Fix javadoc in org.eclipse.jgit annotations and api packages

Change-Id: I2761ea91f8dfed16ea54e7a6646af03a30c15ec9
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

org.eclipse.jgit/src/org/eclipse/jgit/annotations/Nullable.java

@@ -89,7 +89,6 @@ import java.lang.annotation.Target;
  * @see <a href=
  *      "http://types.cs.washington.edu/checker-framework/current/checker-framework-manual.html#faq-array-syntax-meaning">
  *      The checker-framework manual</a>
- *
  * @since 4.2
  */
 @Documented

org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java

@@ -91,8 +91,10 @@ public class AddCommand extends GitCommand<DirCache> {
 	private boolean update = false;
 
 	/**
+	 * Constructor for AddCommand
 	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	public AddCommand(Repository repo) {
 		super(repo);
@@ -119,7 +121,10 @@ public class AddCommand extends GitCommand<DirCache> {
 
 	/**
 	 * Allow clients to provide their own implementation of a FileTreeIterator
+	 *
 	 * @param f
+	 *            a {@link org.eclipse.jgit.treewalk.WorkingTreeIterator}
+	 *            object.
 	 * @return {@code this}
 	 */
 	public AddCommand setWorkingTreeIterator(WorkingTreeIterator f) {
@@ -128,11 +133,11 @@ public class AddCommand extends GitCommand<DirCache> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code Add} command. Each instance of this class should only
 	 * be used for one invocation of the command. Don't call this method twice
 	 * on an instance.
-	 *
-	 * @return the DirCache after Add
 	 */
 	@Override
 	public DirCache call() throws GitAPIException, NoFilepatternException {
@@ -260,17 +265,18 @@ public class AddCommand extends GitCommand<DirCache> {
 	}
 
 	/**
+	 * Set whether to only match against already tracked files
+	 *
 	 * @param update
 	 *            If set to true, the command only matches {@code filepattern}
 	 *            against already tracked files in the index rather than the
 	 *            working tree. That means that it will never stage new files,
 	 *            but that it will stage modified new contents of tracked files
 	 *            and that it will remove files from the index if the
-	 *            corresponding files in the working tree have been removed.
-	 *            In contrast to the git command line a {@code filepattern} must
-	 *            exist also if update is set to true as there is no
-	 *            concept of a working directory here.
-	 *
+	 *            corresponding files in the working tree have been removed. In
+	 *            contrast to the git command line a {@code filepattern} must
+	 *            exist also if update is set to true as there is no concept of
+	 *            a working directory here.
 	 * @return {@code this}
 	 */
 	public AddCommand setUpdate(boolean update) {
@@ -279,7 +285,9 @@ public class AddCommand extends GitCommand<DirCache> {
 	}
 
 	/**
-	 * @return is the parameter update is set
+	 * Whether to only match against already tracked files
+	 *
+	 * @return whether to only match against already tracked files
 	 */
 	public boolean isUpdate() {
 		return update;

org.eclipse.jgit/src/org/eclipse/jgit/api/AddNoteCommand.java

@@ -75,12 +75,16 @@ public class AddNoteCommand extends GitCommand<Note> {
 	private String notesRef = Constants.R_NOTES_COMMITS;
 
 	/**
+	 * Constructor for AddNoteCommand
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected AddNoteCommand(Repository repo) {
 		super(repo);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Note call() throws GitAPIException {
 		checkCallable();
@@ -108,6 +112,7 @@ public class AddNoteCommand extends GitCommand<Note> {
 	 * has a note, the existing note will be replaced.
 	 *
 	 * @param id
+	 *            a {@link org.eclipse.jgit.revwalk.RevObject}
 	 * @return {@code this}
 	 */
 	public AddNoteCommand setObjectId(RevObject id) {
@@ -117,6 +122,8 @@ public class AddNoteCommand extends GitCommand<Note> {
 	}
 
 	/**
+	 * Set the notes message
+	 *
 	 * @param message
 	 *            the notes message used when adding a note
 	 * @return {@code this}
@@ -152,12 +159,13 @@ public class AddNoteCommand extends GitCommand<Note> {
 	}
 
