Fix javadoc in org.eclipse.jgit transport package

Change-Id: Id70e2c27e38bf12f87e66b28fbd0b06908494764
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

109 files changed, 1807 insertions, 755 deletions

diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AbstractAdvertiseRefsHook.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AbstractAdvertiseRefsHook.java
index 6f1369458c..4bf0d2692a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AbstractAdvertiseRefsHook.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AbstractAdvertiseRefsHook.java
@@ -51,12 +51,13 @@ import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.RevWalk;
 
 /**
- * Implementation of {@link AdvertiseRefsHook} that advertises the same refs for
+ * Implementation of {@link org.eclipse.jgit.transport.AdvertiseRefsHook} that advertises the same refs for
  * upload-pack and receive-pack.
  *
  * @since 2.0
  */
 public abstract class AbstractAdvertiseRefsHook implements AdvertiseRefsHook {
+	/** {@inheritDoc} */
 	@Override
 	public void advertiseRefs(UploadPack uploadPack)
 			throws ServiceMayNotContinueException {
@@ -64,6 +65,7 @@ public abstract class AbstractAdvertiseRefsHook implements AdvertiseRefsHook {
 				uploadPack.getRepository(), uploadPack.getRevWalk()));
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void advertiseRefs(BaseReceivePack receivePack)
 			throws ServiceMayNotContinueException {
@@ -82,7 +84,7 @@ public abstract class AbstractAdvertiseRefsHook implements AdvertiseRefsHook {
 	 * @param revWalk
 	 *            open rev walk on the repository.
 	 * @return set of refs to advertise.
-	 * @throws ServiceMayNotContinueException
+	 * @throws org.eclipse.jgit.transport.ServiceMayNotContinueException
 	 *             abort; the message will be sent to the user.
 	 */
 	protected abstract Map<String, Ref> getAdvertisedRefs(
@@ -97,8 +99,8 @@ public abstract class AbstractAdvertiseRefsHook implements AdvertiseRefsHook {
 	 * @param revWalk
 	 *            open rev walk on the repository.
 	 * @return set of additional haves; see
-	 *         {@link ReceivePack#getAdvertisedObjects()}.
-	 * @throws ServiceMayNotContinueException
+	 *         {@link org.eclipse.jgit.transport.ReceivePack#getAdvertisedObjects()}.
+	 * @throws org.eclipse.jgit.transport.ServiceMayNotContinueException
 	 *             abort; the message will be sent to the user.
 	 */
 	protected Set<ObjectId> getAdvertisedHaves(
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHook.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHook.java
index 96d7c240c3..ed05c733f3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHook.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHook.java
@@ -70,10 +70,11 @@ public interface AdvertiseRefsHook {
 	/**
 	 * Advertise refs for upload-pack.
 	 *
-	 * @param uploadPack instance on which to call
-	 *            {@link UploadPack#setAdvertisedRefs(java.util.Map)}
+	 * @param uploadPack
+	 *            instance on which to call
+	 *            {@link org.eclipse.jgit.transport.UploadPack#setAdvertisedRefs(java.util.Map)}
 	 *            if necessary.
-	 * @throws ServiceMayNotContinueException
+	 * @throws org.eclipse.jgit.transport.ServiceMayNotContinueException
 	 *             abort; the message will be sent to the user.
 	 */
 	public void advertiseRefs(UploadPack uploadPack)
@@ -82,10 +83,11 @@ public interface AdvertiseRefsHook {
 	/**
 	 * Advertise refs for receive-pack.
 	 *
-	 * @param receivePack instance on which to call
-	 *            {@link BaseReceivePack#setAdvertisedRefs(java.util.Map,java.util.Set)}
+	 * @param receivePack
+	 *            instance on which to call
+	 *            {@link org.eclipse.jgit.transport.BaseReceivePack#setAdvertisedRefs(java.util.Map,java.util.Set)}
 	 *            if necessary.
-	 * @throws ServiceMayNotContinueException
+	 * @throws org.eclipse.jgit.transport.ServiceMayNotContinueException
 	 *             abort; the message will be sent to the user.
 	 */
 	public void advertiseRefs(BaseReceivePack receivePack)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHookChain.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHookChain.java
index 22ea5cba9a..4ef3e1a974 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHookChain.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHookChain.java
@@ -46,13 +46,14 @@ package org.eclipse.jgit.transport;
 import java.util.List;
 
 /**
- * {@link AdvertiseRefsHook} that delegates to a list of other hooks.
+ * {@link org.eclipse.jgit.transport.AdvertiseRefsHook} that delegates to a list
+ * of other hooks.
  * <p>
  * Hooks are run in the order passed to the constructor. A hook may inspect or
  * modify the results of the previous hooks in the chain by calling
- * {@link UploadPack#getAdvertisedRefs()}, or
- * {@link BaseReceivePack#getAdvertisedRefs()} or
- * {@link BaseReceivePack#getAdvertisedObjects()}.
+ * {@link org.eclipse.jgit.transport.UploadPack#getAdvertisedRefs()}, or
+ * {@link org.eclipse.jgit.transport.BaseReceivePack#getAdvertisedRefs()} or
+ * {@link org.eclipse.jgit.transport.BaseReceivePack#getAdvertisedObjects()}.
  */
 public class AdvertiseRefsHookChain implements AdvertiseRefsHook {
 	private final AdvertiseRefsHook[] hooks;
@@ -79,6 +80,7 @@ public class AdvertiseRefsHookChain implements AdvertiseRefsHook {
 			return new AdvertiseRefsHookChain(newHooks, i);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void advertiseRefs(BaseReceivePack rp)
 			throws ServiceMayNotContinueException {
@@ -86,6 +88,7 @@ public class AdvertiseRefsHookChain implements AdvertiseRefsHook {
 			hooks[i].advertiseRefs(rp);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void advertiseRefs(UploadPack rp)
 			throws ServiceMayNotContinueException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AmazonS3.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AmazonS3.java
index 0690397078..fee71eb362 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/AmazonS3.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/AmazonS3.java
@@ -231,7 +231,6 @@ public class AmazonS3 {
 	 *
 	 * @param props
 	 *            connection properties.
-	 *
 	 */
 	public AmazonS3(final Properties props) {
 		domain = props.getProperty(Keys.DOMAIN, "s3.amazonaws.com"); //$NON-NLS-1$
@@ -281,7 +280,7 @@ public class AmazonS3 {
 	 * @return connection to stream the content of the object. The request
 	 *         properties of the connection may not be modified by the caller as
 	 *         the request parameters have already been signed.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             sending the request was not possible.
 	 */
 	public URLConnection get(final String bucket, final String key)
@@ -310,7 +309,7 @@ public class AmazonS3 {
 	 * @param u
 	 *            connection previously created by {@link #get(String, String)}}.
 	 * @return stream to read plain text from.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             decryption could not be configured.
 	 */
 	public InputStream decrypt(final URLConnection u) throws IOException {
@@ -333,7 +332,7 @@ public class AmazonS3 {
 	 * @return list of keys starting with <code>prefix</code>, after removing
 	 *         <code>prefix</code> (or <code>prefix + "/"</code>)from all
 	 *         of them.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             sending the request was not possible, or the response XML
 	 *             document could not be parsed properly.
 	 */
@@ -357,7 +356,7 @@ public class AmazonS3 {
 	 *            name of the bucket storing the object.
 	 * @param key
 	 *            key of the object within its bucket.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             deletion failed due to communications error.
 	 */
 	public void delete(final String bucket, final String key)
@@ -394,7 +393,7 @@ public class AmazonS3 {
 	 * @param data
 	 *            new data content for the object. Must not be null. Zero length
 	 *            array will create a zero length object.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             creation/updating failed due to communications error.
 	 */
 	public void put(final String bucket, final String key, final byte[] data)
@@ -463,7 +462,7 @@ public class AmazonS3 {
 	 * @param monitorTask
 	 *            (optional) task name to display during the close method.
 	 * @return a stream which accepts the new data, and transmits once closed.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if encryption was enabled it could not be configured.
 	 */
 	public OutputStream beginPut(final String bucket, final String key,
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseConnection.java
index 69028fab31..c8d1d229b5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseConnection.java
@@ -71,31 +71,34 @@ public abstract class BaseConnection implements Connection {
 
 	private Writer messageWriter;
 
+	/** {@inheritDoc} */
 	@Override
 	public Map<String, Ref> getRefsMap() {
 		return advertisedRefs;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public final Collection<Ref> getRefs() {
 		return advertisedRefs.values();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public final Ref getRef(final String name) {
 		return advertisedRefs.get(name);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getMessages() {
 		return messageWriter != null ? messageWriter.toString() : ""; //$NON-NLS-1$
 	}
 
 	/**
-	 * User agent advertised by the remote server.
+	 * {@inheritDoc}
 	 *
-	 * @return agent (version of Git) running on the remote server. Null if the
-	 *         server does not advertise this version.
+	 * User agent advertised by the remote server.
 	 * @since 4.0
 	 */
 	@Override
@@ -114,6 +117,7 @@ public abstract class BaseConnection implements Connection {
 		peerUserAgent = agent;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public abstract void close();
 
@@ -136,7 +140,7 @@ public abstract class BaseConnection implements Connection {
 	 * Helper method for ensuring one-operation per connection. Check whether
 	 * operation was already marked as started, and mark it as started.
 	 *
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             if operation was already marked as started.
 	 */
 	protected void markStartedOperation() throws TransportException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseFetchConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseFetchConnection.java
index 41b8c2d765..6f460251c0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseFetchConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseFetchConnection.java
@@ -64,6 +64,7 @@ import org.eclipse.jgit.lib.Ref;
  */
 abstract class BaseFetchConnection extends BaseConnection implements
 		FetchConnection {
+	/** {@inheritDoc} */
 	@Override
 	public final void fetch(final ProgressMonitor monitor,
 			final Collection<Ref> want, final Set<ObjectId> have)
@@ -71,6 +72,7 @@ abstract class BaseFetchConnection extends BaseConnection implements
 		fetch(monitor, want, have, null);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public final void fetch(final ProgressMonitor monitor,
 			final Collection<Ref> want, final Set<ObjectId> have,
@@ -80,6 +82,8 @@ abstract class BaseFetchConnection extends BaseConnection implements
 	}
 
 	/**
+	 * {@inheritDoc}
+	 *
 	 * Default implementation of {@link FetchConnection#didFetchIncludeTags()} -
 	 * returning false.
 	 */
@@ -98,7 +102,7 @@ abstract class BaseFetchConnection extends BaseConnection implements
 	 *            as in {@link #fetch(ProgressMonitor, Collection, Set)}
 	 * @param have
 	 *            as in {@link #fetch(ProgressMonitor, Collection, Set)}
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             as in {@link #fetch(ProgressMonitor, Collection, Set)}, but
 	 *             implementation doesn't have to care about multiple
 	 *             {@link #fetch(ProgressMonitor, Collection, Set)} calls, as it
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackConnection.java
index c69544930d..e9227e33a3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackConnection.java
@@ -170,9 +170,9 @@ abstract class BasePackConnection extends BaseConnection {
 	 * <p>
 	 * If any errors occur, this connection is automatically closed by invoking
 	 * {@link #close()} and the exception is wrapped (if necessary) and thrown
-	 * as a {@link TransportException}.
+	 * as a {@link org.eclipse.jgit.errors.TransportException}.
 	 *
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the reference list could not be scanned.
 	 */
 	protected void readAdvertisedRefs() throws TransportException {
@@ -267,10 +267,26 @@ abstract class BasePackConnection extends BaseConnection {
 		return new NoRemoteRepositoryException(uri, JGitText.get().notFound);
 	}
 
+	/**
+	 * Whether this option is supported
+	 *
+	 * @param option
+	 *            option string
+	 * @return whether this option is supported
+	 */
 	protected boolean isCapableOf(final String option) {
 		return remoteCapablities.contains(option);
 	}
 
+	/**
+	 * Request capability
+	 *
+	 * @param b
+	 *            buffer
+	 * @param option
+	 *            option we want
+	 * @return {@code true} if the requested option is supported
+	 */
 	protected boolean wantCapability(final StringBuilder b, final String option) {
 		if (!isCapableOf(option))
 			return false;
@@ -279,6 +295,12 @@ abstract class BasePackConnection extends BaseConnection {
 		return true;
 	}
 
+	/**
+	 * Add user agent capability
+	 *
+	 * @param b
+	 *            a {@link java.lang.StringBuilder} object.
+	 */
 	protected void addUserAgentCapability(StringBuilder b) {
 		String a = UserAgent.get();
 		if (a != null && UserAgent.hasAgent(remoteCapablities)) {
@@ -286,6 +308,7 @@ abstract class BasePackConnection extends BaseConnection {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getPeerUserAgent() {
 		return UserAgent.getAgent(remoteCapablities, super.getPeerUserAgent());
@@ -295,6 +318,7 @@ abstract class BasePackConnection extends BaseConnection {
 		return new PackProtocolException(uri, MessageFormat.format(JGitText.get().duplicateAdvertisementsOf, name));
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		if (out != null) {
@@ -334,7 +358,9 @@ abstract class BasePackConnection extends BaseConnection {
 		}
 	}
 
-	/** Tell the peer we are disconnecting, if it cares to know. */
+	/**
+	 * Tell the peer we are disconnecting, if it cares to know.
+	 */
 	protected void endOut() {
 		if (outNeedsEnd && out != null) {
 			try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackFetchConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackFetchConnection.java
index 61c4c4b172..19d8abe9e0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackFetchConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackFetchConnection.java
@@ -94,10 +94,10 @@ import org.eclipse.jgit.util.TemporaryBuffer;
  * easily wrapped up into a local process pipe, anonymous TCP socket, or a
  * command executed through an SSH tunnel.
  * <p>
- * If {@link BasePackConnection#statelessRPC} is {@code true}, this connection
- * can be tunneled over a request-response style RPC system like HTTP.  The RPC
- * call boundary is determined by this class switching from writing to the
- * OutputStream to reading from the InputStream.
+ * If {@link org.eclipse.jgit.transport.BasePackConnection#statelessRPC} is
+ * {@code true}, this connection can be tunneled over a request-response style
+ * RPC system like HTTP. The RPC call boundary is determined by this class
+ * switching from writing to the OutputStream to reading from the InputStream.
  * <p>
  * Concrete implementations should just call
  * {@link #init(java.io.InputStream, java.io.OutputStream)} and
@@ -285,6 +285,7 @@ public abstract class BasePackFetchConnection extends BasePackConnection
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public final void fetch(final ProgressMonitor monitor,
 			final Collection<Ref> want, final Set<ObjectId> have)
@@ -292,9 +293,7 @@ public abstract class BasePackFetchConnection extends BasePackConnection
 		fetch(monitor, want, have, null);
 	}
 
-	/**
-	 * @since 3.0
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public final void fetch(final ProgressMonitor monitor,
 			final Collection<Ref> want, final Set<ObjectId> have,
@@ -303,21 +302,25 @@ public abstract class BasePackFetchConnection extends BasePackConnection
 		doFetch(monitor, want, have, outputStream);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean didFetchIncludeTags() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean didFetchTestConnectivity() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setPackLockMessage(final String message) {
 		lockMessage = message;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Collection<PackLock> getPackLocks() {
 		if (packLock != null)
@@ -330,7 +333,7 @@ public abstract class BasePackFetchConnection extends BasePackConnection
 	 *
 	 * @param monitor
 	 *            progress monitor to receive status updates. If the monitor is
-	 *            the {@link NullProgressMonitor#INSTANCE}, then the no-progress
+	 *            the {@link org.eclipse.jgit.lib.NullProgressMonitor#INSTANCE}, then the no-progress
 	 *            option enabled.
 	 * @param want
 	 *            the advertised remote references the caller wants to fetch.
@@ -340,7 +343,7 @@ public abstract class BasePackFetchConnection extends BasePackConnection
 	 *            destination repository's references.
 	 * @param outputStream
 	 *            ouputStream to write sideband messages to
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             if any exception occurs.
 	 * @since 3.0
 	 */
@@ -380,6 +383,7 @@ public abstract class BasePackFetchConnection extends BasePackConnection
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		if (walk != null)
@@ -776,7 +780,7 @@ public abstract class BasePackFetchConnection extends BasePackConnection
 
 	/**
 	 * Notification event delivered just before the pack is received from the
-	 * network. This event can be used by RPC such as {@link TransportHttp} to
+	 * network. This event can be used by RPC such as {@link org.eclipse.jgit.transport.TransportHttp} to
 	 * disable its request magic and ensure the pack stream is read correctly.
 	 *
 	 * @since 2.0
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackPushConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackPushConnection.java
index 679ea0c8fd..ee6f29ed0a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackPushConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackPushConnection.java
@@ -81,7 +81,8 @@ import org.eclipse.jgit.transport.RemoteRefUpdate.Status;
  * easily wrapped up into a local process pipe, anonymous TCP socket, or a
  * command executed through an SSH tunnel.
  * <p>
- * This implementation honors {@link Transport#isPushThin()} option.
+ * This implementation honors
+ * {@link org.eclipse.jgit.transport.Transport#isPushThin()} option.
  * <p>
  * Concrete implementations should just call
  * {@link #init(java.io.InputStream, java.io.OutputStream)} and
@@ -152,6 +153,7 @@ public abstract class BasePackPushConnection extends BasePackConnection implemen
 		pushOptions = transport.getPushOptions();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void push(final ProgressMonitor monitor,
 			final Map<String, RemoteRefUpdate> refUpdates)
@@ -159,9 +161,7 @@ public abstract class BasePackPushConnection extends BasePackConnection implemen
 		push(monitor, refUpdates, null);
 	}
 
-	/**
-	 * @since 3.0
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public void push(final ProgressMonitor monitor,
 			final Map<String, RemoteRefUpdate> refUpdates, OutputStream outputStream)
@@ -170,6 +170,7 @@ public abstract class BasePackPushConnection extends BasePackConnection implemen
 		doPush(monitor, refUpdates, outputStream);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected TransportException noRepository() {
 		// Sadly we cannot tell the "invalid URI" case from "push not allowed".
@@ -202,7 +203,7 @@ public abstract class BasePackPushConnection extends BasePackConnection implemen
 	 *            update commands to be applied to the remote repository.
 	 * @param outputStream
 	 *            output stream to write sideband messages to
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             if any exception occurs.
 	 * @since 3.0
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java
index 44abcd598b..e97f71a488 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BaseReceivePack.java
@@ -405,15 +405,27 @@ public abstract class BaseReceivePack {
 		}
 	}
 
-	/** @return the process name used for pack lock messages. */
+	/**
+	 * Get the process name used for pack lock messages.
+	 *
+	 * @return the process name used for pack lock messages.
+	 */
 	protected abstract String getLockMessageProcessName();
 
-	/** @return the repository this receive completes into. */
+	/**
+	 * Get the repository this receive completes into.
+	 *
+	 * @return the repository this receive completes into.
+	 */
 	public final Repository getRepository() {
 		return db;
 	}
 
-	/** @return the RevWalk instance used by this connection. */
+	/**
+	 * Get the RevWalk instance used by this connection.
+	 *
+	 * @return the RevWalk instance used by this connection.
+	 */
 	public final RevWalk getRevWalk() {
 		return walk;
 	}
@@ -431,14 +443,15 @@ public abstract class BaseReceivePack {
 	/**
 	 * Set the refs advertised by this ReceivePack.
 	 * <p>
-	 * Intended to be called from a {@link PreReceiveHook}.
+	 * Intended to be called from a
+	 * {@link org.eclipse.jgit.transport.PreReceiveHook}.
 	 *
 	 * @param allRefs
 	 *            explicit set of references to claim as advertised by this
-	 *            ReceivePack instance. This overrides any references that
-	 *            may exist in the source repository. The map is passed
-	 *            to the configured {@link #getRefFilter()}. If null, assumes
-	 *            all refs were advertised.
+	 *            ReceivePack instance. This overrides any references that may
+	 *            exist in the source repository. The map is passed to the
+	 *            configured {@link #getRefFilter()}. If null, assumes all refs
+	 *            were advertised.
 	 * @param additionalHaves
 	 *            explicit set of additional haves to claim as advertised. If
 	 *            null, assumes the default set of additional haves from the
@@ -475,6 +488,9 @@ public abstract class BaseReceivePack {
 	}
 
 	/**
+	 * Whether this instance will validate all referenced, but not supplied by
+	 * the client, objects are reachable from another reference.
+	 *
 	 * @return true if this instance will validate all referenced, but not
 	 *         supplied by the client, objects are reachable from another
 	 *         reference.
@@ -493,8 +509,9 @@ public abstract class BaseReceivePack {
 	 * This feature is useful when the application doesn't trust the client to
 	 * not provide a forged SHA-1 reference to an object, in an attempt to
 	 * access parts of the DAG that they aren't allowed to see and which have
-	 * been hidden from them via the configured {@link AdvertiseRefsHook} or
-	 * {@link RefFilter}.
+	 * been hidden from them via the configured
+	 * {@link org.eclipse.jgit.transport.AdvertiseRefsHook} or
+	 * {@link org.eclipse.jgit.transport.RefFilter}.
 	 * <p>
 	 * Enabling this feature may imply at least some, if not all, of the same
 	 * functionality performed by {@link #setCheckReceivedObjects(boolean)}.
@@ -508,6 +525,9 @@ public abstract class BaseReceivePack {
 	}
 
 	/**
+	 * Whether this class expects a bi-directional pipe opened between the
+	 * client and itself.
+	 *
 	 * @return true if this class expects a bi-directional pipe opened between
 	 *         the client and itself. The default is true.
 	 */
@@ -516,6 +536,10 @@ public abstract class BaseReceivePack {
 	}
 
 	/**
+	 * Whether this class will assume the socket is a fully bidirectional pipe
+	 * between the two peers and takes advantage of that by first transmitting
+	 * the known refs, then waiting to read commands.
+	 *
 	 * @param twoWay
 	 *            if true, this class will assume the socket is a fully
 	 *            bidirectional pipe between the two peers and takes advantage
@@ -528,32 +552,44 @@ public abstract class BaseReceivePack {
 		biDirectionalPipe = twoWay;
 	}
 
-	/** @return true if there is data expected after the pack footer. */
+	/**
+	 * Whether there is data expected after the pack footer.
+	 *
+	 * @return {@code true} if there is data expected after the pack footer.
+	 */
 	public boolean isExpectDataAfterPackFooter() {
 		return expectDataAfterPackFooter;
 	}
 
 	/**
+	 * Whether there is additional data in InputStream after pack.
+	 *
 	 * @param e
-	 *            true if there is additional data in InputStream after pack.
+	 *            {@code true} if there is additional data in InputStream after
+	 *            pack.
 	 */
 	public void setExpectDataAfterPackFooter(boolean e) {
 		expectDataAfterPackFooter = e;
 	}
 
 	/**
-	 * @return true if this instance will verify received objects are formatted
-	 *         correctly. Validating objects requires more CPU time on this side
-	 *         of the connection.
+	 * Whether this instance will verify received objects are formatted
+	 * correctly.
+	 *
+	 * @return {@code true} if this instance will verify received objects are
+	 *         formatted correctly. Validating objects requires more CPU time on
+	 *         this side of the connection.
 	 */
 	public boolean isCheckReceivedObjects() {
 		return objectChecker != null;
 	}
 
 	/**
+	 * Whether to enable checking received objects
+	 *
 	 * @param check
-	 *            true to enable checking received objects; false to assume all
-	 *            received objects are valid.
+	 *            {@code true} to enable checking received objects; false to
+	 *            assume all received objects are valid.
 	 * @see #setObjectChecker(ObjectChecker)
 	 */
 	public void setCheckReceivedObjects(final boolean check) {
@@ -564,42 +600,59 @@ public abstract class BaseReceivePack {
 	}
 
 	/**
-	 * @param impl if non-null the object checking instance to verify each
-	 *        received object with; null to disable object checking.
+	 * Set the object checking instance to verify each received object with
+	 *
+	 * @param impl
+	 *            if non-null the object checking instance to verify each
+	 *            received object with; null to disable object checking.
 	 * @since 3.4
 	 */
 	public void setObjectChecker(ObjectChecker impl) {
 		objectChecker = impl;
 	}
 
-	/** @return true if the client can request refs to be created. */
+	/**
+	 * Whether the client can request refs to be created.
+	 *
+	 * @return {@code true} if the client can request refs to be created.
+	 */
 	public boolean isAllowCreates() {
 		return allowCreates;
 	}
 
 	/**
+	 * Whether to permit create ref commands to be processed.
+	 *
 	 * @param canCreate
-	 *            true to permit create ref commands to be processed.
+	 *            {@code true} to permit create ref commands to be processed.
 	 */
 	public void setAllowCreates(final boolean canCreate) {
 		allowCreates = canCreate;
 	}
 
-	/** @return true if the client can request refs to be deleted. */
+	/**
+	 * Whether the client can request refs to be deleted.
+	 *
+	 * @return {@code true} if the client can request refs to be deleted.
+	 */
 	public boolean isAllowDeletes() {
 		return allowAnyDeletes;
 	}
 
 	/**
+	 * Whether to permit delete ref commands to be processed.
+	 *
 	 * @param canDelete
-	 *            true to permit delete ref commands to be processed.
+	 *            {@code true} to permit delete ref commands to be processed.
 	 */
 	public void setAllowDeletes(final boolean canDelete) {
 		allowAnyDeletes = canDelete;
 	}
 
 	/**
-	 * @return true if the client can delete from {@code refs/heads/}.
+	 * Whether the client can delete from {@code refs/heads/}.
+	 *
+	 * @return {@code true} if the client can delete from {@code refs/heads/}.
 	 * @since 3.6
 	 */
 	public boolean isAllowBranchDeletes() {
@@ -607,8 +660,11 @@ public abstract class BaseReceivePack {
 	}
 
 	/**
+	 * Configure whether to permit deletion of branches from the
+	 * {@code refs/heads/} namespace.
+	 *
 	 * @param canDelete
-	 *            true to permit deletion of branches from the
+	 *            {@code true} to permit deletion of branches from the
 	 *            {@code refs/heads/} namespace.
 	 * @since 3.6
 	 */
@@ -617,25 +673,34 @@ public abstract class BaseReceivePack {
 	}
 
 	/**
-	 * @return true if the client can request non-fast-forward updates of a ref,
-	 *         possibly making objects unreachable.
+	 * Whether the client can request non-fast-forward updates of a ref,
+	 * possibly making objects unreachable.
+	 *
+	 * @return {@code true} if the client can request non-fast-forward updates
+	 *         of a ref, possibly making objects unreachable.
 	 */
 	public boolean isAllowNonFastForwards() {
 		return allowNonFastForwards;
 	}
 
 	/**
+	 * Configure whether to permit the client to ask for non-fast-forward
+	 * updates of an existing ref.
+	 *
 	 * @param canRewind
-	 *            true to permit the client to ask for non-fast-forward updates
-	 *            of an existing ref.
+	 *            {@code true} to permit the client to ask for non-fast-forward
+	 *            updates of an existing ref.
 	 */
 	public void setAllowNonFastForwards(final boolean canRewind) {
 		allowNonFastForwards = canRewind;
 	}
 
 	/**
-	 * @return true if the client's commands should be performed as a single
-	 *         atomic transaction.
+	 * Whether the client's commands should be performed as a single atomic
+	 * transaction.
+	 *
+	 * @return {@code true} if the client's commands should be performed as a
+	 *         single atomic transaction.
 	 * @since 4.4
 	 */
 	public boolean isAtomic() {
@@ -643,16 +708,23 @@ public abstract class BaseReceivePack {
 	}
 
 	/**
+	 * Configure whether to perform the client's commands as a single atomic
+	 * transaction.
+	 *
 	 * @param atomic
-	 *            true to perform the client's commands as a single atomic
-	 *            transaction.
+	 *            {@code true} to perform the client's commands as a single
+	 *            atomic transaction.
 	 * @since 4.4
 	 */
 	public void setAtomic(boolean atomic) {
 		this.atomic = atomic;
 	}
 
-	/** @return identity of the user making the changes in the reflog. */
+	/**
+	 * Get identity of the user making the changes in the reflog.
+	 *
+	 * @return identity of the user making the changes in the reflog.
+	 */
 	public PersonIdent getRefLogIdent() {
 		return refLogIdent;
 	}
@@ -673,12 +745,20 @@ public abstract class BaseReceivePack {
 		refLogIdent = pi;
 	}
 
-	/** @return the hook used while advertising the refs to the client */
+	/**
+	 * Get the hook used while advertising the refs to the client
+	 *
+	 * @return the hook used while advertising the refs to the client
+	 */
 	public AdvertiseRefsHook getAdvertiseRefsHook() {
 		return advertiseRefsHook;
 	}
 
-	/** @return the filter used while advertising the refs to the client */
+	/**
+	 * Get the filter used while advertising the refs to the client
+	 *
+	 * @return the filter used while advertising the refs to the client
+	 */
 	public RefFilter getRefFilter() {
 		return refFilter;
 	}
@@ -686,12 +766,14 @@ public abstract class BaseReceivePack {
 	/**
 	 * Set the hook used while advertising the refs to the client.
 	 * <p>
-	 * If the {@link AdvertiseRefsHook} chooses to call
-	 * {@link #setAdvertisedRefs(Map,Set)}, only refs set by this hook
-	 * <em>and</em> selected by the {@link RefFilter} will be shown to the client.
-	 * Clients may still attempt to create or update a reference not advertised by
-	 * the configured {@link AdvertiseRefsHook}. These attempts should be rejected
-	 * by a matching {@link PreReceiveHook}.
+	 * If the {@link org.eclipse.jgit.transport.AdvertiseRefsHook} chooses to
+	 * call {@link #setAdvertisedRefs(Map,Set)}, only refs set by this hook
+	 * <em>and</em> selected by the {@link org.eclipse.jgit.transport.RefFilter}
+	 * will be shown to the client. Clients may still attempt to create or
+	 * update a reference not advertised by the configured
+	 * {@link org.eclipse.jgit.transport.AdvertiseRefsHook}. These attempts
+	 * should be rejected by a matching
+	 * {@link org.eclipse.jgit.transport.PreReceiveHook}.
 	 *
 	 * @param advertiseRefsHook
 	 *            the hook; may be null to show all refs.
@@ -706,9 +788,9 @@ public abstract class BaseReceivePack {
 	/**
 	 * Set the filter used while advertising the refs to the client.
 	 * <p>
-	 * Only refs allowed by this filter will be shown to the client.
-	 * The filter is run against the refs specified by the
-	 * {@link AdvertiseRefsHook} (if applicable).
+	 * Only refs allowed by this filter will be shown to the client. The filter
+	 * is run against the refs specified by the
+	 * {@link org.eclipse.jgit.transport.AdvertiseRefsHook} (if applicable).
 	 *
 	 * @param refFilter
 	 *            the filter; may be null to show all refs.
@@ -717,7 +799,11 @@ public abstract class BaseReceivePack {
 		this.refFilter = refFilter != null ? refFilter : RefFilter.DEFAULT;
 	}
 
-	/** @return timeout (in seconds) before aborting an IO operation. */
+	/**
+	 * Get timeout (in seconds) before aborting an IO operation.
+	 *
+	 * @return timeout (in seconds) before aborting an IO operation.
+	 */
 	public int getTimeout() {
 		return timeout;
 	}
@@ -786,7 +872,6 @@ public abstract class BaseReceivePack {
 	 *
 	 * @param limit
 	 *            the pack size limit, in bytes
-	 *
 	 * @since 3.3
 	 */
 	public void setMaxPackSizeLimit(final long limit) {
@@ -801,7 +886,7 @@ public abstract class BaseReceivePack {
 	 *
 	 * @return true if the client has advertised a side-band capability, false
 	 *     otherwise.
-	 * @throws RequestNotYetReadException
+	 * @throws org.eclipse.jgit.transport.RequestNotYetReadException
 	 *             if the client's request has not yet been read from the wire, so
 	 *             we do not know if they expect side-band. Note that the client
 	 *             may have already written the request, it just has not been
@@ -813,6 +898,8 @@ public abstract class BaseReceivePack {
 	}
 
 	/**
+	 * Whether clients may request avoiding noisy progress messages.
+	 *
 	 * @return true if clients may request avoiding noisy progress messages.
 	 * @since 4.0
 	 */
@@ -835,6 +922,8 @@ public abstract class BaseReceivePack {
 	}
 
 	/**
+	 * Whether the server supports receiving push options.
+	 *
 	 * @return true if the server supports receiving push options.
 	 * @since 4.5
 	 */
@@ -857,7 +946,7 @@ public abstract class BaseReceivePack {
 	 * True if the client wants less verbose output.
 	 *
 	 * @return true if the client has requested the server to be less verbose.
-	 * @throws RequestNotYetReadException
+	 * @throws org.eclipse.jgit.transport.RequestNotYetReadException
 	 *             if the client's request has not yet been read from the wire,
 	 *             so we do not know if they expect side-band. Note that the
 	 *             client may have already written the request, it just has not
@@ -908,7 +997,11 @@ public abstract class BaseReceivePack {
 		return UserAgent.getAgent(enabledCapabilities, userAgent);
 	}
 
