader.java

@@ -69,11 +69,15 @@
 /**
  * A leader managing consensus across remote followers.
  * <p>
- * A leader instance starts up in {@link State#CANDIDATE} and tries to begin a
+ * A leader instance starts up in
- * new term by sending an {@link ElectionRound} to all replicas. Its term starts
+ * {@link org.eclipse.jgit.internal.ketch.KetchLeader.State#CANDIDATE} and tries
- * if a majority of replicas have accepted this leader instance for the term.
+ * to begin a new term by sending an
+ * {@link org.eclipse.jgit.internal.ketch.ElectionRound} to all replicas. Its
+ * term starts if a majority of replicas have accepted this leader instance for
+ * the term.
  * <p>
- * Once elected by a majority the instance enters {@link State#LEADER} and runs
+ * Once elected by a majority the instance enters
+ * {@link org.eclipse.jgit.internal.ketch.KetchLeader.State#LEADER} and runs
  * proposals offered to {@link #queueProposal(Proposal)}. This continues until
  * the leader is timed out for inactivity, or is deposed by a competing leader
  * gaining its own majority.
@@ -81,36 +85,42 @@
  * Once timed out or deposed this {@code KetchLeader} instance should be
  * discarded, and a new instance takes over.
  * <p>
- * Each leader instance coordinates a group of {@link KetchReplica}s. Replica
+ * Each leader instance coordinates a group of
- * instances are owned by the leader instance and must be discarded when the
+ * {@link org.eclipse.jgit.internal.ketch.KetchReplica}s. Replica instances are
- * leader is discarded.
+ * owned by the leader instance and must be discarded when the leader is
+ * discarded.
  * <p>
  * In Ketch all push requests are issued through the leader. The steps are as
- * follows (see {@link KetchPreReceive} for an example):
+ * follows (see {@link org.eclipse.jgit.internal.ketch.KetchPreReceive} for an
+ * example):
  * <ul>
- * <li>Create a {@link Proposal} with the
+ * <li>Create a {@link org.eclipse.jgit.internal.ketch.Proposal} with the
  * {@link org.eclipse.jgit.transport.ReceiveCommand}s that represent the push.
  * <li>Invoke {@link #queueProposal(Proposal)} on the leader instance.
- * <li>Wait for consensus with {@link Proposal#await()}.
+ * <li>Wait for consensus with
- * <li>To examine the status of the push, check {@link Proposal#getCommands()},
+ * {@link org.eclipse.jgit.internal.ketch.Proposal#await()}.
- * looking at
+ * <li>To examine the status of the push, check
+ * {@link org.eclipse.jgit.internal.ketch.Proposal#getCommands()}, looking at
  * {@link org.eclipse.jgit.internal.storage.reftree.Command#getResult()}.
  * </ul>
  * <p>
  * The leader gains consensus by first pushing the needed objects and a
- * {@link RefTree} representing the desired target repository state to the
+ * {@link org.eclipse.jgit.internal.storage.reftree.RefTree} representing the
- * {@code refs/txn/accepted} branch on each of the replicas. Once a majority has
+ * desired target repository state to the {@code refs/txn/accepted} branch on
- * succeeded, the leader commits the state by either pushing the
+ * each of the replicas. Once a majority has succeeded, the leader commits the
- * {@code refs/txn/accepted} value to {@code refs/txn/committed} (for
+ * state by either pushing the {@code refs/txn/accepted} value to
- * Ketch-aware replicas) or by pushing updates to {@code refs/heads/master},
+ * {@code refs/txn/committed} (for Ketch-aware replicas) or by pushing updates
- * etc. for stock Git replicas.
+ * to {@code refs/heads/master}, etc. for stock Git replicas.
  * <p>
  * Internally, the actual transport to replicas is performed on background
- * threads via the {@link KetchSystem}'s executor service. For performance, the
+ * threads via the {@link org.eclipse.jgit.internal.ketch.KetchSystem}'s
- * {@link KetchLeader}, {@link KetchReplica} and {@link Proposal} objects share
+ * executor service. For performance, the
- * some state, and may invoke each other's methods on different threads. This
+ * {@link org.eclipse.jgit.internal.ketch.KetchLeader},
- * access is protected by the leader's {@link #lock} object. Care must be taken
+ * {@link org.eclipse.jgit.internal.ketch.KetchReplica} and
- * to prevent concurrent access by correctly obtaining the leader's lock.
+ * {@link org.eclipse.jgit.internal.ketch.Proposal} objects share some state,
+ * and may invoke each other's methods on different threads. This access is
+ * protected by the leader's {@link #lock} object. Care must be taken to prevent
+ * concurrent access by correctly obtaining the leader's lock.
  */
 public abstract class KetchLeader {
 	private static final Logger log = LoggerFactory.getLogger(KetchLeader.class);
@@ -295,7 +305,7 @@ private static LocalReplica findLocal(Collection<KetchReplica> voters) {
 	 * The caller will close the repository.
 	 *
 	 * @return opened repository for use by the leader thread.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             cannot reopen the repository for the leader.
 	 */
 	protected abstract Repository openRepository() throws IOException;
@@ -307,16 +317,17 @@ private static LocalReplica findLocal(Collection<KetchReplica> voters) {
 	 * checked to look for risks of conflicts, and then submitted into the queue
 	 * for distribution as soon as possible.
 	 * <p>
-	 * Callers must use {@link Proposal#await()} to see if the proposal is done.
+	 * Callers must use {@link org.eclipse.jgit.internal.ketch.Proposal#await()}
+	 * to see if the proposal is done.
 	 *
 	 * @param proposal
 	 *            the proposed reference updates to queue for consideration.
 	 *            Once execution is complete the individual reference result
 	 *            fields will be populated with the outcome.
-	 * @throws InterruptedException
+	 * @throws java.lang.InterruptedException
 	 *             current thread was interrupted. The proposal may have been
 	 *             aborted if it was not yet queued for execution.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             unrecoverable error preventing proposals from being attempted
 	 *             by this leader.
 	 */
@@ -577,7 +588,11 @@ void nextRound() {
 		}
 	}
 