 	/**
+	 * Set name of a {@code Ref} to read notes from
+	 *
 	 * @param notesRef
 	 *            the ref to read notes from. Note, the default value of
-	 *            {@link Constants#R_NOTES_COMMITS} will be used if nothing is
-	 *            set
+	 *            {@link org.eclipse.jgit.lib.Constants#R_NOTES_COMMITS} will be
+	 *            used if nothing is set
 	 * @return {@code this}
-	 *
 	 * @see Constants#R_NOTES_COMMITS
 	 */
 	public AddNoteCommand setNotesRef(String notesRef) {

org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java

@@ -87,6 +87,8 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 	}
 
 	/**
+	 * Set patch
+	 *
 	 * @param in
 	 *            the patch to apply
 	 * @return this instance
@@ -98,16 +100,13 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code ApplyCommand} command with all the options and
 	 * parameters collected by the setter methods (e.g.
 	 * {@link #setPatch(InputStream)} of this class. Each instance of this class
 	 * should only be used for one invocation of the command. Don't call this
 	 * method twice on an instance.
-	 *
-	 * @return an {@link ApplyResult} object representing the command result
-	 * @throws GitAPIException
-	 * @throws PatchFormatException
-	 * @throws PatchApplyException
 	 */
 	@Override
 	public ApplyResult call() throws GitAPIException, PatchFormatException,

org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyResult.java

@@ -47,7 +47,7 @@ import java.util.ArrayList;
 import java.util.List;
 
 /**
- * Encapsulates the result of a {@link ApplyCommand}
+ * Encapsulates the result of a {@link org.eclipse.jgit.api.ApplyCommand}
  *
  * @since 2.0
  */
@@ -56,6 +56,8 @@ public class ApplyResult {
 	private List<File> updatedFiles = new ArrayList<>();
 
 	/**
+	 * Add updated file
+	 *
 	 * @param f
 	 *            an updated file
 	 * @return this instance
@@ -67,6 +69,8 @@ public class ApplyResult {
 	}
 
 	/**
+	 * Get updated files
+	 *
 	 * @return updated files
 	 */
 	public List<File> getUpdatedFiles() {

org.eclipse.jgit/src/org/eclipse/jgit/api/ArchiveCommand.java

@@ -70,17 +70,14 @@ import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
 /**
  * Create an archive of files from a named tree.
  * <p>
- * Examples (<code>git</code> is a {@link Git} instance):
+ * Examples (<code>git</code> is a {@link org.eclipse.jgit.api.Git} instance):
  * <p>
  * Create a tarball from HEAD:
  *
  * <pre>
  * ArchiveCommand.registerFormat("tar", new TarFormat());
  * try {
- *	git.archive()
- *		.setTree(db.resolve(&quot;HEAD&quot;))
- *		.setOutputStream(out)
- *		.call();
+ * 	git.archive().setTree(db.resolve(&quot;HEAD&quot;)).setOutputStream(out).call();
  * } finally {
  * 	ArchiveCommand.unregisterFormat("tar");
  * }
@@ -103,7 +100,6 @@ import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
  *
  * @see <a href="http://git-htmldocs.googlecode.com/git/git-archive.html" >Git
  *      documentation about archive</a>
- *
  * @since 3.1
  */
 public class ArchiveCommand extends GitCommand<OutputStream> {
@@ -383,7 +379,10 @@ public class ArchiveCommand extends GitCommand<OutputStream> {
 	private String suffix;
 
 	/**
+	 * Constructor for ArchiveCommand
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	public ArchiveCommand(Repository repo) {
 		super(repo);
@@ -440,9 +439,7 @@ public class ArchiveCommand extends GitCommand<OutputStream> {
 		}
 	}
 
-	/**
-	 * @return the stream to which the archive has been written
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public OutputStream call() throws GitAPIException {
 		checkCallable();
@@ -456,6 +453,8 @@ public class ArchiveCommand extends GitCommand<OutputStream> {
 	}
 
 	/**
+	 * Set the tag, commit, or tree object to produce an archive for
+	 *
 	 * @param tree
 	 *            the tag, commit, or tree object to produce an archive for
 	 * @return this
@@ -470,6 +469,8 @@ public class ArchiveCommand extends GitCommand<OutputStream> {
 	}
 
 	/**
+	 * Set string prefixed to filenames in archive
+	 *
 	 * @param prefix
 	 *            string prefixed to filenames in archive (e.g., "master/").
 	 *            null means to not use any leading prefix.
@@ -502,6 +503,8 @@ public class ArchiveCommand extends GitCommand<OutputStream> {
 	}
 
 	/**
+	 * Set output stream
+	 *
 	 * @param out
 	 *            the stream to which to write the archive
 	 * @return this
@@ -512,10 +515,11 @@ public class ArchiveCommand extends GitCommand<OutputStream> {
 	}
 
 	/**
+	 * Set archive format
+	 *
 	 * @param fmt
-	 *	      archive format (e.g., "tar" or "zip").
-	 *	      null means to choose automatically based on
-	 *	      the archive filename.
+	 *            archive format (e.g., "tar" or "zip"). null means to choose
+	 *            automatically based on the archive filename.
 	 * @return this
 	 */
 	public ArchiveCommand setFormat(String fmt) {
@@ -524,6 +528,8 @@ public class ArchiveCommand extends GitCommand<OutputStream> {
 	}
 