-	/** @return all of the command received by the current request. */
+	/**
+	 * Get all of the command received by the current request.
+	 *
+	 * @return all of the command received by the current request.
+	 */
 	public List<ReceiveCommand> getAllCommands() {
 		return Collections.unmodifiableList(commands);
 	}
@@ -926,11 +1019,13 @@ public abstract class BaseReceivePack {
 	 * message will be discarded, with no other indication to the caller or to
 	 * the client.
 	 * <p>
-	 * {@link PreReceiveHook}s should always try to use
-	 * {@link ReceiveCommand#setResult(Result, String)} with a result status of
-	 * {@link Result#REJECTED_OTHER_REASON} to indicate any reasons for
-	 * rejecting an update. Messages attached to a command are much more likely
-	 * to be returned to the client.
+	 * {@link org.eclipse.jgit.transport.PreReceiveHook}s should always try to
+	 * use
+	 * {@link org.eclipse.jgit.transport.ReceiveCommand#setResult(Result, String)}
+	 * with a result status of
+	 * {@link org.eclipse.jgit.transport.ReceiveCommand.Result#REJECTED_OTHER_REASON}
+	 * to indicate any reasons for rejecting an update. Messages attached to a
+	 * command are much more likely to be returned to the client.
 	 *
 	 * @param what
 	 *            string describing the problem identified by the hook. The
@@ -973,7 +1068,11 @@ public abstract class BaseReceivePack {
 		msgOutWrapper.write(Constants.encode(what + "\n")); //$NON-NLS-1$
 	}
 
-	/** @return an underlying stream for sending messages to the client. */
+	/**
+	 * Get an underlying stream for sending messages to the client.
+	 *
+	 * @return an underlying stream for sending messages to the client.
+	 */
 	public OutputStream getMessageOutputStream() {
 		return msgOutWrapper;
 	}
@@ -984,7 +1083,7 @@ public abstract class BaseReceivePack {
 	 * This can only be called if the pack is already received.
 	 *
 	 * @return the size of the received pack including index size
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             if called before the pack has been received
 	 * @since 3.3
 	 */
@@ -1006,12 +1105,20 @@ public abstract class BaseReceivePack {
 		return clientShallowCommits;
 	}
 
-	/** @return true if any commands to be executed have been read. */
+	/**
+	 * Whether any commands to be executed have been read.
+	 *
+	 * @return {@code true} if any commands to be executed have been read.
+	 */
 	protected boolean hasCommands() {
 		return !commands.isEmpty();
 	}
 
-	/** @return true if an error occurred that should be advertised. */
+	/**
+	 * Whether an error occurred that should be advertised.
+	 *
+	 * @return true if an error occurred that should be advertised.
+	 */
 	protected boolean hasError() {
 		return advertiseError != null;
 	}
@@ -1059,7 +1166,11 @@ public abstract class BaseReceivePack {
 		commands = new ArrayList<>();
 	}
 
-	/** @return advertised refs, or the default if not explicitly advertised. */
+	/**
+	 * Get advertised refs, or the default if not explicitly advertised.
+	 *
+	 * @return advertised refs, or the default if not explicitly advertised.
+	 */
 	protected Map<String, Ref> getAdvertisedOrDefaultRefs() {
 		if (refs == null)
 			setAdvertisedRefs(null, null);
@@ -1069,7 +1180,7 @@ public abstract class BaseReceivePack {
 	/**
 	 * Receive a pack from the stream and check connectivity if necessary.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred during unpacking or connectivity checking.
 	 */
 	protected void receivePackAndCheckConnectivity() throws IOException {
@@ -1082,7 +1193,7 @@ public abstract class BaseReceivePack {
 	/**
 	 * Unlock the pack written by this object.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the pack could not be unlocked.
 	 */
 	protected void unlockPack() throws IOException {
@@ -1097,9 +1208,9 @@ public abstract class BaseReceivePack {
 	 *
 	 * @param adv
 	 *            the advertisement formatter.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the formatter failed to write an advertisement.
-	 * @throws ServiceMayNotContinueException
+	 * @throws org.eclipse.jgit.transport.ServiceMayNotContinueException
 	 *             the hook denied advertisement.
 	 */
 	public void sendAdvertisedRefs(final RefAdvertiser adv)
@@ -1160,7 +1271,7 @@ public abstract class BaseReceivePack {
 	/**
 	 * Receive a list of commands from the input.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	protected void recvCommands() throws IOException {
 		PacketLineIn pck = maxCommandBytes > 0
@@ -1289,7 +1400,9 @@ public abstract class BaseReceivePack {
 		// Do nothing by default.
 	}
 
-	/** Enable capabilities based on a previously read capabilities line. */
+	/**
+	 * Enable capabilities based on a previously read capabilities line.
+	 */
 	protected void enableCapabilities() {
 		sideBand = isCapabilityEnabled(CAPABILITY_SIDE_BAND_64K);
 		quiet = allowQuiet && isCapabilityEnabled(CAPABILITY_QUIET);
@@ -1321,7 +1434,11 @@ public abstract class BaseReceivePack {
 			throw new RequestNotYetReadException();
 	}
 
-	/** @return true if a pack is expected based on the list of commands. */
+	/**
+	 * Whether a pack is expected based on the list of commands.
+	 *
+	 * @return {@code true} if a pack is expected based on the list of commands.
+	 */
 	protected boolean needPack() {
 		for (final ReceiveCommand cmd : commands) {
 			if (cmd.getType() != ReceiveCommand.Type.DELETE)
@@ -1475,7 +1592,9 @@ public abstract class BaseReceivePack {
 		}
 	}
 
-	/** Validate the command list. */
+	/**
+	 * Validate the command list.
+	 */
 	protected void validateCommands() {
 		for (final ReceiveCommand cmd : commands) {
 			final Ref ref = cmd.getRef();
@@ -1612,6 +1731,8 @@ public abstract class BaseReceivePack {
 	}
 
 	/**
+	 * Whether any commands have been rejected so far.
+	 *
 	 * @return if any commands have been rejected so far.
 	 * @since 3.6
 	 */
@@ -1625,6 +1746,7 @@ public abstract class BaseReceivePack {
 
 	/**
 	 * Set the result to fail for any command that was not processed yet.
+	 *
 	 * @since 3.6
 	 */
 	protected void failPendingCommands() {
@@ -1643,7 +1765,9 @@ public abstract class BaseReceivePack {
 		return ReceiveCommand.filter(commands, want);
 	}
 
-	/** Execute commands to update references. */
+	/**
+	 * Execute commands to update references.
+	 */
 	protected void executeCommands() {
 		List<ReceiveCommand> toApply = filterCommands(Result.NOT_ATTEMPTED);
 		if (toApply.isEmpty())
@@ -1683,7 +1807,7 @@ public abstract class BaseReceivePack {
 	 *            an error that occurred during unpacking, or {@code null}
 	 * @param out
 	 *            the reporter for sending the status strings.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred writing the status report.
 	 */
 	protected void sendStatusReport(final boolean forClient,
@@ -1770,7 +1894,7 @@ public abstract class BaseReceivePack {
 	/**
 	 * Close and flush (if necessary) the underlying streams.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	protected void close() throws IOException {
 		if (sideBand) {
@@ -1802,7 +1926,7 @@ public abstract class BaseReceivePack {
 	/**
 	 * Release any resources used by this object.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the pack could not be unlocked.
 	 */
 	protected void release() throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleFetchConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleFetchConnection.java
index f37ba01034..39efabf5d8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleFetchConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleFetchConnection.java
@@ -180,11 +180,13 @@ class BundleFetchConnection extends BaseFetchConnection {
 		return line.toString();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean didFetchTestConnectivity() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void doFetch(final ProgressMonitor monitor,
 			final Collection<Ref> want, final Set<ObjectId> have)
@@ -208,11 +210,13 @@ class BundleFetchConnection extends BaseFetchConnection {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setPackLockMessage(final String message) {
 		lockMessage = message;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Collection<PackLock> getPackLocks() {
 		if (packLock != null)
@@ -290,6 +294,7 @@ class BundleFetchConnection extends BaseFetchConnection {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		if (bin != null) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleWriter.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleWriter.java
index 0920f21563..35ac7792e6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleWriter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleWriter.java
@@ -70,7 +70,7 @@ import org.eclipse.jgit.storage.pack.PackConfig;
  * <p>
  * Bundles generated by this class can be later read in from a file URI using
  * the bundle transport, or from an application controlled buffer by the more
- * generic {@link TransportBundleStream}.
+ * generic {@link org.eclipse.jgit.transport.TransportBundleStream}.
  * <p>
  * Applications creating bundles need to call one or more <code>include</code>
  * calls to reflect which objects should be available as refs in the bundle for
@@ -208,13 +208,10 @@ public class BundleWriter {
 	 *            the stream the bundle is written to. The stream should be
 	 *            buffered by the caller. The caller is responsible for closing
 	 *            the stream.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             an error occurred reading a local object's data to include in
 	 *             the bundle, or writing compressed object data to the output
 	 *             stream.
-	 * @throws WriteAbortedException
-	 *             the write operation is aborted by
-	 *             {@link ObjectCountCallback}.
 	 */
 	public void writeBundle(ProgressMonitor monitor, OutputStream os)
 			throws IOException {
@@ -270,17 +267,16 @@ public class BundleWriter {
 	}
 
 	/**
-	 * Set the {@link ObjectCountCallback}.
+	 * Set the {@link org.eclipse.jgit.transport.ObjectCountCallback}.
 	 * <p>
 	 * It should be set before calling
 	 * {@link #writeBundle(ProgressMonitor, OutputStream)}.
 	 * <p>
 	 * This callback will be passed on to
-	 * {@link PackWriter#setObjectCountCallback}.
+	 * {@link org.eclipse.jgit.internal.storage.pack.PackWriter#setObjectCountCallback}.
 	 *
 	 * @param callback
 	 *            the callback to set
-	 *
 	 * @return this object for chaining.
 	 * @since 4.1
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ChainingCredentialsProvider.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ChainingCredentialsProvider.java
index 8cb3d604cf..9f05d5a548 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ChainingCredentialsProvider.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ChainingCredentialsProvider.java
@@ -72,11 +72,7 @@ public class ChainingCredentialsProvider extends CredentialsProvider {
 				Arrays.asList(providers));
 	}
 
-	/**
-	 * @return {@code true} if any of the credential providers in the list is
-	 *         interactive, otherwise {@code false}
-	 * @see org.eclipse.jgit.transport.CredentialsProvider#isInteractive()
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public boolean isInteractive() {
 		for (CredentialsProvider p : credentialProviders)
@@ -85,11 +81,7 @@ public class ChainingCredentialsProvider extends CredentialsProvider {
 		return false;
 	}
 
-	/**
-	 * @return {@code true} if any of the credential providers in the list
-	 *         supports the requested items, otherwise {@code false}
-	 * @see org.eclipse.jgit.transport.CredentialsProvider#supports(org.eclipse.jgit.transport.CredentialItem[])
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public boolean supports(CredentialItem... items) {
 		for (CredentialsProvider p : credentialProviders)
@@ -99,11 +91,11 @@ public class ChainingCredentialsProvider extends CredentialsProvider {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Populates the credential items with the credentials provided by the first
 	 * credential provider in the list which populates them with non-null values
 	 *
-	 * @return {@code true} if any of the credential providers in the list
-	 *         supports the requested items, otherwise {@code false}
 	 * @see org.eclipse.jgit.transport.CredentialsProvider#supports(org.eclipse.jgit.transport.CredentialItem[])
 	 */
 	@Override
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/Connection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/Connection.java
index 9a272a4fdd..bcc5110e73 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/Connection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/Connection.java
@@ -98,6 +98,8 @@ public interface Connection extends AutoCloseable {
 	public Ref getRef(final String name);
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Close any resources used by this connection.
 	 * <p>
 	 * If the remote repository is contacted by a network socket this method
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/CredentialItem.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/CredentialItem.java
index 88e075adc9..3a74f1d9e1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/CredentialItem.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/CredentialItem.java
@@ -48,14 +48,19 @@ import java.util.Arrays;
 import org.eclipse.jgit.internal.JGitText;
 
 /**
- * A credential requested from a {@link CredentialsProvider}.
+ * A credential requested from a
+ * {@link org.eclipse.jgit.transport.CredentialsProvider}.
  *
  * Most users should work with the specialized subclasses:
  * <ul>
- * <li>{@link Username} for usernames</li>
- * <li>{@link Password} for passwords</li>
- * <li>{@link StringType} for other general string information</li>
- * <li>{@link CharArrayType} for other general secret information</li>
+ * <li>{@link org.eclipse.jgit.transport.CredentialItem.Username} for
+ * usernames</li>
+ * <li>{@link org.eclipse.jgit.transport.CredentialItem.Password} for
+ * passwords</li>
+ * <li>{@link org.eclipse.jgit.transport.CredentialItem.StringType} for other
+ * general string information</li>
+ * <li>{@link org.eclipse.jgit.transport.CredentialItem.CharArrayType} for other
+ * general secret information</li>
  * </ul>
  *
  * This class is not thread-safe. Applications should construct their own
@@ -83,17 +88,27 @@ public abstract class CredentialItem {
 		this.valueSecure = maskValue;
 	}
 
-	/** @return prompt to display to the user. */
+	/**
+	 * Get prompt to display to the user.
+	 *
+	 * @return prompt to display to the user.
+	 */
 	public String getPromptText() {
 		return promptText;
 	}
 
-	/** @return true if the value should be masked when entered. */
+	/**
+	 * Whether the value should be masked when entered.
+	 *
+	 * @return true if the value should be masked when entered.
+	 */
 	public boolean isValueSecure() {
 		return valueSecure;
 	}
 
-	/** Clear the stored value, destroying it as much as possible. */
+	/**
+	 * Clear the stored value, destroying it as much as possible.
+	 */
 	public abstract void clear();
 
 	/**
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/CredentialsProvider.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/CredentialsProvider.java
index 4800f6826f..8115946204 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/CredentialsProvider.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/CredentialsProvider.java
@@ -52,9 +52,10 @@ import org.eclipse.jgit.errors.UnsupportedCredentialItem;
  * Provide credentials for use in connecting to Git repositories.
  *
  * Implementors are strongly encouraged to support at least the minimal
- * {@link CredentialItem.Username} and {@link CredentialItem.Password} items.
- * More sophisticated implementors may implement additional types, such as
- * {@link CredentialItem.StringType}.
+ * {@link org.eclipse.jgit.transport.CredentialItem.Username} and
+ * {@link org.eclipse.jgit.transport.CredentialItem.Password} items. More
+ * sophisticated implementors may implement additional types, such as
+ * {@link org.eclipse.jgit.transport.CredentialItem.StringType}.
  *
  * CredentialItems are usually presented in bulk, allowing implementors to
  * combine them into a single UI widget and streamline the authentication
@@ -65,7 +66,11 @@ import org.eclipse.jgit.errors.UnsupportedCredentialItem;
 public abstract class CredentialsProvider {
 	private static volatile CredentialsProvider defaultProvider;
 
-	/** @return the default credentials provider, or null. */
+	/**
+	 * Get the default credentials provider, or null.
+	 *
+	 * @return the default credentials provider, or null.
+	 */
 	public static CredentialsProvider getDefault() {
 		return defaultProvider;
 	}
@@ -81,6 +86,8 @@ public abstract class CredentialsProvider {
 	}
 
 	/**
+	 * Whether any of the passed items is null
+	 *
 	 * @param items
 	 *            credential items to check
 	 * @return {@code true} if any of the passed items is null, {@code false}
@@ -106,12 +113,14 @@ public abstract class CredentialsProvider {
 	public abstract boolean isInteractive();
 
 	/**
-	 * Check if the provider can supply the necessary {@link CredentialItem}s.
+	 * Check if the provider can supply the necessary
+	 * {@link org.eclipse.jgit.transport.CredentialItem}s.
 	 *
 	 * @param items
 	 *            the items the application requires to complete authentication.
-	 * @return {@code true} if this {@link CredentialsProvider} supports all of
-	 *         the items supplied.
+	 * @return {@code true} if this
+	 *         {@link org.eclipse.jgit.transport.CredentialsProvider} supports
+	 *         all of the items supplied.
 	 */
 	public abstract boolean supports(CredentialItem... items);
 
@@ -125,7 +134,7 @@ public abstract class CredentialsProvider {
 	 * @return {@code true} if the request was successful and values were
 	 *         supplied; {@code false} if the user canceled the request and did
 	 *         not supply all requested values.
-	 * @throws UnsupportedCredentialItem
+	 * @throws org.eclipse.jgit.errors.UnsupportedCredentialItem
 	 *             if one of the items supplied is not supported.
 	 */
 	public abstract boolean get(URIish uri, CredentialItem... items)
@@ -141,7 +150,7 @@ public abstract class CredentialsProvider {
 	 * @return {@code true} if the request was successful and values were
 	 *         supplied; {@code false} if the user canceled the request and did
 	 *         not supply all requested values.
-	 * @throws UnsupportedCredentialItem
+	 * @throws org.eclipse.jgit.errors.UnsupportedCredentialItem
 	 *             if one of the items supplied is not supported.
 	 */
 	public boolean get(URIish uri, List<CredentialItem> items)
@@ -153,6 +162,7 @@ public abstract class CredentialsProvider {
 	 * Reset the credentials provider for the given URI
 	 *
 	 * @param uri
+	 *            a {@link org.eclipse.jgit.transport.URIish} object.
 	 */
 	public void reset(URIish uri) {
 		// default does nothing
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/CredentialsProviderUserInfo.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/CredentialsProviderUserInfo.java
index 83586350be..d901021788 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/CredentialsProviderUserInfo.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/CredentialsProviderUserInfo.java
@@ -51,7 +51,10 @@ import com.jcraft.jsch.Session;
 import com.jcraft.jsch.UIKeyboardInteractive;
 import com.jcraft.jsch.UserInfo;
 
-/** A JSch {@link UserInfo} adapter for a {@link CredentialsProvider}. */
+/**
+ * A JSch {@link com.jcraft.jsch.UserInfo} adapter for a
+ * {@link org.eclipse.jgit.transport.CredentialsProvider}.
+ */
 public class CredentialsProviderUserInfo implements UserInfo,
 		UIKeyboardInteractive {
 	private final URIish uri;
@@ -85,16 +88,19 @@ public class CredentialsProviderUserInfo implements UserInfo,
 		return uri;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getPassword() {
 		return password;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getPassphrase() {
 		return passphrase;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean promptPassphrase(String msg) {
 		CredentialItem.StringType v = newPrompt(msg);
@@ -107,6 +113,7 @@ public class CredentialsProviderUserInfo implements UserInfo,
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean promptPassword(String msg) {
 		CredentialItem.Password p = new CredentialItem.Password(msg);
@@ -123,17 +130,20 @@ public class CredentialsProviderUserInfo implements UserInfo,
 		return new CredentialItem.StringType(msg, true);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean promptYesNo(String msg) {
 		CredentialItem.YesNoType v = new CredentialItem.YesNoType(msg);
 		return provider.get(uri, v) && v.getValue();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void showMessage(String msg) {
 		provider.get(uri, new CredentialItem.InformationalMessage(msg));
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String[] promptKeyboardInteractive(String destination, String name,
 			String instruction, String[] prompt, boolean[] echo) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/Daemon.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/Daemon.java
index 896b10a4ec..2fc5eb2b51 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/Daemon.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/Daemon.java
@@ -65,7 +65,9 @@ import org.eclipse.jgit.transport.resolver.ServiceNotAuthorizedException;
 import org.eclipse.jgit.transport.resolver.ServiceNotEnabledException;
 import org.eclipse.jgit.transport.resolver.UploadPackFactory;
 
-/** Basic daemon for the anonymous <code>git://</code> transport protocol. */
+/**
+ * Basic daemon for the anonymous <code>git://</code> transport protocol.
+ */
 public class Daemon {
 	/** 9418: IANA assigned port number for Git. */
 	public static final int DEFAULT_PORT = 9418;
@@ -90,7 +92,9 @@ public class Daemon {
 
 	volatile ReceivePackFactory<DaemonClient> receivePackFactory;
 
-	/** Configure a daemon to listen on any available network port. */
+	/**
+	 * Configure a daemon to listen on any available network port.
+	 */
 	public Daemon() {
 		this(null);
 	}
@@ -175,7 +179,11 @@ public class Daemon {
 				} };
 	}
 
-	/** @return the address connections are received on. */
+	/**
+	 * Get the address connections are received on.
+	 *
+	 * @return the address connections are received on.
+	 */
 	public synchronized InetSocketAddress getAddress() {
 		return myAddress;
 	}
@@ -199,7 +207,11 @@ public class Daemon {
 		return null;
 	}
 
-	/** @return timeout (in seconds) before aborting an IO operation. */
+	/**
+	 * Get timeout (in seconds) before aborting an IO operation.
+	 *
+	 * @return timeout (in seconds) before aborting an IO operation.
+	 */
 	public int getTimeout() {
 		return timeout;
 	}
@@ -216,7 +228,11 @@ public class Daemon {
 		timeout = seconds;
 	}
 
-	/** @return configuration controlling packing, may be null. */
+	/**
+	 * Get configuration controlling packing, may be null.
+	 *
+	 * @return configuration controlling packing, may be null.
+	 */
 	public PackConfig getPackConfig() {
 		return packConfig;
 	}
@@ -333,9 +349,9 @@ public class Daemon {
 	/**
 	 * Start this daemon on a background thread.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the server socket could not be opened.
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             the daemon is already running.
 	 */
 	public synchronized void start() throws IOException {
@@ -359,7 +375,11 @@ public class Daemon {
 		acceptThread = null;
 	}
 
-	/** @return true if this daemon is receiving connections. */
+	/**
+	 * Whether this daemon is receiving connections.
+	 *
+	 * @return {@code true} if this daemon is receiving connections.
+	 */
 	public synchronized boolean isRunning() {
 		return acceptThread != null && acceptThread.isRunning();
 	}
@@ -376,9 +396,8 @@ public class Daemon {
 	/**
 	 * Stops this daemon and waits until it's acceptor thread has finished.
 	 *
-	 * @throws InterruptedException
+	 * @throws java.lang.InterruptedException
 	 *             if waiting for the acceptor thread is interrupted
-	 *
 	 * @since 4.9
 	 */
 	public void stopAndWait() throws InterruptedException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/DaemonClient.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/DaemonClient.java
index 23e3379f91..a9731ac3a4 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/DaemonClient.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/DaemonClient.java
@@ -54,7 +54,9 @@ import java.net.Socket;
 import org.eclipse.jgit.transport.resolver.ServiceNotAuthorizedException;
 import org.eclipse.jgit.transport.resolver.ServiceNotEnabledException;
 
-/** Active network client of {@link Daemon}. */
+/**
+ * Active network client of {@link org.eclipse.jgit.transport.Daemon}.
+ */
 public class DaemonClient {
 	private final Daemon daemon;
 
@@ -72,22 +74,38 @@ public class DaemonClient {
 		peer = ia;
 	}
 
-	/** @return the daemon which spawned this client. */
+	/**
+	 * Get the daemon which spawned this client.
+	 *
+	 * @return the daemon which spawned this client.
+	 */
 	public Daemon getDaemon() {
 		return daemon;
 	}
 
-	/** @return Internet address of the remote client. */
+	/**
+	 * Get Internet address of the remote client.
+	 *
+	 * @return Internet address of the remote client.
+	 */
 	public InetAddress getRemoteAddress() {
 		return peer;
 	}
 
-	/** @return input stream to read from the connected client. */
+	/**
+	 * Get input stream to read from the connected client.
+	 *
+	 * @return input stream to read from the connected client.
+	 */
 	public InputStream getInputStream() {
 		return rawIn;
 	}
 
-	/** @return output stream to send data to the connected client. */
+	/**
+	 * Get output stream to send data to the connected client.
+	 *
+	 * @return output stream to send data to the connected client.
+	 */
 	public OutputStream getOutputStream() {
 		return rawOut;
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/DaemonService.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/DaemonService.java
index 566153a333..e0ec7751b9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/DaemonService.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/DaemonService.java
@@ -52,7 +52,10 @@ import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.transport.resolver.ServiceNotAuthorizedException;
 import org.eclipse.jgit.transport.resolver.ServiceNotEnabledException;
 
-/** A service exposed by {@link Daemon} over anonymous <code>git://</code>. */
+/**
+ * A service exposed by {@link org.eclipse.jgit.transport.Daemon} over anonymous
+ * <code>git://</code>.
+ */
 public abstract class DaemonService {
 	private final String command;
 
@@ -77,34 +80,55 @@ public abstract class DaemonService {
 		}
 	}
 
-	/** @return is this service enabled for invocation? */
+	/**
+	 * Whether this service is enabled for invocation.
+	 *
+	 * @return whether this service is enabled for invocation.
+	 */
 	public boolean isEnabled() {
 		return enabled;
 	}
 
 	/**
+	 * Set if it is allowed to use this service
+	 *
 	 * @param on
-	 *            true to allow this service to be used; false to deny it.
+	 *            {@code true} to allow this service to be used; {@code false}
+	 *            to deny it.
 	 */
 	public void setEnabled(final boolean on) {
 		enabled = on;
 	}
 
 	/** @return can this service be configured in the repository config file? */
+	/**
+	 * Whether this service can be configured in the repository config file
+	 *
+	 * @return whether this service can be configured in the repository config
+	 *         file
+	 */
 	public boolean isOverridable() {
 		return overridable;
 	}
 
 	/**
+	 * Whether to permit repositories to override this service's enabled state
+	 * with the <code>daemon.servicename</code> config setting.
+	 *
 	 * @param on
-	 *            true to permit repositories to override this service's enabled
-	 *            state with the <code>daemon.servicename</code> config setting.
+	 *            {@code true} to permit repositories to override this service's
+	 *            enabled state with the <code>daemon.servicename</code> config
+	 *            setting.
 	 */
 	public void setOverridable(final boolean on) {
 		overridable = on;
 	}
 
-	/** @return name of the command requested by clients. */
+	/**
+	 * Get name of the command requested by clients.
+	 *
+	 * @return name of the command requested by clients.
+	 */
 	public String getCommandName() {
 		return command;
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/DefaultSshSessionFactory.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/DefaultSshSessionFactory.java
index 23fd7e39c5..a749fbcaf0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/DefaultSshSessionFactory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/DefaultSshSessionFactory.java
@@ -59,6 +59,7 @@ import com.jcraft.jsch.Session;
  * connection will immediately fail.
  */
 class DefaultSshSessionFactory extends JschConfigSessionFactory {
+	/** {@inheritDoc} */
 	@Override
 	protected void configure(final OpenSshConfig.Host hc, final Session session) {
 		// No additional configuration required.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchConnection.java
index 2d042400f6..f0c45d5fb6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchConnection.java
@@ -64,9 +64,9 @@ import org.eclipse.jgit.lib.Ref;
  * one-way object transfer service to copy objects from the remote repository
  * into this local repository.
  * <p>
- * Instances of a FetchConnection must be created by a {@link Transport} that
- * implements a specific object transfer protocol that both sides of the
- * connection understand.
+ * Instances of a FetchConnection must be created by a
+ * {@link org.eclipse.jgit.transport.Transport} that implements a specific
+ * object transfer protocol that both sides of the connection understand.
  * <p>
  * FetchConnection instances are not thread safe and may be accessed by only one
  * thread at a time.
@@ -78,7 +78,7 @@ public interface FetchConnection extends Connection {
 	 * Fetch objects we don't have but that are reachable from advertised refs.
 	 * <p>
 	 * Only one call per connection is allowed. Subsequent calls will result in
-	 * {@link TransportException}.
+	 * {@link org.eclipse.jgit.errors.TransportException}.
 	 * </p>
 	 * <p>
 	 * Implementations are free to use network connections as necessary to
@@ -87,7 +87,8 @@ public interface FetchConnection extends Connection {
 	 * avoid replacing/overwriting/duplicating an object already available in
 	 * the local destination repository. Locally available objects and packs
 	 * should always be preferred over remotely available objects and packs.
-	 * {@link Transport#isFetchThin()} should be honored if applicable.
+	 * {@link org.eclipse.jgit.transport.Transport#isFetchThin()} should be
+	 * honored if applicable.
 	 * </p>
 	 *
 	 * @param monitor
@@ -103,7 +104,7 @@ public interface FetchConnection extends Connection {
 	 *            repository, especially if they aren't yet reachable by the ref
 	 *            database. Connections should take this set as an addition to
 	 *            what is reachable through all Refs, not in replace of it.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             objects could not be copied due to a network failure,
 	 *             protocol error, or error on remote side, or connection was
 	 *             already used for fetch.
@@ -116,7 +117,7 @@ public interface FetchConnection extends Connection {
 	 * Fetch objects we don't have but that are reachable from advertised refs.
 	 * <p>
 	 * Only one call per connection is allowed. Subsequent calls will result in
-	 * {@link TransportException}.
+	 * {@link org.eclipse.jgit.errors.TransportException}.
 	 * </p>
 	 * <p>
 	 * Implementations are free to use network connections as necessary to
@@ -125,7 +126,8 @@ public interface FetchConnection extends Connection {
 	 * avoid replacing/overwriting/duplicating an object already available in
 	 * the local destination repository. Locally available objects and packs
 	 * should always be preferred over remotely available objects and packs.
-	 * {@link Transport#isFetchThin()} should be honored if applicable.
+	 * {@link org.eclipse.jgit.transport.Transport#isFetchThin()} should be
+	 * honored if applicable.
 	 * </p>
 	 *
 	 * @param monitor
@@ -143,7 +145,7 @@ public interface FetchConnection extends Connection {
 	 *            what is reachable through all Refs, not in replace of it.
 	 * @param out
 	 *            OutputStream to write sideband messages to
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             objects could not be copied due to a network failure,
 	 *             protocol error, or error on remote side, or connection was
 	 *             already used for fetch.
@@ -157,11 +159,12 @@ public interface FetchConnection extends Connection {
 	 * Did the last {@link #fetch(ProgressMonitor, Collection, Set)} get tags?
 	 * <p>
 	 * Some Git aware transports are able to implicitly grab an annotated tag if
-	 * {@link TagOpt#AUTO_FOLLOW} or {@link TagOpt#FETCH_TAGS} was selected and
-	 * the object the tag peels to (references) was transferred as part of the
-	 * last {@link #fetch(ProgressMonitor, Collection, Set)} call. If it is
-	 * possible for such tags to have been included in the transfer this method
-	 * returns true, allowing the caller to attempt tag discovery.
+	 * {@link org.eclipse.jgit.transport.TagOpt#AUTO_FOLLOW} or
+	 * {@link org.eclipse.jgit.transport.TagOpt#FETCH_TAGS} was selected and the
+	 * object the tag peels to (references) was transferred as part of the last
+	 * {@link #fetch(ProgressMonitor, Collection, Set)} call. If it is possible
+	 * for such tags to have been included in the transfer this method returns
+	 * true, allowing the caller to attempt tag discovery.
 	 * <p>
 	 * By returning only true/false (and not the actual list of tags obtained)
 	 * the transport itself does not need to be aware of whether or not tags
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/HMACSHA1NonceGenerator.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/HMACSHA1NonceGenerator.java
index 7de4d2de1b..6c26b7026a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/HMACSHA1NonceGenerator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/HMACSHA1NonceGenerator.java
@@ -66,8 +66,11 @@ public class HMACSHA1NonceGenerator implements NonceGenerator {
 	private Mac mac;
 
 	/**
+	 * Constructor for HMACSHA1NonceGenerator.
+	 *
 	 * @param seed
-	 * @throws IllegalStateException
+	 *            seed the generator
+	 * @throws java.lang.IllegalStateException
 	 */
 	public HMACSHA1NonceGenerator(String seed) throws IllegalStateException {
 		try {
@@ -82,6 +85,7 @@ public class HMACSHA1NonceGenerator implements NonceGenerator {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public synchronized String createNonce(Repository repo, long timestamp)
 			throws IllegalStateException {
@@ -102,6 +106,7 @@ public class HMACSHA1NonceGenerator implements NonceGenerator {
 		return Long.toString(timestamp) + "-" + toHex(rawHmac); //$NON-NLS-1$
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public NonceStatus verify(String received, String sent,
 			Repository db, boolean allowSlop, int slop) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpAuthMethod.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpAuthMethod.java
index 0c54027c7f..c40d9635de 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpAuthMethod.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpAuthMethod.java
@@ -204,6 +204,12 @@ abstract class HttpAuthMethod {
 
 	protected final Type type;
 
+	/**
+	 * Constructor for HttpAuthMethod.
+	 *
+	 * @param type
+	 *            authentication method type
+	 */
 	protected HttpAuthMethod(Type type) {
 		this.type = type;
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpConfig.java
index db59a54a27..368bdc913c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpConfig.java
@@ -61,10 +61,10 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /**
- * A representation of the "http.*" config values in a git {@link Config}. git
- * provides for setting values for specific URLs through "http.<url>.*
- * subsections. git always considers only the initial original URL for such
- * settings, not any redirected URL.
+ * A representation of the "http.*" config values in a git
+ * {@link org.eclipse.jgit.lib.Config}. git provides for setting values for
+ * specific URLs through "http.<url>.* subsections. git always considers only
+ * the initial original URL for such settings, not any redirected URL.
  *
  * @since 4.9
  */
@@ -154,6 +154,8 @@ public class HttpConfig {
 	private int maxRedirects;
 