-	/** @return snapshot this leader. */
+	/**
+	 * Snapshot this leader
+	 *
+	 * @return snapshot of this leader
+	 */
 	public LeaderSnapshot snapshot() {
 		lock.lock();
 		try {
@@ -599,7 +614,9 @@ public LeaderSnapshot snapshot() {
 		}
 	}
 
-	/** Gracefully shutdown this leader and cancel outstanding operations. */
+	/**
+	 * Gracefully shutdown this leader and cancel outstanding operations.
+	 */
 	public void shutdown() {
 		lock.lock();
 		try {
@@ -617,6 +634,7 @@ public void shutdown() {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		return snapshot().toString();

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/KetchLeaderCache.java

@@ -82,7 +82,7 @@ public KetchLeaderCache(KetchSystem system) {
 	 * @param repo
 	 *            repository to get the leader for.
 	 * @return the leader instance for the repository.
-	 * @throws URISyntaxException
+	 * @throws java.net.URISyntaxException
 	 *             remote configuration contains an invalid URL.
 	 */
 	public KetchLeader get(Repository repo)

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/KetchPreReceive.java

@@ -64,9 +64,10 @@
 /**
  * PreReceiveHook for handling push traffic in a Ketch system.
  * <p>
- * Install an instance on {@link ReceivePack} to capture the commands and other
+ * Install an instance on {@link org.eclipse.jgit.transport.ReceivePack} to
- * connection state and relay them through the {@link KetchLeader}, allowing the
+ * capture the commands and other connection state and relay them through the
- * leader to gain consensus about the new reference state.
+ * {@link org.eclipse.jgit.internal.ketch.KetchLeader}, allowing the leader to
+ * gain consensus about the new reference state.
  */
 public class KetchPreReceive implements PreReceiveHook {
 	private static final Logger log = LoggerFactory.getLogger(KetchPreReceive.class);
@@ -74,7 +75,8 @@ public class KetchPreReceive implements PreReceiveHook {
 	private final KetchLeader leader;
 
 	/**
-	 * Construct a hook executing updates through a {@link KetchLeader}.
+	 * Construct a hook executing updates through a
+	 * {@link org.eclipse.jgit.internal.ketch.KetchLeader}.
 	 *
 	 * @param leader
 	 *            leader for this repository.
@@ -83,6 +85,7 @@ public KetchPreReceive(KetchLeader leader) {
 		this.leader = leader;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void onPreReceive(ReceivePack rp, Collection<ReceiveCommand> cmds) {
 		cmds = ReceiveCommand.filter(cmds, NOT_ATTEMPTED);

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/KetchReplica.java

@@ -82,26 +82,32 @@
 import org.slf4j.LoggerFactory;
 
 /**
- * A Ketch replica, either {@link LocalReplica} or {@link RemoteGitReplica}.
+ * A Ketch replica, either {@link org.eclipse.jgit.internal.ketch.LocalReplica}
+ * or {@link org.eclipse.jgit.internal.ketch.RemoteGitReplica}.
  * <p>
  * Replicas can be either a stock Git replica, or a Ketch-aware replica.
  * <p>
  * A stock Git replica has no special knowledge of Ketch and simply stores
  * objects and references. Ketch communicates with the stock Git replica using
- * the Git push wire protocol. The {@link KetchLeader} commits an agreed upon
+ * the Git push wire protocol. The
+ * {@link org.eclipse.jgit.internal.ketch.KetchLeader} commits an agreed upon
  * state by pushing all references to the Git replica, for example
  * {@code "refs/heads/master"} is pushed during commit. Stock Git replicas use
- * {@link CommitMethod#ALL_REFS} to record the final state.
+ * {@link org.eclipse.jgit.internal.ketch.KetchReplica.CommitMethod#ALL_REFS} to
+ * record the final state.
  * <p>
  * Ketch-aware replicas understand the {@code RefTree} sent during the proposal
  * and during commit are able to update their own reference space to match the
  * state represented by the {@code RefTree}. Ketch-aware replicas typically use
  * a {@link org.eclipse.jgit.internal.storage.reftree.RefTreeDatabase} and
- * {@link CommitMethod#TXN_COMMITTED} to record the final state.
+ * {@link org.eclipse.jgit.internal.ketch.KetchReplica.CommitMethod#TXN_COMMITTED}
+ * to record the final state.
  * <p>
- * KetchReplica instances are tightly coupled with a single {@link KetchLeader}.
+ * KetchReplica instances are tightly coupled with a single
- * Some state may be accessed by the leader thread and uses the leader's own
+ * {@link org.eclipse.jgit.internal.ketch.KetchLeader}. Some state may be
- * {@link KetchLeader#lock} to protect shared data.
+ * accessed by the leader thread and uses the leader's own
+ * {@link org.eclipse.jgit.internal.ketch.KetchLeader#lock} to protect shared
+ * data.
  */
 public abstract class KetchReplica {
 	static final Logger log = LoggerFactory.getLogger(KetchReplica.class);
@@ -223,37 +229,65 @@ protected KetchReplica(KetchLeader leader, String name, ReplicaConfig cfg) {
 		this.queued = new ArrayList<>(4);
 	}
 
