diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/console/ConsoleAuthenticator.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/console/ConsoleAuthenticator.java
index 8bf451c3c..06c95d821 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/console/ConsoleAuthenticator.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/console/ConsoleAuthenticator.java
@@ -58,7 +58,9 @@
  * @since 4.0
  */
 public class ConsoleAuthenticator extends CachedAuthenticator {
-	/** Install this authenticator implementation into the JVM. */
+	/**
+	 * Install this authenticator implementation into the JVM.
+	 */
 	public static void install() {
 		final ConsoleAuthenticator c = new ConsoleAuthenticator();
 		if (c.cons == null)
@@ -69,6 +71,7 @@ public static void install() {
 
 	private final Console cons = System.console();
 
+	/** {@inheritDoc} */
 	@Override
 	protected PasswordAuthentication promptPasswordAuthentication() {
 		final String realm = formatRealm();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/console/ConsoleCredentialsProvider.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/console/ConsoleCredentialsProvider.java
index 0aa0cf484..f8442facb 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/console/ConsoleCredentialsProvider.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/console/ConsoleCredentialsProvider.java
@@ -61,7 +61,9 @@
  * @since 4.0
  */
 public class ConsoleCredentialsProvider extends CredentialsProvider {
-	/** Install this implementation as the default. */
+	/**
+	 * Install this implementation as the default.
+	 */
 	public static void install() {
 		final ConsoleCredentialsProvider c = new ConsoleCredentialsProvider();
 		if (c.cons == null)
@@ -74,11 +76,13 @@ public static void install() {
 
 	private final Console cons = System.console();
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean isInteractive() {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean supports(CredentialItem... items) {
 		for (CredentialItem i : items) {
@@ -100,6 +104,7 @@ else if (i instanceof CredentialItem.InformationalMessage)
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean get(URIish uri, CredentialItem... items)
 			throws UnsupportedCredentialItem {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/AbstractFetchCommand.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/AbstractFetchCommand.java
index 08ec0964f..f0754b192 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/AbstractFetchCommand.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/AbstractFetchCommand.java
@@ -66,6 +66,14 @@ abstract class AbstractFetchCommand extends TextBuiltin {
 	@Option(name = "--verbose", aliases = { "-v" }, usage = "usage_beMoreVerbose")
 	private boolean verbose;
 
+	/**
+	 * Show fetch result.
+	 *
+	 * @param r
+	 *            a {@link org.eclipse.jgit.transport.FetchResult} object.
+	 * @throws java.io.IOException
+	 *             if any.
+	 */
 	protected void showFetchResult(final FetchResult r) throws IOException {
 		try (ObjectReader reader = db.newObjectReader()) {
 			boolean shownURI = false;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Add.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Add.java
index 3c1359030..08a9f48c0 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Add.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Add.java
@@ -60,6 +60,7 @@ class Add extends TextBuiltin {
 	@Argument(required = true, metaVar = "metaVar_filepattern", usage = "usage_filesToAddContentFrom")
 	private List<String> filepatterns = new ArrayList<>();
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/AmazonS3Client.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/AmazonS3Client.java
index e0a9244a8..086c9766a 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/AmazonS3Client.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/AmazonS3Client.java
@@ -75,11 +75,13 @@ class AmazonS3Client extends TextBuiltin {
 	@Argument(index = 3, metaVar = "metaVar_KEY", required = true)
 	private String key;
 
+	/** {@inheritDoc} */
 	@Override
 	protected final boolean requiresRepository() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		final AmazonS3 s3 = new AmazonS3(properties());
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Archive.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Archive.java
index cff0bf6c2..4721b3a0f 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Archive.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Archive.java
@@ -74,6 +74,7 @@ class Archive extends TextBuiltin {
 	@Option(name = "--output", aliases = { "-o" }, metaVar = "metaVar_file", usage = "usage_archiveOutput")
 	private String output;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		if (tree == null)
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
index 419325405..13a38dddf 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
@@ -134,6 +134,7 @@ void ignoreAllSpace(@SuppressWarnings("unused") boolean on) {
 
 	private BlameResult blame;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		if (file == null) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java
index f6e3810a8..e6685c2f6 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java
@@ -87,6 +87,12 @@ class Branch extends TextBuiltin {
 
 	private List<String> delete;
 
+	/**
+	 * Delete branches
+	 *
+	 * @param names
+	 *            a {@link java.util.List} of branch names.
+	 */
 	@Option(name = "--delete", aliases = {
 			"-d" }, metaVar = "metaVar_branchNames", usage = "usage_deleteFullyMergedBranch", handler = OptionWithValuesListHandler.class)
 	public void delete(List<String> names) {
@@ -98,6 +104,12 @@ public void delete(List<String> names) {
 
 	private List<String> deleteForce;
 
+	/**
+	 * Forcefully delete branches
+	 *
+	 * @param names
+	 *            a {@link java.util.List} of branch names.
+	 */
 	@Option(name = "--delete-force", aliases = {
 			"-D" }, metaVar = "metaVar_branchNames", usage = "usage_deleteBranchEvenIfNotMerged", handler = OptionWithValuesListHandler.class)
 	public void deleteForce(List<String> names) {
@@ -107,6 +119,12 @@ public void deleteForce(List<String> names) {
 		deleteForce = names;
 	}
 
+	/**
+	 * Forcefully create a list of branches
+	 *
+	 * @param branchAndStartPoint
+	 *            a branch name and a start point
+	 */
 	@Option(name = "--create-force", aliases = {
 			"-f" }, metaVar = "metaVar_branchAndStartPoint", usage = "usage_forceCreateBranchEvenExists", handler = OptionWithValuesListHandler.class)
 	public void createForce(List<String> branchAndStartPoint) {
@@ -125,6 +143,12 @@ public void createForce(List<String> branchAndStartPoint) {
 		}
 	}
 
+	/**
+	 * Move or rename a branch
+	 *
+	 * @param currentAndNew
+	 *            the current and the new branch name
+	 */
 	@Option(name = "--move", aliases = {
 			"-m" }, metaVar = "metaVar_oldNewBranchNames", usage = "usage_moveRenameABranch", handler = OptionWithValuesListHandler.class)
 	public void moveRename(List<String> currentAndNew) {
@@ -156,6 +180,7 @@ public void moveRename(List<String> currentAndNew) {
 
 	private int maxNameLength;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		if (delete != null || deleteForce != null) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Checkout.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Checkout.java
index 2af1eca80..1f80301f6 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Checkout.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Checkout.java
@@ -80,6 +80,7 @@ class Checkout extends TextBuiltin {
 	@Option(name = "--", metaVar = "metaVar_paths", handler = RestOfArgumentsHandler.class)
 	private List<String> paths = new ArrayList<>();
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		if (createBranch) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clean.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clean.java
index ce4faf83a..6ae078c95 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clean.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clean.java
@@ -62,6 +62,7 @@ class Clean extends TextBuiltin {
 	@Option(name = "--dryRun", aliases = { "-n" })
 	private boolean dryRun = false;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java
index a8eb4742d..393c607a2 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java
@@ -86,11 +86,13 @@ class Clone extends AbstractFetchCommand implements CloneCommand.Callback {
 	@Argument(index = 1, metaVar = "metaVar_directory")
 	private String localName;
 