 	/**
+	 * Get the "http.postBuffer" setting
+	 *
 	 * @return the value of the "http.postBuffer" setting
 	 */
 	public int getPostBuffer() {
@@ -161,6 +163,8 @@ public class HttpConfig {
 	}
 
 	/**
+	 * Get the "http.sslVerify" setting
+	 *
 	 * @return the value of the "http.sslVerify" setting
 	 */
 	public boolean isSslVerify() {
@@ -168,6 +172,8 @@ public class HttpConfig {
 	}
 
 	/**
+	 * Get the "http.followRedirects" setting
+	 *
 	 * @return the value of the "http.followRedirects" setting
 	 */
 	public HttpRedirectMode getFollowRedirects() {
@@ -175,6 +181,8 @@ public class HttpConfig {
 	}
 
 	/**
+	 * Get the "http.maxRedirects" setting
+	 *
 	 * @return the value of the "http.maxRedirects" setting
 	 */
 	public int getMaxRedirects() {
@@ -182,10 +190,11 @@ public class HttpConfig {
 	}
 
 	/**
-	 * Creates a new {@link HttpConfig} tailored to the given {@link URIish}.
+	 * Creates a new {@link org.eclipse.jgit.transport.HttpConfig} tailored to
+	 * the given {@link org.eclipse.jgit.transport.URIish}.
 	 *
 	 * @param config
-	 *            to read the {@link HttpConfig} from
+	 *            to read the {@link org.eclipse.jgit.transport.HttpConfig} from
 	 * @param uri
 	 *            to get the configuration values for
 	 */
@@ -194,8 +203,8 @@ public class HttpConfig {
 	}
 
 	/**
-	 * Creates a {@link HttpConfig} that reads values solely from the user
-	 * config.
+	 * Creates a {@link org.eclipse.jgit.transport.HttpConfig} that reads values
+	 * solely from the user config.
 	 *
 	 * @param uri
 	 *            to get the configuration values for
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpTransport.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpTransport.java
index 006e846328..d1141868fd 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpTransport.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpTransport.java
@@ -62,7 +62,11 @@ public abstract class HttpTransport extends Transport {
 	protected static HttpConnectionFactory connectionFactory = new JDKHttpConnectionFactory();
 
 	/**
-	 * @return the {@link HttpConnectionFactory} used to create new connections
+	 * Get the {@link org.eclipse.jgit.transport.http.HttpConnectionFactory}
+	 * used to create new connections
+	 *
+	 * @return the {@link org.eclipse.jgit.transport.http.HttpConnectionFactory}
+	 *         used to create new connections
 	 * @since 3.3
 	 */
 	public static HttpConnectionFactory getConnectionFactory() {
@@ -70,10 +74,11 @@ public abstract class HttpTransport extends Transport {
 	}
 
 	/**
-	 * Set the {@link HttpConnectionFactory} to be used to create new
-	 * connections
+	 * Set the {@link org.eclipse.jgit.transport.http.HttpConnectionFactory} to
+	 * be used to create new connections
 	 *
 	 * @param cf
+	 *            connection factory
 	 * @since 3.3
 	 */
 	public static void setConnectionFactory(HttpConnectionFactory cf) {
@@ -98,7 +103,7 @@ public abstract class HttpTransport extends Transport {
 	/**
 	 * Create a minimal HTTP transport instance not tied to a single repository.
 	 *
-	 * @param uri
+	 * @param uri a {@link org.eclipse.jgit.transport.URIish} object.
 	 */
 	protected HttpTransport(URIish uri) {
 		super(uri);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/InternalFetchConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/InternalFetchConnection.java
index bea8d60ecd..9fb9062fbb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/InternalFetchConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/InternalFetchConnection.java
@@ -57,6 +57,21 @@ import org.eclipse.jgit.transport.resolver.UploadPackFactory;
 class InternalFetchConnection<C> extends BasePackFetchConnection {
 	private Thread worker;
 
+	/**
+	 * Constructor for InternalFetchConnection.
+	 *
+	 * @param transport
+	 *            a {@link org.eclipse.jgit.transport.PackTransport}
+	 * @param uploadPackFactory
+	 *            a
+	 *            {@link org.eclipse.jgit.transport.resolver.UploadPackFactory}
+	 * @param req
+	 *            request
+	 * @param remote
+	 *            the remote {@link org.eclipse.jgit.lib.Repository}
+	 * @throws org.eclipse.jgit.errors.TransportException
+	 *             if any.
+	 */
 	public InternalFetchConnection(PackTransport transport,
 			final UploadPackFactory<C> uploadPackFactory,
 			final C req, final Repository remote) throws TransportException {
@@ -125,6 +140,7 @@ class InternalFetchConnection<C> extends BasePackFetchConnection {
 		readAdvertisedRefs();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		super.close();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/InternalPushConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/InternalPushConnection.java
index 8a1884e5fc..732be63dc1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/InternalPushConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/InternalPushConnection.java
@@ -57,6 +57,21 @@ import org.eclipse.jgit.transport.resolver.ServiceNotEnabledException;
 class InternalPushConnection<C> extends BasePackPushConnection {
 	private Thread worker;
 
+	/**
+	 * Constructor for InternalPushConnection.
+	 *
+	 * @param transport
+	 *            a {@link org.eclipse.jgit.transport.PackTransport}
+	 * @param receivePackFactory
+	 *            a
+	 *            {@link org.eclipse.jgit.transport.resolver.ReceivePackFactory}
+	 * @param req
+	 *            a request
+	 * @param remote
+	 *            the {@link org.eclipse.jgit.lib.Repository}
+	 * @throws org.eclipse.jgit.errors.TransportException
+	 *             if any.
+	 */
 	public InternalPushConnection(PackTransport transport,
 			final ReceivePackFactory<C> receivePackFactory,
 			final C req, final Repository remote) throws TransportException {
@@ -115,6 +130,7 @@ class InternalPushConnection<C> extends BasePackPushConnection {
 		readAdvertisedRefs();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		super.close();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschConfigSessionFactory.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschConfigSessionFactory.java
index eadfd69b58..38dc457553 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschConfigSessionFactory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschConfigSessionFactory.java
@@ -70,7 +70,6 @@ import org.slf4j.LoggerFactory;
 import com.jcraft.jsch.JSch;
 import com.jcraft.jsch.JSchException;
 import com.jcraft.jsch.Session;
-import com.jcraft.jsch.UserInfo;
 
 /**
  * The base session factory that loads known hosts and private keys from
@@ -81,8 +80,8 @@ import com.jcraft.jsch.UserInfo;
  * used by C Git.
  * <p>
  * The factory does not provide UI behavior. Override the method
- * {@link #configure(org.eclipse.jgit.transport.OpenSshConfig.Host, Session)}
- * to supply appropriate {@link UserInfo} to the session.
+ * {@link #configure(org.eclipse.jgit.transport.OpenSshConfig.Host, Session)} to
+ * supply appropriate {@link com.jcraft.jsch.UserInfo} to the session.
  */
 public abstract class JschConfigSessionFactory extends SshSessionFactory {
 
@@ -95,6 +94,7 @@ public abstract class JschConfigSessionFactory extends SshSessionFactory {
 
 	private OpenSshConfig config;
 
+	/** {@inheritDoc} */
 	@Override
 	public synchronized RemoteSession getSession(URIish uri,
 			CredentialsProvider credentialsProvider, FS fs, int tms)
@@ -248,7 +248,7 @@ public abstract class JschConfigSessionFactory extends SshSessionFactory {
 	 *            the file system abstraction which will be necessary to
 	 *            perform certain file system operations.
 	 * @return new session instance, but otherwise unconfigured.
-	 * @throws JSchException
+	 * @throws com.jcraft.jsch.JSchException
 	 *             the session could not be created.
 	 */
 	protected Session createSession(final OpenSshConfig.Host hc,
@@ -272,7 +272,8 @@ public abstract class JschConfigSessionFactory extends SshSessionFactory {
 
 	/**
 	 * Provide additional configuration for the session based on the host
-	 * information. This method could be used to supply {@link UserInfo}.
+	 * information. This method could be used to supply
+	 * {@link com.jcraft.jsch.UserInfo}.
 	 *
 	 * @param hc
 	 *            host configuration
@@ -290,7 +291,7 @@ public abstract class JschConfigSessionFactory extends SshSessionFactory {
 	 *            the file system abstraction which will be necessary to
 	 *            perform certain file system operations.
 	 * @return the JSch instance to use.
-	 * @throws JSchException
+	 * @throws com.jcraft.jsch.JSchException
 	 *             the user configuration could not be created.
 	 */
 	protected JSch getJSch(final OpenSshConfig.Host hc, FS fs) throws JSchException {
@@ -323,11 +324,13 @@ public abstract class JschConfigSessionFactory extends SshSessionFactory {
 	}
 
 	/**
+	 * Create default instance of jsch
+	 *
 	 * @param fs
-	 *            the file system abstraction which will be necessary to
-	 *            perform certain file system operations.
+	 *            the file system abstraction which will be necessary to perform
+	 *            certain file system operations.
 	 * @return the new default JSch implementation.
-	 * @throws JSchException
+	 * @throws com.jcraft.jsch.JSchException
 	 *             known host keys cannot be loaded.
 	 */
 	protected JSch createDefaultJSch(FS fs) throws JSchException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschSession.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschSession.java
index a8cc032006..081d05748c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschSession.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/JschSession.java
@@ -66,8 +66,8 @@ import com.jcraft.jsch.Session;
  * Run remote commands using Jsch.
  * <p>
  * This class is the default session implementation using Jsch. Note that
- * {@link JschConfigSessionFactory} is used to create the actual session passed
- * to the constructor.
+ * {@link org.eclipse.jgit.transport.JschConfigSessionFactory} is used to create
+ * the actual session passed to the constructor.
  */
 public class JschSession implements RemoteSession {
 	final Session sock;
@@ -87,11 +87,13 @@ public class JschSession implements RemoteSession {
 		this.uri = uri;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Process exec(String command, int timeout) throws IOException {
 		return new JschProcess(command, timeout);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void disconnect() {
 		if (sock.isConnected())
@@ -99,12 +101,13 @@ public class JschSession implements RemoteSession {
 	}
 
 	/**
-	 * A kludge to allow {@link TransportSftp} to get an Sftp channel from Jsch.
-	 * Ideally, this method would be generic, which would require implementing
-	 * generic Sftp channel operations in the RemoteSession class.
+	 * A kludge to allow {@link org.eclipse.jgit.transport.TransportSftp} to get
+	 * an Sftp channel from Jsch. Ideally, this method would be generic, which
+	 * would require implementing generic Sftp channel operations in the
+	 * RemoteSession class.
 	 *
 	 * @return a channel suitable for Sftp operations.
-	 * @throws JSchException
+	 * @throws com.jcraft.jsch.JSchException
 	 *             on problems getting the channel.
 	 */
 	public Channel getSftpChannel() throws JSchException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java
index 5727b034b3..e3f287bef8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java
@@ -143,7 +143,9 @@ public class NetRC {
 		COMMAND, MACHINE, LOGIN, PASSWORD, DEFAULT, ACCOUNT, MACDEF
 	}
 
-	/** */
+	/**
+	 * <p>Constructor for NetRC.</p>
+	 */
 	public NetRC() {
 		netrc = getDefaultFile();
 		if (netrc != null)
@@ -151,6 +153,8 @@ public class NetRC {
 	}
 
 	/**
+	 * <p>Constructor for NetRC.</p>
+	 *
 	 * @param netrc
 	 *            the .netrc file
 	 */
@@ -176,6 +180,7 @@ public class NetRC {
 	 * Get entry by host name
 	 *
 	 * @param host
+	 *            the host name
 	 * @return entry associated with host name or null
 	 */
 	public NetRCEntry getEntry(String host) {
@@ -194,6 +199,8 @@ public class NetRC {
 	}
 
 	/**
+	 * Get all entries collected from .netrc file
+	 *
 	 * @return all entries collected from .netrc file
 	 */
 	public Collection<NetRCEntry> getEntries() {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRCCredentialsProvider.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRCCredentialsProvider.java
index 4037545e9d..6531b17e23 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRCCredentialsProvider.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRCCredentialsProvider.java
@@ -54,7 +54,9 @@ public class NetRCCredentialsProvider extends CredentialsProvider {
 
 	NetRC netrc = new NetRC();
 
-	/** */
+	/**
+	 * <p>Constructor for NetRCCredentialsProvider.</p>
+	 */
 	public NetRCCredentialsProvider() {
 	}
 
@@ -65,6 +67,7 @@ public class NetRCCredentialsProvider extends CredentialsProvider {
 		CredentialsProvider.setDefault(new NetRCCredentialsProvider());
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean supports(CredentialItem... items) {
 		for (CredentialItem i : items) {
@@ -78,6 +81,7 @@ public class NetRCCredentialsProvider extends CredentialsProvider {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean get(URIish uri, CredentialItem... items)
 			throws UnsupportedCredentialItem {
@@ -108,6 +112,7 @@ public class NetRCCredentialsProvider extends CredentialsProvider {
 		return !isAnyNull(items);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isInteractive() {
 		return false;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NonceGenerator.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NonceGenerator.java
index d1ea089068..51fe9070c0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NonceGenerator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NonceGenerator.java
@@ -55,6 +55,8 @@ import org.eclipse.jgit.transport.PushCertificate.NonceStatus;
 public interface NonceGenerator {
 
 	/**
+	 * Create nonce to be signed by the pusher
+	 *
 	 * @param db
 	 *            The repository which should be used to obtain a unique String
 	 *            such that the pusher cannot forge nonces by pushing to another
@@ -62,12 +64,14 @@ public interface NonceGenerator {
 	 * @param timestamp
 	 *            The current time in seconds.
 	 * @return The nonce to be signed by the pusher
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 */
 	public String createNonce(Repository db, long timestamp)
 			throws IllegalStateException;
 
 	/**
+	 * Verify trustworthiness of the received nonce.
+	 *
 	 * @param received
 	 *            The nonce which was received from the server
 	 * @param sent
@@ -76,7 +80,6 @@ public interface NonceGenerator {
 	 *            The repository which should be used to obtain a unique String
 	 *            such that the pusher cannot forge nonces by pushing to another
 	 *            repository at the same time as well and reusing the nonce.
-	 *
 	 * @param allowSlop
 	 *            If the receiving backend is is able to generate slop. This is
 	 *            the case for serving via http protocol using more than one
@@ -85,7 +88,6 @@ public interface NonceGenerator {
 	 * @param slop
 	 *            If `allowSlop` is true, this specifies the number of seconds
 	 *            which we allow as slop.
-	 *
 	 * @return a NonceStatus indicating the trustworthiness of the received
 	 *         nonce.
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ObjectCountCallback.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ObjectCountCallback.java
index cf81adbcd0..3856bb2204 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ObjectCountCallback.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ObjectCountCallback.java
@@ -45,7 +45,6 @@ package org.eclipse.jgit.transport;
 
 import java.io.OutputStream;
 
-import org.eclipse.jgit.internal.storage.pack.PackWriter;
 import org.eclipse.jgit.lib.ProgressMonitor;
 
 /**
@@ -55,19 +54,20 @@ import org.eclipse.jgit.lib.ProgressMonitor;
  */
 public interface ObjectCountCallback {
 	/**
-	 * Invoked when the {@link PackWriter} has counted the objects to be
-	 * written to pack.
+	 * Invoked when the
+	 * {@link org.eclipse.jgit.internal.storage.pack.PackWriter} has counted the
+	 * objects to be written to pack.
 	 * <p>
-	 * An {@code ObjectCountCallback} can use this information to decide
-	 * whether the
-	 * {@link PackWriter#writePack(ProgressMonitor, ProgressMonitor, OutputStream)}
+	 * An {@code ObjectCountCallback} can use this information to decide whether
+	 * the
+	 * {@link org.eclipse.jgit.internal.storage.pack.PackWriter#writePack(ProgressMonitor, ProgressMonitor, OutputStream)}
 	 * operation should be aborted.
 	 * <p>
 	 * This callback will be called exactly once.
 	 *
 	 * @param objectCount
 	 *            the count of the objects.
-	 * @throws WriteAbortedException
+	 * @throws org.eclipse.jgit.transport.WriteAbortedException
 	 *             to indicate that the write operation should be aborted.
 	 */
 	void setObjectCount(long objectCount) throws WriteAbortedException;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java
index 79fab01297..58024c4dc8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/OpenSshConfig.java
@@ -85,9 +85,11 @@ import com.jcraft.jsch.ConfigRepository;
  * </ul>
  * <p>
  * Therefore implement our own parser to read an OpenSSH configuration file. It
- * makes the critical options available to {@link SshSessionFactory} via
- * {@link Host} objects returned by {@link #lookup(String)}, and implements a
- * fully conforming {@link ConfigRepository} providing
+ * makes the critical options available to
+ * {@link org.eclipse.jgit.transport.SshSessionFactory} via
+ * {@link org.eclipse.jgit.transport.OpenSshConfig.Host} objects returned by
+ * {@link #lookup(String)}, and implements a fully conforming
+ * {@link com.jcraft.jsch.ConfigRepository} providing
  * {@link com.jcraft.jsch.ConfigRepository.Config}s via
  * {@link #getConfig(String)}.
  * </p>
@@ -104,7 +106,7 @@ import com.jcraft.jsch.ConfigRepository;
  * ConfigRepository OTOH treats all option values as plain strings, so any
  * validation must happen in Jsch outside of the parser. Thus this parser does
  * not validate option values, except for a few options when constructing a
- * {@link Host} object.
+ * {@link org.eclipse.jgit.transport.OpenSshConfig.Host} object.
  * </p>
  * <p>
  * This config does %-substitutions for the following tokens:
@@ -961,12 +963,11 @@ public class OpenSshConfig implements ConfigRepository {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Retrieves the full {@link com.jcraft.jsch.ConfigRepository.Config Config}
 	 * for the given host name. Should be called only by Jsch and tests.
 	 *
-	 * @param hostName
-	 *            to get the config for
-	 * @return the configuration for the host
 	 * @since 4.9
 	 */
 	@Override
@@ -975,6 +976,7 @@ public class OpenSshConfig implements ConfigRepository {
 		return new JschBugFixingConfig(host.getConfig());
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	@SuppressWarnings("nls")
 	public String toString() {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackParser.java
index d2ec39c0c5..af5a0b7c98 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackParser.java
@@ -76,7 +76,6 @@ import org.eclipse.jgit.lib.ObjectDatabase;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectIdOwnerMap;
 import org.eclipse.jgit.lib.ObjectIdSubclassMap;
-import org.eclipse.jgit.lib.ObjectInserter;
 import org.eclipse.jgit.lib.ObjectLoader;
 import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.ObjectStream;
@@ -88,14 +87,16 @@ import org.eclipse.jgit.util.NB;
 import org.eclipse.jgit.util.sha1.SHA1;
 
 /**
- * Parses a pack stream and imports it for an {@link ObjectInserter}.
+ * Parses a pack stream and imports it for an
+ * {@link org.eclipse.jgit.lib.ObjectInserter}.
  * <p>
  * Applications can acquire an instance of a parser from ObjectInserter's
- * {@link ObjectInserter#newPackParser(InputStream)} method.
+ * {@link org.eclipse.jgit.lib.ObjectInserter#newPackParser(InputStream)}
+ * method.
  * <p>
- * Implementations of {@link ObjectInserter} should subclass this type and
- * provide their own logic for the various {@code on*()} event methods declared
- * to be abstract.
+ * Implementations of {@link org.eclipse.jgit.lib.ObjectInserter} should
+ * subclass this type and provide their own logic for the various {@code on*()}
+ * event methods declared to be abstract.
  */
 public abstract class PackParser {
 	/** Size of the internal stream buffer. */
@@ -213,7 +214,11 @@ public abstract class PackParser {
 		checkObjectCollisions = true;
 	}
 
-	/** @return true if a thin pack (missing base objects) is permitted. */
+	/**
+	 * Whether a thin pack (missing base objects) is permitted.
+	 *
+	 * @return {@code true} if a thin pack (missing base objects) is permitted.
+	 */
 	public boolean isAllowThin() {
 		return allowThin;
 	}
@@ -232,6 +237,8 @@ public abstract class PackParser {
 	}
 
 	/**
+	 * Whether received objects are verified to prevent collisions.
+	 *
 	 * @return if true received objects are verified to prevent collisions.
 	 * @since 4.1
 	 */
@@ -300,7 +307,11 @@ public abstract class PackParser {
 		this.needBaseObjectIds = b;
 	}
 
-	/** @return true if the EOF should be read from the input after the footer. */
+	/**
+	 * Whether the EOF should be read from the input after the footer.
+	 *
+	 * @return true if the EOF should be read from the input after the footer.
+	 */
 	public boolean isCheckEofAfterPackFooter() {
 		return checkEofAfterPackFooter;
 	}
@@ -315,12 +326,18 @@ public abstract class PackParser {
 		checkEofAfterPackFooter = b;
 	}
 
-	/** @return true if there is data expected after the pack footer. */
+	/**
+	 * Whether there is data expected after the pack footer.
+	 *
+	 * @return true if there is data expected after the pack footer.
+	 */
 	public boolean isExpectDataAfterPackFooter() {
 		return expectDataAfterPackFooter;
 	}
 
 	/**
+	 * Set if there is additional data in InputStream after pack.
+	 *
 	 * @param e
 	 *            true if there is additional data in InputStream after pack.
 	 *            This requires the InputStream to support the mark and reset
@@ -330,14 +347,22 @@ public abstract class PackParser {
 		expectDataAfterPackFooter = e;
 	}
 
-	/** @return the new objects that were sent by the user */
+	/**
+	 * Get the new objects that were sent by the user
+	 *
+	 * @return the new objects that were sent by the user
+	 */
 	public ObjectIdSubclassMap<ObjectId> getNewObjectIds() {
 		if (newObjectIds != null)
 			return newObjectIds;
 		return new ObjectIdSubclassMap<>();
 	}
 
-	/** @return set of objects the incoming pack assumed for delta purposes */
+	/**
+	 * Get set of objects the incoming pack assumed for delta purposes
+	 *
+	 * @return set of objects the incoming pack assumed for delta purposes
+	 */
 	public ObjectIdSubclassMap<ObjectId> getBaseObjectIds() {
 		if (baseObjectIds != null)
 			return baseObjectIds;
@@ -378,7 +403,11 @@ public abstract class PackParser {
 		setObjectChecker(on ? new ObjectChecker() : null);
 	}
 
-	/** @return the message to record with the pack lock. */
+	/**
+	 * Get the message to record with the pack lock.
+	 *
+	 * @return the message to record with the pack lock.
+	 */
 	public String getLockMessage() {
 		return lockMessage;
 	}
@@ -420,7 +449,7 @@ public abstract class PackParser {
 		return entryCount;
 	}
 
-	/***
+	/**
 	 * Get the information about the requested object.
 	 * <p>
 	 * The object information is only available after
@@ -477,7 +506,7 @@ public abstract class PackParser {
 	 * <p>
 	 * This should only be called after pack parsing is finished.
 	 *
-	 * @return {@link ReceivedPackStatistics}
+	 * @return {@link org.eclipse.jgit.transport.ReceivedPackStatistics}
 	 * @since 4.6
 	 */
 	public ReceivedPackStatistics getReceivedPackStatistics() {
@@ -489,10 +518,10 @@ public abstract class PackParser {
 	 *
 	 * @param progress
 	 *            callback to provide progress feedback during parsing. If null,
-	 *            {@link NullProgressMonitor} will be used.
+	 *            {@link org.eclipse.jgit.lib.NullProgressMonitor} will be used.
 	 * @return the pack lock, if one was requested by setting
 	 *         {@link #setLockMessage(String)}.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream is malformed, or contains corrupt objects.
 	 * @since 3.0
 	 */
@@ -505,13 +534,13 @@ public abstract class PackParser {
 	 *
 	 * @param receiving
 	 *            receives progress feedback during the initial receiving
-	 *            objects phase. If null, {@link NullProgressMonitor} will be
-	 *            used.
+	 *            objects phase. If null,
+	 *            {@link org.eclipse.jgit.lib.NullProgressMonitor} will be used.
 	 * @param resolving
 	 *            receives progress feedback during the resolving objects phase.
 	 * @return the pack lock, if one was requested by setting
 	 *         {@link #setLockMessage(String)}.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream is malformed, or contains corrupt objects.
 	 * @since 3.0
 	 */
@@ -737,7 +766,7 @@ public abstract class PackParser {
 	 * @param info
 	 *            the info object to populate.
 	 * @return {@code info}, after populating.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the size cannot be read.
 	 */
 	protected ObjectTypeAndSize readObjectHeader(ObjectTypeAndSize info)
@@ -1097,9 +1126,8 @@ public abstract class PackParser {
 	 *            the type of the object.
 	 * @param data
 	 *            raw content of the object.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 * @since 4.9
-	 *
 	 */
 	protected void verifySafeObject(final AnyObjectId id, final int type,
 			final byte[] data) throws CorruptObjectException {
@@ -1265,7 +1293,11 @@ public abstract class PackParser {
 		bOffset = 0;
 	}
 
-	/** @return a temporary byte array for use by the caller. */
+	/**
+	 * Get a temporary byte array for use by the caller.
+	 *
+	 * @return a temporary byte array for use by the caller.
+	 */
 	protected byte[] buffer() {
 		return tempBuffer;
 	}
@@ -1302,7 +1334,7 @@ public abstract class PackParser {
 	 * If external implementation wants to overwrite the expectedObjectCount,
 	 * they should call this method during {@link #onPackHeader(long)}.
 	 *
-	 * @param expectedObjectCount
+	 * @param expectedObjectCount a long.
 	 * @since 4.9
 	 */
 	protected void setExpectedObjectCount(long expectedObjectCount) {
@@ -1327,7 +1359,7 @@ public abstract class PackParser {
 	 *            first offset within the buffer that is valid.
 	 * @param len
 	 *            number of bytes in the buffer that are valid.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream cannot be archived.
 	 */
 	protected abstract void onStoreStream(byte[] raw, int pos, int len)
@@ -1347,7 +1379,7 @@ public abstract class PackParser {
 	 *            first offset within buffer that is valid.
 	 * @param len
 	 *            number of bytes in buffer that are valid.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream cannot be archived.
 	 */
 	protected abstract void onObjectHeader(Source src, byte[] raw, int pos,
@@ -1370,7 +1402,7 @@ public abstract class PackParser {
 	 *            first offset within buffer that is valid.
 	 * @param len
 	 *            number of bytes in buffer that are valid.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream cannot be archived.
 	 */
 	protected abstract void onObjectData(Source src, byte[] raw, int pos,
@@ -1385,7 +1417,7 @@ public abstract class PackParser {
 	 *            the type of the object.
 	 * @param data
 	 *            inflated data for the object.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object cannot be archived.
 	 */
 	protected abstract void onInflatedObjectData(PackedObjectInfo obj,
@@ -1396,7 +1428,7 @@ public abstract class PackParser {
 	 *
 	 * @param objCnt
 	 *            number of objects expected in the stream.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the implementation refuses to work with this many objects.
 	 */
 	protected abstract void onPackHeader(long objCnt) throws IOException;
@@ -1407,7 +1439,7 @@ public abstract class PackParser {
 	 * @param hash
 	 *            the trailing 20 bytes of the pack, this is a SHA-1 checksum of
 	 *            all of the pack data.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream cannot be archived.
 	 */
 	protected abstract void onPackFooter(byte[] hash) throws IOException;
@@ -1430,7 +1462,7 @@ public abstract class PackParser {
 	 * @return true if the {@code info} should be included in the object list
 	 *         returned by {@link #getSortedObjectList(Comparator)}, false if it
 	 *         should not be included.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the base could not be included into the pack.
 	 */
 	protected abstract boolean onAppendBase(int typeCode, byte[] data,
@@ -1443,7 +1475,7 @@ public abstract class PackParser {
 	 * external from the pack. The event is called after all of those deltas
 	 * have been resolved.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the pack cannot be archived.
 	 */
 	protected abstract void onEndThinPack() throws IOException;
@@ -1460,7 +1492,7 @@ public abstract class PackParser {
 	 * @param info
 	 *            object to populate with type and size.
 	 * @return the {@code info} object.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the database cannot reposition to this location.
 	 */
 	protected abstract ObjectTypeAndSize seekDatabase(PackedObjectInfo obj,
@@ -1478,7 +1510,7 @@ public abstract class PackParser {
 	 * @param info
 	 *            object to populate with type and size.
 	 * @return the {@code info} object.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the database cannot reposition to this location.
 	 */
 	protected abstract ObjectTypeAndSize seekDatabase(UnresolvedDelta delta,
@@ -1495,7 +1527,7 @@ public abstract class PackParser {
 	 *            ideal target number of bytes to read. Actual read length may
 	 *            be shorter.
 	 * @return number of bytes stored.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the database cannot be accessed.
 	 */
 	protected abstract int readDatabase(byte[] dst, int pos, int cnt)
@@ -1525,13 +1557,15 @@ public abstract class PackParser {
 	 * @param streamPosition
 	 *            position of this object in the incoming stream.
 	 * @param type
-	 *            type of the object; one of {@link Constants#OBJ_COMMIT},
-	 *            {@link Constants#OBJ_TREE}, {@link Constants#OBJ_BLOB}, or
-	 *            {@link Constants#OBJ_TAG}.
+	 *            type of the object; one of
+	 *            {@link org.eclipse.jgit.lib.Constants#OBJ_COMMIT},
+	 *            {@link org.eclipse.jgit.lib.Constants#OBJ_TREE},
+	 *            {@link org.eclipse.jgit.lib.Constants#OBJ_BLOB}, or
+	 *            {@link org.eclipse.jgit.lib.Constants#OBJ_TAG}.
 	 * @param inflatedSize
 	 *            size of the object when fully inflated. The size stored within
 	 *            the pack may be larger or smaller, and is not yet known.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object cannot be recorded.
 	 */
 	protected abstract void onBeginWholeObject(long streamPosition, int type,
@@ -1542,7 +1576,7 @@ public abstract class PackParser {
 	 *
 	 *@param info
 	 *            object information.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object cannot be recorded.
 	 */
 	protected abstract void onEndWholeObject(PackedObjectInfo info)
@@ -1561,7 +1595,7 @@ public abstract class PackParser {
 	 * @param inflatedSize
 	 *            size of the delta when fully inflated. The size stored within
 	 *            the pack may be larger or smaller, and is not yet known.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object cannot be recorded.
 	 */
 	protected abstract void onBeginOfsDelta(long deltaStreamPosition,
@@ -1579,7 +1613,7 @@ public abstract class PackParser {
 	 * @param inflatedSize
 	 *            size of the delta when fully inflated. The size stored within
 	 *            the pack may be larger or smaller, and is not yet known.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object cannot be recorded.
 	 */
 	protected abstract void onBeginRefDelta(long deltaStreamPosition,
@@ -1590,7 +1624,7 @@ public abstract class PackParser {
 	 *
 	 *@return object information that must be populated with at least the
 	 *         offset.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the object cannot be recorded.
 	 */
 	protected UnresolvedDelta onEndDelta() throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackedObjectInfo.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackedObjectInfo.java
index 381c22893b..80fc0b42ad 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackedObjectInfo.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PackedObjectInfo.java
@@ -80,6 +80,8 @@ public class PackedObjectInfo extends ObjectIdOwnerMap.Entry {
 	}
 
 	/**
+	 * Get offset in pack when object has been already written
+	 *
 	 * @return offset in pack when object has been already written, or 0 if it
 	 *         has not been written yet
 	 */
@@ -98,6 +100,8 @@ public class PackedObjectInfo extends ObjectIdOwnerMap.Entry {
 	}
 
 	/**
+	 * Get the 32 bit CRC checksum for the packed data.
+	 *
 	 * @return the 32 bit CRC checksum for the packed data.
 	 */
 	public int getCRC() {
@@ -117,6 +121,8 @@ public class PackedObjectInfo extends ObjectIdOwnerMap.Entry {
 	}
 