-	/** @return system configuration. */
+	/**
+	 * Get system configuration.
+	 *
+	 * @return system configuration.
+	 */
 	public KetchSystem getSystem() {
 		return getLeader().getSystem();
 	}
 
-	/** @return leader instance this replica follows. */
+	/**
+	 * Get leader instance this replica follows.
+	 *
+	 * @return leader instance this replica follows.
+	 */
 	public KetchLeader getLeader() {
 		return leader;
 	}
 
-	/** @return unique-ish name for debugging. */
+	/**
+	 * Get unique-ish name for debugging.
+	 *
+	 * @return unique-ish name for debugging.
+	 */
 	public String getName() {
 		return replicaName;
 	}
 
-	/** @return description of this replica for error/debug logging purposes. */
+	/**
+	 * Get description of this replica for error/debug logging purposes.
+	 *
+	 * @return description of this replica for error/debug logging purposes.
+	 */
 	protected String describeForLog() {
 		return getName();
 	}
 
-	/** @return how the replica participates in this Ketch system. */
+	/**
+	 * Get how the replica participates in this Ketch system.
+	 *
+	 * @return how the replica participates in this Ketch system.
+	 */
 	public Participation getParticipation() {
 		return participation;
 	}
 
-	/** @return how Ketch will commit to the repository. */
+	/**
+	 * Get how Ketch will commit to the repository.
+	 *
+	 * @return how Ketch will commit to the repository.
+	 */
 	public CommitMethod getCommitMethod() {
 		return commitMethod;
 	}
 
-	/** @return when Ketch will commit to the repository. */
+	/**
+	 * Get when Ketch will commit to the repository.
+	 *
+	 * @return when Ketch will commit to the repository.
+	 */
 	public CommitSpeed getCommitSpeed() {
 		return commitSpeed;
 	}
@@ -264,7 +298,8 @@ public CommitSpeed getCommitSpeed() {
 	 * Default implementation cancels any scheduled retry. Subclasses may add
 	 * additional logic before or after calling {@code super.shutdown()}.
 	 * <p>
-	 * Called with {@link KetchLeader#lock} held by caller.
+	 * Called with {@link org.eclipse.jgit.internal.ketch.KetchLeader#lock} held
+	 * by caller.
 	 */
 	protected void shutdown() {
 		Future<?> f = retryFuture;
@@ -541,8 +576,8 @@ private void doRetryPush() {
 	/**
 	 * Begin executing a single push.
 	 * <p>
-	 * This method must move processing onto another thread.
+	 * This method must move processing onto another thread. Called with
-	 * Called with {@link KetchLeader#lock} held by caller.
+	 * {@link org.eclipse.jgit.internal.ketch.KetchLeader#lock} held by caller.
 	 *
 	 * @param req
 	 *            the request to send to the replica.
@@ -666,20 +701,21 @@ private static ObjectId readId(ReplicaPushRequest req,
 	/**
 	 * Fetch objects from the remote using the calling thread.
 	 * <p>
-	 * Called without {@link KetchLeader#lock}.
+	 * Called without {@link org.eclipse.jgit.internal.ketch.KetchLeader#lock}.
 	 *
 	 * @param repo
 	 *            local repository to fetch objects into.
 	 * @param req
 	 *            the request to fetch from a replica.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             communication with the replica was not possible.
 	 */
 	protected abstract void blockingFetch(Repository repo,
 			ReplicaFetchRequest req) throws IOException;
 
 	/**
-	 * Build a list of commands to commit {@link CommitMethod#ALL_REFS}.
+	 * Build a list of commands to commit
+	 * {@link org.eclipse.jgit.internal.ketch.KetchReplica.CommitMethod#ALL_REFS}.
 	 *
 	 * @param git
 	 *            local leader repository to read committed state from.
@@ -689,7 +725,7 @@ protected abstract void blockingFetch(Repository repo,
 	 * @param committed
 	 *            state being pushed to {@code refs/txn/committed}.
 	 * @return commands to update during commit.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             cannot read the committed state.
 	 */
 	protected Collection<ReceiveCommand> prepareCommit(Repository git,

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/KetchSystem.java

@@ -81,12 +81,17 @@
  * Full scale installations are expected to subclass and override methods to
  * provide consistent configuration across all managed repositories.
  * <p>
- * Servers should configure their own {@link ScheduledExecutorService}.
+ * Servers should configure their own
+ * {@link java.util.concurrent.ScheduledExecutorService}.
  */
 public class KetchSystem {
 	private static final Random RNG = new Random();
 
-	/** @return default executor, one thread per available processor. */
+	/**
+	 * Get default executor, one thread per available processor.
+	 *
+	 * @return default executor, one thread per available processor.
+	 */
 	public static ScheduledExecutorService defaultExecutor() {
 		return DefaultExecutorHolder.I;
 	}
@@ -98,7 +103,9 @@ public static ScheduledExecutorService defaultExecutor() {
 	private final String txnCommitted;
 	private final String txnStage;
 
-	/** Create a default system with a thread pool of 1 thread per CPU. */
+	/**
+	 * Create a default system with a thread pool of 1 thread per CPU.
+	 */
 	public KetchSystem() {
 		this(defaultExecutor(), new MonotonicSystemClock(), DEFAULT_TXN_NAMESPACE);
 	}
@@ -125,17 +132,29 @@ public KetchSystem(ScheduledExecutorService executor, MonotonicClock clock,
 		this.txnStage = txnNamespace + STAGE;
 	}
 