+	/** {@inheritDoc} */
 	@Override
 	protected final boolean requiresRepository() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		if (localName != null && gitdir != null)
@@ -148,6 +150,7 @@ protected void run() throws Exception {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void initializedSubmodules(Collection<String> submodules) {
 		try {
@@ -161,6 +164,7 @@ public void initializedSubmodules(Collection<String> submodules) {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void cloningSubmodule(String path) {
 		try {
@@ -172,6 +176,7 @@ public void cloningSubmodule(String path) {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void checkingOut(AnyObjectId commit, String path) {
 		try {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Command.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Command.java
index 0562416a8..d7adaf841 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Command.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Command.java
@@ -50,7 +50,7 @@
 import java.lang.annotation.Target;
 
 /**
- * Annotation to document a {@link TextBuiltin}.
+ * Annotation to document a {@link org.eclipse.jgit.pgm.TextBuiltin}.
  * <p>
  * This is an optional annotation for TextBuiltin subclasses and it carries
  * documentation forward into the runtime system describing what the command is
@@ -60,6 +60,8 @@
 @Target( { TYPE })
 public @interface Command {
 	/**
+	 * Get the command name
+	 *
 	 * @return name the command is invoked as from the command line. If the
 	 *         (default) empty string is supplied the name will be generated
 	 *         from the class name.
@@ -67,11 +69,15 @@
 	public String name() default "";
 
 	/**
+	 * Get command description
+	 *
 	 * @return one line description of the command's feature set.
 	 */
 	public String usage() default "";
 
 	/**
+	 * If this command is considered to be commonly used
+	 *
 	 * @return true if this command is considered to be commonly used.
 	 */
 	public boolean common() default false;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CommandCatalog.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CommandCatalog.java
index cf4c6e333..7bab69210 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CommandCatalog.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CommandCatalog.java
@@ -60,9 +60,10 @@
 /**
  * List of all commands known by jgit's command line tools.
  * <p>
- * Commands are implementations of {@link TextBuiltin}, with an optional
- * {@link Command} class annotation to insert additional documentation or
- * override the default command name (which is guessed from the class name).
+ * Commands are implementations of {@link org.eclipse.jgit.pgm.TextBuiltin},
+ * with an optional {@link org.eclipse.jgit.pgm.Command} class annotation to
+ * insert additional documentation or override the default command name (which
+ * is guessed from the class name).
  * <p>
  * Commands may be registered by adding them to a services file in the same JAR
  * (or classes directory) as the command implementation. The service file name
@@ -90,6 +91,8 @@ public static CommandRef get(final String name) {
 	}
 
 	/**
+	 * Get all commands sorted by their name
+	 *
 	 * @return all known commands, sorted by command name.
 	 */
 	public static CommandRef[] all() {
@@ -97,6 +100,8 @@ public static CommandRef[] all() {
 	}
 
 	/**
+	 * Get all common commands sorted by their name
+	 *
 	 * @return all common commands, sorted by command name.
 	 */
 	public static CommandRef[] common() {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CommandRef.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CommandRef.java
index e5f85324e..2c9bc0dc7 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CommandRef.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CommandRef.java
@@ -50,7 +50,8 @@
 import org.eclipse.jgit.pgm.internal.CLIText;
 
 /**
- * Description of a command (a {@link TextBuiltin} subclass.
+ * Description of a command (a {@link org.eclipse.jgit.pgm.TextBuiltin}
+ * subclass).
  * <p>
  * These descriptions are lightweight compared to creating a command instance
  * and are therefore suitable for catalogs of "known" commands without linking
@@ -102,6 +103,8 @@ private static String guessName(final Class<? extends TextBuiltin> clazz) {
 	}
 
 	/**
+	 * Get the <code>name</code>.
+	 *
 	 * @return name the command is invoked as from the command line.
 	 */
 	public String getName() {
@@ -109,6 +112,8 @@ public String getName() {
 	}
 
 	/**
+	 * Get <code>usage</code>.
+	 *
 	 * @return one line description of the command's feature set.
 	 */
 	public String getUsage() {
@@ -116,6 +121,8 @@ public String getUsage() {
 	}
 
 	/**
+	 * Is this command commonly used
+	 *
 	 * @return true if this command is considered to be commonly used.
 	 */
 	public boolean isCommon() {
@@ -123,6 +130,8 @@ public boolean isCommon() {
 	}
 
 	/**
+	 * Get implementation class name
+	 *
 	 * @return name of the Java class which implements this command.
 	 */
 	public String getImplementationClassName() {
@@ -130,6 +139,8 @@ public String getImplementationClassName() {
 	}
 
 	/**
+	 * Get implementation class loader
+	 *
 	 * @return loader for {@link #getImplementationClassName()}.
 	 */
 	public ClassLoader getImplementationClassLoader() {
@@ -137,6 +148,8 @@ public ClassLoader getImplementationClassLoader() {
 	}
 
 	/**
+	 * Create an instance of the command implementation
+	 *
 	 * @return a new instance of the command implementation.
 	 */
 	public TextBuiltin create() {
@@ -166,6 +179,7 @@ public TextBuiltin create() {
 		return r;
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Commit.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Commit.java
index befc4ec27..2e67c02cb 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Commit.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Commit.java
@@ -77,6 +77,7 @@ class Commit extends TextBuiltin {
 	@Argument(metaVar = "metaVar_commitPaths", usage = "usage_CommitPaths")
 	private List<String> paths = new ArrayList<>();
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws NoHeadException, NoMessageException,
 			ConcurrentRefUpdateException, JGitInternalException, Exception {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Config.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Config.java
index f5c3f9aeb..f762c0d05 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Config.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Config.java
@@ -68,6 +68,7 @@ class Config extends TextBuiltin {
 	@Option(name = "--file", aliases = { "-f" }, metaVar = "metaVar_file", usage = "usage_configFile")
 	private File configFile;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		if (list)
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Daemon.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Daemon.java
index 51bb9792d..d0ada67fc 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Daemon.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Daemon.java
@@ -111,11 +111,13 @@ enum KetchServerType {
 	@Argument(required = true, metaVar = "metaVar_directory", usage = "usage_directoriesToExport")
 	List<File> directory = new ArrayList<>();
 
+	/** {@inheritDoc} */
 	@Override
 	protected boolean requiresRepository() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		PackConfig packConfig = new PackConfig();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Describe.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Describe.java
index 03e271199..f9c1cf5d3 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Describe.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Describe.java
@@ -65,6 +65,7 @@ class Describe extends TextBuiltin {
 	@Option(name = "--match", usage = "usage_Match", metaVar = "metaVar_pattern")
 	private List<String> patterns = new ArrayList<>();
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Die.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Die.java
index a25f1e930..59de80c96 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Die.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Die.java
@@ -45,7 +45,8 @@
 package org.eclipse.jgit.pgm;
 
 /**
- * Indicates a {@link TextBuiltin} implementation has failed during execution.
+ * Indicates a {@link org.eclipse.jgit.pgm.TextBuiltin} implementation has
+ * failed during execution.
  * <p>
  * Typically the stack trace for a Die exception is not shown to the user as it
  * may indicate a simple error condition that the end-user can fix on their own,
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Diff.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Diff.java
index 16284d572..ed6f7b426 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Diff.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Diff.java
@@ -168,12 +168,14 @@ void noPrefix(@SuppressWarnings("unused") boolean on) {
 