 	/**
+	 * Get the object type.
+	 *
 	 * @return the object type. The default type is OBJ_BAD, which is considered
 	 *         as unknown or invalid type.
 	 * @since 4.9
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineIn.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineIn.java
index e70925693b..87064e122b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineIn.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineIn.java
@@ -148,7 +148,7 @@ public class PacketLineIn {
 	 *
 	 * @return the string. {@link #END} if the string was the magic flush
 	 *         packet.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream cannot be read.
 	 */
 	public String readString() throws IOException {
@@ -186,7 +186,7 @@ public class PacketLineIn {
 	 *
 	 * @return the string. {@link #END} if the string was the magic flush
 	 *         packet.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream cannot be read.
 	 */
 	public String readStringRaw() throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineOut.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineOut.java
index a6bd342851..48bdd01f55 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineOut.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineOut.java
@@ -100,7 +100,7 @@ public class PacketLineOut {
 	 *
 	 * @param s
 	 *            string to write.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the packet could not be written, the stream is corrupted as
 	 *             the packet may have been only partially written.
 	 */
@@ -114,7 +114,7 @@ public class PacketLineOut {
 	 * @param packet
 	 *            the packet to write; the length of the packet is equal to the
 	 *            size of the byte array.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the packet could not be written, the stream is corrupted as
 	 *             the packet may have been only partially written.
 	 */
@@ -131,7 +131,7 @@ public class PacketLineOut {
 	 *            first index within {@code buf}.
 	 * @param len
 	 *            number of bytes to write.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the packet could not be written, the stream is corrupted as
 	 *             the packet may have been only partially written.
 	 * @since 4.5
@@ -155,7 +155,7 @@ public class PacketLineOut {
 	 * Implicitly performs a flush on the underlying OutputStream to ensure the
 	 * peer will receive all data written thus far.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the end marker could not be written, the stream is corrupted
 	 *             as the end marker may have been only partially written.
 	 */
@@ -173,7 +173,7 @@ public class PacketLineOut {
 	 * Performs a flush on the underlying OutputStream to ensure the peer will
 	 * receive all data written thus far.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the underlying stream failed to flush.
 	 */
 	public void flush() throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostReceiveHook.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostReceiveHook.java
index 8e395018cd..5cbb6f5dfb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostReceiveHook.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostReceiveHook.java
@@ -46,11 +46,13 @@ package org.eclipse.jgit.transport;
 import java.util.Collection;
 
 /**
- * Hook invoked by {@link ReceivePack} after all updates are executed.
+ * Hook invoked by {@link org.eclipse.jgit.transport.ReceivePack} after all
+ * updates are executed.
  * <p>
  * The hook is called after all commands have been processed. Only commands with
- * a status of {@link ReceiveCommand.Result#OK} are passed into the hook. To get
- * all commands within the hook, see {@link ReceivePack#getAllCommands()}.
+ * a status of {@link org.eclipse.jgit.transport.ReceiveCommand.Result#OK} are
+ * passed into the hook. To get all commands within the hook, see
+ * {@link org.eclipse.jgit.transport.ReceivePack#getAllCommands()}.
  * <p>
  * Any post-receive hook implementation should not update the status of a
  * command, as the command has already completed or failed, and the status has
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostReceiveHookChain.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostReceiveHookChain.java
index 3bdcd68959..0bdf7d4f6b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostReceiveHookChain.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostReceiveHookChain.java
@@ -47,7 +47,8 @@ import java.util.Collection;
 import java.util.List;
 
 /**
- * {@link PostReceiveHook} that delegates to a list of other hooks.
+ * {@link org.eclipse.jgit.transport.PostReceiveHook} that delegates to a list
+ * of other hooks.
  * <p>
  * Hooks are run in the order passed to the constructor.
  */
@@ -77,6 +78,7 @@ public class PostReceiveHookChain implements PostReceiveHook {
 			return new PostReceiveHookChain(newHooks, i);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void onPostReceive(ReceivePack rp,
 			Collection<ReceiveCommand> commands) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostUploadHook.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostUploadHook.java
index 5b37bcdf0c..09667eb01a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostUploadHook.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostUploadHook.java
@@ -42,11 +42,11 @@
 
 package org.eclipse.jgit.transport;
 
-import org.eclipse.jgit.internal.storage.pack.PackWriter;
 import org.eclipse.jgit.storage.pack.PackStatistics;
 
 /**
- * Hook invoked by {@link UploadPack} after the pack has been uploaded.
+ * Hook invoked by {@link org.eclipse.jgit.transport.UploadPack} after the pack
+ * has been uploaded.
  * <p>
  * Implementors of the interface are responsible for associating the current
  * thread to a particular connection, if they need to also include connection
@@ -68,8 +68,9 @@ public interface PostUploadHook {
 	 * Notifies the hook that a pack has been sent.
 	 *
 	 * @param stats
-	 *            the statistics gathered by {@link PackWriter} for the uploaded
-	 *            pack
+	 *            the statistics gathered by
+	 *            {@link org.eclipse.jgit.internal.storage.pack.PackWriter} for
+	 *            the uploaded pack
 	 */
 	public void onPostUpload(PackStatistics stats);
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostUploadHookChain.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostUploadHookChain.java
index 26323badc6..542abe7563 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostUploadHookChain.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PostUploadHookChain.java
@@ -47,7 +47,8 @@ import java.util.List;
 import org.eclipse.jgit.storage.pack.PackStatistics;
 
 /**
- * {@link PostUploadHook} that delegates to a list of other hooks.
+ * {@link org.eclipse.jgit.transport.PostUploadHook} that delegates to a list of
+ * other hooks.
  * <p>
  * Hooks are run in the order passed to the constructor.
  *
@@ -78,6 +79,7 @@ public class PostUploadHookChain implements PostUploadHook {
 			return new PostUploadHookChain(newHooks, i);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void onPostUpload(PackStatistics stats) {
 		for (int i = 0; i < count; i++)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreReceiveHook.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreReceiveHook.java
index 27b2df08ce..77c1a8af29 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreReceiveHook.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreReceiveHook.java
@@ -46,7 +46,8 @@ package org.eclipse.jgit.transport;
 import java.util.Collection;
 
 /**
- * Hook invoked by {@link ReceivePack} before any updates are executed.
+ * Hook invoked by {@link org.eclipse.jgit.transport.ReceivePack} before any
+ * updates are executed.
  * <p>
  * The hook is called with any commands that are deemed valid after parsing them
  * from the client and applying the standard receive configuration options to
@@ -57,23 +58,24 @@ import java.util.Collection;
  * </ul>
  * This means the hook will not receive a non-fast-forward update command if
  * denyNonFastForwards is set to true in the configuration file. To get all
- * commands within the hook, see {@link ReceivePack#getAllCommands()}.
+ * commands within the hook, see
+ * {@link org.eclipse.jgit.transport.ReceivePack#getAllCommands()}.
  * <p>
  * As the hook is invoked prior to the commands being executed, the hook may
  * choose to block any command by setting its result status with
- * {@link ReceiveCommand#setResult(ReceiveCommand.Result)}.
+ * {@link org.eclipse.jgit.transport.ReceiveCommand#setResult(ReceiveCommand.Result)}.
  * <p>
  * The hook may also choose to perform the command itself (or merely pretend
  * that it has performed the command), by setting the result status to
- * {@link ReceiveCommand.Result#OK}.
+ * {@link org.eclipse.jgit.transport.ReceiveCommand.Result#OK}.
  * <p>
  * Hooks should run quickly, as they block the caller thread and the client
  * process from completing.
  * <p>
  * Hooks may send optional messages back to the client via methods on
- * {@link ReceivePack}. Implementors should be aware that not all network
- * transports support this output, so some (or all) messages may simply be
- * discarded. These messages should be advisory only.
+ * {@link org.eclipse.jgit.transport.ReceivePack}. Implementors should be aware
+ * that not all network transports support this output, so some (or all)
+ * messages may simply be discarded. These messages should be advisory only.
  */
 public interface PreReceiveHook {
 	/** A simple no-op hook. */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreReceiveHookChain.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreReceiveHookChain.java
index 7b1c8fb3f2..47b94c6e49 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreReceiveHookChain.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreReceiveHookChain.java
@@ -47,7 +47,8 @@ import java.util.Collection;
 import java.util.List;
 
 /**
- * {@link PreReceiveHook} that delegates to a list of other hooks.
+ * {@link org.eclipse.jgit.transport.PreReceiveHook} that delegates to a list of
+ * other hooks.
  * <p>
  * Hooks are run in the order passed to the constructor.
  */
@@ -76,6 +77,7 @@ public class PreReceiveHookChain implements PreReceiveHook {
 			return new PreReceiveHookChain(newHooks, i);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void onPreReceive(ReceivePack rp,
 			Collection<ReceiveCommand> commands) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreUploadHook.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreUploadHook.java
index 7d9638cfc0..2e1cd5800a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreUploadHook.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreUploadHook.java
@@ -48,9 +48,11 @@ import java.util.Collection;
 import org.eclipse.jgit.lib.ObjectId;
 
 /**
- * Hook invoked by {@link UploadPack} before during critical phases.
+ * Hook invoked by {@link org.eclipse.jgit.transport.UploadPack} before during
+ * critical phases.
  * <p>
- * If any hook function throws {@link ServiceMayNotContinueException} then
+ * If any hook function throws
+ * {@link org.eclipse.jgit.transport.ServiceMayNotContinueException} then
  * processing stops immediately and the exception is thrown up the call stack.
  * Most phases of UploadPack will try to report the exception's message text to
  * the end-user over the client's protocol connection.
@@ -91,7 +93,7 @@ public interface PreUploadHook {
 	 *            the list of wanted objects.
 	 * @param cntOffered
 	 *            number of objects the client has offered.
-	 * @throws ServiceMayNotContinueException
+	 * @throws org.eclipse.jgit.transport.ServiceMayNotContinueException
 	 *             abort; the message will be sent to the user.
 	 */
 	public void onBeginNegotiateRound(UploadPack up,
@@ -115,7 +117,7 @@ public interface PreUploadHook {
 	 * @param ready
 	 *            true if a pack is ready to be sent (the commit graph was
 	 *            successfully cut).
-	 * @throws ServiceMayNotContinueException
+	 * @throws org.eclipse.jgit.transport.ServiceMayNotContinueException
 	 *             abort; the message will be sent to the user.
 	 */
 	public void onEndNegotiateRound(UploadPack up,
@@ -136,7 +138,7 @@ public interface PreUploadHook {
 	 *            the list of common objects. Empty on an initial clone request.
 	 *            These may be RevObject or RevCommit if the processed parsed
 	 *            them. Implementors should not rely on the values being parsed.
-	 * @throws ServiceMayNotContinueException
+	 * @throws org.eclipse.jgit.transport.ServiceMayNotContinueException
 	 *             abort; the message will be sent to the user.
 	 */
 	public void onSendPack(UploadPack up, Collection<? extends ObjectId> wants,
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreUploadHookChain.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreUploadHookChain.java
index c9f88dd164..bfd52af74a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreUploadHookChain.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PreUploadHookChain.java
@@ -49,7 +49,8 @@ import java.util.List;
 import org.eclipse.jgit.lib.ObjectId;
 
 /**
- * {@link PreUploadHook} that delegates to a list of other hooks.
+ * {@link org.eclipse.jgit.transport.PreUploadHook} that delegates to a list of
+ * other hooks.
  * <p>
  * Hooks are run in the order passed to the constructor. If running a method on
  * one hook throws an exception, execution of remaining hook methods is aborted.
@@ -79,6 +80,7 @@ public class PreUploadHookChain implements PreUploadHook {
 			return new PreUploadHookChain(newHooks, i);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void onBeginNegotiateRound(UploadPack up,
 			Collection<? extends ObjectId> wants, int cntOffered)
@@ -87,6 +89,7 @@ public class PreUploadHookChain implements PreUploadHook {
 			hooks[i].onBeginNegotiateRound(up, wants, cntOffered);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void onEndNegotiateRound(UploadPack up,
 			Collection<? extends ObjectId> wants, int cntCommon,
@@ -96,6 +99,7 @@ public class PreUploadHookChain implements PreUploadHook {
 			hooks[i].onEndNegotiateRound(up, wants, cntCommon, cntNotFound, ready);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void onSendPack(UploadPack up,
 			Collection<? extends ObjectId> wants,
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ProgressSpinner.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ProgressSpinner.java
index ac048a14a9..41af8078c8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ProgressSpinner.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ProgressSpinner.java
@@ -104,7 +104,9 @@ public class ProgressSpinner {
 		}
 	}
 
-	/** Update the spinner if it is showing. */
+	/**
+	 * Update the spinner if it is showing.
+	 */
 	public void update() {
 		long now = System.currentTimeMillis();
 		if (now >= nextUpdateMillis) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificate.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificate.java
index e450345b56..a9397a599b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificate.java
@@ -132,6 +132,8 @@ public class PushCertificate {
 	}
 
 	/**
+	 * Get the certificate version string.
+	 *
 	 * @return the certificate version string.
 	 * @since 4.1
 	 */
@@ -140,6 +142,8 @@ public class PushCertificate {
 	}
 
 	/**
+	 * Get the raw line that signed the cert, as a string.
+	 *
 	 * @return the raw line that signed the cert, as a string.
 	 * @since 4.0
 	 */
@@ -148,6 +152,8 @@ public class PushCertificate {
 	}
 
 	/**
+	 * Get identity of the pusher who signed the cert.
+	 *
 	 * @return identity of the pusher who signed the cert.
 	 * @since 4.1
 	 */
@@ -156,6 +162,8 @@ public class PushCertificate {
 	}
 
 	/**
+	 * Get URL of the repository the push was originally sent to.
+	 *
 	 * @return URL of the repository the push was originally sent to.
 	 * @since 4.0
 	 */
@@ -164,6 +172,8 @@ public class PushCertificate {
 	}
 
 	/**
+	 * Get the raw nonce value that was presented by the pusher.
+	 *
 	 * @return the raw nonce value that was presented by the pusher.
 	 * @since 4.1
 	 */
@@ -172,6 +182,8 @@ public class PushCertificate {
 	}
 
 	/**
+	 * Get verification status of the nonce embedded in the certificate.
+	 *
 	 * @return verification status of the nonce embedded in the certificate.
 	 * @since 4.0
 	 */
@@ -180,6 +192,9 @@ public class PushCertificate {
 	}
 
 	/**
+	 * Get the list of commands as one string to be feed into the signature
+	 * verifier.
+	 *
 	 * @return the list of commands as one string to be feed into the signature
 	 *         verifier.
 	 * @since 4.1
@@ -189,9 +204,11 @@ public class PushCertificate {
 	}
 
 	/**
+	 * Get the raw signature
+	 *
 	 * @return the raw signature, consisting of the lines received between the
-	 *     lines {@code "----BEGIN GPG SIGNATURE-----\n"} and
-	 *     {@code "----END GPG SIGNATURE-----\n}", inclusive.
+	 *         lines {@code "----BEGIN GPG SIGNATURE-----\n"} and
+	 *         {@code "----END GPG SIGNATURE-----\n}", inclusive.
 	 * @since 4.0
 	 */
 	public String getSignature() {
@@ -199,6 +216,8 @@ public class PushCertificate {
 	}
 
 	/**
+	 * Get text payload of the certificate for the signature verifier.
+	 *
 	 * @return text payload of the certificate for the signature verifier.
 	 * @since 4.1
 	 */
@@ -207,8 +226,11 @@ public class PushCertificate {
 	}
 
 	/**
+	 * Get original text payload plus signature
+	 *
 	 * @return original text payload plus signature; the final output will be
-	 *     valid as input to {@link PushCertificateParser#fromString(String)}.
+	 *         valid as input to
+	 *         {@link org.eclipse.jgit.transport.PushCertificateParser#fromString(String)}.
 	 * @since 4.1
 	 */
 	public String toTextWithSignature() {
@@ -233,11 +255,13 @@ public class PushCertificate {
 		return sb;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int hashCode() {
 		return signature.hashCode();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean equals(Object o) {
 		if (!(o instanceof PushCertificate)) {
@@ -268,6 +292,7 @@ public class PushCertificate {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		return getClass().getSimpleName() + '['
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificateIdent.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificateIdent.java
index 4c8acd2cc2..f9fddbe889 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificateIdent.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificateIdent.java
@@ -58,18 +58,19 @@ import org.eclipse.jgit.util.RawParseUtils;
 /**
  * Identity in a push certificate.
  * <p>
- * This is similar to a {@link PersonIdent} in that it contains a name,
- * timestamp, and timezone offset, but differs in the following ways:
+ * This is similar to a {@link org.eclipse.jgit.lib.PersonIdent} in that it
+ * contains a name, timestamp, and timezone offset, but differs in the following
+ * ways:
  * <ul>
  * <li>It is always parsed from a UTF-8 string, rather than a raw commit
- *   buffer.</li>
+ * buffer.</li>
  * <li>It is not guaranteed to contain a name and email portion, since any UTF-8
- *   string is a valid OpenPGP User ID (RFC4880 5.1.1). The raw User ID is
- *   always available as {@link #getUserId()}, but {@link #getEmailAddress()}
- *   may return null.</li>
- * <li>The raw text from which the identity was parsed is available with {@link
- *   #getRaw()}. This is necessary for losslessly reconstructing the signed push
- *   certificate payload.</li>
+ * string is a valid OpenPGP User ID (RFC4880 5.1.1). The raw User ID is always
+ * available as {@link #getUserId()}, but {@link #getEmailAddress()} may return
+ * null.</li>
+ * <li>The raw text from which the identity was parsed is available with
+ * {@link #getRaw()}. This is necessary for losslessly reconstructing the signed
+ * push certificate payload.</li>
  * <li>
  * </ul>
  *
@@ -79,18 +80,18 @@ public class PushCertificateIdent {
 	/**
 	 * Parse an identity from a string.
 	 * <p>
-	 * Spaces are trimmed when parsing the timestamp and timezone offset, with one
-	 * exception. The timestamp must be preceded by a single space, and the rest
-	 * of the string prior to that space (including any additional whitespace) is
-	 * treated as the OpenPGP User ID.
+	 * Spaces are trimmed when parsing the timestamp and timezone offset, with
+	 * one exception. The timestamp must be preceded by a single space, and the
+	 * rest of the string prior to that space (including any additional
+	 * whitespace) is treated as the OpenPGP User ID.
 	 * <p>
-	 * If either the timestamp or timezone offsets are missing, mimics {@link
-	 * RawParseUtils#parsePersonIdent(String)} behavior and sets them both to
-	 * zero.
+	 * If either the timestamp or timezone offsets are missing, mimics
+	 * {@link RawParseUtils#parsePersonIdent(String)} behavior and sets them
+	 * both to zero.
 	 *
 	 * @param str
 	 *            string to parse.
-	 * @return identity, never null.
+	 * @return a {@link org.eclipse.jgit.transport.PushCertificateIdent} object.
 	 */
 	public static PushCertificateIdent parse(String str) {
 		MutableInteger p = new MutableInteger();
@@ -181,15 +182,21 @@ public class PushCertificateIdent {
 		return raw;
 	}
 
-	/** @return the OpenPGP User ID, which may be any string. */
+	/**
+	 * Get the OpenPGP User ID, which may be any string.
+	 *
+	 * @return the OpenPGP User ID, which may be any string.
+	 */
 	public String getUserId() {
 		return userId;
 	}
 
 	/**
+	 * Get the name portion of the User ID.
+	 *
 	 * @return the name portion of the User ID. If no email address would be
-	 *         parsed by {@link #getEmailAddress()}, returns the full User ID with
-	 *         spaces trimmed.
+	 *         parsed by {@link #getEmailAddress()}, returns the full User ID
+	 *         with spaces trimmed.
 	 */
 	public String getName() {
 		int nameEnd = userId.indexOf('<');
@@ -208,6 +215,8 @@ public class PushCertificateIdent {
 	}
 
 	/**
+	 * Get the email portion of the User ID
+	 *
 	 * @return the email portion of the User ID, if one was successfully parsed
 	 *         from {@link #getUserId()}, or null.
 	 */
@@ -223,19 +232,28 @@ public class PushCertificateIdent {
 		return userId.substring(emailBegin + 1, emailEnd);
 	}
 
-	/** @return the timestamp of the identity. */
+	/**
+	 * Get the timestamp of the identity.
+	 *
+	 * @return the timestamp of the identity.
+	 */
 	public Date getWhen() {
 		return new Date(when);
 	}
 
 	/**
-	 * @return this person's declared time zone; null if the timezone is unknown.
+	 * Get this person's declared time zone
+	 *
+	 * @return this person's declared time zone; null if the timezone is
+	 *         unknown.
 	 */
 	public TimeZone getTimeZone() {
 		return PersonIdent.getTimeZone(tzOffset);
 	}
 
 	/**
+	 * Get this person's declared time zone as minutes east of UTC.
+	 *
 	 * @return this person's declared time zone as minutes east of UTC. If the
 	 *         timezone is to the west of UTC it is negative.
 	 */
@@ -243,17 +261,20 @@ public class PushCertificateIdent {
 		return tzOffset;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean equals(Object o) {
 		return (o instanceof PushCertificateIdent)
 			&& raw.equals(((PushCertificateIdent) o).raw);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int hashCode() {
 		return raw.hashCode();
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificateParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificateParser.java
index 5174f85627..89c1a93788 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificateParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificateParser.java
@@ -133,11 +133,12 @@ public class PushCertificateParser {
 	/**
 	 * Parse a push certificate from a reader.
 	 * <p>
-	 * Differences from the {@link PacketLineIn} receiver methods:
+	 * Differences from the {@link org.eclipse.jgit.transport.PacketLineIn}
+	 * receiver methods:
 	 * <ul>
 	 * <li>Does not use pkt-line framing.</li>
 	 * <li>Reads an entire cert in one call rather than depending on a loop in
-	 *   the caller.</li>
+	 * the caller.</li>
 	 * <li>Does not assume a {@code "push-cert-end"} line.</li>
 	 * </ul>
 	 *
@@ -145,9 +146,9 @@ public class PushCertificateParser {
 	 *            input reader; consumed only up until the end of the next
 	 *            signature in the input.
 	 * @return the parsed certificate, or null if the reader was at EOF.
-	 * @throws PackProtocolException
+	 * @throws org.eclipse.jgit.errors.PackProtocolException
 	 *             if the certificate is malformed.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if there was an error reading from the input.
 	 * @since 4.1
 	 */
@@ -163,9 +164,9 @@ public class PushCertificateParser {
 	 * @param str
 	 *            input string.
 	 * @return the parsed certificate.
-	 * @throws PackProtocolException
+	 * @throws org.eclipse.jgit.errors.PackProtocolException
 	 *             if the certificate is malformed.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if there was an error reading from the input.
 	 * @since 4.1
 	 */
@@ -207,6 +208,8 @@ public class PushCertificateParser {
 	private final List<ReceiveCommand> commands = new ArrayList<>();
 
 	/**
+	 * <p>Constructor for PushCertificateParser.</p>
+	 *
 	 * @param into
 	 *            destination repository for the push.
 	 * @param cfg
@@ -240,9 +243,9 @@ public class PushCertificateParser {
 	 *            input reader; consumed only up until the end of the next
 	 *            signature in the input.
 	 * @return the parsed certificate, or null if the reader was at EOF.
-	 * @throws PackProtocolException
+	 * @throws org.eclipse.jgit.errors.PackProtocolException
 	 *             if the certificate is malformed.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if there was an error reading from the input.
 	 * @since 4.1
 	 */
@@ -267,8 +270,11 @@ public class PushCertificateParser {
 	}
 
 	/**
-	 * @return the parsed certificate, or null if push certificates are disabled.
-	 * @throws IOException
+	 * Build the parsed certificate
+	 *
+	 * @return the parsed certificate, or null if push certificates are
+	 *         disabled.
+	 * @throws java.io.IOException
 	 *             if the push certificate has missing or invalid fields.
 	 * @since 4.1
 	 */
@@ -285,6 +291,9 @@ public class PushCertificateParser {
 	}
 
 	/**
+	 * Whether the repository is configured to use signed pushes in this
+	 * context.
+	 *
 	 * @return if the repository is configured to use signed pushes in this
 	 *         context.
 	 * @since 4.0
@@ -294,6 +303,9 @@ public class PushCertificateParser {
 	}
 
 	/**
+	 * Get the whole string for the nonce to be included into the capability
+	 * advertisement
+	 *
 	 * @return the whole string for the nonce to be included into the capability
 	 *         advertisement, or null if push certificates are disabled.
 	 * @since 4.0
@@ -348,7 +360,7 @@ public class PushCertificateParser {
 	 *            {@code NonceGenerator} will allow for some time skew caused by
 	 *            clients disconnected and reconnecting in the stateless smart
 	 *            HTTP protocol.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if the certificate from the client is badly malformed or the
 	 *             client disconnects before sending the entire certificate.
 	 * @since 4.0
@@ -410,7 +422,7 @@ public class PushCertificateParser {
 	 *
 	 * @param pckIn
 	 *            where we read the signature from.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if the signature is invalid.
 	 * @since 4.0
 	 */
@@ -455,7 +467,7 @@ public class PushCertificateParser {
 	 * @param line
 	 *            the line read from the wire that produced this
 	 *            command, with optional trailing newline already trimmed.
-	 * @throws PackProtocolException
+	 * @throws org.eclipse.jgit.errors.PackProtocolException
 	 *             if the raw line cannot be parsed to a command.
 	 * @since 4.0
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificateStore.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificateStore.java
index 706e727060..ab58a3317a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificateStore.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushCertificateStore.java
@@ -135,10 +135,12 @@ public class PushCertificateStore implements AutoCloseable {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Close resources opened by this store.
 	 * <p>
-	 * If {@link #get(String)} was called, closes the cached object reader created
-	 * by that method. Does not close the underlying repository.
+	 * If {@link #get(String)} was called, closes the cached object reader
+	 * created by that method. Does not close the underlying repository.
 	 */
 	@Override
 	public void close() {
@@ -160,7 +162,7 @@ public class PushCertificateStore implements AutoCloseable {
 	 *            the ref name to get the certificate for.
 	 * @return last certificate affecting the ref, or null if no cert was recorded
 	 *         for the last update to this ref.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if a problem occurred reading the repository.
 	 */
 	public PushCertificate get(String refName) throws IOException {
@@ -298,20 +300,20 @@ public class PushCertificateStore implements AutoCloseable {
 	/**
 	 * Put a certificate to be saved to the store.
 	 * <p>
-	 * Writes the contents of this certificate for each ref mentioned. It is up to
-	 * the caller to ensure this certificate accurately represents the state of
-	 * the ref.
+	 * Writes the contents of this certificate for each ref mentioned. It is up
+	 * to the caller to ensure this certificate accurately represents the state
+	 * of the ref.
 	 * <p>
-	 * Pending certificates added to this method are not returned by {@link
-	 * #get(String)} and {@link #getAll(String)} until after calling {@link
-	 * #save()}.
+	 * Pending certificates added to this method are not returned by
+	 * {@link #get(String)} and {@link #getAll(String)} until after calling
+	 * {@link #save()}.
 	 *
 	 * @param cert
 	 *            certificate to store.
 	 * @param ident
 	 *            identity for the commit that stores this certificate. Pending
-	 *            certificates are sorted by identity timestamp during {@link
-	 *            #save()}.
+	 *            certificates are sorted by identity timestamp during
+	 *            {@link #save()}.
 	 */
 	public void put(PushCertificate cert, PersonIdent ident) {
 		put(cert, ident, null);
@@ -325,16 +327,16 @@ public class PushCertificateStore implements AutoCloseable {
 	 * list that exactly matches the old/new values mentioned in the push
 	 * certificate.
 	 * <p>
-	 * Pending certificates added to this method are not returned by {@link
-	 * #get(String)} and {@link #getAll(String)} until after calling {@link
-	 * #save()}.
+	 * Pending certificates added to this method are not returned by
+	 * {@link #get(String)} and {@link #getAll(String)} until after calling
+	 * {@link #save()}.
 	 *
 	 * @param cert
 	 *            certificate to store.
 	 * @param ident
 	 *            identity for the commit that stores this certificate. Pending
-	 *            certificates are sorted by identity timestamp during {@link
-	 *            #save()}.
+	 *            certificates are sorted by identity timestamp during
+	 *            {@link #save()}.
 	 * @param matching
 	 *            only store certs for the refs listed in this list whose values
 	 *            match the commands in the cert.
@@ -347,15 +349,15 @@ public class PushCertificateStore implements AutoCloseable {
 	/**
 	 * Save pending certificates to the store.
 	 * <p>
-	 * One commit is created per certificate added with {@link
-	 * #put(PushCertificate, PersonIdent)}, in order of identity timestamps, and
-	 * a single ref update is performed.
+	 * One commit is created per certificate added with
+	 * {@link #put(PushCertificate, PersonIdent)}, in order of identity
+	 * timestamps, and a single ref update is performed.
 	 * <p>
-	 * The pending list is cleared if and only the ref update fails, which allows
-	 * for easy retries in case of lock failure.
+	 * The pending list is cleared if and only the ref update fails, which
+	 * allows for easy retries in case of lock failure.
 	 *
 	 * @return the result of attempting to update the ref.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if there was an error reading from or writing to the
 	 *             repository.
 	 */
@@ -384,18 +386,19 @@ public class PushCertificateStore implements AutoCloseable {
 	/**
 	 * Save pending certificates to the store in an existing batch ref update.
 	 * <p>
-	 * One commit is created per certificate added with {@link
-	 * #put(PushCertificate, PersonIdent)}, in order of identity timestamps, all
-	 * commits are flushed, and a single command is added to the batch.
+	 * One commit is created per certificate added with
+	 * {@link #put(PushCertificate, PersonIdent)}, in order of identity
+	 * timestamps, all commits are flushed, and a single command is added to the
+	 * batch.
 	 * <p>
-	 * The cached ref value and pending list are <em>not</em> cleared. If the ref
-	 * update succeeds, the caller is responsible for calling {@link #close()}
-	 * and/or {@link #clear()}.
+	 * The cached ref value and pending list are <em>not</em> cleared. If the
+	 * ref update succeeds, the caller is responsible for calling
+	 * {@link #close()} and/or {@link #clear()}.
 	 *
 	 * @param batch
 	 *            update to save to.
 	 * @return whether a command was added to the batch.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if there was an error reading from or writing to the
 	 *             repository.
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushConnection.java
index c2a885f622..ff2939a3d6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushConnection.java
@@ -49,7 +49,6 @@ import java.util.Map;
 
 import org.eclipse.jgit.errors.TransportException;
 import org.eclipse.jgit.lib.ProgressMonitor;
-import org.eclipse.jgit.transport.RemoteRefUpdate.Status;
 
 /**
  * Lists known refs from the remote and sends objects to the remote.
@@ -60,9 +59,9 @@ import org.eclipse.jgit.transport.RemoteRefUpdate.Status;
  * into the remote repository, as well as a way to modify the refs stored by the
  * remote repository.
  * <p>
- * Instances of a PushConnection must be created by a {@link Transport} that
- * implements a specific object transfer protocol that both sides of the
- * connection understand.
+ * Instances of a PushConnection must be created by a
+ * {@link org.eclipse.jgit.transport.Transport} that implements a specific
+ * object transfer protocol that both sides of the connection understand.
  * <p>
  * PushConnection instances are not thread safe and may be accessed by only one
  * thread at a time.
@@ -79,13 +78,14 @@ public interface PushConnection extends Connection {
 	 * <p>
 	 * <p>
 	 * Only one call per connection is allowed. Subsequent calls will result in
-	 * {@link TransportException}.
+	 * {@link org.eclipse.jgit.errors.TransportException}.
 	 * </p>
 	 * <p>
 	 * Implementation may use local repository to send a minimum set of objects
 	 * needed by remote repository in efficient way.
-	 * {@link Transport#isPushThin()} should be honored if applicable.
-	 * refUpdates should be filled with information about status of each update.
+	 * {@link org.eclipse.jgit.transport.Transport#isPushThin()} should be
+	 * honored if applicable. refUpdates should be filled with information about
+	 * status of each update.
 	 * </p>
 	 *
 	 * @param monitor
@@ -97,12 +97,16 @@ public interface PushConnection extends Connection {
 	 *            map of remote refnames to remote refs update
 	 *            specifications/statuses. Can't be empty. This indicate what
 	 *            refs caller want to update on remote side. Only refs updates
-	 *            with {@link Status#NOT_ATTEMPTED} should passed.
-	 *            Implementation must ensure that and appropriate status with
-	 *            optional message should be set during call. No refUpdate with
-	 *            {@link Status#AWAITING_REPORT} or {@link Status#NOT_ATTEMPTED}
+	 *            with
+	 *            {@link org.eclipse.jgit.transport.RemoteRefUpdate.Status#NOT_ATTEMPTED}
+	 *            should passed. Implementation must ensure that and appropriate
+	 *            status with optional message should be set during call. No
+	 *            refUpdate with
+	 *            {@link org.eclipse.jgit.transport.RemoteRefUpdate.Status#AWAITING_REPORT}
+	 *            or
+	 *            {@link org.eclipse.jgit.transport.RemoteRefUpdate.Status#NOT_ATTEMPTED}
 	 *            can be leaved by implementation after return from this call.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             objects could not be copied due to a network failure,
 	 *             critical protocol error, or error on remote side, or
 	 *             connection was already used for push - new connection must be
@@ -121,13 +125,14 @@ public interface PushConnection extends Connection {
 	 * <p>
 	 * <p>
 	 * Only one call per connection is allowed. Subsequent calls will result in
-	 * {@link TransportException}.
+	 * {@link org.eclipse.jgit.errors.TransportException}.
 	 * </p>
 	 * <p>
 	 * Implementation may use local repository to send a minimum set of objects
 	 * needed by remote repository in efficient way.
-	 * {@link Transport#isPushThin()} should be honored if applicable.
-	 * refUpdates should be filled with information about status of each update.
+	 * {@link org.eclipse.jgit.transport.Transport#isPushThin()} should be
+	 * honored if applicable. refUpdates should be filled with information about
+	 * status of each update.
 	 * </p>
 	 *
 	 * @param monitor
@@ -139,14 +144,18 @@ public interface PushConnection extends Connection {
 	 *            map of remote refnames to remote refs update
 	 *            specifications/statuses. Can't be empty. This indicate what
 	 *            refs caller want to update on remote side. Only refs updates
-	 *            with {@link Status#NOT_ATTEMPTED} should passed.
-	 *            Implementation must ensure that and appropriate status with
-	 *            optional message should be set during call. No refUpdate with
-	 *            {@link Status#AWAITING_REPORT} or {@link Status#NOT_ATTEMPTED}
+	 *            with
+	 *            {@link org.eclipse.jgit.transport.RemoteRefUpdate.Status#NOT_ATTEMPTED}
+	 *            should passed. Implementation must ensure that and appropriate
+	 *            status with optional message should be set during call. No
+	 *            refUpdate with
+	 *            {@link org.eclipse.jgit.transport.RemoteRefUpdate.Status#AWAITING_REPORT}
+	 *            or
+	 *            {@link org.eclipse.jgit.transport.RemoteRefUpdate.Status#NOT_ATTEMPTED}
 	 *            can be leaved by implementation after return from this call.
 	 * @param out
 	 *            output stream to write sideband messages to
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             objects could not be copied due to a network failure,
 	 *             critical protocol error, or error on remote side, or
 	 *             connection was already used for push - new connection must be
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushResult.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushResult.java
index 41aa73cc3b..8bae5a5e09 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushResult.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PushResult.java
@@ -51,7 +51,8 @@ import java.util.Map;
 