-	/** @return executor to perform background operations. */
+	/**
+	 * Get executor to perform background operations.
+	 *
+	 * @return executor to perform background operations.
+	 */
 	public ScheduledExecutorService getExecutor() {
 		return executor;
 	}
 
-	/** @return clock to obtain timestamps from. */
+	/**
+	 * Get clock to obtain timestamps from.
+	 *
+	 * @return clock to obtain timestamps from.
+	 */
 	public MonotonicClock getClock() {
 		return clock;
 	}
 
 	/**
+	 * Get how long the leader will wait for the {@link #getClock()}'s
+	 * {@code ProposedTimestamp} used in commits proposed to the RefTree graph
+	 * ({@link #getTxnAccepted()})
+	 *
 	 * @return how long the leader will wait for the {@link #getClock()}'s
 	 *         {@code ProposedTimestamp} used in commits proposed to the RefTree
 	 *         graph ({@link #getTxnAccepted()}). Defaults to 5 seconds.
@@ -145,8 +164,12 @@ public Duration getMaxWaitForMonotonicClock() {
 	}
 
 	/**
-	 * @return true if elections should require monotonically increasing commit
+	 * Whether elections should require monotonically increasing commit
-	 *         timestamps. This requires a very good {@link MonotonicClock}.
+	 * timestamps
+	 *
+	 * @return {@code true} if elections should require monotonically increasing
+	 *         commit timestamps. This requires a very good
+	 *         {@link org.eclipse.jgit.util.time.MonotonicClock}.
 	 */
 	public boolean requireMonotonicLeaderElections() {
 		return false;
@@ -161,22 +184,36 @@ public String getTxnNamespace() {
 		return txnNamespace;
 	}
 
-	/** @return name of the accepted RefTree graph. */
+	/**
+	 * Get name of the accepted RefTree graph.
+	 *
+	 * @return name of the accepted RefTree graph.
+	 */
 	public String getTxnAccepted() {
 		return txnAccepted;
 	}
 
-	/** @return name of the committed RefTree graph. */
+	/**
+	 * Get name of the committed RefTree graph.
+	 *
+	 * @return name of the committed RefTree graph.
+	 */
 	public String getTxnCommitted() {
 		return txnCommitted;
 	}
 
-	/** @return prefix for staged objects, e.g. {@code "refs/txn/stage/"}. */
+	/**
+	 * Get prefix for staged objects, e.g. {@code "refs/txn/stage/"}.
+	 *
+	 * @return prefix for staged objects, e.g. {@code "refs/txn/stage/"}.
+	 */
 	public String getTxnStage() {
 		return txnStage;
 	}
 
 	/**
+	 * Create new committer {@code PersonIdent} for ketch system
+	 *
 	 * @param time
 	 *            timestamp for the committer.
 	 * @return identity line for the committer header of a RefTreeGraph.
@@ -220,7 +257,7 @@ public String newLeaderTag() {
 	 * @param repo
 	 *            local repository stored by the leader.
 	 * @return leader instance.
-	 * @throws URISyntaxException
+	 * @throws java.net.URISyntaxException
 	 *             a follower configuration contains an unsupported URI.
 	 */
 	public KetchLeader createLeader(final Repository repo)
@@ -246,7 +283,7 @@ protected Repository openRepository() {
 	 * @param repo
 	 *            repository to get the replicas of.
 	 * @return collection of replicas for the specified repository.
-	 * @throws URISyntaxException
+	 * @throws java.net.URISyntaxException
 	 *             a configured URI is invalid.
 	 */
 	protected List<KetchReplica> createReplicas(KetchLeader leader,

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/KetchText.java

@@ -46,9 +46,15 @@
 import org.eclipse.jgit.nls.NLS;
 import org.eclipse.jgit.nls.TranslationBundle;
 
-/** Translation bundle for the Ketch implementation. */
+/**
+ * Translation bundle for the Ketch implementation.
+ */
 public class KetchText extends TranslationBundle {
-	/** @return instance of this translation bundle. */
+	/**
+	 * Get an instance of this translation bundle.
+	 *
+	 * @return instance of this translation bundle.
+	 */
 	public static KetchText get() {
 		return NLS.getBundleFor(KetchText.class);
 	}

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/LagCheck.java

@@ -86,6 +86,7 @@ private void initRevWalk() {
 		rw.setRetainBody(false);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		if (rw != null) {

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/LeaderSnapshot.java

@@ -53,7 +53,9 @@
 import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.lib.ObjectId;
 
-/** A snapshot of a leader and its view of the world. */
+/**
+ * A snapshot of a leader and its view of the world.
+ */
 public class LeaderSnapshot {
 	final List<ReplicaSnapshot> replicas = new ArrayList<>();
 	KetchLeader.State state;
@@ -65,17 +67,28 @@ public class LeaderSnapshot {
 	LeaderSnapshot() {
 	}
 
-	/** @return unmodifiable view of configured replicas. */
+	/**
+	 * Get unmodifiable view of configured replicas.
+	 *
+	 * @return unmodifiable view of configured replicas.
+	 */
 	public Collection<ReplicaSnapshot> getReplicas() {
 		return Collections.unmodifiableList(replicas);
 	}
 
-	/** @return current state of the leader. */
+	/**
+	 * Get current state of the leader.
+	 *
+	 * @return current state of the leader.
+	 */
 	public KetchLeader.State getState() {
 		return state;
 	}
 