 	// END -- Options shared with Log
 
+	/** {@inheritDoc} */
 	@Override
 	protected void init(final Repository repository, final String gitDir) {
 		super.init(repository, gitDir);
 		diffFmt = new DiffFormatter(new BufferedOutputStream(outs));
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		diffFmt.setRepository(db);
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/DiffTree.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/DiffTree.java
index 443240599..510406345 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/DiffTree.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/DiffTree.java
@@ -72,6 +72,7 @@ void tree_0(final AbstractTreeIterator c) {
 	@Option(name = "--", metaVar = "metaVar_path", handler = PathTreeFilterHandler.class)
 	private TreeFilter pathFilter = TreeFilter.ALL;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (final TreeWalk walk = new TreeWalk(db)) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Fetch.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Fetch.java
index f4b7708d3..bc7637286 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Fetch.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Fetch.java
@@ -131,6 +131,7 @@ void noRecurseSubmodules(@SuppressWarnings("unused")
 	@Argument(index = 1, metaVar = "metaVar_refspec")
 	private List<RefSpec> toget;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
@@ -164,6 +165,7 @@ protected void run() throws Exception {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void fetchingSubmodule(String name) {
 		try {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Gc.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Gc.java
index 7289abb62..56172f57c 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Gc.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Gc.java
@@ -58,6 +58,7 @@ class Gc extends TextBuiltin {
 	@Option(name = "--prune-preserved", usage = "usage_PrunePreserved")
 	private boolean prunePreserved;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		Git git = Git.wrap(db);
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Glog.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Glog.java
index 7b715751d..a081b7813 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Glog.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Glog.java
@@ -102,6 +102,7 @@ public void actionPerformed(ActionEvent e) {
 		frame.getContentPane().add(world);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected int walkLoop() throws Exception {
 		graphPane.getCommitList().source(walk);
@@ -113,11 +114,13 @@ protected int walkLoop() throws Exception {
 		return graphPane.getCommitList().size();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void show(final RevCommit c) throws Exception {
 		throw new UnsupportedOperationException();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected RevWalk createWalk() {
 		if (objects)
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/IndexPack.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/IndexPack.java
index 22f3be9af..26276718d 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/IndexPack.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/IndexPack.java
@@ -60,6 +60,7 @@ class IndexPack extends TextBuiltin {
 	@Option(name = "--index-version", usage = "usage_indexFileFormatToCreate")
 	private int indexVersion = -1;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		BufferedInputStream in = new BufferedInputStream(ins);
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java
index a7bee7f7b..f880fc207 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Init.java
@@ -66,11 +66,13 @@ class Init extends TextBuiltin {
 	@Argument(index = 0, metaVar = "metaVar_directory")
 	private String directory;
 
+	/** {@inheritDoc} */
 	@Override
 	protected final boolean requiresRepository() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		InitCommand command = Git.init();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Log.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Log.java
index 1108ddd10..75542d445 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Log.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Log.java
@@ -184,12 +184,14 @@ void noPrefix(@SuppressWarnings("unused") boolean on) {
 		dateFormatter = new GitDateFormatter(Format.DEFAULT);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void init(final Repository repository, final String gitDir) {
 		super.init(repository, gitDir);
 		diffFmt = new DiffFormatter(new BufferedOutputStream(outs));
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		diffFmt.setRepository(db);
@@ -237,6 +239,7 @@ private void addNoteMap(String notesRef) throws IOException {
 				NoteMap.read(argWalk.getObjectReader(), notesCommit));
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void show(final RevCommit c) throws Exception {
 		outw.print(CLIText.get().commitLabel);
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsRemote.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsRemote.java
index 7a5f3d811..9013ff6cf 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsRemote.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsRemote.java
@@ -70,6 +70,7 @@ class LsRemote extends TextBuiltin {
 	@Argument(index = 0, metaVar = "metaVar_uriish", required = true)
 	private String remote;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		LsRemoteCommand command = Git.lsRemoteRepository().setRemote(remote)
@@ -89,6 +90,7 @@ public int compare(Ref r1, Ref r2) {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected boolean requiresRepository() {
 		return false;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsTree.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsTree.java
index 398d305f6..c57f9f2c3 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsTree.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/LsTree.java
@@ -70,6 +70,7 @@ class LsTree extends TextBuiltin {
 	@Option(name = "--", metaVar = "metaVar_paths", handler = StopOptionHandler.class)
 	private List<String> paths = new ArrayList<>();
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (final TreeWalk walk = new TreeWalk(db)) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java
index 9d44dc08c..b29b09747 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java
@@ -80,7 +80,9 @@
 import org.kohsuke.args4j.Option;
 import org.kohsuke.args4j.OptionHandlerFilter;
 
-/** Command line entry point. */
+/**
+ * Command line entry point.
+ */
 public class Main {
 	@Option(name = "--help", usage = "usage_displayThisHelpText", aliases = { "-h" })
 	private boolean help;
@@ -105,7 +107,7 @@ public class Main {
 	private ExecutorService gcExecutor;
 
 	/**
-	 *
+	 * <p>Constructor for Main.</p>
 	 */
 	public Main() {
 		HttpTransport.setConnectionFactory(new HttpClientConnectionFactory());
@@ -129,7 +131,7 @@ public Thread newThread(Runnable taskBody) {
 	 *
 	 * @param argv
 	 *            arguments.
-	 * @throws Exception
+	 * @throws java.lang.Exception
 	 */
 	public static void main(final String[] argv) throws Exception {
 		new Main().run(argv);
@@ -150,7 +152,7 @@ public static void main(final String[] argv) throws Exception {
 	 *
 	 * @param argv
 	 *            arguments.
-	 * @throws Exception
+	 * @throws java.lang.Exception
 	 */
 	protected void run(final String[] argv) throws Exception {
 		writer = createErrorWriter();
@@ -309,7 +311,7 @@ void exit(int status, Exception t) throws Exception {
 	 *            the {@code --git-dir} option given on the command line. May be
 	 *            null if it was not supplied.
 	 * @return the repository to operate on.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository cannot be opened.
 	 */
 	protected Repository openGitDir(String aGitdir) throws IOException {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Merge.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Merge.java
index 1aab748a0..de059e941 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Merge.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Merge.java
@@ -101,6 +101,7 @@ void ffonly(@SuppressWarnings("unused") final boolean ignored) {
 	@Option(name = "-m", usage = "usage_message")
 	private String message;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		if (squash && ff == FastForwardMode.NO_FF)
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MergeBase.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MergeBase.java
index 975d5deee..62a88aeed 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MergeBase.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MergeBase.java
@@ -65,6 +65,7 @@ void commit_0(final RevCommit c) {
 	@Argument(index = 1, metaVar = "metaVar_commitish", required = true)
 	private List<RevCommit> commits = new ArrayList<>();
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		for (final RevCommit c : commits)
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Push.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Push.java
index 389708e6e..309dca2a7 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Push.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Push.java
@@ -113,6 +113,7 @@ void nothin(@SuppressWarnings("unused") final boolean ignored) {
 
 	private boolean shownURI;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ReceivePack.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ReceivePack.java
index d7f895a30..f3baafb0b 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ReceivePack.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ReceivePack.java
@@ -58,11 +58,13 @@ class ReceivePack extends TextBuiltin {
 	@Argument(index = 0, required = true, metaVar = "metaVar_directory", usage = "usage_RepositoryToReceiveInto")
 	File dstGitdir;
 