 /**
  * Result of push operation to the remote repository. Holding information of
- * {@link OperationResult} and remote refs updates status.
+ * {@link org.eclipse.jgit.transport.OperationResult} and remote refs updates
+ * status.
  *
  * @see Transport#push(org.eclipse.jgit.lib.ProgressMonitor, Collection)
  */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceiveCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceiveCommand.java
index a6eb2f0855..e14d18f3a6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceiveCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceiveCommand.java
@@ -64,10 +64,11 @@ import org.eclipse.jgit.revwalk.RevObject;
 import org.eclipse.jgit.revwalk.RevWalk;
 
 /**
- * A command being processed by {@link BaseReceivePack}.
+ * A command being processed by
+ * {@link org.eclipse.jgit.transport.BaseReceivePack}.
  * <p>
  * This command instance roughly translates to the server side representation of
- * the {@link RemoteRefUpdate} created by the client.
+ * the {@link org.eclipse.jgit.transport.RemoteRefUpdate} created by the client.
  */
 public class ReceiveCommand {
 	/** Type of operation requested. */
@@ -176,8 +177,10 @@ public class ReceiveCommand {
 	/**
 	 * Set unprocessed commands as failed due to transaction aborted.
 	 * <p>
-	 * If a command is still {@link Result#NOT_ATTEMPTED} it will be set to
-	 * {@link Result#REJECTED_OTHER_REASON}.
+	 * If a command is still
+	 * {@link org.eclipse.jgit.transport.ReceiveCommand.Result#NOT_ATTEMPTED} it
+	 * will be set to
+	 * {@link org.eclipse.jgit.transport.ReceiveCommand.Result#REJECTED_OTHER_REASON}.
 	 *
 	 * @param commands
 	 *            commands to mark as failed.
@@ -286,14 +289,17 @@ public class ReceiveCommand {
 	private Boolean forceRefLog;
 
 	/**
-	 * Create a new command for {@link BaseReceivePack}.
+	 * Create a new command for
+	 * {@link org.eclipse.jgit.transport.BaseReceivePack}.
 	 *
 	 * @param oldId
 	 *            the expected old object id; must not be null. Use
-	 *            {@link ObjectId#zeroId()} to indicate a ref creation.
+	 *            {@link org.eclipse.jgit.lib.ObjectId#zeroId()} to indicate a
+	 *            ref creation.
 	 * @param newId
 	 *            the new object id; must not be null. Use
-	 *            {@link ObjectId#zeroId()} to indicate a ref deletion.
+	 *            {@link org.eclipse.jgit.lib.ObjectId#zeroId()} to indicate a
+	 *            ref deletion.
 	 * @param name
 	 *            name of the ref being affected.
 	 */
@@ -327,20 +333,26 @@ public class ReceiveCommand {
 	}
 
 	/**
-	 * Create a new command for {@link BaseReceivePack}.
+	 * Create a new command for
+	 * {@link org.eclipse.jgit.transport.BaseReceivePack}.
 	 *
 	 * @param oldId
 	 *            the old object id; must not be null. Use
-	 *            {@link ObjectId#zeroId()} to indicate a ref creation.
+	 *            {@link org.eclipse.jgit.lib.ObjectId#zeroId()} to indicate a
+	 *            ref creation.
 	 * @param newId
 	 *            the new object id; must not be null. Use
-	 *            {@link ObjectId#zeroId()} to indicate a ref deletion.
+	 *            {@link org.eclipse.jgit.lib.ObjectId#zeroId()} to indicate a
+	 *            ref deletion.
 	 * @param name
 	 *            name of the ref being affected.
 	 * @param type
-	 *            type of the command. Must be {@link Type#CREATE} if {@code
-	 *            oldId} is zero, or {@link Type#DELETE} if {@code newId} is
-	 *            zero.
+	 *            type of the command. Must be
+	 *            {@link org.eclipse.jgit.transport.ReceiveCommand.Type#CREATE}
+	 *            if {@code
+	 *            oldId} is zero, or
+	 *            {@link org.eclipse.jgit.transport.ReceiveCommand.Type#DELETE}
+	 *            if {@code newId} is zero.
 	 * @since 2.0
 	 */
 	public ReceiveCommand(final ObjectId oldId, final ObjectId newId,
@@ -500,12 +512,18 @@ public class ReceiveCommand {
 		typeIsCorrect = true;
 	}
 
-	/** @return the old value the client thinks the ref has. */
+	/**
+	 * Get the old value the client thinks the ref has.
+	 *
+	 * @return the old value the client thinks the ref has.
+	 */
 	public ObjectId getOldId() {
 		return oldId;
 	}
 
 	/**
+	 * Get expected old target for a symbolic reference.
+	 *
 	 * @return expected old target for a symbolic reference.
 	 * @since 4.10
 	 */
@@ -514,12 +532,18 @@ public class ReceiveCommand {
 		return oldSymref;
 	}
 
-	/** @return the requested new value for this ref. */
+	/**
+	 * Get the requested new value for this ref.
+	 *
+	 * @return the requested new value for this ref.
+	 */
 	public ObjectId getNewId() {
 		return newId;
 	}
 
 	/**
+	 * Get requested new target for a symbolic reference.
+	 *
 	 * @return requested new target for a symbolic reference.
 	 * @since 4.10
 	 */
@@ -528,27 +552,47 @@ public class ReceiveCommand {
 		return newSymref;
 	}
 
-	/** @return the name of the ref being updated. */
+	/**
+	 * Get the name of the ref being updated.
+	 *
+	 * @return the name of the ref being updated.
+	 */
 	public String getRefName() {
 		return name;
 	}
 
-	/** @return the type of this command; see {@link Type}. */
+	/**
+	 * Get the type of this command; see {@link Type}.
+	 *
+	 * @return the type of this command; see {@link Type}.
+	 */
 	public Type getType() {
 		return type;
 	}
 
-	/** @return the ref, if this was advertised by the connection. */
+	/**
+	 * Get the ref, if this was advertised by the connection.
+	 *
+	 * @return the ref, if this was advertised by the connection.
+	 */
 	public Ref getRef() {
 		return ref;
 	}
 
-	/** @return the current status code of this command. */
+	/**
+	 * Get the current status code of this command.
+	 *
+	 * @return the current status code of this command.
+	 */
 	public Result getResult() {
 		return status;
 	}
 
-	/** @return the message associated with a failure status. */
+	/**
+	 * Get the message associated with a failure status.
+	 *
+	 * @return the message associated with a failure status.
+	 */
 	public String getMessage() {
 		return message;
 	}
@@ -692,12 +736,13 @@ public class ReceiveCommand {
 	 * If the command's current type is UPDATE, a merge test will be performed
 	 * using the supplied RevWalk to determine if {@link #getOldId()} is fully
 	 * merged into {@link #getNewId()}. If some commits are not merged the
-	 * update type is changed to {@link Type#UPDATE_NONFASTFORWARD}.
+	 * update type is changed to
+	 * {@link org.eclipse.jgit.transport.ReceiveCommand.Type#UPDATE_NONFASTFORWARD}.
 	 *
 	 * @param walk
 	 *            an instance to perform the merge test with. The caller must
 	 *            allocate and release this object.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             either oldId or newId is not accessible in the repository
 	 *             used by the RevWalk. This usually indicates data corruption,
 	 *             and the command cannot be processed.
@@ -837,6 +882,7 @@ public class ReceiveCommand {
 				JGitText.get().lockError, err.getMessage()));
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java
index 169df3be26..7c5f32ac0d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java
@@ -130,7 +130,11 @@ public class ReceivePack extends BaseReceivePack {
 		pushOptions = options;
 	}
 
-	/** @return the hook invoked before updates occur. */
+	/**
+	 * Get the hook invoked before updates occur.
+	 *
+	 * @return the hook invoked before updates occur.
+	 */
 	public PreReceiveHook getPreReceiveHook() {
 		return preReceive;
 	}
@@ -141,7 +145,8 @@ public class ReceivePack extends BaseReceivePack {
 	 * Only valid commands (those which have no obvious errors according to the
 	 * received input and this instance's configuration) are passed into the
 	 * hook. The hook may mark a command with a result of any value other than
-	 * {@link Result#NOT_ATTEMPTED} to block its execution.
+	 * {@link org.eclipse.jgit.transport.ReceiveCommand.Result#NOT_ATTEMPTED} to
+	 * block its execution.
 	 * <p>
 	 * The hook may be called with an empty command collection if the current
 	 * set is completely invalid.
@@ -153,7 +158,11 @@ public class ReceivePack extends BaseReceivePack {
 		preReceive = h != null ? h : PreReceiveHook.NULL;
 	}
 
-	/** @return the hook invoked after updates occur. */
+	/**
+	 * Get the hook invoked after updates occur.
+	 *
+	 * @return the hook invoked after updates occur.
+	 */
 	public PostReceiveHook getPostReceiveHook() {
 		return postReceive;
 	}
@@ -161,9 +170,10 @@ public class ReceivePack extends BaseReceivePack {
 	/**
 	 * Set the hook which is invoked after commands are executed.
 	 * <p>
-	 * Only successful commands (type is {@link Result#OK}) are passed into the
-	 * hook. The hook may be called with an empty command collection if the
-	 * current set all resulted in an error.
+	 * Only successful commands (type is
+	 * {@link org.eclipse.jgit.transport.ReceiveCommand.Result#OK}) are passed
+	 * into the hook. The hook may be called with an empty command collection if
+	 * the current set all resulted in an error.
 	 *
 	 * @param h
 	 *            the hook instance; may be null to disable the hook.
@@ -173,6 +183,9 @@ public class ReceivePack extends BaseReceivePack {
 	}
 
 	/**
+	 * Set whether this class will report command failures as warning messages
+	 * before sending the command results.
+	 *
 	 * @param echo
 	 *            if true this class will report command failures as warning
 	 *            messages before sending the command results. This is usually
@@ -199,7 +212,7 @@ public class ReceivePack extends BaseReceivePack {
 	 *            through. When run over SSH this should be tied back to the
 	 *            standard error channel of the command execution. For most
 	 *            other network connections this should be null.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void receive(final InputStream input, final OutputStream output,
 			final OutputStream messages) throws IOException {
@@ -215,6 +228,7 @@ public class ReceivePack extends BaseReceivePack {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void enableCapabilities() {
 		reportStatus = isCapabilityEnabled(CAPABILITY_REPORT_STATUS);
@@ -325,6 +339,7 @@ public class ReceivePack extends BaseReceivePack {
 		repo.autoGC(NullProgressMonitor.INSTANCE);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected String getLockMessageProcessName() {
 		return "jgit receive-pack"; //$NON-NLS-1$
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivedPackStatistics.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivedPackStatistics.java
index 052d5506f8..dec528970a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivedPackStatistics.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivedPackStatistics.java
@@ -46,7 +46,7 @@ package org.eclipse.jgit.transport;
 import org.eclipse.jgit.lib.Constants;
 
 /**
- * Statistics about {@link PackParser}.
+ * Statistics about {@link org.eclipse.jgit.transport.PackParser}.
  *
  * @since 4.6
  */
@@ -65,57 +65,101 @@ public class ReceivedPackStatistics {
 	private long numDeltaBlob;
 	private long numDeltaTag;
 
-	/** @return number of bytes read from the input stream */
+	/**
+	 * Get number of bytes read from the input stream
+	 *
+	 * @return number of bytes read from the input stream
+	 */
 	public long getNumBytesRead() {
 		return numBytesRead;
 	}
 
-	/** @return number of whole commit objects in the pack */
+	/**
+	 * Get number of whole commit objects in the pack
+	 *
+	 * @return number of whole commit objects in the pack
+	 */
 	public long getNumWholeCommit() {
 		return numWholeCommit;
 	}
 
-	/** @return number of whole tree objects in the pack */
+	/**
+	 * Get number of whole tree objects in the pack
+	 *
+	 * @return number of whole tree objects in the pack
+	 */
 	public long getNumWholeTree() {
 		return numWholeTree;
 	}
 
-	/** @return number of whole blob objects in the pack */
+	/**
+	 * Get number of whole blob objects in the pack
+	 *
+	 * @return number of whole blob objects in the pack
+	 */
 	public long getNumWholeBlob() {
 		return numWholeBlob;
 	}
 
-	/** @return number of whole tag objects in the pack */
+	/**
+	 * Get number of whole tag objects in the pack
+	 *
+	 * @return number of whole tag objects in the pack
+	 */
 	public long getNumWholeTag() {
 		return numWholeTag;
 	}
 
-	/** @return number of offset delta objects in the pack */
+	/**
+	 * Get number of offset delta objects in the pack
+	 *
+	 * @return number of offset delta objects in the pack
+	 */
 	public long getNumOfsDelta() {
 		return numOfsDelta;
 	}
 
-	/** @return number of ref delta objects in the pack */
+	/**
+	 * Get number of ref delta objects in the pack
+	 *
+	 * @return number of ref delta objects in the pack
+	 */
 	public long getNumRefDelta() {
 		return numRefDelta;
 	}
 
-	/** @return number of delta commit objects in the pack */
+	/**
+	 * Get number of delta commit objects in the pack
+	 *
+	 * @return number of delta commit objects in the pack
+	 */
 	public long getNumDeltaCommit() {
 		return numDeltaCommit;
 	}
 
-	/** @return number of delta tree objects in the pack */
+	/**
+	 * Get number of delta tree objects in the pack
+	 *
+	 * @return number of delta tree objects in the pack
+	 */
 	public long getNumDeltaTree() {
 		return numDeltaTree;
 	}
 
-	/** @return number of delta blob objects in the pack */
+	/**
+	 * Get number of delta blob objects in the pack
+	 *
+	 * @return number of delta blob objects in the pack
+	 */
 	public long getNumDeltaBlob() {
 		return numDeltaBlob;
 	}
 
-	/** @return number of delta tag objects in the pack */
+	/**
+	 * Get number of delta tag objects in the pack
+	 *
+	 * @return number of delta tag objects in the pack
+	 */
 	public long getNumDeltaTag() {
 		return numDeltaTag;
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefAdvertiser.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefAdvertiser.java
index 745e813c41..5eb1661738 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefAdvertiser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefAdvertiser.java
@@ -67,7 +67,10 @@ import org.eclipse.jgit.lib.RefComparator;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.util.RefMap;
 
-/** Support for the start of {@link UploadPack} and {@link ReceivePack}. */
+/**
+ * Support for the start of {@link org.eclipse.jgit.transport.UploadPack} and
+ * {@link org.eclipse.jgit.transport.ReceivePack}.
+ */
 public abstract class RefAdvertiser {
 	/** Advertiser which frames lines in a {@link PacketLineOut} format. */
 	public static class PacketLineOutRefAdvertiser extends RefAdvertiser {
@@ -247,7 +250,6 @@ public abstract class RefAdvertiser {
 	 *            The symbolic ref, e.g. "HEAD"
 	 * @param to
 	 *            The real ref it points to, e.g. "refs/heads/master"
-	 *
 	 * @since 3.6
 	 */
 	public void addSymref(String from, String to) {
@@ -262,7 +264,7 @@ public abstract class RefAdvertiser {
 	 *            sorted before display if necessary, and therefore may appear
 	 *            in any order.
 	 * @return set of ObjectIds that were advertised to the client.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the underlying output stream failed to write out an
 	 *             advertisement record.
 	 */
@@ -305,7 +307,7 @@ public abstract class RefAdvertiser {
 	 *
 	 * @param id
 	 *            identity of the object that is assumed to exist.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the underlying output stream failed to write out an
 	 *             advertisement record.
 	 */
@@ -313,7 +315,11 @@ public abstract class RefAdvertiser {
 		advertiseAnyOnce(id, ".have"); //$NON-NLS-1$
 	}
 
-	/** @return true if no advertisements have been sent yet. */
+	/**
+	 * Whether no advertisements have been sent yet.
+	 *
+	 * @return true if no advertisements have been sent yet.
+	 */
 	public boolean isEmpty() {
 		return first;
 	}
@@ -341,7 +347,7 @@ public abstract class RefAdvertiser {
 	 * @param refName
 	 *            name of the reference to advertise the object as, can be any
 	 *            string not including the NUL byte.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the underlying output stream failed to write out an
 	 *             advertisement record.
 	 */
@@ -372,7 +378,7 @@ public abstract class RefAdvertiser {
 	 * @param line
 	 *            the advertisement line to be written. The line always ends
 	 *            with LF. Never null or the empty string.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the underlying output stream failed to write out an
 	 *             advertisement record.
 	 */
@@ -381,7 +387,7 @@ public abstract class RefAdvertiser {
 	/**
 	 * Mark the end of the advertisements.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the underlying output stream failed to write out an
 	 *             advertisement record.
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefFilter.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefFilter.java
index d4f85f2af5..bbe4f84bc8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefFilter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefFilter.java
@@ -50,14 +50,17 @@ import org.eclipse.jgit.lib.Ref;
 /**
  * Filters the list of refs that are advertised to the client.
  * <p>
- * The filter is called by {@link ReceivePack} and {@link UploadPack} to ensure
- * that the refs are filtered before they are advertised to the client.
+ * The filter is called by {@link org.eclipse.jgit.transport.ReceivePack} and
+ * {@link org.eclipse.jgit.transport.UploadPack} to ensure that the refs are
+ * filtered before they are advertised to the client.
  * <p>
  * This can be used by applications to control visibility of certain refs based
  * on a custom set of rules.
  */
 public interface RefFilter {
-	/** The default filter, allows all refs to be shown. */
+	/**
+	 * The default filter, allows all refs to be shown.
+	 */
 	public static final RefFilter DEFAULT = new RefFilter() {
 		@Override
 		public Map<String, Ref> filter (final Map<String, Ref> refs) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefLeaseSpec.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefLeaseSpec.java
index 734f523c4c..ea0f84a97f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefLeaseSpec.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefLeaseSpec.java
@@ -47,6 +47,7 @@ import java.io.Serializable;
 
 /**
  * Describes the expected value for a ref being pushed.
+ *
  * @since 4.7
  */
 public class RefLeaseSpec implements Serializable {
@@ -59,6 +60,7 @@ public class RefLeaseSpec implements Serializable {
 	private final String expected;
 
 	/**
+	 * <p>Constructor for RefLeaseSpec.</p>
 	 *
 	 * @param ref
 	 *            ref being pushed
@@ -89,6 +91,7 @@ public class RefLeaseSpec implements Serializable {
 		return expected;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		final StringBuilder r = new StringBuilder();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefSpec.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefSpec.java
index 64f6c3fb97..e1b306ea90 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefSpec.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefSpec.java
@@ -153,7 +153,7 @@ public class RefSpec implements Serializable {
 	 * @param mode
 	 *            whether to allow a wildcard on one side without a wildcard on
 	 *            the other.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             the specification is invalid.
 	 * @since 4.5
 	 */
@@ -219,7 +219,7 @@ public class RefSpec implements Serializable {
 	 *
 	 * @param spec
 	 *            string describing the specification.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             the specification is invalid.
 	 */
 	public RefSpec(final String spec) {
@@ -288,7 +288,7 @@ public class RefSpec implements Serializable {
 	 * @param source
 	 *            new value for source in the returned instance.
 	 * @return a new RefSpec with source as specified.
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             There is already a destination configured, and the wildcard
 	 *             status of the existing destination disagrees with the
 	 *             wildcard status of the new source.
@@ -327,7 +327,7 @@ public class RefSpec implements Serializable {
 	 * @param destination
 	 *            new value for destination in the returned instance.
 	 * @return a new RefSpec with destination as specified.
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             There is already a source configured, and the wildcard status
 	 *             of the existing source disagrees with the wildcard status of
 	 *             the new destination.
@@ -350,7 +350,7 @@ public class RefSpec implements Serializable {
 	 * @param destination
 	 *            new value for destination in the returned instance.
 	 * @return a new RefSpec with destination as specified.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             The wildcard status of the new source disagrees with the
 	 *             wildcard status of the new destination.
 	 */
@@ -421,7 +421,7 @@ public class RefSpec implements Serializable {
 	 * @return a new specification expanded from provided ref name. Result
 	 *         specification is wildcard if and only if provided ref name is
 	 *         wildcard.
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             when the RefSpec was constructed with wildcard mode that
 	 *             doesn't require matching wildcards.
 	 */
@@ -453,7 +453,7 @@ public class RefSpec implements Serializable {
 	 * @return a new specification expanded from provided ref name. Result
 	 *         specification is wildcard if and only if provided ref name is
 	 *         wildcard.
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             when the RefSpec was constructed with wildcard mode that
 	 *             doesn't require matching wildcards.
 	 */
@@ -473,7 +473,7 @@ public class RefSpec implements Serializable {
 	 * @return a new specification expanded from provided ref name. Result
 	 *         specification is wildcard if and only if provided ref name is
 	 *         wildcard.
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             when the RefSpec was constructed with wildcard mode that
 	 *             doesn't require matching wildcards.
 	 */
@@ -504,7 +504,7 @@ public class RefSpec implements Serializable {
 	 * @return a new specification expanded from provided ref name. Result
 	 *         specification is wildcard if and only if provided ref name is
 	 *         wildcard.
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             when the RefSpec was constructed with wildcard mode that
 	 *             doesn't require matching wildcards.
 	 */
@@ -556,6 +556,7 @@ public class RefSpec implements Serializable {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int hashCode() {
 		int hc = 0;
@@ -566,6 +567,7 @@ public class RefSpec implements Serializable {
 		return hc;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean equals(final Object obj) {
 		if (!(obj instanceof RefSpec))
@@ -590,6 +592,7 @@ public class RefSpec implements Serializable {
 		return a.equals(b);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		final StringBuilder r = new StringBuilder();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteConfig.java
index c968ba37cf..7b882ec8d5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteConfig.java
@@ -109,7 +109,7 @@ public class RemoteConfig implements Serializable {
 	 * @return all remotes configurations existing in provided repository
 	 *         configuration. Returned configurations are ordered
 	 *         lexicographically by names.
-	 * @throws URISyntaxException
+	 * @throws java.net.URISyntaxException
 	 *             one of the URIs within the remote's configuration is invalid.
 	 */
 	public static List<RemoteConfig> getAllRemoteConfigs(final Config rc)
@@ -157,7 +157,7 @@ public class RemoteConfig implements Serializable {
 	 *            The configuration must already be loaded into memory.
 	 * @param remoteName
 	 *            subsection key indicating the name of this remote.
-	 * @throws URISyntaxException
+	 * @throws java.net.URISyntaxException
 	 *             one of the URIs within the remote's configuration is invalid.
 	 */
 	public RemoteConfig(final Config rc, final String remoteName)
@@ -525,6 +525,9 @@ public class RemoteConfig implements Serializable {
 	}
 
 	/**
+	 * Whether pushing to the remote automatically deletes remote refs which
+	 * don't exist on the source side.
+	 *
 	 * @return true if pushing to the remote automatically deletes remote refs
 	 *         which don't exist on the source side.
 	 */
@@ -542,7 +545,11 @@ public class RemoteConfig implements Serializable {
 		mirror = m;
 	}
 
-	/** @return timeout (in seconds) before aborting an IO operation. */
+	/**
+	 * Get timeout (in seconds) before aborting an IO operation.
+	 *
+	 * @return timeout (in seconds) before aborting an IO operation.
+	 */
 	public int getTimeout() {
 		return timeout;
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteRefUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteRefUpdate.java
index 5c58346189..3e9b16ee49 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteRefUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteRefUpdate.java
@@ -55,17 +55,18 @@ import org.eclipse.jgit.revwalk.RevWalk;
 
 /**
  * Represent request and status of a remote ref update. Specification is
- * provided by client, while status is handled by {@link PushProcess} class,
- * being read-only for client.
+ * provided by client, while status is handled by
+ * {@link org.eclipse.jgit.transport.PushProcess} class, being read-only for
+ * client.
  * <p>
  * Client can create instances of this class directly, basing on user
- * specification and advertised refs ({@link Connection} or through
- * {@link Transport} helper methods. Apply this specification on remote
- * repository using
- * {@link Transport#push(org.eclipse.jgit.lib.ProgressMonitor, java.util.Collection)}
+ * specification and advertised refs
+ * ({@link org.eclipse.jgit.transport.Connection} or through
+ * {@link org.eclipse.jgit.transport.Transport} helper methods. Apply this
+ * specification on remote repository using
+ * {@link org.eclipse.jgit.transport.Transport#push(org.eclipse.jgit.lib.ProgressMonitor, java.util.Collection)}
  * method.
  * </p>
- *
  */
 public class RemoteRefUpdate {
 	/**
@@ -149,16 +150,19 @@ public class RemoteRefUpdate {
 
 	/**
 	 * Construct remote ref update request by providing an update specification.
-	 * Object is created with default {@link Status#NOT_ATTEMPTED} status and no
-	 * message.
+	 * Object is created with default
+	 * {@link org.eclipse.jgit.transport.RemoteRefUpdate.Status#NOT_ATTEMPTED}
+	 * status and no message.
 	 *
 	 * @param localDb
 	 *            local repository to push from.
 	 * @param srcRef
 	 *            source revision - any string resolvable by
-	 *            {@link Repository#resolve(String)}. This resolves to the new
-	 *            object that the caller want remote ref to be after update. Use
-	 *            null or {@link ObjectId#zeroId()} string for delete request.
+	 *            {@link org.eclipse.jgit.lib.Repository#resolve(String)}. This
+	 *            resolves to the new object that the caller want remote ref to
+	 *            be after update. Use null or
+	 *            {@link org.eclipse.jgit.lib.ObjectId#zeroId()} string for
+	 *            delete request.
 	 * @param remoteName
 	 *            full name of a remote ref to update, e.g. "refs/heads/master"
 	 *            (no wildcard, no short name).
@@ -176,13 +180,14 @@ public class RemoteRefUpdate {
 	 *            advertised by remote side before update; update will take
 	 *            place ONLY if remote side advertise exactly this expected id;
 	 *            null if caller doesn't care what object id remote side
-	 *            advertise. Use {@link ObjectId#zeroId()} when expecting no
-	 *            remote ref with this name.
-	 * @throws IOException
+	 *            advertise. Use {@link org.eclipse.jgit.lib.ObjectId#zeroId()}
+	 *            when expecting no remote ref with this name.
+	 * @throws java.io.IOException
 	 *             when I/O error occurred during creating
-	 *             {@link TrackingRefUpdate} for local tracking branch or srcRef
-	 *             can't be resolved to any object.
-	 * @throws IllegalArgumentException
+	 *             {@link org.eclipse.jgit.transport.TrackingRefUpdate} for
+	 *             local tracking branch or srcRef can't be resolved to any
+	 *             object.
+	 * @throws java.lang.IllegalArgumentException
 	 *             if some required parameter was null
 	 */
 	public RemoteRefUpdate(final Repository localDb, final String srcRef,
@@ -196,8 +201,9 @@ public class RemoteRefUpdate {
 
 	/**
 	 * Construct remote ref update request by providing an update specification.
-	 * Object is created with default {@link Status#NOT_ATTEMPTED} status and no
-	 * message.
+	 * Object is created with default
+	 * {@link org.eclipse.jgit.transport.RemoteRefUpdate.Status#NOT_ATTEMPTED}
+	 * status and no message.
 	 *
 	 * @param localDb
 	 *            local repository to push from.
@@ -220,13 +226,14 @@ public class RemoteRefUpdate {
 	 *            advertised by remote side before update; update will take
 	 *            place ONLY if remote side advertise exactly this expected id;
 	 *            null if caller doesn't care what object id remote side
-	 *            advertise. Use {@link ObjectId#zeroId()} when expecting no
-	 *            remote ref with this name.
-	 * @throws IOException
+	 *            advertise. Use {@link org.eclipse.jgit.lib.ObjectId#zeroId()}
+	 *            when expecting no remote ref with this name.
+	 * @throws java.io.IOException
 	 *             when I/O error occurred during creating
-	 *             {@link TrackingRefUpdate} for local tracking branch or srcRef
-	 *             can't be resolved to any object.
-	 * @throws IllegalArgumentException
+	 *             {@link org.eclipse.jgit.transport.TrackingRefUpdate} for
+	 *             local tracking branch or srcRef can't be resolved to any
+	 *             object.
+	 * @throws java.lang.IllegalArgumentException
 	 *             if some required parameter was null
 	 */
 	public RemoteRefUpdate(final Repository localDb, final Ref srcRef,
@@ -240,8 +247,9 @@ public class RemoteRefUpdate {
 
 	/**
 	 * Construct remote ref update request by providing an update specification.
-	 * Object is created with default {@link Status#NOT_ATTEMPTED} status and no
-	 * message.
+	 * Object is created with default
+	 * {@link org.eclipse.jgit.transport.RemoteRefUpdate.Status#NOT_ATTEMPTED}
+	 * status and no message.
 	 *
 	 * @param localDb
 	 *            local repository to push from.
@@ -250,7 +258,8 @@ public class RemoteRefUpdate {
 	 *            be used instead.
 	 * @param srcId
 	 *            The new object that the caller wants remote ref to be after
-	 *            update. Use null or {@link ObjectId#zeroId()} for delete
+	 *            update. Use null or
+	 *            {@link org.eclipse.jgit.lib.ObjectId#zeroId()} for delete
 	 *            request.
 	 * @param remoteName
 	 *            full name of a remote ref to update, e.g. "refs/heads/master"
@@ -269,13 +278,14 @@ public class RemoteRefUpdate {
 	 *            advertised by remote side before update; update will take
 	 *            place ONLY if remote side advertise exactly this expected id;
 	 *            null if caller doesn't care what object id remote side
-	 *            advertise. Use {@link ObjectId#zeroId()} when expecting no
-	 *            remote ref with this name.
-	 * @throws IOException
+	 *            advertise. Use {@link org.eclipse.jgit.lib.ObjectId#zeroId()}
+	 *            when expecting no remote ref with this name.
+	 * @throws java.io.IOException
 	 *             when I/O error occurred during creating
-	 *             {@link TrackingRefUpdate} for local tracking branch or srcRef
-	 *             can't be resolved to any object.
-	 * @throws IllegalArgumentException
+	 *             {@link org.eclipse.jgit.transport.TrackingRefUpdate} for
+	 *             local tracking branch or srcRef can't be resolved to any
+	 *             object.
+	 * @throws java.lang.IllegalArgumentException
 	 *             if some required parameter was null
 	 */
 	public RemoteRefUpdate(final Repository localDb, final String srcRef,
@@ -333,10 +343,11 @@ public class RemoteRefUpdate {
 	 *            configuration base.
 	 * @param newExpectedOldObjectId
 	 *            new expected object id value.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             when I/O error occurred during creating
-	 *             {@link TrackingRefUpdate} for local tracking branch or srcRef
-	 *             of base object no longer can be resolved to any object.
+	 *             {@link org.eclipse.jgit.transport.TrackingRefUpdate} for
+	 *             local tracking branch or srcRef of base object no longer can
+	 *             be resolved to any object.
 	 */
 	public RemoteRefUpdate(final RemoteRefUpdate base,
 			final ObjectId newExpectedOldObjectId) throws IOException {
@@ -346,6 +357,8 @@ public class RemoteRefUpdate {
 	}
 