 	/**
+	 * Whether the leader is not running a round to reach consensus, and has no
+	 * rounds queued.
+	 *
 	 * @return {@code true} if the leader is not running a round to reach
 	 *         consensus, and has no rounds queued.
 	 */
@@ -84,14 +97,19 @@ public boolean isIdle() {
 	}
 
 	/**
+	 * Get term of this leader
+	 *
 	 * @return term of this leader. Valid only if {@link #getState()} is
-	 *         currently {@link KetchLeader.State#LEADER}.
+	 *         currently
+	 *         {@link org.eclipse.jgit.internal.ketch.KetchLeader.State#LEADER}.
 	 */
 	public long getTerm() {
 		return term;
 	}
 
 	/**
+	 * Get end of the leader's log
+	 *
 	 * @return end of the leader's log; null if leader hasn't started up enough
 	 *         to begin its own election.
 	 */
@@ -101,6 +119,9 @@ public LogIndex getHead() {
 	}
 
 	/**
+	 * Get state the leader knows is committed on a majority of participant
+	 * replicas
+	 *
 	 * @return state the leader knows is committed on a majority of participant
 	 *         replicas. Null until the leader instance has committed a log
 	 *         index within its own term.
@@ -110,6 +131,7 @@ public LogIndex getCommitted() {
 		return committedIndex;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		StringBuilder s = new StringBuilder();

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/LocalReplica.java

@@ -67,7 +67,10 @@
 import org.eclipse.jgit.util.time.MonotonicClock;
 import org.eclipse.jgit.util.time.ProposedTimestamp;
 
-/** Ketch replica running on the same system as the {@link KetchLeader}. */
+/**
+ * Ketch replica running on the same system as the
+ * {@link org.eclipse.jgit.internal.ketch.KetchLeader}.
+ */
 public class LocalReplica extends KetchReplica {
 	/**
 	 * Configure a local replica.
@@ -83,6 +86,7 @@ public LocalReplica(KetchLeader leader, String name, ReplicaConfig cfg) {
 		super(leader, name, cfg);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected String describeForLog() {
 		return String.format("%s (leader)", getName()); //$NON-NLS-1$
@@ -116,6 +120,7 @@ void initialize(Repository repo) throws IOException {
 				getSystem().getTxnCommitted()));
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void startPush(final ReplicaPushRequest req) {
 		getSystem().getExecutor().execute(new Runnable() {
@@ -137,6 +142,7 @@ public void run() {
 		});
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void blockingFetch(Repository repo, ReplicaFetchRequest req)
 			throws IOException {

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/LogIndex.java

@@ -54,17 +54,18 @@
  * LogIndex provides a performance optimization for Ketch, the same information
  * can be obtained from {@link org.eclipse.jgit.revwalk.RevWalk}.
  * <p>
- * Index values are only valid within a single {@link KetchLeader} instance
+ * Index values are only valid within a single
- * after it has won an election. By restricting scope to a single leader new
+ * {@link org.eclipse.jgit.internal.ketch.KetchLeader} instance after it has won
- * leaders do not need to traverse the entire history to determine the next
+ * an election. By restricting scope to a single leader new leaders do not need
- * {@code index} for new proposals. This differs from Raft, where leader
+ * to traverse the entire history to determine the next {@code index} for new
- * election uses the log index and the term number to determine which replica
+ * proposals. This differs from Raft, where leader election uses the log index
- * holds a sufficiently up-to-date log. Since Ketch uses Git objects for storage
+ * and the term number to determine which replica holds a sufficiently
- * of its replicated log, it keeps the term number as Raft does but uses
+ * up-to-date log. Since Ketch uses Git objects for storage of its replicated
- * standard Git operations to imply the log index.
+ * log, it keeps the term number as Raft does but uses standard Git operations
+ * to imply the log index.
  * <p>
- * {@link Round#runAsync(AnyObjectId)} bumps the index as each new round is
+ * {@link org.eclipse.jgit.internal.ketch.Round#runAsync(AnyObjectId)} bumps the
- * constructed.
+ * index as each new round is constructed.
  */
 public class LogIndex extends ObjectId {
 	static LogIndex unknown(AnyObjectId id) {
@@ -82,7 +83,11 @@ LogIndex nextIndex(AnyObjectId id) {
 		return new LogIndex(id, index + 1);
 	}
 
-	/** @return index provided by the current leader instance. */
+	/**
+	 * Get index provided by the current leader instance.
+	 *
+	 * @return index provided by the current leader instance.
+	 */
 	public long getIndex() {
 		return index;
 	}
@@ -103,6 +108,9 @@ boolean isBefore(LogIndex c) {
 	}
 
 	/**
+	 * Create string suitable for debug logging containing the log index and
+	 * abbreviated ObjectId.
+	 *
 	 * @return string suitable for debug logging containing the log index and
 	 *         abbreviated ObjectId.
 	 */
@@ -111,6 +119,7 @@ public String describeForLog() {
 		return String.format("%5d/%s", index, abbreviate(6).name()); //$NON-NLS-1$
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("boxing")
 	@Override
 	public String toString() {