+	/** {@inheritDoc} */
 	@Override
 	protected final boolean requiresRepository() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		final org.eclipse.jgit.transport.ReceivePack rp;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reflog.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reflog.java
index 86a021dee..6f4fcc248 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reflog.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reflog.java
@@ -57,6 +57,7 @@ class Reflog extends TextBuiltin {
 	@Argument(metaVar = "metaVar_ref")
 	private String ref;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Remote.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Remote.java
index 24916bd1c..948cbc554 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Remote.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Remote.java
@@ -84,6 +84,7 @@ class Remote extends TextBuiltin {
 	@Argument(index = 2, metaVar = "metaVar_uriish")
 	private String uri;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
@@ -143,6 +144,7 @@ protected void run() throws Exception {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void printUsage(final String message, final CmdLineParser clp)
 			throws IOException {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Repo.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Repo.java
index bec5003a1..f557211fd 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Repo.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Repo.java
@@ -58,6 +58,7 @@ class Repo extends TextBuiltin {
 	@Argument(required = true, metaVar = "metaVar_path", usage = "usage_pathToXml")
 	private String path;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		new RepoCommand(db)
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reset.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reset.java
index 4c19883c8..f84c84806 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reset.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reset.java
@@ -72,6 +72,7 @@ class Reset extends TextBuiltin {
 	@Option(name = "--", metaVar = "metaVar_paths", handler = RestOfArgumentsHandler.class)
 	private List<String> paths = new ArrayList<>();
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevList.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevList.java
index 4420abec1..8c88a5cdc 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevList.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevList.java
@@ -51,6 +51,7 @@
 
 @Command(usage = "usage_RevList")
 class RevList extends RevWalkTextBuiltin {
+	/** {@inheritDoc} */
 	@Override
 	protected void show(final RevCommit c) throws Exception {
 		if (c.has(RevFlag.UNINTERESTING))
@@ -64,6 +65,7 @@ protected void show(final RevCommit c) throws Exception {
 		outw.println();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void show(final ObjectWalk ow, final RevObject obj)
 			throws Exception {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevParse.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevParse.java
index 215703409..21adf738e 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevParse.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevParse.java
@@ -70,6 +70,7 @@ class RevParse extends TextBuiltin {
 	@Argument(index = 0, metaVar = "metaVar_commitish")
 	private List<ObjectId> commits = new ArrayList<>();
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		if (all) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevWalkTextBuiltin.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevWalkTextBuiltin.java
index 6b0744d51..3fc91013a 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevWalkTextBuiltin.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevWalkTextBuiltin.java
@@ -149,6 +149,7 @@ void addCMessageRevFilter(final String msg) {
 	@Option(name = "--max-count", aliases = "-n", metaVar = "metaVar_n")
 	private int maxCount = -1;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		walk = createWalk();
@@ -210,6 +211,11 @@ else if (revLimiter.size() > 1)
 		}
 	}
 
+	/**
+	 * Create RevWalk
+	 *
+	 * @return a {@link org.eclipse.jgit.revwalk.RevWalk} object.
+	 */
 	protected RevWalk createWalk() {
 		RevWalk result;
 		if (objects)
@@ -222,6 +228,13 @@ else if (argWalk != null)
 		return result;
 	}
 
+	/**
+	 * Loop the walk
+	 *
+	 * @return number of RevCommits walked
+	 * @throws java.lang.Exception
+	 *             if any.
+	 */
 	protected int walkLoop() throws Exception {
 		int n = 0;
 		for (final RevCommit c : walk) {
@@ -248,8 +261,8 @@ protected int walkLoop() throws Exception {
 	 * RevWalkTextBuiltin.
 	 *
 	 * @param c
-	 *            The current {@link RevCommit}
-	 * @throws Exception
+	 *            The current {@link org.eclipse.jgit.revwalk.RevCommit}
+	 * @throws java.lang.Exception
 	 */
 	protected abstract void show(final RevCommit c) throws Exception;
 
@@ -260,10 +273,11 @@ protected int walkLoop() throws Exception {
 	 * process RevCommits.
 	 *
 	 * @param objectWalk
-	 *            the {@link ObjectWalk} used by {@link #walkLoop()}
+	 *            the {@link org.eclipse.jgit.revwalk.ObjectWalk} used by
+	 *            {@link #walkLoop()}
 	 * @param currentObject
-	 *            The current {@link RevObject}
-	 * @throws Exception
+	 *            The current {@link org.eclipse.jgit.revwalk.RevObject}
+	 * @throws java.lang.Exception
 	 */
 	protected void show(final ObjectWalk objectWalk,
 			final RevObject currentObject) throws Exception {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Rm.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Rm.java
index 32a5631e5..f59161039 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Rm.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Rm.java
@@ -59,6 +59,7 @@ class Rm extends TextBuiltin {
 	@Option(name = "--", handler = StopOptionHandler.class)
 	private List<String> paths = new ArrayList<>();
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java
index 5eda36f39..de04045e4 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java
@@ -165,12 +165,14 @@ void noPrefix(@SuppressWarnings("unused") boolean on) {
 		fmt = new SimpleDateFormat("EEE MMM dd HH:mm:ss yyyy ZZZZZ", Locale.US); //$NON-NLS-1$
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void init(final Repository repository, final String gitDir) {
 		super.init(repository, gitDir);
 		diffFmt = new DiffFormatter(new BufferedOutputStream(outs));
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("boxing")
 	@Override
 	protected void run() throws Exception {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ShowRef.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ShowRef.java
index e9d9df6a1..7b59d437a 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ShowRef.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ShowRef.java
@@ -58,6 +58,7 @@
 
 @Command(usage = "usage_ShowRef")
 class ShowRef extends TextBuiltin {
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		for (final Ref r : getSortedRefs()) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Status.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Status.java
index adcfea4dc..4238f207e 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Status.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Status.java
@@ -86,6 +86,7 @@ class Status extends TextBuiltin {
 	@Option(name = "--", metaVar = "metaVar_paths", handler = RestOfArgumentsHandler.class)
 	protected List<String> filterPaths;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
@@ -261,6 +262,15 @@ private void printLongStatus(org.eclipse.jgit.api.Status status)
 		}
 	}
 
+	/**
+	 * Print section header
+	 *
+	 * @param pattern
+	 *            a {@link java.lang.String} object.
+	 * @param arguments
+	 *            a {@link java.lang.Object} object.
+	 * @throws java.io.IOException
+	 */
 	protected void printSectionHeader(String pattern, Object... arguments)
 			throws IOException {
 		if (!porcelain) {
@@ -272,6 +282,14 @@ protected void printSectionHeader(String pattern, Object... arguments)
 		}
 	}
 
+	/**
+	 * Print String list
+	 *
+	 * @param list
+	 *            a {@link java.util.Collection} object.
+	 * @return a int.
+	 * @throws java.io.IOException
+	 */
 	protected int printList(Collection<String> list) throws IOException {
 		if (!list.isEmpty()) {
 			List<String> sortedList = new ArrayList<>(list);
@@ -286,6 +304,26 @@ protected int printList(Collection<String> list) throws IOException {
 			return 0;
 	}
 