 	/**
+	 * Get expected old object id
+	 *
 	 * @return expectedOldObjectId required to be advertised by remote side, as
 	 *         set in constructor; may be null.
 	 */
@@ -354,6 +367,9 @@ public class RemoteRefUpdate {
 	}
 
 	/**
+	 * Whether some object is required to be advertised by remote side, as set
+	 * in constructor
+	 *
 	 * @return true if some object is required to be advertised by remote side,
 	 *         as set in constructor; false otherwise.
 	 */
@@ -362,6 +378,8 @@ public class RemoteRefUpdate {
 	}
 
 	/**
+	 * Get new object id
+	 *
 	 * @return newObjectId for remote ref, as set in constructor.
 	 */
 	public ObjectId getNewObjectId() {
@@ -369,6 +387,8 @@ public class RemoteRefUpdate {
 	}
 
 	/**
+	 * Whether this update is a deleting update
+	 *
 	 * @return true if this update is deleting update; false otherwise.
 	 */
 	public boolean isDelete() {
@@ -376,6 +396,8 @@ public class RemoteRefUpdate {
 	}
 
 	/**
+	 * Get name of remote ref to update
+	 *
 	 * @return name of remote ref to update, as set in constructor.
 	 */
 	public String getRemoteName() {
@@ -383,6 +405,8 @@ public class RemoteRefUpdate {
 	}
 
 	/**
+	 * Get tracking branch update if localName was set in constructor.
+	 *
 	 * @return local tracking branch update if localName was set in constructor.
 	 */
 	public TrackingRefUpdate getTrackingRefUpdate() {
@@ -390,9 +414,12 @@ public class RemoteRefUpdate {
 	}
 
 	/**
+	 * Get source revision as specified by user (in constructor)
+	 *
 	 * @return source revision as specified by user (in constructor), could be
-	 *         any string parseable by {@link Repository#resolve(String)}; can
-	 *         be null if specified that way in constructor - this stands for
+	 *         any string parseable by
+	 *         {@link org.eclipse.jgit.lib.Repository#resolve(String)}; can be
+	 *         null if specified that way in constructor - this stands for
 	 *         delete request.
 	 */
 	public String getSrcRef() {
@@ -400,6 +427,8 @@ public class RemoteRefUpdate {
 	}
 
 	/**
+	 * Whether user specified a local tracking branch for remote update
+	 *
 	 * @return true if user specified a local tracking branch for remote update;
 	 *         false otherwise.
 	 */
@@ -408,6 +437,8 @@ public class RemoteRefUpdate {
 	}
 
 	/**
+	 * Whether this update is forced regardless of old remote ref object
+	 *
 	 * @return true if this update is forced regardless of old remote ref
 	 *         object; false otherwise.
 	 */
@@ -416,6 +447,8 @@ public class RemoteRefUpdate {
 	}
 
 	/**
+	 * Get status of remote ref update operation.
+	 *
 	 * @return status of remote ref update operation.
 	 */
 	public Status getStatus() {
@@ -424,7 +457,8 @@ public class RemoteRefUpdate {
 
 	/**
 	 * Check whether update was fast-forward. Note that this result is
-	 * meaningful only after successful update (when status is {@link Status#OK}).
+	 * meaningful only after successful update (when status is
+	 * {@link org.eclipse.jgit.transport.RemoteRefUpdate.Status#OK}).
 	 *
 	 * @return true if update was fast-forward; false otherwise.
 	 */
@@ -433,6 +467,9 @@ public class RemoteRefUpdate {
 	}
 
 	/**
+	 * Get message describing reasons of status when needed/possible; may be
+	 * null.
+	 *
 	 * @return message describing reasons of status when needed/possible; may be
 	 *         null.
 	 */
@@ -461,7 +498,7 @@ public class RemoteRefUpdate {
 	 *
 	 * @param walk
 	 *            walker used for checking update properties.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             when I/O error occurred during update
 	 */
 	protected void updateTrackingRef(final RevWalk walk) throws IOException {
@@ -471,6 +508,7 @@ public class RemoteRefUpdate {
 			trackingRefUpdate.setResult(localUpdate.update(walk));
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteSession.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteSession.java
index d6a2fe6a80..525c895f45 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteSession.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RemoteSession.java
@@ -65,17 +65,18 @@ public interface RemoteSession {
 	 * Generate a new remote process to execute the given command. This function
 	 * should also start execution and may need to create the streams prior to
 	 * execution.
+	 *
 	 * @param commandName
 	 *            command to execute
 	 * @param timeout
 	 *            timeout value, in seconds, for command execution
 	 * @return a new remote process
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             may be thrown in several cases. For example, on problems
 	 *             opening input or output streams or on problems connecting or
 	 *             communicating with the remote host. For the latter two cases,
 	 *             a TransportException may be thrown (a subclass of
-	 *             IOException).
+	 *             java.io.IOException).
 	 */
 	public Process exec(String commandName, int timeout) throws IOException;
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RequestNotYetReadException.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RequestNotYetReadException.java
index 8b45174c01..428af960b9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RequestNotYetReadException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RequestNotYetReadException.java
@@ -51,12 +51,16 @@ package org.eclipse.jgit.transport;
 public class RequestNotYetReadException extends IllegalStateException {
 	private static final long serialVersionUID = 1L;
 
-	/** Initialize with no message. */
+	/**
+	 * Initialize with no message.
+	 */
 	public RequestNotYetReadException() {
 		// Do not set a message.
 	}
 
 	/**
+	 * <p>Constructor for RequestNotYetReadException.</p>
+	 *
 	 * @param msg
 	 *            a message explaining the state. This message should not
 	 *            be shown to an end-user.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ServiceMayNotContinueException.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ServiceMayNotContinueException.java
index 87c9a50038..940d2e2648 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ServiceMayNotContinueException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ServiceMayNotContinueException.java
@@ -59,13 +59,17 @@ public class ServiceMayNotContinueException extends IOException {
 	private final int statusCode;
 	private boolean output;
 
-	/** Initialize with no message. */
+	/**
+	 * Initialize with no message.
+	 */
 	public ServiceMayNotContinueException() {
 		// Do not set a message.
 		statusCode = FORBIDDEN;
 	}
 
 	/**
+	 * <p>Constructor for ServiceMayNotContinueException.</p>
+	 *
 	 * @param msg
 	 *            a message explaining why it cannot continue. This message may
 	 *            be shown to an end-user.
@@ -76,6 +80,8 @@ public class ServiceMayNotContinueException extends IOException {
 	}
 
 	/**
+	 * <p>Constructor for ServiceMayNotContinueException.</p>
+	 *
 	 * @param msg
 	 *            a message explaining why it cannot continue. This message may
 	 *            be shown to an end-user.
@@ -89,6 +95,8 @@ public class ServiceMayNotContinueException extends IOException {
 	}
 
 	/**
+	 * <p>Constructor for ServiceMayNotContinueException.</p>
+	 *
 	 * @param msg
 	 *            a message explaining why it cannot continue. This message may
 	 *            be shown to an end-user.
@@ -102,6 +110,8 @@ public class ServiceMayNotContinueException extends IOException {
 	}
 
 	/**
+	 * <p>Constructor for ServiceMayNotContinueException.</p>
+	 *
 	 * @param msg
 	 *            a message explaining why it cannot continue. This message may
 	 *            be shown to an end-user.
@@ -128,17 +138,25 @@ public class ServiceMayNotContinueException extends IOException {
 		this(JGitText.get().internalServerError, cause);
 	}
 
-	/** @return true if the message was already output to the client. */
+	/**
+	 * Whether the message was already output to the client.
+	 *
+	 * @return {@code true} if the message was already output to the client.
+	 */
 	public boolean isOutput() {
 		return output;
 	}
 
-	/** Mark this message has being sent to the client. */
+	/**
+	 * Mark this message has being sent to the client.
+	 */
 	public void setOutput() {
 		output = true;
 	}
 
 	/**
+	 * Get status code
+	 *
 	 * @return true if the message was already output to the client.
 	 * @since 4.5
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandInputStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandInputStream.java
index fe9f2a3155..25486cb64f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandInputStream.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandInputStream.java
@@ -120,6 +120,7 @@ class SideBandInputStream extends InputStream {
 		out = outputStream;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read() throws IOException {
 		needDataPacket();
@@ -129,6 +130,7 @@ class SideBandInputStream extends InputStream {
 		return rawIn.read();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int read(final byte[] b, int off, int len) throws IOException {
 		int r = 0;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandOutputStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandOutputStream.java
index 0303eed9a7..af65827ca6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandOutputStream.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandOutputStream.java
@@ -127,12 +127,14 @@ public class SideBandOutputStream extends OutputStream {
 			writeBuffer();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void flush() throws IOException {
 		flushBuffer();
 		out.flush();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(final byte[] b, int off, int len) throws IOException {
 		while (0 < len) {
@@ -159,6 +161,7 @@ public class SideBandOutputStream extends OutputStream {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void write(final int b) throws IOException {
 		if (cnt == buffer.length)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandProgressMonitor.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandProgressMonitor.java
index aa800657e1..365545a092 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandProgressMonitor.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SideBandProgressMonitor.java
@@ -60,6 +60,7 @@ class SideBandProgressMonitor extends BatchingProgressMonitor {
 		write = true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onUpdate(String taskName, int workCurr) {
 		StringBuilder s = new StringBuilder();
@@ -68,6 +69,7 @@ class SideBandProgressMonitor extends BatchingProgressMonitor {
 		send(s);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onEndTask(String taskName, int workCurr) {
 		StringBuilder s = new StringBuilder();
@@ -82,6 +84,7 @@ class SideBandProgressMonitor extends BatchingProgressMonitor {
 		s.append(workCurr);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onUpdate(String taskName, int cmp, int totalWork, int pcnt) {
 		StringBuilder s = new StringBuilder();
@@ -90,6 +93,7 @@ class SideBandProgressMonitor extends BatchingProgressMonitor {
 		send(s);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void onEndTask(String taskName, int cmp, int totalWork, int pcnt) {
 		StringBuilder s = new StringBuilder();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SignedPushConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SignedPushConfig.java
index 1ecbed95c7..f404737d14 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SignedPushConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SignedPushConfig.java
@@ -60,7 +60,9 @@ public class SignedPushConfig {
 	private int certNonceSlopLimit;
 	private NonceGenerator nonceGenerator;
 
-	/** Create a new config with default values disabling push verification. */
+	/**
+	 * Create a new config with default values disabling push verification.
+	 */
 	public SignedPushConfig() {
 	}
 
@@ -73,9 +75,10 @@ public class SignedPushConfig {
 	 * Set the seed used by the nonce verifier.
 	 * <p>
 	 * Setting this to a non-null value enables push certificate verification
-	 * using the default {@link HMACSHA1NonceGenerator} implementation, if a
-	 * different implementation was not set using {@link
-	 * #setNonceGenerator(NonceGenerator)}.
+	 * using the default
+	 * {@link org.eclipse.jgit.transport.HMACSHA1NonceGenerator} implementation,
+	 * if a different implementation was not set using
+	 * {@link #setNonceGenerator(NonceGenerator)}.
 	 *
 	 * @param seed
 	 *            new seed value.
@@ -84,7 +87,11 @@ public class SignedPushConfig {
 		certNonceSeed = seed;
 	}
 
-	/** @return the configured seed. */
+	/**
+	 * Get the configured seed.
+	 *
+	 * @return the configured seed.
+	 */
 	public String getCertNonceSeed() {
 		return certNonceSeed;
 	}
@@ -101,18 +108,23 @@ public class SignedPushConfig {
 		certNonceSlopLimit = limit;
 	}
 
-	/** @return the configured nonce slop limit. */
+	/**
+	 * Get the configured nonce slop limit.
+	 *
+	 * @return the configured nonce slop limit.
+	 */
 	public int getCertNonceSlopLimit() {
 		return certNonceSlopLimit;
 	}
 
 	/**
-	 * Set the {@link NonceGenerator} used for signed pushes.
+	 * Set the {@link org.eclipse.jgit.transport.NonceGenerator} used for signed
+	 * pushes.
 	 * <p>
-	 * Setting this to a non-null value enables push certificate verification. If
-	 * this method is called, this implementation will be used instead of the
-	 * default {@link HMACSHA1NonceGenerator} even if {@link
-	 * #setCertNonceSeed(String)} was called.
+	 * Setting this to a non-null value enables push certificate verification.
+	 * If this method is called, this implementation will be used instead of the
+	 * default {@link org.eclipse.jgit.transport.HMACSHA1NonceGenerator} even if
+	 * {@link #setCertNonceSeed(String)} was called.
 	 *
 	 * @param generator
 	 *            new nonce generator.
@@ -122,12 +134,13 @@ public class SignedPushConfig {
 	}
 
 	/**
-	 * Get the {@link NonceGenerator} used for signed pushes.
+	 * Get the {@link org.eclipse.jgit.transport.NonceGenerator} used for signed
+	 * pushes.
 	 * <p>
 	 * If {@link #setNonceGenerator(NonceGenerator)} was used to set a non-null
-	 * implementation, that will be returned. If no custom implementation was set
-	 * but {@link #setCertNonceSeed(String)} was called, returns a newly-created
-	 * {@link HMACSHA1NonceGenerator}.
+	 * implementation, that will be returned. If no custom implementation was
+	 * set but {@link #setCertNonceSeed(String)} was called, returns a
+	 * newly-created {@link org.eclipse.jgit.transport.HMACSHA1NonceGenerator}.
 	 *
 	 * @return the configured nonce generator.
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshSessionFactory.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshSessionFactory.java
index 2d5029a010..e0022333ef 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshSessionFactory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshSessionFactory.java
@@ -54,9 +54,9 @@ import org.eclipse.jgit.util.FS;
  * communicating with the end-user as well as reading their personal SSH
  * configuration settings, such as known hosts and private keys.
  * <p>
- * A {@link RemoteSession} must be returned to the factory that created it.
- * Callers are encouraged to retain the SshSessionFactory for the duration of
- * the period they are using the Session.
+ * A {@link org.eclipse.jgit.transport.RemoteSession} must be returned to the
+ * factory that created it. Callers are encouraged to retain the
+ * SshSessionFactory for the duration of the period they are using the Session.
  */
 public abstract class SshSessionFactory {
 	private static SshSessionFactory INSTANCE = new DefaultSshSessionFactory();
@@ -106,7 +106,7 @@ public abstract class SshSessionFactory {
 	 * @param tms
 	 *            Timeout value, in milliseconds.
 	 * @return a session that can contact the remote host.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the session could not be created.
 	 */
 	public abstract RemoteSession getSession(URIish uri,
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshTransport.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshTransport.java
index 74865dc6dc..62a6f0e175 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshTransport.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/SshTransport.java
@@ -99,7 +99,7 @@ public abstract class SshTransport extends TcpTransport {
 	 *
 	 * @param factory
 	 *            a factory to set, must not be null
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             if session has been already created.
 	 */
 	public void setSshSessionFactory(SshSessionFactory factory) {
@@ -112,7 +112,10 @@ public abstract class SshTransport extends TcpTransport {
 	}
 
 	/**
-	 * @return the SSH session factory that will be used for creating SSH sessions
+	 * Get the SSH session factory
+	 *
+	 * @return the SSH session factory that will be used for creating SSH
+	 *         sessions
 	 */
 	public SshSessionFactory getSshSessionFactory() {
 		return sch;
@@ -122,7 +125,7 @@ public abstract class SshTransport extends TcpTransport {
 	 * Get the default SSH session
 	 *
 	 * @return a remote session
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             in case of error with opening SSH session
 	 */
 	protected RemoteSession getSession() throws TransportException {
@@ -138,6 +141,7 @@ public abstract class SshTransport extends TcpTransport {
 		return sock;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		if (sock != null) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TagOpt.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TagOpt.java
index 384e9fc4b2..e1134e8fa8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TagOpt.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TagOpt.java
@@ -48,7 +48,9 @@ import java.text.MessageFormat;
 
 import org.eclipse.jgit.internal.JGitText;
 
-/** Specification of annotated tag behavior during fetch. */
+/**
+ * Specification of annotated tag behavior during fetch.
+ */
 public enum TagOpt {
 	/**
 	 * Automatically follow tags if we fetch the thing they point at.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TestProtocol.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TestProtocol.java
index 8a28e3a7d7..b186f9ecd3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TestProtocol.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TestProtocol.java
@@ -60,15 +60,16 @@ import org.eclipse.jgit.transport.resolver.UploadPackFactory;
 /**
  * Protocol for transport between manually-specified repositories in tests.
  * <p>
- * Remote repositories are registered using {@link #register(Object,
- * Repository)}, after which they can be accessed using the returned URI. As
- * this class provides both the client side (the protocol) and the server side,
- * the caller is responsible for setting up and passing the connection context,
- * whatever form that may take.
+ * Remote repositories are registered using
+ * {@link #register(Object, Repository)}, after which they can be accessed using
+ * the returned URI. As this class provides both the client side (the protocol)
+ * and the server side, the caller is responsible for setting up and passing the
+ * connection context, whatever form that may take.
  * <p>
  * Unlike the other built-in protocols, which are automatically-registered
  * singletons, callers are expected to register/unregister specific protocol
- * instances on demand with {@link Transport#register(TransportProtocol)}.
+ * instances on demand with
+ * {@link org.eclipse.jgit.transport.Transport#register(TransportProtocol)}.
  *
  * @param <C>
  *            the connection type
@@ -92,12 +93,16 @@ public class TestProtocol<C> extends TransportProtocol {
 	private final HashMap<URIish, Handle> handles;
 
 	/**
+	 * Constructor for TestProtocol.
+	 *
 	 * @param uploadPackFactory
-	 *            factory for creating {@link UploadPack} used by all connections
-	 *            from this protocol instance.
+	 *            factory for creating
+	 *            {@link org.eclipse.jgit.transport.UploadPack} used by all
+	 *            connections from this protocol instance.
 	 * @param receivePackFactory
-	 *            factory for creating {@link ReceivePack} used by all connections
-	 *            from this protocol instance.
+	 *            factory for creating
+	 *            {@link org.eclipse.jgit.transport.ReceivePack} used by all
+	 *            connections from this protocol instance.
 	 */
 	public TestProtocol(UploadPackFactory<C> uploadPackFactory,
 			ReceivePackFactory<C> receivePackFactory) {
@@ -106,16 +111,19 @@ public class TestProtocol<C> extends TransportProtocol {
 		this.handles = new HashMap<>();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getName() {
 		return JGitText.get().transportProtoTest;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Set<String> getSchemes() {
 		return Collections.singleton(SCHEME);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Transport open(URIish uri, Repository local, String remoteName)
 			throws NotSupportedException, TransportException {
@@ -127,11 +135,13 @@ public class TestProtocol<C> extends TransportProtocol {
 		return new TransportInternal(local, uri, h);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Set<URIishField> getRequiredFields() {
 		return EnumSet.of(URIishField.HOST, URIishField.PATH);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Set<URIishField> getOptionalFields() {
 		return Collections.emptySet();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TrackingRefUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TrackingRefUpdate.java
index 5aae5ea21a..ba2a673a18 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TrackingRefUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TrackingRefUpdate.java
@@ -49,7 +49,9 @@ import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.RefUpdate;
 
-/** Update of a locally stored tracking branch. */
+/**
+ * Update of a locally stored tracking branch.
+ */
 public class TrackingRefUpdate {
 	private final String remoteName;
 	final String localName;
@@ -132,6 +134,8 @@ public class TrackingRefUpdate {
 	}
 
 	/**
+	 * Get this update wrapped by a ReceiveCommand.
+	 *
 	 * @return this update wrapped by a ReceiveCommand.
 	 * @since 3.4
 	 */
@@ -201,6 +205,7 @@ public class TrackingRefUpdate {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransferConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransferConfig.java
index 099629c056..4c70725e42 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransferConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransferConfig.java
@@ -157,6 +157,8 @@ public class TransferConfig {
 	}
 
 	/**
+	 * Create checker to verify fetched objects
+	 *
 	 * @return checker to verify fetched objects, or null if checking is not
 	 *         enabled in the repository configuration.
 	 * @since 3.6
@@ -167,6 +169,8 @@ public class TransferConfig {
 	}
 
 	/**
+	 * Create checker to verify objects pushed into this repository
+	 *
 	 * @return checker to verify objects pushed into this repository, or null if
 	 *         checking is not enabled in the repository configuration.
 	 * @since 4.2
@@ -196,6 +200,8 @@ public class TransferConfig {
 	}
 
 	/**
+	 * Whether to allow clients to request non-advertised tip SHA-1s
+	 *
 	 * @return allow clients to request non-advertised tip SHA-1s?
 	 * @since 3.1
 	 */
@@ -204,6 +210,8 @@ public class TransferConfig {
 	}
 
 	/**
+	 * Whether to allow clients to request non-tip SHA-1s
+	 *
 	 * @return allow clients to request non-tip SHA-1s?
 	 * @since 4.1
 	 */
@@ -212,7 +220,11 @@ public class TransferConfig {
 	}
 
 	/**
-	 * @return {@link RefFilter} respecting configured hidden refs.
+	 * Get {@link org.eclipse.jgit.transport.RefFilter} respecting configured
+	 * hidden refs.
+	 *
+	 * @return {@link org.eclipse.jgit.transport.RefFilter} respecting
+	 *         configured hidden refs.
 	 * @since 3.1
 	 */
 	public RefFilter getRefFilter() {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/Transport.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/Transport.java
index 649e840626..8db796a83f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/Transport.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/Transport.java
@@ -78,7 +78,6 @@ import org.eclipse.jgit.hooks.Hooks;
 import org.eclipse.jgit.hooks.PrePushHook;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
-import org.eclipse.jgit.lib.NullProgressMonitor;
 import org.eclipse.jgit.lib.ObjectChecker;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ProgressMonitor;
@@ -215,7 +214,8 @@ public abstract class Transport implements AutoCloseable {
 	 * Protocol definitions are held by WeakReference, allowing them to be
 	 * garbage collected when the calling application drops all strongly held
 	 * references to the TransportProtocol. Therefore applications should use a
-	 * singleton pattern as described in {@link TransportProtocol}'s class
+	 * singleton pattern as described in
+	 * {@link org.eclipse.jgit.transport.TransportProtocol}'s class
 	 * documentation to ensure their protocol does not get disabled by garbage
 	 * collection earlier than expected.
 	 * <p>
@@ -270,7 +270,8 @@ public abstract class Transport implements AutoCloseable {
 	/**
 	 * Open a new transport instance to connect two repositories.
 	 * <p>
-	 * This method assumes {@link Operation#FETCH}.
+	 * This method assumes
+	 * {@link org.eclipse.jgit.transport.Transport.Operation#FETCH}.
 	 *
 	 * @param local
 	 *            existing local repository.
@@ -279,12 +280,12 @@ public abstract class Transport implements AutoCloseable {
 	 *            configuration name.
 	 * @return the new transport instance. Never null. In case of multiple URIs
 	 *         in remote configuration, only the first is chosen.
-	 * @throws URISyntaxException
+	 * @throws java.net.URISyntaxException
 	 *             the location is not a remote defined in the configuration
 	 *             file and is not a well-formed URL.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             the protocol specified is not supported.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the transport cannot open this URI.
 	 */
 	public static Transport open(final Repository local, final String remote)
@@ -306,12 +307,12 @@ public abstract class Transport implements AutoCloseable {
 	 *            based on the type of connection desired.
 	 * @return the new transport instance. Never null. In case of multiple URIs
 	 *         in remote configuration, only the first is chosen.
-	 * @throws URISyntaxException
+	 * @throws java.net.URISyntaxException
 	 *             the location is not a remote defined in the configuration
 	 *             file and is not a well-formed URL.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             the protocol specified is not supported.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the transport cannot open this URI.
 	 */
 	public static Transport open(final Repository local, final String remote,
@@ -330,7 +331,8 @@ public abstract class Transport implements AutoCloseable {
 	/**
 	 * Open new transport instances to connect two repositories.
 	 * <p>
-	 * This method assumes {@link Operation#FETCH}.
+	 * This method assumes
+	 * {@link org.eclipse.jgit.transport.Transport.Operation#FETCH}.
 	 *
 	 * @param local
 	 *            existing local repository.
@@ -339,12 +341,12 @@ public abstract class Transport implements AutoCloseable {
 	 *            configuration name.
 	 * @return the list of new transport instances for every URI in remote
 	 *         configuration.
-	 * @throws URISyntaxException
+	 * @throws java.net.URISyntaxException
 	 *             the location is not a remote defined in the configuration
 	 *             file and is not a well-formed URL.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             the protocol specified is not supported.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the transport cannot open this URI.
 	 */
 	public static List<Transport> openAll(final Repository local,
@@ -366,12 +368,12 @@ public abstract class Transport implements AutoCloseable {
 	 *            based on the type of connection desired.
 	 * @return the list of new transport instances for every URI in remote
 	 *         configuration.
-	 * @throws URISyntaxException
+	 * @throws java.net.URISyntaxException
 	 *             the location is not a remote defined in the configuration
 	 *             file and is not a well-formed URL.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             the protocol specified is not supported.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the transport cannot open this URI.
 	 */
 	public static List<Transport> openAll(final Repository local,
@@ -390,7 +392,8 @@ public abstract class Transport implements AutoCloseable {
 	/**
 	 * Open a new transport instance to connect two repositories.
 	 * <p>
-	 * This method assumes {@link Operation#FETCH}.
+	 * This method assumes
+	 * {@link org.eclipse.jgit.transport.Transport.Operation#FETCH}.
 	 *
 	 * @param local
 	 *            existing local repository.
@@ -399,11 +402,11 @@ public abstract class Transport implements AutoCloseable {
 	 *            repository.
 	 * @return the new transport instance. Never null. In case of multiple URIs
 	 *         in remote configuration, only the first is chosen.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             the protocol specified is not supported.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the transport cannot open this URI.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             if provided remote configuration doesn't have any URI
 	 *             associated.
 	 */
@@ -425,11 +428,11 @@ public abstract class Transport implements AutoCloseable {
 	 *            based on the type of connection desired.
 	 * @return the new transport instance. Never null. In case of multiple URIs
 	 *         in remote configuration, only the first is chosen.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             the protocol specified is not supported.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the transport cannot open this URI.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             if provided remote configuration doesn't have any URI
 	 *             associated.
 	 */
@@ -448,7 +451,8 @@ public abstract class Transport implements AutoCloseable {
 	/**
 	 * Open new transport instances to connect two repositories.
 	 * <p>
-	 * This method assumes {@link Operation#FETCH}.
+	 * This method assumes
+	 * {@link org.eclipse.jgit.transport.Transport.Operation#FETCH}.
 	 *
 	 * @param local
 	 *            existing local repository.
@@ -457,9 +461,9 @@ public abstract class Transport implements AutoCloseable {
 	 *            repository.
 	 * @return the list of new transport instances for every URI in remote
 	 *         configuration.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             the protocol specified is not supported.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the transport cannot open this URI.
 	 */
 	public static List<Transport> openAll(final Repository local,
@@ -481,9 +485,9 @@ public abstract class Transport implements AutoCloseable {
 	 *            based on the type of connection desired.
 	 * @return the list of new transport instances for every URI in remote
 	 *         configuration.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             the protocol specified is not supported.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the transport cannot open this URI.
 	 */
 	public static List<Transport> openAll(final Repository local,
@@ -527,9 +531,9 @@ public abstract class Transport implements AutoCloseable {
 	 * @param uri
 	 *            location of the remote repository.
 	 * @return the new transport instance. Never null.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             the protocol specified is not supported.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the transport cannot open this URI.
 	 */
 	public static Transport open(final Repository local, final URIish uri)
@@ -548,9 +552,9 @@ public abstract class Transport implements AutoCloseable {
 	 *            name of the remote, if the remote as configured in
 	 *            {@code local}; otherwise null.
 	 * @return the new transport instance. Never null.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             the protocol specified is not supported.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the transport cannot open this URI.
 	 */
 	public static Transport open(Repository local, URIish uri, String remoteName)
@@ -580,10 +584,10 @@ public abstract class Transport implements AutoCloseable {
 	 * Note that the resulting transport instance can not be used for fetching
 	 * or pushing, but only for reading remote refs.
 	 *
-	 * @param uri
+	 * @param uri a {@link org.eclipse.jgit.transport.URIish} object.
 	 * @return new Transport instance
-	 * @throws NotSupportedException
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 */
 	public static Transport open(URIish uri) throws NotSupportedException, TransportException {
 		for (WeakReference<TransportProtocol> ref : protocols) {
@@ -601,12 +605,13 @@ public abstract class Transport implements AutoCloseable {
 	}
 
 	/**
-	 * Convert push remote refs update specification from {@link RefSpec} form
-	 * to {@link RemoteRefUpdate}. Conversion expands wildcards by matching
-	 * source part to local refs. expectedOldObjectId in RemoteRefUpdate is
-	 * set when specified in leases. Tracking branch is configured if RefSpec
-	 * destination matches source of any fetch ref spec for this transport
-	 * remote configuration.
+	 * Convert push remote refs update specification from
+	 * {@link org.eclipse.jgit.transport.RefSpec} form to
+	 * {@link org.eclipse.jgit.transport.RemoteRefUpdate}. Conversion expands
+	 * wildcards by matching source part to local refs. expectedOldObjectId in
+	 * RemoteRefUpdate is set when specified in leases. Tracking branch is
+	 * configured if RefSpec destination matches source of any fetch ref spec
+	 * for this transport remote configuration.
 	 *
 	 * @param db
 	 *            local database.
@@ -617,8 +622,9 @@ public abstract class Transport implements AutoCloseable {
 	 * @param fetchSpecs
 	 *            fetch specifications used for finding localtracking refs. May
 	 *            be null or empty collection.
-	 * @return collection of set up {@link RemoteRefUpdate}.
-	 * @throws IOException
+	 * @return collection of set up
+	 *         {@link org.eclipse.jgit.transport.RemoteRefUpdate}.
+	 * @throws java.io.IOException
 	 *             when problem occurred during conversion or specification set
 	 *             up: most probably, missing objects or refs.
 	 * @since 4.7
@@ -668,12 +674,13 @@ public abstract class Transport implements AutoCloseable {
 	}
 
 	/**
-	 * Convert push remote refs update specification from {@link RefSpec} form
-	 * to {@link RemoteRefUpdate}. Conversion expands wildcards by matching
-	 * source part to local refs. expectedOldObjectId in RemoteRefUpdate is
-	 * always set as null. Tracking branch is configured if RefSpec destination
-	 * matches source of any fetch ref spec for this transport remote
-	 * configuration.
+	 * Convert push remote refs update specification from
+	 * {@link org.eclipse.jgit.transport.RefSpec} form to
+	 * {@link org.eclipse.jgit.transport.RemoteRefUpdate}. Conversion expands
+	 * wildcards by matching source part to local refs. expectedOldObjectId in
+	 * RemoteRefUpdate is always set as null. Tracking branch is configured if
+	 * RefSpec destination matches source of any fetch ref spec for this
+	 * transport remote configuration.
 	 *
 	 * @param db
 	 *            local database.
@@ -682,8 +689,9 @@ public abstract class Transport implements AutoCloseable {
 	 * @param fetchSpecs
 	 *            fetch specifications used for finding localtracking refs. May
 	 *            be null or empty collection.
-	 * @return collection of set up {@link RemoteRefUpdate}.
-	 * @throws IOException
+	 * @return collection of set up
+	 *         {@link org.eclipse.jgit.transport.RemoteRefUpdate}.
+	 * @throws java.io.IOException
 	 *             when problem occurred during conversion or specification set
 	 *             up: most probably, missing objects or refs.
 	 */
@@ -838,6 +846,7 @@ public abstract class Transport implements AutoCloseable {
 	 * Create a minimal transport instance not tied to a single repository.
 	 *
 	 * @param uri
+	 *            a {@link org.eclipse.jgit.transport.URIish} object.
 	 */
 	protected Transport(final URIish uri) {
 		this.uri = uri;
@@ -923,6 +932,8 @@ public abstract class Transport implements AutoCloseable {
 	}
 
 	/**
+	 * Whether fetch will verify if received objects are formatted correctly.
+	 *
 	 * @return true if fetch will verify received objects are formatted
 	 *         correctly. Validating objects requires more CPU time on the
 	 *         client side of the connection.
@@ -932,6 +943,8 @@ public abstract class Transport implements AutoCloseable {
 	}
 
 	/**
+	 * Configure if checking received objects is enabled
+	 *
 	 * @param check
 	 *            true to enable checking received objects; false to assume all
 	 *            received objects are valid.
@@ -945,6 +958,8 @@ public abstract class Transport implements AutoCloseable {
 	}
 
 	/**
+	 * Get configured object checker for received objects
+	 *
 	 * @return configured object checker for received objects, or null.
 	 * @since 3.6
 	 */
@@ -953,6 +968,8 @@ public abstract class Transport implements AutoCloseable {
 	}
 
 	/**
+	 * Set the object checker to verify each received object with
+	 *
 	 * @param impl
 	 *            if non-null the object checking instance to verify each
 	 *            received object with; null to disable object checking.
@@ -963,7 +980,8 @@ public abstract class Transport implements AutoCloseable {
 	}
 