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/Proposal.java

@@ -78,10 +78,11 @@
  * area under the {@code refs/txn/stage/} namespace. If the proposal succeeds
  * then the changes are durable and the leader can commit the proposal.
  * <p>
- * Proposals are executed by {@link KetchLeader#queueProposal(Proposal)}, which
+ * Proposals are executed by
- * runs them asynchronously in the background. Proposals are thread-safe futures
+ * {@link org.eclipse.jgit.internal.ketch.KetchLeader#queueProposal(Proposal)},
- * allowing callers to {@link #await()} for results or be notified by callback
+ * which runs them asynchronously in the background. Proposals are thread-safe
- * using {@link #addListener(Runnable)}.
+ * futures allowing callers to {@link #await()} for results or be notified by
+ * callback using {@link #addListener(Runnable)}.
  */
 public class Proposal {
 	/** Current state of the proposal. */
@@ -146,9 +147,9 @@ public Proposal(List<Command> cmds) {
 	 *            walker to assist in preparing commands.
 	 * @param cmds
 	 *            list of pending commands.
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             newId of a command is not found locally.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             local objects cannot be accessed.
 	 */
 	public Proposal(RevWalk rw, Collection<ReceiveCommand> cmds)
@@ -166,12 +167,20 @@ private static List<Command> asCommandList(RevWalk rw,
 		return Collections.unmodifiableList(commands);
 	}
 
-	/** @return commands from this proposal. */
+	/**
+	 * Get commands from this proposal.
+	 *
+	 * @return commands from this proposal.
+	 */
 	public Collection<Command> getCommands() {
 		return commands;
 	}
 
-	/** @return optional author of the proposal. */
+	/**
+	 * Get optional author of the proposal.
+	 *
+	 * @return optional author of the proposal.
+	 */
 	@Nullable
 	public PersonIdent getAuthor() {
 		return author;
@@ -189,7 +198,11 @@ public Proposal setAuthor(@Nullable PersonIdent who) {
 		return this;
 	}
 
-	/** @return optional message for the commit log of the RefTree. */
+	/**
+	 * Get optional message for the commit log of the RefTree.
+	 *
+	 * @return optional message for the commit log of the RefTree.
+	 */
 	@Nullable
 	public String getMessage() {
 		return message;
@@ -207,7 +220,11 @@ public Proposal setMessage(@Nullable String msg) {
 		return this;
 	}
 
-	/** @return optional certificate signing the references. */
+	/**
+	 * Get optional certificate signing the references.
+	 *
+	 * @return optional certificate signing the references.
+	 */
 	@Nullable
 	public PushCertificate getPushCertificate() {
 		return pushCert;
@@ -226,6 +243,8 @@ public Proposal setPushCertificate(@Nullable PushCertificate cert) {
 	}
 
 	/**
+	 * Get timestamps that Ketch must block for.
+	 *
 	 * @return timestamps that Ketch must block for. These may have been used as
 	 *         commit times inside the objects involved in the proposal.
 	 */
@@ -240,6 +259,7 @@ public List<ProposedTimestamp> getProposedTimestamps() {
 	 * Request the proposal to wait for the affected timestamps to resolve.
 	 *
 	 * @param ts
+	 *            a {@link org.eclipse.jgit.util.time.ProposedTimestamp} object.
 	 * @return {@code this}.
 	 */
 	public Proposal addProposedTimestamp(ProposedTimestamp ts) {
@@ -253,9 +273,11 @@ public Proposal addProposedTimestamp(ProposedTimestamp ts) {
 	/**
 	 * Add a callback to be invoked when the proposal is done.
 	 * <p>
-	 * A proposal is done when it has entered either {@link State#EXECUTED} or
+	 * A proposal is done when it has entered either
-	 * {@link State#ABORTED} state. If the proposal is already done
+	 * {@link org.eclipse.jgit.internal.ketch.Proposal.State#EXECUTED} or
-	 * {@code callback.run()} is immediately invoked on the caller's thread.
+	 * {@link org.eclipse.jgit.internal.ketch.Proposal.State#ABORTED} state. If
+	 * the proposal is already done {@code callback.run()} is immediately
+	 * invoked on the caller's thread.
 	 *
 	 * @param callback
 	 *            method to run after the proposal is done. The callback may be
@@ -291,12 +313,18 @@ void abort() {
 		notifyState(ABORTED);
 	}
 
-	/** @return read the current state of the proposal. */
+	/**
+	 * Read the current state of the proposal.
+	 *
+	 * @return read the current state of the proposal.
+	 */
 	public State getState() {
 		return state.get();
 	}
 
 	/**
+	 * Whether the proposal was attempted
+	 *
 	 * @return {@code true} if the proposal was attempted. A true value does not
 	 *         mean consensus was reached, only that the proposal was considered
 	 *         and will not be making any more progress beyond its current
@@ -309,7 +337,7 @@ public boolean isDone() {
 	/**
 	 * Wait for the proposal to be attempted and {@link #isDone()} to be true.
 	 *
-	 * @throws InterruptedException
+	 * @throws java.lang.InterruptedException
 	 *             caller was interrupted before proposal executed.
 	 */
 	public void await() throws InterruptedException {
@@ -328,7 +356,7 @@ public void await() throws InterruptedException {
 	 * @param unit
 	 *            unit describing the wait time.
 	 * @return true if the proposal is done; false if the method timed out.
-	 * @throws InterruptedException
+	 * @throws java.lang.InterruptedException
 	 *             caller was interrupted before proposal executed.
 	 */
 	public boolean await(long wait, TimeUnit unit) throws InterruptedException {
@@ -351,7 +379,7 @@ public boolean await(long wait, TimeUnit unit) throws InterruptedException {
 	 * @param unit
 	 *            unit describing the wait time.
 	 * @return true if the proposal exited the state; false on time out.
-	 * @throws InterruptedException
+	 * @throws java.lang.InterruptedException
 	 *             caller was interrupted before proposal executed.
 	 */
 	public boolean awaitStateChange(State notIn, long wait, TimeUnit unit)
@@ -378,6 +406,7 @@ void notifyState(State s) {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		StringBuilder s = new StringBuilder();