+	/**
+	 * Print String list
+	 *
+	 * @param status1
+	 *            a {@link java.lang.String} object.
+	 * @param status2
+	 *            a {@link java.lang.String} object.
+	 * @param status3
+	 *            a {@link java.lang.String} object.
+	 * @param list
+	 *            a {@link java.util.Collection} object.
+	 * @param set1
+	 *            a {@link java.util.Collection} object.
+	 * @param set2
+	 *            a {@link java.util.Collection} object.
+	 * @param set3
+	 *            a {@link java.util.Collection} object.
+	 * @return a int.
+	 * @throws java.io.IOException
+	 */
 	protected int printList(String status1, String status2, String status3,
 			Collection<String> list, Collection<String> set1,
 			Collection<String> set2,
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Tag.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Tag.java
index dc4b037cf..43c1f54ab 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Tag.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Tag.java
@@ -80,6 +80,7 @@ class Tag extends TextBuiltin {
 	@Argument(index = 1, metaVar = "metaVar_object")
 	private ObjectId object;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java
index c3b45e8de..bc3755d34 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java
@@ -133,7 +133,11 @@ final void setCommandName(final String name) {
 		commandName = name;
 	}
 
-	/** @return true if {@link #db}/{@link #getRepository()} is required. */
+	/**
+	 * If this command requires a repository.
+	 *
+	 * @return true if {@link #db}/{@link #getRepository()} is required
+	 */
 	protected boolean requiresRepository() {
 		return true;
 	}
@@ -214,7 +218,7 @@ protected void init(final Repository repository, final String gitDir) {
 	 *
 	 * @param args
 	 *            command line arguments passed after the command name.
-	 * @throws Exception
+	 * @throws java.lang.Exception
 	 *             an error occurred while processing the command. The main
 	 *             framework will catch the exception and print a message on
 	 *             standard error.
@@ -233,7 +237,7 @@ public final void execute(String[] args) throws Exception {
 	 *
 	 * @param args
 	 *            the arguments supplied on the command line, if any.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	protected void parseArguments(final String[] args) throws IOException {
 		final CmdLineParser clp = new CmdLineParser(this);
@@ -260,7 +264,8 @@ protected void parseArguments(final String[] args) throws IOException {
 	 * Print the usage line
 	 *
 	 * @param clp
-	 * @throws IOException
+	 *            a {@link org.eclipse.jgit.pgm.opt.CmdLineParser} object.
+	 * @throws java.io.IOException
 	 */
 	public void printUsageAndExit(final CmdLineParser clp) throws IOException {
 		printUsageAndExit("", clp); //$NON-NLS-1$
@@ -270,8 +275,10 @@ public void printUsageAndExit(final CmdLineParser clp) throws IOException {
 	 * Print an error message and the usage line
 	 *
 	 * @param message
+	 *            a {@link java.lang.String} object.
 	 * @param clp
-	 * @throws IOException
+	 *            a {@link org.eclipse.jgit.pgm.opt.CmdLineParser} object.
+	 * @throws java.io.IOException
 	 */
 	public void printUsageAndExit(final String message, final CmdLineParser clp) throws IOException {
 		printUsage(message, clp);
@@ -279,11 +286,13 @@ public void printUsageAndExit(final String message, final CmdLineParser clp) thr
 	}
 
 	/**
+	 * Print usage help text.
+	 *
 	 * @param message
 	 *            non null
 	 * @param clp
 	 *            parser used to print options
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 * @since 4.2
 	 */
 	protected void printUsage(final String message, final CmdLineParser clp)
@@ -302,6 +311,8 @@ protected void printUsage(final String message, final CmdLineParser clp)
 	}
 
 	/**
+	 * Get error writer
+	 *
 	 * @return error writer, typically this is standard error.
 	 * @since 4.2
 	 */
@@ -310,6 +321,8 @@ public ThrowingPrintWriter getErrorWriter() {
 	}
 
 	/**
+	 * Get output writer
+	 *
 	 * @return output writer, typically this is standard output.
 	 * @since 4.9
 	 */
@@ -318,6 +331,8 @@ public ThrowingPrintWriter getOutputWriter() {
 	}
 
 	/**
+	 * Get resource bundle with localized texts
+	 *
 	 * @return the resource bundle that will be passed to args4j for purpose of
 	 *         string localization
 	 */
@@ -330,7 +345,7 @@ protected ResourceBundle getResourceBundle() {
 	 * <p>
 	 * This method should only be invoked by {@link #execute(String[])}.
 	 *
-	 * @throws Exception
+	 * @throws java.lang.Exception
 	 *             an error occurred while processing the command. The main
 	 *             framework will catch the exception and print a message on
 	 *             standard error.
@@ -338,6 +353,8 @@ protected ResourceBundle getResourceBundle() {
 	protected abstract void run() throws Exception;
 
 	/**
+	 * Get the repository
+	 *
 	 * @return the repository this command accesses.
 	 */
 	public Repository getRepository() {
@@ -352,6 +369,8 @@ ObjectId resolve(final String s) throws IOException {
 	}
 
 	/**
+	 * Exit the command with an error message
+	 *
 	 * @param why
 	 *            textual explanation
 	 * @return a runtime exception the caller is expected to throw
@@ -361,6 +380,8 @@ protected static Die die(final String why) {
 	}
 
 	/**
+	 * Exit the command with an error message and an exception
+	 *
 	 * @param why
 	 *            textual explanation
 	 * @param cause
@@ -372,8 +393,11 @@ protected static Die die(final String why, final Throwable cause) {
 	}
 
 	/**
+	 * Exit the command
+	 *
 	 * @param aborted
-	 *            boolean indicating that the execution has been aborted before running
+	 *            boolean indicating that the execution has been aborted before
+	 *            running
 	 * @return a runtime exception the caller is expected to throw
 	 * @since 3.4
 	 */
@@ -382,6 +406,8 @@ protected static Die die(boolean aborted) {
 	}
 
 	/**
+	 * Exit the command
+	 *
 	 * @param aborted
 	 *            boolean indicating that the execution has been aborted before
 	 *            running
@@ -405,6 +431,8 @@ else if (abbreviateRemote && dst.startsWith(R_REMOTES))
 	}
 
 	/**
+	 * Check if the arguments contain a help option
+	 *
 	 * @param args
 	 *            non null
 	 * @return true if the given array contains help option
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/UploadPack.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/UploadPack.java
index 447374d69..5d032d208 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/UploadPack.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/UploadPack.java
@@ -62,11 +62,13 @@ class UploadPack extends TextBuiltin {
 	@Argument(index = 0, required = true, metaVar = "metaVar_directory", usage = "usage_RepositoryToReadFrom")
 	File srcGitdir;
 
+	/** {@inheritDoc} */
 	@Override
 	protected final boolean requiresRepository() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		final org.eclipse.jgit.transport.UploadPack up;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Version.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Version.java
index 6bed9c602..5efc03b28 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Version.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Version.java
@@ -55,6 +55,7 @@
 
 @Command(common = true, usage = "usage_DisplayTheVersionOfJgit")
 class Version extends TextBuiltin {
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		// read the Implementation-Version from Manifest
@@ -73,6 +74,7 @@ protected void run() throws Exception {
 		outw.println(MessageFormat.format(CLIText.get().jgitVersion, version));
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected final boolean requiresRepository() {
 		return false;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/BenchmarkReftable.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/BenchmarkReftable.java
index 71c8db8e4..248eaac8a 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/BenchmarkReftable.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/BenchmarkReftable.java
@@ -95,6 +95,7 @@ enum Test {
 	@Argument(index = 1)
 	private String reftablePath;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		switch (test) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/DiffAlgorithms.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/DiffAlgorithms.java
index 8de57e322..5f8ebdb1a 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/DiffAlgorithms.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/DiffAlgorithms.java
@@ -130,11 +130,13 @@ DiffAlgorithm create() {
 
 	private ThreadMXBean mxBean;
 