 	/**
-	 * Default setting is: {@link RemoteConfig#DEFAULT_RECEIVE_PACK}
+	 * Default setting is:
+	 * {@link org.eclipse.jgit.transport.RemoteConfig#DEFAULT_RECEIVE_PACK}
 	 *
 	 * @return remote executable providing receive-pack service for pack
 	 *         transports.
@@ -975,7 +993,8 @@ public abstract class Transport implements AutoCloseable {
 
 	/**
 	 * Set remote executable providing receive-pack service for pack transports.
-	 * Default setting is: {@link RemoteConfig#DEFAULT_RECEIVE_PACK}
+	 * Default setting is:
+	 * {@link org.eclipse.jgit.transport.RemoteConfig#DEFAULT_RECEIVE_PACK}
 	 *
 	 * @param optionReceivePack
 	 *            remote executable, if null or empty default one is set;
@@ -1036,6 +1055,9 @@ public abstract class Transport implements AutoCloseable {
 	}
 
 	/**
+	 * Whether destination refs should be removed if they no longer exist at the
+	 * source repository.
+	 *
 	 * @return true if destination refs should be removed if they no longer
 	 *         exist at the source repository.
 	 */
@@ -1075,6 +1097,9 @@ public abstract class Transport implements AutoCloseable {
 	}
 
 	/**
+	 * Whether push operation should just check for possible result and not
+	 * really update remote refs
+	 *
 	 * @return true if push operation should just check for possible result and
 	 *         not really update remote refs, false otherwise - when push should
 	 *         act normally.
@@ -1095,7 +1120,11 @@ public abstract class Transport implements AutoCloseable {
 		this.dryRun = dryRun;
 	}
 
-	/** @return timeout (in seconds) before aborting an IO operation. */
+	/**
+	 * Get timeout (in seconds) before aborting an IO operation.
+	 *
+	 * @return timeout (in seconds) before aborting an IO operation.
+	 */
 	public int getTimeout() {
 		return timeout;
 	}
@@ -1159,6 +1188,8 @@ public abstract class Transport implements AutoCloseable {
 	}
 
 	/**
+	 * Get the option strings associated with the push operation
+	 *
 	 * @return the option strings associated with the push operation
 	 * @since 4.5
 	 */
@@ -1182,22 +1213,24 @@ public abstract class Transport implements AutoCloseable {
 	 * <p>
 	 * This is a utility function providing standard fetch behavior. Local
 	 * tracking refs associated with the remote repository are automatically
-	 * updated if this transport was created from a {@link RemoteConfig} with
-	 * fetch RefSpecs defined.
+	 * updated if this transport was created from a
+	 * {@link org.eclipse.jgit.transport.RemoteConfig} with fetch RefSpecs
+	 * defined.
 	 *
 	 * @param monitor
 	 *            progress monitor to inform the user about our processing
-	 *            activity. Must not be null. Use {@link NullProgressMonitor} if
-	 *            progress updates are not interesting or necessary.
+	 *            activity. Must not be null. Use
+	 *            {@link org.eclipse.jgit.lib.NullProgressMonitor} if progress
+	 *            updates are not interesting or necessary.
 	 * @param toFetch
 	 *            specification of refs to fetch locally. May be null or the
 	 *            empty collection to use the specifications from the
 	 *            RemoteConfig. Source for each RefSpec can't be null.
 	 * @return information describing the tracking refs updated.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             this transport implementation does not support fetching
 	 *             objects.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the remote connection could not be established or object
 	 *             copying (if necessary) failed or update specification was
 	 *             incorrect.
@@ -1252,17 +1285,18 @@ public abstract class Transport implements AutoCloseable {
 	 * For setting up remote ref update specification from ref spec, see helper
 	 * method {@link #findRemoteRefUpdatesFor(Collection)}, predefined refspecs
 	 * ({@link #REFSPEC_TAGS}, {@link #REFSPEC_PUSH_ALL}) or consider using
-	 * directly {@link RemoteRefUpdate} for more possibilities.
+	 * directly {@link org.eclipse.jgit.transport.RemoteRefUpdate} for more
+	 * possibilities.
 	 * <p>
 	 * When {@link #isDryRun()} is true, result of this operation is just
 	 * estimation of real operation result, no real action is performed.
 	 *
 	 * @see RemoteRefUpdate
-	 *
 	 * @param monitor
 	 *            progress monitor to inform the user about our processing
-	 *            activity. Must not be null. Use {@link NullProgressMonitor} if
-	 *            progress updates are not interesting or necessary.
+	 *            activity. Must not be null. Use
+	 *            {@link org.eclipse.jgit.lib.NullProgressMonitor} if progress
+	 *            updates are not interesting or necessary.
 	 * @param toPush
 	 *            specification of refs to push. May be null or the empty
 	 *            collection to use the specifications from the RemoteConfig
@@ -1273,10 +1307,10 @@ public abstract class Transport implements AutoCloseable {
 	 *            output stream to write messages to
 	 * @return information about results of remote refs updates, tracking refs
 	 *         updates and refs advertised by remote repository.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             this transport implementation does not support pushing
 	 *             objects.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the remote connection could not be established or object
 	 *             copying (if necessary) failed at I/O or protocol level or
 	 *             update specification was incorrect.
@@ -1322,30 +1356,30 @@ public abstract class Transport implements AutoCloseable {
 	 * For setting up remote ref update specification from ref spec, see helper
 	 * method {@link #findRemoteRefUpdatesFor(Collection)}, predefined refspecs
 	 * ({@link #REFSPEC_TAGS}, {@link #REFSPEC_PUSH_ALL}) or consider using
-	 * directly {@link RemoteRefUpdate} for more possibilities.
+	 * directly {@link org.eclipse.jgit.transport.RemoteRefUpdate} for more
+	 * possibilities.
 	 * <p>
 	 * When {@link #isDryRun()} is true, result of this operation is just
 	 * estimation of real operation result, no real action is performed.
 	 *
 	 * @see RemoteRefUpdate
-	 *
 	 * @param monitor
 	 *            progress monitor to inform the user about our processing
-	 *            activity. Must not be null. Use {@link NullProgressMonitor} if
-	 *            progress updates are not interesting or necessary.
+	 *            activity. Must not be null. Use
+	 *            {@link org.eclipse.jgit.lib.NullProgressMonitor} if progress
+	 *            updates are not interesting or necessary.
 	 * @param toPush
 	 *            specification of refs to push. May be null or the empty
 	 *            collection to use the specifications from the RemoteConfig
 	 *            converted by {@link #findRemoteRefUpdatesFor(Collection)}. No
 	 *            more than 1 RemoteRefUpdate with the same remoteName is
 	 *            allowed. These objects are modified during this call.
-	 *
 	 * @return information about results of remote refs updates, tracking refs
 	 *         updates and refs advertised by remote repository.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             this transport implementation does not support pushing
 	 *             objects.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the remote connection could not be established or object
 	 *             copying (if necessary) failed at I/O or protocol level or
 	 *             update specification was incorrect.
@@ -1357,20 +1391,22 @@ public abstract class Transport implements AutoCloseable {
 	}
 
 	/**
-	 * Convert push remote refs update specification from {@link RefSpec} form
-	 * to {@link RemoteRefUpdate}. Conversion expands wildcards by matching
-	 * source part to local refs. expectedOldObjectId in RemoteRefUpdate is
-	 * always set as null. Tracking branch is configured if RefSpec destination
-	 * matches source of any fetch ref spec for this transport remote
-	 * configuration.
+	 * Convert push remote refs update specification from
+	 * {@link org.eclipse.jgit.transport.RefSpec} form to
+	 * {@link org.eclipse.jgit.transport.RemoteRefUpdate}. Conversion expands
+	 * wildcards by matching source part to local refs. expectedOldObjectId in
+	 * RemoteRefUpdate is always set as null. Tracking branch is configured if
+	 * RefSpec destination matches source of any fetch ref spec for this
+	 * transport remote configuration.
 	 * <p>
 	 * Conversion is performed for context of this transport (database, fetch
 	 * specifications).
 	 *
 	 * @param specs
 	 *            collection of RefSpec to convert.
-	 * @return collection of set up {@link RemoteRefUpdate}.
-	 * @throws IOException
+	 * @return collection of set up
+	 *         {@link org.eclipse.jgit.transport.RemoteRefUpdate}.
+	 * @throws java.io.IOException
 	 *             when problem occurred during conversion or specification set
 	 *             up: most probably, missing objects or refs.
 	 */
@@ -1381,12 +1417,13 @@ public abstract class Transport implements AutoCloseable {
 	}
 
 	/**
-	 * Convert push remote refs update specification from {@link RefSpec} form
-	 * to {@link RemoteRefUpdate}. Conversion expands wildcards by matching
-	 * source part to local refs. expectedOldObjectId in RemoteRefUpdate is
-	 * set according to leases. Tracking branch is configured if RefSpec destination
-	 * matches source of any fetch ref spec for this transport remote
-	 * configuration.
+	 * Convert push remote refs update specification from
+	 * {@link org.eclipse.jgit.transport.RefSpec} form to
+	 * {@link org.eclipse.jgit.transport.RemoteRefUpdate}. Conversion expands
+	 * wildcards by matching source part to local refs. expectedOldObjectId in
+	 * RemoteRefUpdate is set according to leases. Tracking branch is configured
+	 * if RefSpec destination matches source of any fetch ref spec for this
+	 * transport remote configuration.
 	 * <p>
 	 * Conversion is performed for context of this transport (database, fetch
 	 * specifications).
@@ -1395,8 +1432,9 @@ public abstract class Transport implements AutoCloseable {
 	 *            collection of RefSpec to convert.
 	 * @param leases
 	 *            map from ref to lease (containing expected old object id)
-	 * @return collection of set up {@link RemoteRefUpdate}.
-	 * @throws IOException
+	 * @return collection of set up
+	 *         {@link org.eclipse.jgit.transport.RemoteRefUpdate}.
+	 * @throws java.io.IOException
 	 *             when problem occurred during conversion or specification set
 	 *             up: most probably, missing objects or refs.
 	 * @since 4.7
@@ -1415,9 +1453,9 @@ public abstract class Transport implements AutoCloseable {
 	 * be used for reading remote refs.
 	 *
 	 * @return a fresh connection to fetch from the remote repository.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             the implementation does not support fetching.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the remote connection could not be established.
 	 */
 	public abstract FetchConnection openFetch() throws NotSupportedException,
@@ -1427,15 +1465,17 @@ public abstract class Transport implements AutoCloseable {
 	 * Begins a new connection for pushing into the remote repository.
 	 *
 	 * @return a fresh connection to push into the remote repository.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             the implementation does not support pushing.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the remote connection could not be established
 	 */
 	public abstract PushConnection openPush() throws NotSupportedException,
 			TransportException;
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Close any resources used by this transport.
 	 * <p>
 	 * If the remote repository is contacted by a network socket this method
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportAmazonS3.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportAmazonS3.java
index 6cd119bd2f..c6191eceb0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportAmazonS3.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportAmazonS3.java
@@ -86,8 +86,9 @@ import org.eclipse.jgit.lib.SymbolicRef;
  * extended HTTP/1.1 semantics. This make it possible to read or write Git data
  * from a remote repository that is stored on S3.
  * <p>
- * Unlike the HTTP variant (see {@link TransportHttp}) we rely upon being able
- * to list objects in a bucket, as the S3 API supports this function. By listing
+ * Unlike the HTTP variant (see
+ * {@link org.eclipse.jgit.transport.TransportHttp}) we rely upon being able to
+ * list objects in a bucket, as the S3 API supports this function. By listing
  * the bucket contents we can avoid relying on <code>objects/info/packs</code>
  * or <code>info/refs</code> in the remote repository.
  * <p>
@@ -201,6 +202,7 @@ public class TransportAmazonS3 extends HttpTransport implements WalkTransport {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public FetchConnection openFetch() throws TransportException {
 		final DatabaseS3 c = new DatabaseS3(bucket, keyPrefix + "/objects"); //$NON-NLS-1$
@@ -209,6 +211,7 @@ public class TransportAmazonS3 extends HttpTransport implements WalkTransport {
 		return r;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public PushConnection openPush() throws TransportException {
 		final DatabaseS3 c = new DatabaseS3(bucket, keyPrefix + "/objects"); //$NON-NLS-1$
@@ -217,6 +220,7 @@ public class TransportAmazonS3 extends HttpTransport implements WalkTransport {
 		return r;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		// No explicit connections are maintained.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleFile.java
index f2ddc0d0d1..58f021c0ae 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleFile.java
@@ -125,11 +125,20 @@ class TransportBundleFile extends Transport implements TransportBundle {
 		bundle = bundlePath;
 	}
 
+	/**
+	 * Constructor for TransportBundleFile.
+	 *
+	 * @param uri
+	 *            a {@link org.eclipse.jgit.transport.URIish} object.
+	 * @param bundlePath
+	 *            transport bundle path
+	 */
 	public TransportBundleFile(URIish uri, File bundlePath) {
 		super(uri);
 		bundle = bundlePath;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public FetchConnection openFetch() throws NotSupportedException,
 			TransportException {
@@ -142,12 +151,14 @@ class TransportBundleFile extends Transport implements TransportBundle {
 		return new BundleFetchConnection(this, src);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public PushConnection openPush() throws NotSupportedException {
 		throw new NotSupportedException(
 				JGitText.get().pushIsNotSupportedForBundleTransport);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		// Resources must be established per-connection.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleStream.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleStream.java
index a9d881f9b9..573367ec06 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleStream.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportBundleStream.java
@@ -90,6 +90,7 @@ public class TransportBundleStream extends Transport implements TransportBundle
 		src = in;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public FetchConnection openFetch() throws TransportException {
 		if (src == null)
@@ -101,12 +102,14 @@ public class TransportBundleStream extends Transport implements TransportBundle
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public PushConnection openPush() throws NotSupportedException {
 		throw new NotSupportedException(
 				JGitText.get().pushIsNotSupportedForBundleTransport);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		if (src != null) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportGitAnon.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportGitAnon.java
index 7bf5b947d8..816187ee0c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportGitAnon.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportGitAnon.java
@@ -121,16 +121,19 @@ class TransportGitAnon extends TcpTransport implements PackTransport {
 		super(uri);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public FetchConnection openFetch() throws TransportException {
 		return new TcpFetchConnection();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public PushConnection openPush() throws TransportException {
 		return new TcpPushConnection();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		// Resources must be established per-connection.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportGitSsh.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportGitSsh.java
index b1b910ea22..bc85e6f60f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportGitSsh.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportGitSsh.java
@@ -164,11 +164,13 @@ public class TransportGitSsh extends SshTransport implements PackTransport {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public FetchConnection openFetch() throws TransportException {
 		return new SshFetchConnection();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public PushConnection openPush() throws TransportException {
 		return new SshPushConnection();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportHttp.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportHttp.java
index 35bbd10d79..db43edc4ca 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportHttp.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportHttp.java
@@ -291,8 +291,11 @@ public class TransportHttp extends HttpTransport implements WalkTransport,
 	}
 
 	/**
+	 * Set uri a {@link org.eclipse.jgit.transport.URIish} object.
+	 *
 	 * @param uri
-	 * @throws NotSupportedException
+	 *            a {@link org.eclipse.jgit.transport.URIish} object.
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 * @since 4.9
 	 */
 	protected void setURI(final URIish uri) throws NotSupportedException {
@@ -333,6 +336,7 @@ public class TransportHttp extends HttpTransport implements WalkTransport,
 		useSmartHttp = on;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public FetchConnection openFetch() throws TransportException,
 			NotSupportedException {
@@ -427,6 +431,7 @@ public class TransportHttp extends HttpTransport implements WalkTransport,
 		return new BufferedReader(new InputStreamReader(in, Constants.CHARSET));
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public PushConnection openPush() throws NotSupportedException,
 			TransportException {
@@ -465,6 +470,7 @@ public class TransportHttp extends HttpTransport implements WalkTransport,
 		return p;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		// No explicit connections are maintained.
@@ -803,7 +809,7 @@ public class TransportHttp extends HttpTransport implements WalkTransport,
 	 * @param method HTTP request method
 	 * @param u url of the HTTP connection
 	 * @return the HTTP connection
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 3.3
 	 * @deprecated use {@link #httpOpen(String, URL, AcceptEncoding)} instead.
 	 */
@@ -819,7 +825,7 @@ public class TransportHttp extends HttpTransport implements WalkTransport,
 	 * @param u url of the HTTP connection
 	 * @param acceptEncoding accept-encoding header option
 	 * @return the HTTP connection
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 4.6
 	 */
 	protected HttpConnection httpOpen(String method, URL u,
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportLocal.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportLocal.java
index f483ec7f9f..20eb898fbe 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportLocal.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportLocal.java
@@ -178,6 +178,7 @@ class TransportLocal extends Transport implements PackTransport {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public FetchConnection openFetch() throws TransportException {
 		final String up = getOptionUploadPack();
@@ -194,6 +195,7 @@ class TransportLocal extends Transport implements PackTransport {
 		return new InternalFetchConnection<>(this, upf, null, openRepo());
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public PushConnection openPush() throws TransportException {
 		final String rp = getOptionReceivePack();
@@ -210,11 +212,21 @@ class TransportLocal extends Transport implements PackTransport {
 		return new InternalPushConnection<>(this, rpf, null, openRepo());
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		// Resources must be established per-connection.
 	}
 
+	/**
+	 * Spawn process
+	 *
+	 * @param cmd
+	 *            command
+	 * @return a {@link java.lang.Process} object.
+	 * @throws org.eclipse.jgit.errors.TransportException
+	 *             if any.
+	 */
 	protected Process spawn(final String cmd)
 			throws TransportException {
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportProtocol.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportProtocol.java
index e08efc4eaf..de58aa9e1b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportProtocol.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportProtocol.java
@@ -72,11 +72,12 @@ import org.eclipse.jgit.lib.Repository;
  *
  * <p>
  * Applications may register additional protocols for use by JGit by calling
- * {@link Transport#register(TransportProtocol)}. Because that API holds onto
- * the protocol object by a WeakReference, applications must ensure their own
- * ClassLoader retains the TransportProtocol for the life of the application.
- * Using a static singleton pattern as above will ensure the protocol is valid
- * so long as the ClassLoader that defines it remains valid.
+ * {@link org.eclipse.jgit.transport.Transport#register(TransportProtocol)}.
+ * Because that API holds onto the protocol object by a WeakReference,
+ * applications must ensure their own ClassLoader retains the TransportProtocol
+ * for the life of the application. Using a static singleton pattern as above
+ * will ensure the protocol is valid so long as the ClassLoader that defines it
+ * remains valid.
  * <p>
  * Applications may automatically register additional protocols by filling in
  * the names of their TransportProtocol defining classes using the services file
@@ -102,25 +103,45 @@ public abstract class TransportProtocol {
 		PATH,
 	}
 
-	/** @return text name of the protocol suitable for display to a user. */
+	/**
+	 * Get text name of the protocol suitable for display to a user.
+	 *
+	 * @return text name of the protocol suitable for display to a user.
+	 */
 	public abstract String getName();
 
-	/** @return immutable set of schemes supported by this protocol. */
+	/**
+	 * Get immutable set of schemes supported by this protocol.
+	 *
+	 * @return immutable set of schemes supported by this protocol.
+	 */
 	public Set<String> getSchemes() {
 		return Collections.emptySet();
 	}
 
-	/** @return immutable set of URIishFields that must be filled in. */
+	/**
+	 * Get immutable set of URIishFields that must be filled in.
+	 *
+	 * @return immutable set of URIishFields that must be filled in.
+	 */
 	public Set<URIishField> getRequiredFields() {
 		return Collections.unmodifiableSet(EnumSet.of(URIishField.PATH));
 	}
 
-	/** @return immutable set of URIishFields that may be filled in. */
+	/**
+	 * Get immutable set of URIishFields that may be filled in.
+	 *
+	 * @return immutable set of URIishFields that may be filled in.
+	 */
 	public Set<URIishField> getOptionalFields() {
 		return Collections.emptySet();
 	}
 
-	/** @return if a port is supported, the default port, else -1. */
+	/**
+	 * Get the default port if the protocol supports a port, else -1.
+	 *
+	 * @return the default port if the protocol supports a port, else -1.
+	 */
 	public int getDefaultPort() {
 		return -1;
 	}
@@ -246,9 +267,9 @@ public abstract class TransportProtocol {
 	 *            name of the remote, if the remote as configured in
 	 *            {@code local}; otherwise null.
 	 * @return the transport.
-	 * @throws NotSupportedException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
 	 *             this protocol does not support the URI.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             the transport cannot open this URI.
 	 */
 	public abstract Transport open(URIish uri, Repository local,
@@ -260,9 +281,10 @@ public abstract class TransportProtocol {
 	 * configuration instead of reading from configuration files.
 	 *
 	 * @param uri
+	 *            a {@link org.eclipse.jgit.transport.URIish} object.
 	 * @return new Transport
-	 * @throws NotSupportedException
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.NotSupportedException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 */
 	public Transport open(URIish uri)
 			throws NotSupportedException, TransportException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportSftp.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportSftp.java
index c46f94b7da..306c6c452c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportSftp.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportSftp.java
@@ -86,11 +86,12 @@ import com.jcraft.jsch.SftpException;
  * repository that is available over SSH, but whose remote host does not have
  * Git installed.
  * <p>
- * Unlike the HTTP variant (see {@link TransportHttp}) we rely upon being able
- * to list files in directories, as the SFTP protocol supports this function. By
+ * Unlike the HTTP variant (see
+ * {@link org.eclipse.jgit.transport.TransportHttp}) we rely upon being able to
+ * list files in directories, as the SFTP protocol supports this function. By
  * listing files through SFTP we can avoid needing to have current
- * <code>objects/info/packs</code> or <code>info/refs</code> files on the
- * remote repository and access the data directly, much as Git itself would.
+ * <code>objects/info/packs</code> or <code>info/refs</code> files on the remote
+ * repository and access the data directly, much as Git itself would.
  * <p>
  * Concurrent pushing over this transport is not supported. Multiple concurrent
  * push operations may cause confusion in the repository state.
@@ -137,6 +138,7 @@ public class TransportSftp extends SshTransport implements WalkTransport {
 		super(local, uri);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public FetchConnection openFetch() throws TransportException {
 		final SftpObjectDB c = new SftpObjectDB(uri.getPath());
@@ -145,6 +147,7 @@ public class TransportSftp extends SshTransport implements WalkTransport {
 		return r;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public PushConnection openPush() throws TransportException {
 		final SftpObjectDB c = new SftpObjectDB(uri.getPath());
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java
index ffd4d41f2a..f96d2698e1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java
@@ -200,10 +200,12 @@ public class URIish implements Serializable {
 	private String host;
 
 	/**
-	 * Parse and construct an {@link URIish} from a string
+	 * Parse and construct an {@link org.eclipse.jgit.transport.URIish} from a
+	 * string
 	 *
 	 * @param s
-	 * @throws URISyntaxException
+	 *            a {@link java.lang.String} object.
+	 * @throws java.net.URISyntaxException
 	 */
 	public URIish(String s) throws URISyntaxException {
 		if (StringUtils.isEmptyOrNull(s)) {
@@ -395,7 +397,9 @@ public class URIish implements Serializable {
 		host = u.getHost();
 	}
 
-	/** Create an empty, non-configured URI. */
+	/**
+	 * Create an empty, non-configured URI.
+	 */
 	public URIish() {
 		// Configure nothing.
 	}
@@ -411,6 +415,8 @@ public class URIish implements Serializable {
 	}
 
 	/**
+	 * Whether this URI references a repository on another system.
+	 *
 	 * @return true if this URI references a repository on another system.
 	 */
 	public boolean isRemote() {
@@ -418,6 +424,8 @@ public class URIish implements Serializable {
 	}
 
 	/**
+	 * Get host name part.
+	 *
 	 * @return host name part or null
 	 */
 	public String getHost() {
@@ -438,6 +446,8 @@ public class URIish implements Serializable {
 	}
 
 	/**
+	 * Get protocol name
+	 *
 	 * @return protocol name or null for local references
 	 */
 	public String getScheme() {
@@ -458,6 +468,8 @@ public class URIish implements Serializable {
 	}
 
 	/**
+	 * Get path name component
+	 *
 	 * @return path name component
 	 */
 	public String getPath() {
@@ -465,6 +477,8 @@ public class URIish implements Serializable {
 	}
 
 	/**
+	 * Get path name component
+	 *
 	 * @return path name component
 	 */
 	public String getRawPath() {
@@ -491,7 +505,7 @@ public class URIish implements Serializable {
 	 * @param n
 	 *            the new value for path.
 	 * @return a new URI with the updated value.
-	 * @throws URISyntaxException
+	 * @throws java.net.URISyntaxException
 	 */
 	public URIish setRawPath(final String n) throws URISyntaxException {
 		final URIish r = new URIish(this);
@@ -501,6 +515,8 @@ public class URIish implements Serializable {
 	}
 
 	/**
+	 * Get user name requested for transfer
+	 *
 	 * @return user name requested for transfer or null
 	 */
 	public String getUser() {
@@ -521,6 +537,8 @@ public class URIish implements Serializable {
 	}
 
 	/**
+	 * Get password requested for transfer
+	 *
 	 * @return password requested for transfer or null
 	 */
 	public String getPass() {
@@ -541,6 +559,8 @@ public class URIish implements Serializable {
 	}
 
 	/**
+	 * Get port number requested for transfer or -1 if not explicit
+	 *
 	 * @return port number requested for transfer or -1 if not explicit
 	 */
 	public int getPort() {
@@ -560,6 +580,7 @@ public class URIish implements Serializable {
 		return r;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int hashCode() {
 		int hc = 0;
@@ -578,6 +599,7 @@ public class URIish implements Serializable {
 		return hc;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean equals(final Object obj) {
 		if (!(obj instanceof URIish))
@@ -617,6 +639,7 @@ public class URIish implements Serializable {
 		return format(true, false);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		return format(false, false);
@@ -666,6 +689,8 @@ public class URIish implements Serializable {
 	}
 
 	/**
+	 * <Get the URI as an ASCII string.
+	 *
 	 * @return the URI as an ASCII string. Password is not included.
 	 */
 	public String toASCIIString() {
@@ -673,6 +698,9 @@ public class URIish implements Serializable {
 	}
 
 	/**
+	 * Convert the URI including password, formatted with only ASCII characters
+	 * such that it will be valid for use over the network.
+	 *
 	 * @return the URI including password, formatted with only ASCII characters
 	 *         such that it will be valid for use over the network.
 	 */
@@ -713,7 +741,7 @@ public class URIish implements Serializable {
 	 *
 	 * @return the "humanish" part of the path. May be an empty string. Never
 	 *         {@code null}.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             if it's impossible to determine a humanish part, or path is
 	 *             {@code null} or empty
 	 * @see #getPath
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java
index cab532288b..822d47c7c2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java
@@ -346,12 +346,20 @@ public class UploadPack {
 		setTransferConfig(null);
 	}
 
-	/** @return the repository this upload is reading from. */
+	/**
+	 * Get the repository this upload is reading from.
+	 *
+	 * @return the repository this upload is reading from.
+	 */
 	public final Repository getRepository() {
 		return db;
 	}
 
-	/** @return the RevWalk instance used by this connection. */
+	/**
+	 * Get the RevWalk instance used by this connection.
+	 *
+	 * @return the RevWalk instance used by this connection.
+	 */
 	public final RevWalk getRevWalk() {
 		return walk;
 	}
@@ -369,14 +377,15 @@ public class UploadPack {
 	/**
 	 * Set the refs advertised by this UploadPack.
 	 * <p>
-	 * Intended to be called from a {@link PreUploadHook}.
+	 * Intended to be called from a
+	 * {@link org.eclipse.jgit.transport.PreUploadHook}.
 	 *
 	 * @param allRefs
 	 *            explicit set of references to claim as advertised by this
-	 *            UploadPack instance. This overrides any references that
-	 *            may exist in the source repository. The map is passed
-	 *            to the configured {@link #getRefFilter()}. If null, assumes
-	 *            all refs were advertised.
+	 *            UploadPack instance. This overrides any references that may
+	 *            exist in the source repository. The map is passed to the
+	 *            configured {@link #getRefFilter()}. If null, assumes all refs
+	 *            were advertised.
 	 */
 	public void setAdvertisedRefs(Map<String, Ref> allRefs) {
 		if (allRefs != null)
@@ -389,7 +398,11 @@ public class UploadPack {
 			refs = refFilter.filter(refs);
 	}
 
-	/** @return timeout (in seconds) before aborting an IO operation. */
+	/**
+	 * Get timeout (in seconds) before aborting an IO operation.
+	 *
+	 * @return timeout (in seconds) before aborting an IO operation.
+	 */
 	public int getTimeout() {
 		return timeout;
 	}
@@ -407,6 +420,9 @@ public class UploadPack {
 	}
 
 	/**
+	 * Whether this class expects a bi-directional pipe opened between the
+	 * client and itself.
+	 *
 	 * @return true if this class expects a bi-directional pipe opened between
 	 *         the client and itself. The default is true.
 	 */
@@ -415,6 +431,9 @@ public class UploadPack {
 	}
 
 	/**
+	 * Set whether this class will assume the socket is a fully bidirectional
+	 * pipe between the two peers
+	 *
 	 * @param twoWay
 	 *            if true, this class will assume the socket is a fully
 	 *            bidirectional pipe between the two peers and takes advantage
@@ -428,8 +447,10 @@ public class UploadPack {
 	}
 
 	/**
-	 * @return policy used by the service to validate client requests, or null for
-	 *         a custom request validator.
+	 * Get policy used by the service to validate client requests
+	 *
+	 * @return policy used by the service to validate client requests, or null
+	 *         for a custom request validator.
 	 */
 	public RequestPolicy getRequestPolicy() {
 		if (requestValidator instanceof AdvertisedRequestValidator)
@@ -446,15 +467,21 @@ public class UploadPack {
 	}
 
 	/**
+	 * Set the policy used to enforce validation of a client's want list.
+	 *
 	 * @param policy
 	 *            the policy used to enforce validation of a client's want list.
-	 *            By default the policy is {@link RequestPolicy#ADVERTISED},
+	 *            By default the policy is
+	 *            {@link org.eclipse.jgit.transport.UploadPack.RequestPolicy#ADVERTISED},
 	 *            which is the Git default requiring clients to only ask for an
-	 *            object that a reference directly points to. This may be relaxed
-	 *            to {@link RequestPolicy#REACHABLE_COMMIT} or
-	 *            {@link RequestPolicy#REACHABLE_COMMIT_TIP} when callers have
-	 *            {@link #setBiDirectionalPipe(boolean)} set to false.
-	 *            Overrides any policy specified in a {@link TransferConfig}.
+	 *            object that a reference directly points to. This may be
+	 *            relaxed to
+	 *            {@link org.eclipse.jgit.transport.UploadPack.RequestPolicy#REACHABLE_COMMIT}
+	 *            or
+	 *            {@link org.eclipse.jgit.transport.UploadPack.RequestPolicy#REACHABLE_COMMIT_TIP}
+	 *            when callers have {@link #setBiDirectionalPipe(boolean)} set
+	 *            to false. Overrides any policy specified in a
+	 *            {@link org.eclipse.jgit.transport.TransferConfig}.
 	 */
 	public void setRequestPolicy(RequestPolicy policy) {
 		switch (policy) {
@@ -478,6 +505,8 @@ public class UploadPack {
 	}
 
 	/**
+	 * Set custom validator for client want list.
+	 *
 	 * @param validator
 	 *            custom validator for client want list.
 	 * @since 3.1
@@ -487,12 +516,20 @@ public class UploadPack {
 				: new AdvertisedRequestValidator();
 	}
 
-	/** @return the hook used while advertising the refs to the client */
+	/**
+	 * Get the hook used while advertising the refs to the client.
+	 *
+	 * @return the hook used while advertising the refs to the client.
+	 */
 	public AdvertiseRefsHook getAdvertiseRefsHook() {
 		return advertiseRefsHook;
 	}
 
-	/** @return the filter used while advertising the refs to the client */
+	/**
+	 * Get the filter used while advertising the refs to the client.
+	 *
+	 * @return the filter used while advertising the refs to the client.
+	 */
 	public RefFilter getRefFilter() {
 		return refFilter;
 	}
@@ -500,9 +537,10 @@ public class UploadPack {
 	/**
 	 * Set the hook used while advertising the refs to the client.
 	 * <p>
-	 * If the {@link AdvertiseRefsHook} chooses to call
-	 * {@link #setAdvertisedRefs(Map)}, only refs set by this hook <em>and</em>
-	 * selected by the {@link RefFilter} will be shown to the client.
+	 * If the {@link org.eclipse.jgit.transport.AdvertiseRefsHook} chooses to
+	 * call {@link #setAdvertisedRefs(Map)}, only refs set by this hook
+	 * <em>and</em> selected by the {@link org.eclipse.jgit.transport.RefFilter}
+	 * will be shown to the client.
 	 *
 	 * @param advertiseRefsHook
 	 *            the hook; may be null to show all refs.
@@ -517,10 +555,11 @@ public class UploadPack {
 	/**
 	 * Set the filter used while advertising the refs to the client.
 	 * <p>
-	 * Only refs allowed by this filter will be sent to the client.
-	 * The filter is run against the refs specified by the
-	 * {@link AdvertiseRefsHook} (if applicable). If null or not set, uses the
-	 * filter implied by the {@link TransferConfig}.
+	 * Only refs allowed by this filter will be sent to the client. The filter
+	 * is run against the refs specified by the
+	 * {@link org.eclipse.jgit.transport.AdvertiseRefsHook} (if applicable). If
+	 * null or not set, uses the filter implied by the
+	 * {@link org.eclipse.jgit.transport.TransferConfig}.
 	 *
 	 * @param refFilter
 	 *            the filter; may be null to show all refs.
@@ -529,7 +568,11 @@ public class UploadPack {
 		this.refFilter = refFilter != null ? refFilter : RefFilter.DEFAULT;
 	}
 