 	/**
+	 * Set archive format options
+	 *
 	 * @param options
 	 *            archive format options (e.g., level=9 for zip compression).
 	 * @return this

org.eclipse.jgit/src/org/eclipse/jgit/api/BlameCommand.java

@@ -69,7 +69,8 @@ import org.eclipse.jgit.util.IO;
 import org.eclipse.jgit.util.io.AutoLFInputStream;
 
 /**
- * Blame command for building a {@link BlameResult} for a file path.
+ * Blame command for building a {@link org.eclipse.jgit.blame.BlameResult} for a
+ * file path.
  */
 public class BlameCommand extends GitCommand<BlameResult> {
 
@@ -86,7 +87,10 @@ public class BlameCommand extends GitCommand<BlameResult> {
 	private Boolean followFileRenames;
 
 	/**
+	 * Constructor for BlameCommand
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	public BlameCommand(Repository repo) {
 		super(repo);
@@ -108,6 +112,7 @@ public class BlameCommand extends GitCommand<BlameResult> {
 	 * Set diff algorithm
 	 *
 	 * @param diffAlgorithm
+	 *            a {@link org.eclipse.jgit.diff.DiffAlgorithm} object.
 	 * @return this command
 	 */
 	public BlameCommand setDiffAlgorithm(DiffAlgorithm diffAlgorithm) {
@@ -119,6 +124,7 @@ public class BlameCommand extends GitCommand<BlameResult> {
 	 * Set raw text comparator
 	 *
 	 * @param textComparator
+	 *            a {@link org.eclipse.jgit.diff.RawTextComparator}
 	 * @return this command
 	 */
 	public BlameCommand setTextComparator(RawTextComparator textComparator) {
@@ -130,6 +136,7 @@ public class BlameCommand extends GitCommand<BlameResult> {
 	 * Set start commit id
 	 *
 	 * @param commit
+	 *            id of a commit
 	 * @return this command
 	 */
 	public BlameCommand setStartCommit(AnyObjectId commit) {
@@ -164,7 +171,7 @@ public class BlameCommand extends GitCommand<BlameResult> {
 	 *            most recent commit to stop traversal at. Usually an active
 	 *            branch tip, tag, or HEAD.
 	 * @return {@code this}
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository cannot be read.
 	 */
 	public BlameCommand reverse(AnyObjectId start, AnyObjectId end)
@@ -182,7 +189,7 @@ public class BlameCommand extends GitCommand<BlameResult> {
 	 *            most recent commits to stop traversal at. Usually an active
 	 *            branch tip, tag, or HEAD.
 	 * @return {@code this}
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository cannot be read.
 	 */
 	public BlameCommand reverse(AnyObjectId start, Collection<ObjectId> end)
@@ -193,10 +200,10 @@ public class BlameCommand extends GitCommand<BlameResult> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Generate a list of lines with information about when the lines were
 	 * introduced into the file path.
-	 *
-	 * @return list of lines
 	 */
 	@Override
 	public BlameResult call() throws GitAPIException {

org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java

@@ -91,7 +91,7 @@ import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
 /**
  * Checkout a branch to the working tree.
  * <p>
- * Examples (<code>git</code> is a {@link Git} instance):
+ * Examples (<code>git</code> is a {@link org.eclipse.jgit.api.Git} instance):
  * <p>
  * Check out an existing branch:
  *
@@ -126,9 +126,9 @@ import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
  * 		.setStartPoint(&quot;origin/stable&quot;).call();
  * </pre>
  *
- * @see <a
- *      href="http://www.kernel.org/pub/software/scm/git/docs/git-checkout.html"
- *      >Git documentation about Checkout</a>
+ * @see <a href=
+ *      "http://www.kernel.org/pub/software/scm/git/docs/git-checkout.html" >Git
+ *      documentation about Checkout</a>
  */
 public class CheckoutCommand extends GitCommand<Ref> {
 
@@ -183,26 +183,17 @@ public class CheckoutCommand extends GitCommand<Ref> {
 	private Set<String> actuallyModifiedPaths;
 
 	/**
+	 * Constructor for CheckoutCommand
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected CheckoutCommand(Repository repo) {
 		super(repo);
 		this.paths = new LinkedList<>();
 	}
 