+	/** {@inheritDoc} */
 	@Override
 	protected boolean requiresRepository() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		mxBean = ManagementFactory.getThreadMXBean();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/LfsStore.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/LfsStore.java
index 9dc47210d..973b0d765 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/LfsStore.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/LfsStore.java
@@ -214,11 +214,13 @@ private static enum StorageClass {
 
 	String secretKey;
 
+	/** {@inheritDoc} */
 	@Override
 	protected boolean requiresRepository() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		AppServer server = new AppServer(port);
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/MakeCacheTree.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/MakeCacheTree.java
index d3a0a3e14..127e54174 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/MakeCacheTree.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/MakeCacheTree.java
@@ -57,6 +57,7 @@
 
 @Command(usage = "usage_MakeCacheTree")
 class MakeCacheTree extends TextBuiltin {
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		final DirCache cache = db.readDirCache();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ReadDirCache.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ReadDirCache.java
index 07bfc4b5f..0194cca49 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ReadDirCache.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ReadDirCache.java
@@ -54,6 +54,7 @@
 
 @Command(usage = "usage_ReadDirCache")
 class ReadDirCache extends TextBuiltin {
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		final int cnt = 100;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ReadReftable.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ReadReftable.java
index 9b8db3e0f..fda19017d 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ReadReftable.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ReadReftable.java
@@ -63,6 +63,7 @@ class ReadReftable extends TextBuiltin {
 	@Argument(index = 1, required = false)
 	private String ref;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (FileInputStream in = new FileInputStream(input);
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java
index da602d0b8..2e41eec7c 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java
@@ -114,6 +114,7 @@ class RebuildCommitGraph extends TextBuiltin {
 
 	private Map<ObjectId, ObjectId> rewrites = new HashMap<>();
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		if (!really && !db.getRefDatabase().getRefs(ALL).isEmpty()) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
index 8cde5138a..317248395 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java
@@ -73,6 +73,7 @@ class RebuildRefTree extends TextBuiltin {
 	private String txnNamespace;
 	private String txnCommitted;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		try (ObjectReader reader = db.newObjectReader();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowCacheTree.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowCacheTree.java
index e287425d7..20fa4a3fe 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowCacheTree.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowCacheTree.java
@@ -57,6 +57,7 @@
 
 @Command(usage = "usage_ShowCacheTree")
 class ShowCacheTree extends TextBuiltin {
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		final DirCache cache = db.readDirCache();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowCommands.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowCommands.java
index 415c7d320..a960ec6dd 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowCommands.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowCommands.java
@@ -59,6 +59,7 @@ class ShowCommands extends TextBuiltin {
 	@Option(name = "--pretty", metaVar = "metaVar_commandDetail", usage = "usage_alterTheDetailShown")
 	private Format pretty = Format.USAGE;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		final CommandRef[] list = CommandCatalog.all();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowDirCache.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowDirCache.java
index bb4f73d7d..7f99d76bd 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowDirCache.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowDirCache.java
@@ -64,6 +64,7 @@ class ShowDirCache extends TextBuiltin {
 	@Option(name = "--millis", aliases = { "-m" }, usage = "usage_showTimeInMilliseconds")
 	private boolean millis = false;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		final SimpleDateFormat fmt;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowPackDelta.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowPackDelta.java
index 150fe6eec..bbc1b0f33 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowPackDelta.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowPackDelta.java
@@ -72,6 +72,7 @@ class ShowPackDelta extends TextBuiltin {
 	@Argument(index = 0)
 	private ObjectId objectId;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		ObjectReader reader = db.newObjectReader();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java
index ce582010f..83b7bcea2 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/TextHashFunctions.java
@@ -262,11 +262,13 @@ public int fold(int hash, int bits) {
 	@Option(name = "--repository", aliases = { "-r" }, metaVar = "GIT_DIR", usage = "Repository to scan")
 	List<File> gitDirs = new ArrayList<>();
 
+	/** {@inheritDoc} */
 	@Override
 	protected boolean requiresRepository() {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		if (gitDirs.isEmpty()) {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/VerifyReftable.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/VerifyReftable.java
index dffb57989..b38de14af 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/VerifyReftable.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/VerifyReftable.java
@@ -75,6 +75,7 @@ class VerifyReftable extends TextBuiltin {
 	@Argument(index = 1)
 	private String reftablePath;
 
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		List<Ref> refs = WriteReftable.readRefs(lsRemotePath);
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteDirCache.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteDirCache.java
index 42428c774..d3b0005ef 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteDirCache.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteDirCache.java
@@ -51,6 +51,7 @@
 
 @Command(usage = "usage_WriteDirCache")
 class WriteDirCache extends TextBuiltin {
+	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
 		final DirCache cache = db.readDirCache();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteReftable.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteReftable.java
index 76ffa194a..6cbc1b082 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteReftable.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteReftable.java
@@ -104,6 +104,7 @@ class WriteReftable extends TextBuiltin {
 	@Argument(index = 1)
 	private String out;
 
+	/** {@inheritDoc} */
 	@SuppressWarnings({ "nls", "boxing" })
 	@Override
 	protected void run() throws Exception {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/CLIText.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/CLIText.java
index dfb489d82..b3ad8bf40 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/CLIText.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/CLIText.java
@@ -79,6 +79,8 @@ public String format(Object... args) {
 	}
 
 	/**
+	 * Format text
+	 *
 	 * @param text
 	 *            the text to format.
 	 * @return a new Format instance.
@@ -88,6 +90,8 @@ public static Format format(String text) {
 	}
 
 	/**
+	 * Get an instance of this translation bundle
+	 *
 	 * @return an instance of this translation bundle
 	 */
 	public static CLIText get() {
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/AbstractTreeIteratorHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/AbstractTreeIteratorHandler.java
index 587f98ca5..6fe792716 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/AbstractTreeIteratorHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/AbstractTreeIteratorHandler.java
@@ -68,7 +68,8 @@
 import org.kohsuke.args4j.spi.Setter;
 