-	/** @return the configured pre upload hook. */
+	/**
+	 * Get the configured pre upload hook.
+	 *
+	 * @return the configured pre upload hook.
+	 */
 	public PreUploadHook getPreUploadHook() {
 		return preUploadHook;
 	}
@@ -545,6 +588,8 @@ public class UploadPack {
 	}
 
 	/**
+	 * Get the configured post upload hook.
+	 *
 	 * @return the configured post upload hook.
 	 * @since 4.1
 	 */
@@ -575,6 +620,8 @@ public class UploadPack {
 	}
 
 	/**
+	 * Set configuration controlling transfer options.
+	 *
 	 * @param tc
 	 *            configuration controlling transfer options. If null the source
 	 *            repository's settings will be used.
@@ -592,8 +639,9 @@ public class UploadPack {
 	}
 
 	/**
-	 * @return the configured logger.
+	 * Get the configured logger.
 	 *
+	 * @return the configured logger.
 	 * @deprecated Use {@link #getPreUploadHook()}.
 	 */
 	@Deprecated
@@ -618,7 +666,7 @@ public class UploadPack {
 	 *
 	 * @return true if the client has advertised a side-band capability, false
 	 *     otherwise.
-	 * @throws RequestNotYetReadException
+	 * @throws org.eclipse.jgit.transport.RequestNotYetReadException
 	 *             if the client's request has not yet been read from the wire, so
 	 *             we do not know if they expect side-band. Note that the client
 	 *             may have already written the request, it just has not been
@@ -646,7 +694,7 @@ public class UploadPack {
 	 *            through. When run over SSH this should be tied back to the
 	 *            standard error channel of the command execution. For most
 	 *            other network connections this should be null.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void upload(final InputStream input, OutputStream output,
 			final OutputStream messages) throws IOException {
@@ -889,9 +937,9 @@ public class UploadPack {
 	 *
 	 * @param adv
 	 *            the advertisement formatter.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the formatter failed to write an advertisement.
-	 * @throws ServiceMayNotContinueException
+	 * @throws org.eclipse.jgit.transport.ServiceMayNotContinueException
 	 *             the hook denied advertisement.
 	 */
 	public void sendAdvertisedRefs(final RefAdvertiser adv) throws IOException,
@@ -957,6 +1005,8 @@ public class UploadPack {
 	}
 
 	/**
+	 * Get an underlying stream for sending messages to the client
+	 *
 	 * @return an underlying stream for sending messages to the client, or null.
 	 * @since 3.1
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPackInternalServerErrorException.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPackInternalServerErrorException.java
index acdfe04f89..181352122c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPackInternalServerErrorException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPackInternalServerErrorException.java
@@ -45,7 +45,9 @@ package org.eclipse.jgit.transport;
 
 import java.io.IOException;
 
-/** UploadPack has already reported an error to the client.*/
+/**
+ * UploadPack has already reported an error to the client.
+ */
 public class UploadPackInternalServerErrorException extends IOException {
 	private static final long serialVersionUID = 1L;
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPackLogger.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPackLogger.java
index afc9965183..611418d22c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPackLogger.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPackLogger.java
@@ -46,14 +46,15 @@ package org.eclipse.jgit.transport;
 import org.eclipse.jgit.internal.storage.pack.PackWriter;
 
 /**
- * Logs activity that occurred within {@link UploadPack}.
+ * Logs activity that occurred within
+ * {@link org.eclipse.jgit.transport.UploadPack}.
  * <p>
  * Implementors of the interface are responsible for associating the current
  * thread to a particular connection, if they need to also include connection
  * information. One method is to use a {@link java.lang.ThreadLocal} to remember
  * the connection information before invoking UploadPack.
  *
- * @deprecated use {@link PostUploadHook} instead
+ * @deprecated use {@link org.eclipse.jgit.transport.PostUploadHook} instead
  */
 @Deprecated
 public interface UploadPackLogger { // TODO remove in JGit 5.0
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPackLoggerChain.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPackLoggerChain.java
index 9a8c12c648..9e14672dc5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPackLoggerChain.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPackLoggerChain.java
@@ -52,7 +52,8 @@ import org.eclipse.jgit.internal.storage.pack.PackWriter;
  * <p>
  * loggers are run in the order passed to the constructor.
  *
- * @deprecated Use {@link PostUploadHookChain} instead.
+ * @deprecated Use {@link org.eclipse.jgit.transport.PostUploadHookChain}
+ *             instead.
  */
 @Deprecated
 public class UploadPackLoggerChain implements UploadPackLogger {
@@ -81,9 +82,7 @@ public class UploadPackLoggerChain implements UploadPackLogger {
 			return new UploadPackLoggerChain(newLoggers, i);
 	}
 
-	/**
-	 * @since 3.0
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public void onPackStatistics(PackWriter.Statistics stats) {
 		for (int i = 0; i < count; i++)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UsernamePasswordCredentialsProvider.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UsernamePasswordCredentialsProvider.java
index 6caa5aa146..4445c3d561 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UsernamePasswordCredentialsProvider.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UsernamePasswordCredentialsProvider.java
@@ -48,7 +48,8 @@ import java.util.Arrays;
 import org.eclipse.jgit.errors.UnsupportedCredentialItem;
 
 /**
- * Simple {@link CredentialsProvider} that always uses the same information.
+ * Simple {@link org.eclipse.jgit.transport.CredentialsProvider} that always
+ * uses the same information.
  */
 public class UsernamePasswordCredentialsProvider extends CredentialsProvider {
 	private String username;
@@ -59,7 +60,9 @@ public class UsernamePasswordCredentialsProvider extends CredentialsProvider {
 	 * Initialize the provider with a single username and password.
 	 *
 	 * @param username
+	 *            user name
 	 * @param password
+	 *            password
 	 */
 	public UsernamePasswordCredentialsProvider(String username, String password) {
 		this(username, password.toCharArray());
@@ -69,18 +72,22 @@ public class UsernamePasswordCredentialsProvider extends CredentialsProvider {
 	 * Initialize the provider with a single username and password.
 	 *
 	 * @param username
+	 *            user name
 	 * @param password
+	 *            password
 	 */
 	public UsernamePasswordCredentialsProvider(String username, char[] password) {
 		this.username = username;
 		this.password = password;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isInteractive() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean supports(CredentialItem... items) {
 		for (CredentialItem i : items) {
@@ -96,6 +103,7 @@ public class UsernamePasswordCredentialsProvider extends CredentialsProvider {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean get(URIish uri, CredentialItem... items)
 			throws UnsupportedCredentialItem {
@@ -121,7 +129,9 @@ public class UsernamePasswordCredentialsProvider extends CredentialsProvider {
 		return true;
 	}
 
-	/** Destroy the saved username and password.. */
+	/**
+	 * Destroy the saved username and password..
+	 */
 	public void clear() {
 		username = null;
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkEncryption.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkEncryption.java
index 38e8e9f152..615e46b982 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkEncryption.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkEncryption.java
@@ -95,6 +95,20 @@ abstract class WalkEncryption {
 	// consider permitting mixed ciphers to facilitate algorithm migration
 	// i.e. user keeps the password, but changes the algorithm
 	// then existing remote entries will still be readable
+	/**
+	 * Validate
+	 *
+	 * @param u
+	 *            a {@link java.net.HttpURLConnection} object.
+	 * @param prefix
+	 *            a {@link java.lang.String} object.
+	 * @param version
+	 *            a {@link java.lang.String} object.
+	 * @param name
+	 *            a {@link java.lang.String} object.
+	 * @throws java.io.IOException
+	 *             if any.
+	 */
 	protected void validateImpl(final HttpURLConnection u, final String prefix,
 			final String version, final String name) throws IOException {
 		String v;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkFetchConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkFetchConnection.java
index 3d60aedcca..6708964d5e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkFetchConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkFetchConnection.java
@@ -223,11 +223,13 @@ class WalkFetchConnection extends BaseFetchConnection {
 		workQueue = new LinkedList<>();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean didFetchTestConnectivity() {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void doFetch(final ProgressMonitor monitor,
 			final Collection<Ref> want, final Set<ObjectId> have)
@@ -249,16 +251,19 @@ class WalkFetchConnection extends BaseFetchConnection {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Collection<PackLock> getPackLocks() {
 		return packLocks;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setPackLockMessage(final String message) {
 		lockMessage = message;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		inserter.close();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkPushConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkPushConnection.java
index 5c4e14ca31..cf50c51d5d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkPushConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkPushConnection.java
@@ -134,6 +134,7 @@ class WalkPushConnection extends BaseConnection implements PushConnection {
 		dest = w;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void push(final ProgressMonitor monitor,
 			final Map<String, RemoteRefUpdate> refUpdates)
@@ -141,6 +142,7 @@ class WalkPushConnection extends BaseConnection implements PushConnection {
 		push(monitor, refUpdates, null);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void push(final ProgressMonitor monitor,
 			final Map<String, RemoteRefUpdate> refUpdates, OutputStream out)
@@ -212,6 +214,7 @@ class WalkPushConnection extends BaseConnection implements PushConnection {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void close() {
 		dest.close();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkRemoteObjectDatabase.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkRemoteObjectDatabase.java
index 17f8c3ec19..a0ad2f3662 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkRemoteObjectDatabase.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkRemoteObjectDatabase.java
@@ -417,7 +417,7 @@ abstract class WalkRemoteObjectDatabase {
 	 * @param avail
 	 *            return collection of references. Any existing entries will be
 	 *            replaced if they are found in the packed-refs file.
-	 * @throws TransportException
+	 * @throws org.eclipse.jgit.errors.TransportException
 	 *             an error occurred reading from the packed refs file.
 	 */
 	protected void readPackedRefs(final Map<String, Ref> avail)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkTransport.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkTransport.java
index f1c4357113..8262d0024d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkTransport.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkTransport.java
@@ -53,8 +53,9 @@ package org.eclipse.jgit.transport;
  * from the loose objects directory, or entire packs if the source side does not
  * have the object as a loose object.
  * <p>
- * WalkTransports are not as efficient as {@link PackTransport} instances, but
- * can be useful in situations where a pack transport is not acceptable.
+ * WalkTransports are not as efficient as
+ * {@link org.eclipse.jgit.transport.PackTransport} instances, but can be useful
+ * in situations where a pack transport is not acceptable.
  *
  * @see WalkFetchConnection
  */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WantNotValidException.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WantNotValidException.java
index f0f64344b8..601b0d0a5b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WantNotValidException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WantNotValidException.java
@@ -54,7 +54,7 @@ import org.eclipse.jgit.lib.AnyObjectId;
  * <p>
  * Typically visible only inside of the server implementation; clients are
  * usually looking at the text message from the server in a generic
- * {@link PackProtocolException}.
+ * {@link org.eclipse.jgit.errors.PackProtocolException}.
  *
  * @since 4.3
  */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WriteAbortedException.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WriteAbortedException.java
index 267bf7a380..e3987ea070 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WriteAbortedException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WriteAbortedException.java
@@ -49,7 +49,7 @@ import java.io.IOException;
  * An exception to be thrown when the write operation is aborted.
  * <p>
  * That can be thrown inside
- * {@link ObjectCountCallback#setObjectCount(long)}.
+ * {@link org.eclipse.jgit.transport.ObjectCountCallback#setObjectCount(long)}.
  *
  * @since 4.1
  */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/HttpConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/HttpConnection.java
index 35a1ee15ed..d815bc354e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/HttpConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/HttpConnection.java
@@ -56,13 +56,12 @@ import java.util.Map;
 
 import javax.net.ssl.HostnameVerifier;
 import javax.net.ssl.KeyManager;
-import javax.net.ssl.SSLContext;
 import javax.net.ssl.TrustManager;
 
 /**
  * The interface of connections used during HTTP communication. This interface
- * is that subset of the interface exposed by {@link HttpURLConnection} which is
- * used by JGit
+ * is that subset of the interface exposed by {@link java.net.HttpURLConnection}
+ * which is used by JGit
  *
  * @since 3.3
  */
@@ -114,32 +113,42 @@ public interface HttpConnection {
 	public static final int HTTP_FORBIDDEN = java.net.HttpURLConnection.HTTP_FORBIDDEN;
 
 	/**
+	 * Get response code
+	 *
 	 * @see HttpURLConnection#getResponseCode()
 	 * @return the HTTP Status-Code, or -1
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public int getResponseCode() throws IOException;
 
 	/**
+	 * Get URL
+	 *
 	 * @see HttpURLConnection#getURL()
 	 * @return the URL.
 	 */
 	public URL getURL();
 
 	/**
+	 * Get response message
+	 *
 	 * @see HttpURLConnection#getResponseMessage()
 	 * @return the HTTP response message, or <code>null</code>
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public String getResponseMessage() throws IOException;
 
 	/**
+	 * Get list of header fields
+	 *
 	 * @see HttpURLConnection#getHeaderFields()
 	 * @return a Map of header fields
 	 */
 	public Map<String, List<String>> getHeaderFields();
 
 	/**
+	 * Set request property
+	 *
 	 * @see HttpURLConnection#setRequestProperty(String, String)
 	 * @param key
 	 *            the keyword by which the request is known (e.g., "
@@ -150,17 +159,23 @@ public interface HttpConnection {
 	public void setRequestProperty(String key, String value);
 
 	/**
+	 * Set request method
+	 *
 	 * @see HttpURLConnection#setRequestMethod(String)
 	 * @param method
 	 *            the HTTP method
 	 * @exception ProtocolException
 	 *                if the method cannot be reset or if the requested method
 	 *                isn't valid for HTTP.
+	 * @throws java.net.ProtocolException
+	 *             if any.
 	 */
 	public void setRequestMethod(String method)
 			throws ProtocolException;
 
 	/**
+	 * Set if to use caches
+	 *
 	 * @see HttpURLConnection#setUseCaches(boolean)
 	 * @param usecaches
 	 *            a <code>boolean</code> indicating whether or not to allow
@@ -169,6 +184,8 @@ public interface HttpConnection {
 	public void setUseCaches(boolean usecaches);
 
 	/**
+	 * Set connect timeout
+	 *
 	 * @see HttpURLConnection#setConnectTimeout(int)
 	 * @param timeout
 	 *            an <code>int</code> that specifies the connect timeout value
@@ -177,6 +194,8 @@ public interface HttpConnection {
 	public void setConnectTimeout(int timeout);
 
 	/**
+	 * Set read timeout
+	 *
 	 * @see HttpURLConnection#setReadTimeout(int)
 	 * @param timeout
 	 *            an <code>int</code> that specifies the timeout value to be
@@ -185,6 +204,8 @@ public interface HttpConnection {
 	public void setReadTimeout(int timeout);
 
 	/**
+	 * Get content type
+	 *
 	 * @see HttpURLConnection#getContentType()
 	 * @return the content type of the resource that the URL references, or
 	 *         <code>null</code> if not known.
@@ -192,14 +213,20 @@ public interface HttpConnection {
 	public String getContentType();
 
 	/**
+	 * Get input stream
+	 *
 	 * @see HttpURLConnection#getInputStream()
 	 * @return an input stream that reads from this open connection.
 	 * @exception IOException
 	 *                if an I/O error occurs while creating the input stream.
+	 * @throws java.io.IOException
+	 *             if any.
 	 */
 	public InputStream getInputStream() throws IOException;
 
 	/**
+	 * Get header field
+	 *
 	 * @see HttpURLConnection#getHeaderField(String)
 	 * @param name
 	 *            the name of a header field.
@@ -209,6 +236,8 @@ public interface HttpConnection {
 	public String getHeaderField(String name);
 
 	/**
+	 * Get content length
+	 *
 	 * @see HttpURLConnection#getContentLength()
 	 * @return the content length of the resource that this connection's URL
 	 *         references, {@code -1} if the content length is not known, or if
@@ -217,6 +246,8 @@ public interface HttpConnection {
 	public int getContentLength();
 
 	/**
+	 * Set whether or not to follow HTTP redirects.
+	 *
 	 * @see HttpURLConnection#setInstanceFollowRedirects(boolean)
 	 * @param followRedirects
 	 *            a <code>boolean</code> indicating whether or not to follow
@@ -225,27 +256,35 @@ public interface HttpConnection {
 	public void setInstanceFollowRedirects(boolean followRedirects);
 
 	/**
+	 * Set if to do output
+	 *
 	 * @see HttpURLConnection#setDoOutput(boolean)
-     * @param   dooutput   the new value.
+	 * @param dooutput
+	 *            the new value.
 	 */
 	public void setDoOutput(boolean dooutput);
 
 	/**
+	 * Set fixed length streaming mode
+	 *
 	 * @see HttpURLConnection#setFixedLengthStreamingMode(int)
 	 * @param contentLength
 	 *            The number of bytes which will be written to the OutputStream.
-	 *
 	 */
 	public void setFixedLengthStreamingMode(int contentLength);
 
 	/**
+	 * Get output stream
+	 *
 	 * @see HttpURLConnection#getOutputStream()
 	 * @return an output stream that writes to this connection.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public OutputStream getOutputStream() throws IOException;
 
 	/**
+	 * Set chunked streaming mode
+	 *
 	 * @see HttpURLConnection#setChunkedStreamingMode(int)
 	 * @param chunklen
 	 *            The number of bytes to write in each chunk. If chunklen is
@@ -254,20 +293,26 @@ public interface HttpConnection {
 	public void setChunkedStreamingMode(int chunklen);
 
 	/**
+	 * Get request method
+	 *
 	 * @see HttpURLConnection#getRequestMethod()
 	 * @return the HTTP request method
 	 */
 	public String getRequestMethod();
 
 	/**
+	 * Whether we use a proxy
+	 *
 	 * @see HttpURLConnection#usingProxy()
 	 * @return a boolean indicating if the connection is using a proxy.
 	 */
 	public boolean usingProxy();
 
 	/**
+	 * Connect
+	 *
 	 * @see HttpURLConnection#connect()
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void connect() throws IOException;
 
@@ -283,21 +328,22 @@ public interface HttpConnection {
 	 *            whether credentials presented by a peer should be accepted.
 	 * @param random
 	 *            the source of randomness for this generator or null. See
-	 *            {@link SSLContext#init(KeyManager[], TrustManager[], SecureRandom)}
-	 *
-	 * @throws NoSuchAlgorithmException
-	 * @throws KeyManagementException
+	 *            {@link javax.net.ssl.SSLContext#init(KeyManager[], TrustManager[], SecureRandom)}
+	 * @throws java.security.NoSuchAlgorithmException
+	 * @throws java.security.KeyManagementException
 	 */
 	public void configure(KeyManager[] km, TrustManager[] tm,
 			SecureRandom random) throws NoSuchAlgorithmException,
 			KeyManagementException;
 
 	/**
-	 * Set the {@link HostnameVerifier} used during https communication
+	 * Set the {@link javax.net.ssl.HostnameVerifier} used during https
+	 * communication
 	 *
 	 * @param hostnameverifier
-	 * @throws NoSuchAlgorithmException
-	 * @throws KeyManagementException
+	 *            a {@link javax.net.ssl.HostnameVerifier} object.
+	 * @throws java.security.NoSuchAlgorithmException
+	 * @throws java.security.KeyManagementException
 	 */
 	public void setHostnameVerifier(HostnameVerifier hostnameverifier)
 			throws NoSuchAlgorithmException, KeyManagementException;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/HttpConnectionFactory.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/HttpConnectionFactory.java
index 591353c18d..bd9d61fe66 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/HttpConnectionFactory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/HttpConnectionFactory.java
@@ -47,30 +47,33 @@ import java.net.Proxy;
 import java.net.URL;
 
 /**
- * The interface of a factory returning {@link HttpConnection}
+ * The interface of a factory returning
+ * {@link org.eclipse.jgit.transport.http.HttpConnection}
  *
  * @since 3.3
  */
 public interface HttpConnectionFactory {
 	/**
-	 * Creates a new connection to a destination defined by a {@link URL}
+	 * Creates a new connection to a destination defined by a
+	 * {@link java.net.URL}
 	 *
 	 * @param url
-	 * @return a {@link HttpConnection}
-	 * @throws IOException
+	 *            a {@link java.net.URL} object.
+	 * @return a {@link org.eclipse.jgit.transport.http.HttpConnection}
+	 * @throws java.io.IOException
 	 */
 	public HttpConnection create(URL url) throws IOException;
 
 	/**
-	 * Creates a new connection to a destination defined by a {@link URL} using
-	 * a proxy
+	 * Creates a new connection to a destination defined by a
+	 * {@link java.net.URL} using a proxy
 	 *
 	 * @param url
+	 *            a {@link java.net.URL} object.
 	 * @param proxy
 	 *            the proxy to be used
-	 * @return a {@link HttpConnection}
-	 *
-	 * @throws IOException
+	 * @return a {@link org.eclipse.jgit.transport.http.HttpConnection}
+	 * @throws java.io.IOException
 	 */
 	public HttpConnection create(URL url, Proxy proxy)
 			throws IOException;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/JDKHttpConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/JDKHttpConnection.java
index 534e3d734f..8241c59d2b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/JDKHttpConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/JDKHttpConnection.java
@@ -63,8 +63,9 @@ import javax.net.ssl.SSLContext;
 import javax.net.ssl.TrustManager;
 
 /**
- * A {@link HttpConnection} which simply delegates every call to a
- * {@link HttpURLConnection}. This is the default implementation used by JGit
+ * A {@link org.eclipse.jgit.transport.http.HttpConnection} which simply
+ * delegates every call to a {@link java.net.HttpURLConnection}. This is the
+ * default implementation used by JGit
  *
  * @since 3.3
  */
@@ -72,9 +73,12 @@ public class JDKHttpConnection implements HttpConnection {
 	HttpURLConnection wrappedUrlConnection;
 
 	/**
+	 * Constructor for JDKHttpConnection.
+	 *
 	 * @param url
-	 * @throws MalformedURLException
-	 * @throws IOException
+	 *            a {@link java.net.URL} object.
+	 * @throws java.net.MalformedURLException
+	 * @throws java.io.IOException
 	 */
 	protected JDKHttpConnection(URL url)
 			throws MalformedURLException,
@@ -83,10 +87,14 @@ public class JDKHttpConnection implements HttpConnection {
 	}
 
 	/**
+	 * Constructor for JDKHttpConnection.
+	 *
 	 * @param url
+	 *            a {@link java.net.URL} object.
 	 * @param proxy
-	 * @throws MalformedURLException
-	 * @throws IOException
+	 *            a {@link java.net.Proxy} object.
+	 * @throws java.net.MalformedURLException
+	 * @throws java.io.IOException
 	 */
 	protected JDKHttpConnection(URL url, Proxy proxy)
 			throws MalformedURLException, IOException {
@@ -94,117 +102,140 @@ public class JDKHttpConnection implements HttpConnection {
 				.openConnection(proxy);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int getResponseCode() throws IOException {
 		return wrappedUrlConnection.getResponseCode();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public URL getURL() {
 		return wrappedUrlConnection.getURL();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getResponseMessage() throws IOException {
 		return wrappedUrlConnection.getResponseMessage();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Map<String, List<String>> getHeaderFields() {
 		return wrappedUrlConnection.getHeaderFields();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setRequestProperty(String key, String value) {
 		wrappedUrlConnection.setRequestProperty(key, value);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setRequestMethod(String method) throws ProtocolException {
 		wrappedUrlConnection.setRequestMethod(method);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setUseCaches(boolean usecaches) {
 		wrappedUrlConnection.setUseCaches(usecaches);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setConnectTimeout(int timeout) {
 		wrappedUrlConnection.setConnectTimeout(timeout);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setReadTimeout(int timeout) {
 		wrappedUrlConnection.setReadTimeout(timeout);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getContentType() {
 		return wrappedUrlConnection.getContentType();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public InputStream getInputStream() throws IOException {
 		return wrappedUrlConnection.getInputStream();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getHeaderField(String name) {
 		return wrappedUrlConnection.getHeaderField(name);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int getContentLength() {
 		return wrappedUrlConnection.getContentLength();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setInstanceFollowRedirects(boolean followRedirects) {
 		wrappedUrlConnection.setInstanceFollowRedirects(followRedirects);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setDoOutput(boolean dooutput) {
 		wrappedUrlConnection.setDoOutput(dooutput);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setFixedLengthStreamingMode(int contentLength) {
 		wrappedUrlConnection.setFixedLengthStreamingMode(contentLength);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public OutputStream getOutputStream() throws IOException {
 		return wrappedUrlConnection.getOutputStream();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setChunkedStreamingMode(int chunklen) {
 		wrappedUrlConnection.setChunkedStreamingMode(chunklen);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getRequestMethod() {
 		return wrappedUrlConnection.getRequestMethod();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean usingProxy() {
 		return wrappedUrlConnection.usingProxy();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void connect() throws IOException {
 		wrappedUrlConnection.connect();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void setHostnameVerifier(HostnameVerifier hostnameverifier) {
 		((HttpsURLConnection) wrappedUrlConnection)
 				.setHostnameVerifier(hostnameverifier);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void configure(KeyManager[] km, TrustManager[] tm,
 			SecureRandom random) throws NoSuchAlgorithmException,
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/JDKHttpConnectionFactory.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/JDKHttpConnectionFactory.java
index b9f009f1b7..ef88947aad 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/JDKHttpConnectionFactory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/http/JDKHttpConnectionFactory.java
@@ -47,16 +47,19 @@ import java.net.Proxy;
 import java.net.URL;
 
 /**
- * A factory returning instances of {@link JDKHttpConnection}
+ * A factory returning instances of
+ * {@link org.eclipse.jgit.transport.http.JDKHttpConnection}
  *
  * @since 3.3
  */
 public class JDKHttpConnectionFactory implements HttpConnectionFactory {
+	/** {@inheritDoc} */
 	@Override
 	public HttpConnection create(URL url) throws IOException {
 		return new JDKHttpConnection(url);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public HttpConnection create(URL url, Proxy proxy)
 			throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/FileResolver.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/FileResolver.java
index 8ab112e5f9..16a6f4ab73 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/FileResolver.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/FileResolver.java
@@ -70,7 +70,9 @@ public class FileResolver<C> implements RepositoryResolver<C> {
 
 	private final Collection<File> exportBase;
 
-	/** Initialize an empty file based resolver. */
+	/**
+	 * Initialize an empty file based resolver.
+	 */
 	public FileResolver() {
 		exports = new ConcurrentHashMap<>();
 		exportBase = new CopyOnWriteArrayList<>();
@@ -91,6 +93,7 @@ public class FileResolver<C> implements RepositoryResolver<C> {
 		setExportAll(exportAll);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Repository open(final C req, final String name)
 			throws RepositoryNotFoundException, ServiceNotEnabledException {
@@ -148,6 +151,9 @@ public class FileResolver<C> implements RepositoryResolver<C> {
 	}
 
 	/**
+	 * Whether <code>git-daemon-export-ok</code> is required to export a
+	 * repository
+	 *
 	 * @return false if <code>git-daemon-export-ok</code> is required to export
 	 *         a repository; true if <code>git-daemon-export-ok</code> is
 	 *         ignored.
@@ -167,7 +173,7 @@ public class FileResolver<C> implements RepositoryResolver<C> {
 	 * If true, all repositories are available through the daemon, whether or
 	 * not <code>git-daemon-export-ok</code> exists.
 	 *
-	 * @param export
+	 * @param export a boolean.
 	 */
 	public void setExportAll(final boolean export) {
 		exportAll = export;
@@ -214,7 +220,7 @@ public class FileResolver<C> implements RepositoryResolver<C> {
 	 * @param db
 	 *            the opened repository instance.
 	 * @return true if the repository is accessible; false if not.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository could not be accessed, the caller will claim
 	 *             the repository does not exist.
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/ReceivePackFactory.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/ReceivePackFactory.java
index 73c2ed80c9..4967169776 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/ReceivePackFactory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/ReceivePackFactory.java
@@ -47,13 +47,16 @@ import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.transport.ReceivePack;
 
 /**
- * Create and configure {@link ReceivePack} service instance.
+ * Create and configure {@link org.eclipse.jgit.transport.ReceivePack} service
+ * instance.
  *
  * @param <C>
  *            type of connection
  */
 public interface ReceivePackFactory<C> {
-	/** A factory disabling the ReceivePack service for all repositories */
+	/**
+	 * A factory disabling the ReceivePack service for all repositories
+	 */
 	public static final ReceivePackFactory<?> DISABLED = new ReceivePackFactory<Object>() {
 		@Override
 		public ReceivePack create(Object req, Repository db)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/RepositoryResolver.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/RepositoryResolver.java
index 80211e5812..a305e4cea3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/RepositoryResolver.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/RepositoryResolver.java
@@ -48,13 +48,15 @@ import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.transport.ServiceMayNotContinueException;
 
 /**
- * Locate a Git {@link Repository} by name from the URL.
+ * Locate a Git {@link org.eclipse.jgit.lib.Repository} by name from the URL.
  *
  * @param <C>
  *            type of connection.
  */
 public interface RepositoryResolver<C> {
-	/** Resolver configured to open nothing. */
+	/**
+	 * Resolver configured to open nothing.
+	 */
 	public static final RepositoryResolver<?> NONE = new RepositoryResolver<Object>() {
 		@Override
 		public Repository open(Object req, String name)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/ServiceNotAuthorizedException.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/ServiceNotAuthorizedException.java
index 57a61928b5..d2d1b99d2f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/ServiceNotAuthorizedException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/ServiceNotAuthorizedException.java
@@ -56,8 +56,12 @@ public class ServiceNotAuthorizedException extends Exception {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for ServiceNotAuthorizedException.
+	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable} object.
 	 * @since 4.1
 	 */
 	public ServiceNotAuthorizedException(String message, Throwable cause) {
@@ -65,14 +69,19 @@ public class ServiceNotAuthorizedException extends Exception {
 	}
 
 	/**
+	 * Constructor for ServiceNotAuthorizedException.
+	 *
 	 * @param message
+	 *            error message
 	 * @since 4.1
 	 */
 	public ServiceNotAuthorizedException(String message) {
 		super(message);
 	}
 
-	/** Indicates that the requested service requires authentication. */
+	/**
+	 * Indicates that the requested service requires authentication.
+	 */
 	public ServiceNotAuthorizedException() {
 		super(JGitText.get().unauthorized);
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/ServiceNotEnabledException.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/ServiceNotEnabledException.java
index 78ae303ed0..4473452d07 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/ServiceNotEnabledException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/ServiceNotEnabledException.java
@@ -45,13 +45,19 @@ package org.eclipse.jgit.transport.resolver;
 
 import org.eclipse.jgit.internal.JGitText;
 
-/** Indicates the request service is not enabled on a repository. */
+/**
+ * Indicates the request service is not enabled on a repository.
+ */
 public class ServiceNotEnabledException extends Exception {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for ServiceNotEnabledException.
+	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable} object.
 	 * @since 4.1
 	 */
 	public ServiceNotEnabledException(String message, Throwable cause) {
@@ -59,14 +65,19 @@ public class ServiceNotEnabledException extends Exception {
 	}
 
 	/**
+	 * Constructor for ServiceNotEnabledException.
+	 *
 	 * @param message
+	 *            error message
 	 * @since 4.1
 	 */
 	public ServiceNotEnabledException(String message) {
 		super(message);
 	}
 
-	/** Indicates the request service is not available. */
+	/**
+	 * Indicates the request service is not available.
+	 */
 	public ServiceNotEnabledException() {
 		super(JGitText.get().serviceNotEnabledNoName);
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/UploadPackFactory.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/UploadPackFactory.java
index d7ed0f68cf..40d1ffdc56 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/UploadPackFactory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/resolver/UploadPackFactory.java
@@ -47,13 +47,16 @@ import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.transport.UploadPack;
 
 /**
- * Create and configure {@link UploadPack} service instance.
+ * Create and configure {@link org.eclipse.jgit.transport.UploadPack} service
+ * instance.
  *
  * @param <C>
  *            the connection type
  */
 public interface UploadPackFactory<C> {
-	/** A factory disabling the UploadPack service for all repositories. */
+	/**
+	 * A factory disabling the UploadPack service for all repositories.
+	 */
 	public static final UploadPackFactory<?> DISABLED = new UploadPackFactory<Object>() {
 		@Override
 		public UploadPack create(Object req, Repository db)