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/RemoteGitReplica.java

@@ -80,7 +80,8 @@
 /**
  * Representation of a Git repository on a remote replica system.
  * <p>
- * {@link KetchLeader} will contact the replica using the Git wire protocol.
+ * {@link org.eclipse.jgit.internal.ketch.KetchLeader} will contact the replica
+ * using the Git wire protocol.
  * <p>
  * The remote replica may be fully Ketch-aware, or a standard Git server.
  */
@@ -110,22 +111,32 @@ public RemoteGitReplica(KetchLeader leader, String name, URIish uri,
 		this.remoteConfig = rc;
 	}
 
-	/** @return URI to contact the remote peer repository. */
+	/**
+	 * Get URI to contact the remote peer repository.
+	 *
+	 * @return URI to contact the remote peer repository.
+	 */
 	public URIish getURI() {
 		return uri;
 	}
 
-	/** @return optional configuration describing how to contact the peer. */
+	/**
+	 * Get optional configuration describing how to contact the peer.
+	 *
+	 * @return optional configuration describing how to contact the peer.
+	 */
 	@Nullable
 	protected RemoteConfig getRemoteConfig() {
 		return remoteConfig;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected String describeForLog() {
 		return String.format("%s @ %s", getName(), getURI()); //$NON-NLS-1$
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void startPush(final ReplicaPushRequest req) {
 		getSystem().getExecutor().execute(new Runnable() {
@@ -240,6 +251,7 @@ private static void abort(List<RemoteCommand> cmds) {
 		ReceiveCommand.abort(tmp);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void blockingFetch(Repository repo, ReplicaFetchRequest req)
 			throws NotSupportedException, TransportException {

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/ReplicaConfig.java

@@ -65,7 +65,9 @@
 import org.eclipse.jgit.internal.ketch.KetchReplica.Participation;
 import org.eclipse.jgit.lib.Config;
 
-/** Configures a {@link KetchReplica}. */
+/**
+ * Configures a {@link org.eclipse.jgit.internal.ketch.KetchReplica}.
+ */
 public class ReplicaConfig {
 	/**
 	 * Read a configuration from a config block.
@@ -86,17 +88,29 @@ public static ReplicaConfig newFromConfig(Config cfg, String name) {
 	private long minRetry = SECONDS.toMillis(5);
 	private long maxRetry = MINUTES.toMillis(1);
 
-	/** @return participation of the replica in the system. */
+	/**
+	 * Get participation of the replica in the system.
+	 *
+	 * @return participation of the replica in the system.
+	 */
 	public Participation getParticipation() {
 		return participation;
 	}
 
-	/** @return how Ketch should apply committed changes. */
+	/**
+	 * Get how Ketch should apply committed changes.
+	 *
+	 * @return how Ketch should apply committed changes.
+	 */
 	public CommitMethod getCommitMethod() {
 		return commitMethod;
 	}
 
-	/** @return how quickly should Ketch commit. */
+	/**
+	 * Get how quickly should Ketch commit.
+	 *
+	 * @return how quickly should Ketch commit.
+	 */
 	public CommitSpeed getCommitSpeed() {
 		return commitSpeed;
 	}

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/ReplicaFetchRequest.java

@@ -50,7 +50,9 @@
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
 
-/** A fetch request to obtain objects from a replica, and its result. */
+/**
+ * A fetch request to obtain objects from a replica, and its result.
+ */
 public class ReplicaFetchRequest {
 	private final Set<String> wantRefs;
 	private final Set<ObjectId> wantObjects;
@@ -70,23 +72,37 @@ public ReplicaFetchRequest(Set<String> wantRefs,
 		this.wantObjects = wantObjects;
 	}
 
-	/** @return references to be fetched. */
+	/**
+	 * Get references to be fetched.
+	 *
+	 * @return references to be fetched.
+	 */
 	public Set<String> getWantRefs() {
 		return wantRefs;
 	}
 
-	/** @return objects to be fetched. */
+	/**
+	 * Get objects to be fetched.
+	 *
+	 * @return objects to be fetched.
+	 */
 	public Set<ObjectId> getWantObjects() {
 		return wantObjects;
 	}
 
-	/** @return remote references, usually from the advertisement. */
+	/**
+	 * Get remote references, usually from the advertisement.
+	 *
+	 * @return remote references, usually from the advertisement.
+	 */
 	@Nullable
 	public Map<String, Ref> getRefs() {
 		return refs;
 	}
 
 	/**
+	 * Set references observed from the replica.
+	 *
 	 * @param refs
 	 *            references observed from the replica.
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/ReplicaPushRequest.java

@@ -54,8 +54,8 @@
 /**
  * A push request sending objects to a replica, and its result.
  * <p>
- * Implementors of {@link KetchReplica} must populate the command result fields,
+ * Implementors of {@link org.eclipse.jgit.internal.ketch.KetchReplica} must
- * {@link #setRefs(Map)}, and call one of
+ * populate the command result fields, {@link #setRefs(Map)}, and call one of
  * {@link #setException(Repository, Throwable)} or {@link #done(Repository)} to
  * finish processing.
  */
@@ -80,18 +80,28 @@ public ReplicaPushRequest(KetchReplica replica,
 		this.commands = commands;
 	}
 
-	/** @return commands to be executed, and their results. */
+	/**
+	 * Get commands to be executed, and their results.
+	 *
+	 * @return commands to be executed, and their results.
+	 */
 	public Collection<ReceiveCommand> getCommands() {
 		return commands;
 	}
 