 /**
- * Custom argument handler {@link AbstractTreeIterator} from string values.
+ * Custom argument handler
+ * {@link org.eclipse.jgit.treewalk.AbstractTreeIterator} from string values.
  * <p>
  * Assumes the parser has been initialized with a Repository.
  */
@@ -82,8 +83,11 @@ public class AbstractTreeIteratorHandler extends
 	 * This constructor is used only by args4j.
 	 *
 	 * @param parser
+	 *            a {@link org.kohsuke.args4j.CmdLineParser} object.
 	 * @param option
+	 *            a {@link org.kohsuke.args4j.OptionDef} object.
 	 * @param setter
+	 *            a {@link org.kohsuke.args4j.spi.Setter} object.
 	 */
 	public AbstractTreeIteratorHandler(final CmdLineParser parser,
 			final OptionDef option,
@@ -92,6 +96,7 @@ public AbstractTreeIteratorHandler(final CmdLineParser parser,
 		clp = (org.eclipse.jgit.pgm.opt.CmdLineParser) parser;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int parseArguments(final Parameters params) throws CmdLineException {
 		final String name = params.getParameter(0);
@@ -144,6 +149,7 @@ public int parseArguments(final Parameters params) throws CmdLineException {
 		return 1;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getDefaultMetaVariable() {
 		return CLIText.get().metaVar_treeish;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/CmdLineParser.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/CmdLineParser.java
index 3dcb2a314..e071bdf83 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/CmdLineParser.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/CmdLineParser.java
@@ -61,11 +61,9 @@
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.treewalk.AbstractTreeIterator;
-import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.CmdLineException;
 import org.kohsuke.args4j.IllegalAnnotationError;
 import org.kohsuke.args4j.NamedOptionDef;
-import org.kohsuke.args4j.Option;
 import org.kohsuke.args4j.OptionDef;
 import org.kohsuke.args4j.OptionHandlerRegistry;
 import org.kohsuke.args4j.spi.OptionHandler;
@@ -105,9 +103,10 @@ public class CmdLineParser extends org.kohsuke.args4j.CmdLineParser {
 	 * them into the given object.
 	 *
 	 * @param bean
-	 *            instance of a class annotated by {@link Option} and
-	 *            {@link Argument}. this object will receive values.
-	 *
+	 *            instance of a class annotated by
+	 *            {@link org.kohsuke.args4j.Option} and
+	 *            {@link org.kohsuke.args4j.Argument}. this object will receive
+	 *            values.
 	 * @throws IllegalAnnotationError
 	 *             if the option bean class is using args4j annotations
 	 *             incorrectly.
@@ -121,8 +120,10 @@ public CmdLineParser(final Object bean) {
 	 * them into the given object.
 	 *
 	 * @param bean
-	 *            instance of a class annotated by {@link Option} and
-	 *            {@link Argument}. this object will receive values.
+	 *            instance of a class annotated by
+	 *            {@link org.kohsuke.args4j.Option} and
+	 *            {@link org.kohsuke.args4j.Argument}. this object will receive
+	 *            values.
 	 * @param repo
 	 *            repository this parser can translate options through.
 	 * @throws IllegalAnnotationError
@@ -140,6 +141,7 @@ public CmdLineParser(final Object bean, Repository repo) {
 		this.db = repo;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void parseArgument(final String... args) throws CmdLineException {
 		final ArrayList<String> tmp = new ArrayList<>(args.length);
@@ -223,6 +225,8 @@ private void restoreRequiredOptions(List<OptionHandler> backup) {
 	}
 
 	/**
+	 * Check if array contains help option
+	 *
 	 * @param args
 	 *            non null
 	 * @return true if the given array contains help option
@@ -292,6 +296,7 @@ public boolean required() {
 		}
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected OptionHandler createOptionHandler(OptionDef o, Setter setter) {
 		if (o instanceof NamedOptionDef)
@@ -301,6 +306,7 @@ protected OptionHandler createOptionHandler(OptionDef o, Setter setter) {
 
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public void printSingleLineUsage(Writer w, ResourceBundle rb) {
 		List<OptionHandler> options = getOptions();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/ObjectIdHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/ObjectIdHandler.java
index 74bab2d2e..0e5b0f5b1 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/ObjectIdHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/ObjectIdHandler.java
@@ -56,7 +56,8 @@
 import org.kohsuke.args4j.spi.Setter;
 
 /**
- * Custom argument handler {@link ObjectId} from string values.
+ * Custom argument handler {@link org.eclipse.jgit.lib.ObjectId} from string
+ * values.
  * <p>
  * Assumes the parser has been initialized with a Repository.
  */
@@ -69,8 +70,11 @@ public class ObjectIdHandler extends OptionHandler<ObjectId> {
 	 * This constructor is used only by args4j.
 	 *
 	 * @param parser
+	 *            a {@link org.kohsuke.args4j.CmdLineParser} object.
 	 * @param option
+	 *            a {@link org.kohsuke.args4j.OptionDef} object.
 	 * @param setter
+	 *            a {@link org.kohsuke.args4j.spi.Setter} object.
 	 */
 	public ObjectIdHandler(final CmdLineParser parser, final OptionDef option,
 			final Setter<? super ObjectId> setter) {
@@ -78,6 +82,7 @@ public ObjectIdHandler(final CmdLineParser parser, final OptionDef option,
 		clp = (org.eclipse.jgit.pgm.opt.CmdLineParser) parser;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int parseArguments(final Parameters params) throws CmdLineException {
 		final String name = params.getParameter(0);
@@ -96,6 +101,7 @@ public int parseArguments(final Parameters params) throws CmdLineException {
 				CLIText.format(CLIText.get().notAnObject), name);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getDefaultMetaVariable() {
 		return CLIText.get().metaVar_object;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/OptionWithValuesListHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/OptionWithValuesListHandler.java
index 3de7a8109..7d7c80650 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/OptionWithValuesListHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/OptionWithValuesListHandler.java
@@ -19,15 +19,21 @@
 public class OptionWithValuesListHandler extends OptionHandler<List<?>> {
 
 	/**
+	 * Constructor for OptionWithValuesListHandler.
+	 *
 	 * @param parser
+	 *            a {@link org.kohsuke.args4j.CmdLineParser} object.
 	 * @param option
+	 *            a {@link org.kohsuke.args4j.OptionDef} object.
 	 * @param setter
+	 *            a {@link org.kohsuke.args4j.spi.Setter} object.
 	 */
 	public OptionWithValuesListHandler(CmdLineParser parser,
 			OptionDef option, Setter<List<?>> setter) {
 		super(parser, option, setter);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int parseArguments(Parameters params) throws CmdLineException {
 		final List<String> list = new ArrayList<>();
@@ -44,6 +50,7 @@ public int parseArguments(Parameters params) throws CmdLineException {
 		return list.size();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getDefaultMetaVariable() {
 		return CLIText.get().metaVar_values;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/PathTreeFilterHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/PathTreeFilterHandler.java
index b873c3dc2..1a6b65625 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/PathTreeFilterHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/PathTreeFilterHandler.java
@@ -59,10 +59,11 @@
 import org.kohsuke.args4j.spi.Setter;
 
 /**
- * Create a {@link TreeFilter} to patch math names.
+ * Create a {@link org.eclipse.jgit.treewalk.filter.TreeFilter} to patch math
+ * names.
  * <p>
  * This handler consumes all arguments to the end of the command line, and is
- * meant to be used on an {@link Option} of name "--".
+ * meant to be used on an {@link org.kohsuke.args4j.Option} of name "--".
  */
 public class PathTreeFilterHandler extends OptionHandler<TreeFilter> {
 	/**
@@ -71,14 +72,18 @@ public class PathTreeFilterHandler extends OptionHandler<TreeFilter> {
 	 * This constructor is used only by args4j.
 	 *
 	 * @param parser
+	 *            a {@link org.kohsuke.args4j.CmdLineParser} object.
 	 * @param option
+	 *            a {@link org.kohsuke.args4j.OptionDef} object.
 	 * @param setter
+	 *            a {@link org.kohsuke.args4j.spi.Setter} object.
 	 */
 	public PathTreeFilterHandler(final CmdLineParser parser,
 			final OptionDef option, final Setter<? super TreeFilter> setter) {
 		super(parser, option, setter);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int parseArguments(final Parameters params) throws CmdLineException {
 		final List<PathFilter> filters = new ArrayList<>();
@@ -102,6 +107,7 @@ public int parseArguments(final Parameters params) throws CmdLineException {
 		return filters.size();
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getDefaultMetaVariable() {
 		return CLIText.get().metaVar_paths;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RefSpecHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RefSpecHandler.java
index f50c7aded..dd8520af7 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RefSpecHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RefSpecHandler.java
@@ -53,7 +53,8 @@
 import org.kohsuke.args4j.spi.Setter;
 
 /**
- * Custom argument handler {@link RefSpec} from string values.
+ * Custom argument handler {@link org.eclipse.jgit.transport.RefSpec} from
+ * string values.
  * <p>
  * Assumes the parser has been initialized with a Repository.
  */
@@ -64,20 +65,25 @@ public class RefSpecHandler extends OptionHandler<RefSpec> {
 	 * This constructor is used only by args4j.
 	 *
 	 * @param parser
+	 *            a {@link org.kohsuke.args4j.CmdLineParser} object.
 	 * @param option
+	 *            a {@link org.kohsuke.args4j.OptionDef} object.
 	 * @param setter
+	 *            a {@link org.kohsuke.args4j.spi.Setter} object.
 	 */
 	public RefSpecHandler(final CmdLineParser parser, final OptionDef option,
 			final Setter<? super RefSpec> setter) {
 		super(parser, option, setter);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int parseArguments(final Parameters params) throws CmdLineException {
 		setter.addValue(new RefSpec(params.getParameter(0)));
 		return 1;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getDefaultMetaVariable() {
 		return CLIText.get().metaVar_refspec;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevCommitHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevCommitHandler.java
index 27555e344..d2fa76432 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevCommitHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevCommitHandler.java
@@ -60,7 +60,8 @@
 import org.kohsuke.args4j.spi.Setter;
 
 /**
- * Custom argument handler {@link RevCommit} from string values.
+ * Custom argument handler {@link org.eclipse.jgit.revwalk.RevCommit} from
+ * string values.
  * <p>
  * Assumes the parser has been initialized with a Repository.
  */
@@ -73,8 +74,11 @@ public class RevCommitHandler extends OptionHandler<RevCommit> {
 	 * This constructor is used only by args4j.
 	 *
 	 * @param parser
+	 *            a {@link org.kohsuke.args4j.CmdLineParser} object.
 	 * @param option
+	 *            a {@link org.kohsuke.args4j.OptionDef} object.
 	 * @param setter
+	 *            a {@link org.kohsuke.args4j.spi.Setter} object.
 	 */
 	public RevCommitHandler(final CmdLineParser parser, final OptionDef option,
 			final Setter<? super RevCommit> setter) {
@@ -82,6 +86,7 @@ public RevCommitHandler(final CmdLineParser parser, final OptionDef option,
 		clp = (org.eclipse.jgit.pgm.opt.CmdLineParser) parser;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int parseArguments(final Parameters params) throws CmdLineException {
 		String name = params.getParameter(0);
@@ -145,6 +150,7 @@ private void addOne(final String name, final boolean interesting)
 		setter.addValue(c);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getDefaultMetaVariable() {
 		return CLIText.get().metaVar_commitish;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevTreeHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevTreeHandler.java
index 15ed5890e..9444363be 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevTreeHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/RevTreeHandler.java
@@ -59,7 +59,8 @@
 import org.kohsuke.args4j.spi.Setter;
 
 /**
- * Custom argument handler {@link RevTree} from string values.
+ * Custom argument handler {@link org.eclipse.jgit.revwalk.RevTree} from string
+ * values.
  * <p>
  * Assumes the parser has been initialized with a Repository.
  */
@@ -72,8 +73,11 @@ public class RevTreeHandler extends OptionHandler<RevTree> {
 	 * This constructor is used only by args4j.
 	 *
 	 * @param parser
+	 *            a {@link org.kohsuke.args4j.CmdLineParser} object.
 	 * @param option
+	 *            a {@link org.kohsuke.args4j.OptionDef} object.
 	 * @param setter
+	 *            a {@link org.kohsuke.args4j.spi.Setter} object.
 	 */
 	public RevTreeHandler(final CmdLineParser parser, final OptionDef option,
 			final Setter<? super RevTree> setter) {
@@ -81,6 +85,7 @@ public RevTreeHandler(final CmdLineParser parser, final OptionDef option,
 		clp = (org.eclipse.jgit.pgm.opt.CmdLineParser) parser;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int parseArguments(final Parameters params) throws CmdLineException {
 		final String name = params.getParameter(0);
@@ -112,6 +117,7 @@ public int parseArguments(final Parameters params) throws CmdLineException {
 		return 1;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getDefaultMetaVariable() {
 		return CLIText.get().metaVar_treeish;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/SubcommandHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/SubcommandHandler.java
index ae5263fba..d60071f17 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/SubcommandHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/SubcommandHandler.java
@@ -57,8 +57,9 @@
 /**
  * Custom Argument handler for jgit command selection.
  * <p>
- * Translates a single argument string to a {@link TextBuiltin} instance which
- * we can execute at runtime with the remaining arguments of the parser.
+ * Translates a single argument string to a
+ * {@link org.eclipse.jgit.pgm.TextBuiltin} instance which we can execute at
+ * runtime with the remaining arguments of the parser.
  */
 public class SubcommandHandler extends OptionHandler<TextBuiltin> {
 	private final org.eclipse.jgit.pgm.opt.CmdLineParser clp;
@@ -69,8 +70,11 @@ public class SubcommandHandler extends OptionHandler<TextBuiltin> {
 	 * This constructor is used only by args4j.
 	 *
 	 * @param parser
+	 *            a {@link org.kohsuke.args4j.CmdLineParser} object.
 	 * @param option
+	 *            a {@link org.kohsuke.args4j.OptionDef} object.
 	 * @param setter
+	 *            a {@link org.kohsuke.args4j.spi.Setter} object.
 	 */
 	public SubcommandHandler(final CmdLineParser parser,
 			final OptionDef option, final Setter<? super TextBuiltin> setter) {
@@ -78,6 +82,7 @@ public SubcommandHandler(final CmdLineParser parser,
 		clp = (org.eclipse.jgit.pgm.opt.CmdLineParser) parser;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int parseArguments(final Parameters params) throws CmdLineException {
 		final String name = params.getParameter(0);
@@ -95,6 +100,7 @@ public int parseArguments(final Parameters params) throws CmdLineException {
 		return 1;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getDefaultMetaVariable() {
 		return CLIText.get().metaVar_command;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/UntrackedFilesHandler.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/UntrackedFilesHandler.java
index e22b2e49b..2487a926d 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/UntrackedFilesHandler.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/UntrackedFilesHandler.java
@@ -71,6 +71,8 @@
 public class UntrackedFilesHandler extends StringOptionHandler {
 
 	/**
+	 * <p>Constructor for UntrackedFilesHandler.</p>
+	 *
 	 * @param parser
 	 *            The parser to which this handler belongs to.
 	 * @param option
@@ -83,6 +85,7 @@ public UntrackedFilesHandler(CmdLineParser parser, OptionDef option,
 		super(parser, option, setter);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int parseArguments(Parameters params) throws CmdLineException {
 		String alias = params.getParameter(-1);