-	/** @return remote references, usually from the advertisement. */
+	/**
+	 * Get remote references, usually from the advertisement.
+	 *
+	 * @return remote references, usually from the advertisement.
+	 */
 	@Nullable
 	public Map<String, Ref> getRefs() {
 		return refs;
 	}
 
 	/**
+	 * Set references observed from the replica.
+	 *
 	 * @param refs
 	 *            references observed from the replica.
 	 */
@@ -99,7 +109,11 @@ public void setRefs(Map<String, Ref> refs) {
 		this.refs = refs;
 	}
 
-	/** @return exception thrown, if any. */
+	/**
+	 * Get exception thrown, if any.
+	 *
+	 * @return exception thrown, if any.
+	 */
 	@Nullable
 	public Throwable getException() {
 		return exception;

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/ReplicaSnapshot.java

@@ -65,31 +65,50 @@ public class ReplicaSnapshot {
 		this.replica = replica;
 	}
 
-	/** @return the replica this snapshot describes the state of. */
+	/**
+	 * Get the replica this snapshot describes the state of
+	 *
+	 * @return the replica this snapshot describes the state of
+	 */
 	public KetchReplica getReplica() {
 		return replica;
 	}
 
-	/** @return current state of the replica. */
+	/**
+	 * Get current state of the replica
+	 *
+	 * @return current state of the replica
+	 */
 	public KetchReplica.State getState() {
 		return state;
 	}
 
-	/** @return last known Git commit at {@code refs/txn/accepted}. */
+	/**
+	 * Get last known Git commit at {@code refs/txn/accepted}
+	 *
+	 * @return last known Git commit at {@code refs/txn/accepted}
+	 */
 	@Nullable
 	public ObjectId getAccepted() {
 		return accepted;
 	}
 
-	/** @return last known Git commit at {@code refs/txn/committed}. */
+	/**
+	 * Get last known Git commit at {@code refs/txn/committed}
+	 *
+	 * @return last known Git commit at {@code refs/txn/committed}
+	 */
 	@Nullable
 	public ObjectId getCommitted() {
 		return committed;
 	}
 
 	/**
-	 * @return if {@link #getState()} == {@link KetchReplica.State#OFFLINE} an
+	 * Get error message
-	 *         optional human-readable message from the transport system
+	 *
+	 * @return if {@link #getState()} ==
+	 *         {@link org.eclipse.jgit.internal.ketch.KetchReplica.State#OFFLINE}
+	 *         an optional human-readable message from the transport system
 	 *         explaining the failure.
 	 */
 	@Nullable
@@ -98,6 +117,9 @@ public String getErrorMessage() {
 	}
 
 	/**
+	 * Get when the leader will retry communication with the offline or lagging
+	 * replica
+	 *
 	 * @return time (usually in the future) when the leader will retry
 	 *         communication with the offline or lagging replica; null if no
 	 *         retry is scheduled or necessary.

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/StageBuilder.java

@@ -66,7 +66,9 @@
 import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.jgit.treewalk.filter.TreeFilter;
 
-/** Constructs a set of commands to stage content during a proposal. */
+/**
+ * Constructs a set of commands to stage content during a proposal.
+ */
 public class StageBuilder {
 	/**
 	 * Acceptable number of references to send in a single stage transaction.
@@ -119,14 +121,15 @@ public StageBuilder(String txnStageNamespace, ObjectId txnId) {
 	 *            from.
 	 * @param oldTree
 	 *            accepted RefTree on the replica ({@code refs/txn/accepted}).
-	 *            Use {@link ObjectId#zeroId()} if the remote does not have any
+	 *            Use {@link org.eclipse.jgit.lib.ObjectId#zeroId()} if the
-	 *            ref tree, e.g. a new replica catching up.
+	 *            remote does not have any ref tree, e.g. a new replica catching
+	 *            up.
 	 * @param newTree
 	 *            RefTree being sent to the replica. The trees will be compared.
 	 * @return list of commands to create {@code "refs/txn/stage/..."}
 	 *         references on replicas anchoring new objects into the repository
 	 *         while a transaction gains consensus.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             {@code git} cannot be accessed to compare {@code oldTree} and
 	 *             {@code newTree} to build the object set.
 	 */
@@ -172,7 +175,7 @@ public List<ReceiveCommand> makeStageList(Repository git, ObjectId oldTree,
 	 * @return list of commands to create {@code "refs/txn/stage/..."}
 	 *         references on replicas anchoring {@code newObjs} into the
 	 *         repository while a transaction gains consensus.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             {@code git} cannot be accessed to perform minification of
 	 *             {@code newObjs}.
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/internal/revwalk/AddToBitmapFilter.java

@@ -73,6 +73,7 @@ public AddToBitmapFilter(BitmapBuilder bitmap) {
 		this.bitmap = bitmap;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public final boolean include(RevWalk walker, RevCommit cmit) {
 		Bitmap visitedBitmap;
@@ -93,11 +94,13 @@ public final boolean include(RevWalk walker, RevCommit cmit) {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public final RevFilter clone() {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public final boolean requiresCommitBody() {
 		return false;

org.eclipse.jgit/src/org/eclipse/jgit/internal/revwalk/AddUnseenToBitmapFilter.java

@@ -81,6 +81,7 @@ public AddUnseenToBitmapFilter(BitmapBuilder seen, BitmapBuilder bitmap) {
 		this.bitmap = bitmap;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public final boolean include(RevWalk walker, RevCommit cmit) {
 		Bitmap visitedBitmap;
@@ -101,11 +102,13 @@ public final boolean include(RevWalk walker, RevCommit cmit) {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public final RevFilter clone() {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public final boolean requiresCommitBody() {
 		return false;