-	/**
-	 * @throws RefAlreadyExistsException
-	 *             when trying to create (without force) a branch with a name
-	 *             that already exists
-	 * @throws RefNotFoundException
-	 *             if the start point or branch can not be found
-	 * @throws InvalidRefNameException
-	 *             if the provided name is <code>null</code> or otherwise
-	 *             invalid
-	 * @throws CheckoutConflictException
-	 *             if the checkout results in a conflict
-	 * @return the newly created branch
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public Ref call() throws GitAPIException, RefAlreadyExistsException,
 			RefNotFoundException, InvalidRefNameException,
@@ -418,11 +409,12 @@ public class CheckoutCommand extends GitCommand<Ref> {
 
 	/**
 	 * Checkout paths into index and working directory, firing a
-	 * {@link WorkingTreeModifiedEvent} if the working tree was modified.
+	 * {@link org.eclipse.jgit.events.WorkingTreeModifiedEvent} if the working
+	 * tree was modified.
 	 *
 	 * @return this instance
-	 * @throws IOException
-	 * @throws RefNotFoundException
+	 * @throws java.io.IOException
+	 * @throws org.eclipse.jgit.api.errors.RefNotFoundException
 	 */
 	protected CheckoutCommand checkoutPaths() throws IOException,
 			RefNotFoundException {
@@ -739,6 +731,8 @@ public class CheckoutCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * <p>getResult.</p>
+	 *
 	 * @return the result, never <code>null</code>
 	 */
 	public CheckoutResult getResult() {

org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutResult.java

@@ -46,8 +46,7 @@ import java.util.ArrayList;
 import java.util.List;
 
 /**
- * Encapsulates the result of a {@link CheckoutCommand}
- *
+ * Encapsulates the result of a {@link org.eclipse.jgit.api.CheckoutCommand}
  */
 public class CheckoutResult {
 
@@ -168,6 +167,8 @@ public class CheckoutResult {
 	}
 
 	/**
+	 * Get status
+	 *
 	 * @return the status
 	 */
 	public Status getStatus() {
@@ -175,33 +176,44 @@ public class CheckoutResult {
 	}
 
 	/**
+	 * Get list of file that created a checkout conflict
+	 *
 	 * @return the list of files that created a checkout conflict, or an empty
-	 *         list if {@link #getStatus()} is not {@link Status#CONFLICTS};
+	 *         list if {@link #getStatus()} is not
+	 *         {@link org.eclipse.jgit.api.CheckoutResult.Status#CONFLICTS};
 	 */
 	public List<String> getConflictList() {
 		return conflictList;
 	}
 
 	/**
+	 * Get the list of files that could not be deleted during checkout
+	 *
 	 * @return the list of files that could not be deleted during checkout, or
 	 *         an empty list if {@link #getStatus()} is not
-	 *         {@link Status#NONDELETED};
+	 *         {@link org.eclipse.jgit.api.CheckoutResult.Status#NONDELETED};
 	 */
 	public List<String> getUndeletedList() {
 		return undeletedList;
 	}
 
 	/**
+	 * Get the list of files that where modified during checkout
+	 *
 	 * @return the list of files that where modified during checkout, or an
-	 *         empty list if {@link #getStatus()} is not {@link Status#OK}
+	 *         empty list if {@link #getStatus()} is not
+	 *         {@link org.eclipse.jgit.api.CheckoutResult.Status#OK}
 	 */
 	public List<String> getModifiedList() {
 		return modifiedList;
 	}
 
 	/**
+	 * Get the list of files that where removed during checkout
+	 *
 	 * @return the list of files that where removed during checkout, or an empty
-	 *         list if {@link #getStatus()} is not {@link Status#OK}
+	 *         list if {@link #getStatus()} is not
+	 *         {@link org.eclipse.jgit.api.CheckoutResult.Status#OK}
 	 */
 	public List<String> getRemovedList() {
 		return removedList;

org.eclipse.jgit/src/org/eclipse/jgit/api/CherryPickCommand.java

@@ -96,25 +96,22 @@ public class CherryPickCommand extends GitCommand<CherryPickResult> {
 	private boolean noCommit = false;
 
 	/**
+	 * Constructor for CherryPickCommand
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected CherryPickCommand(Repository repo) {
 		super(repo);
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code Cherry-Pick} command with all the options and
 	 * parameters collected by the setter methods (e.g. {@link #include(Ref)} of
 	 * this class. Each instance of this class should only be used for one
 	 * invocation of the command. Don't call this method twice on an instance.
-	 *
-	 * @return the result of the cherry-pick
-	 * @throws GitAPIException
-	 * @throws WrongRepositoryStateException
-	 * @throws ConcurrentRefUpdateException
-	 * @throws UnmergedPathsException
-	 * @throws NoMessageException
-	 * @throws NoHeadException
 	 */
 	@Override
 	public CherryPickResult call() throws GitAPIException, NoMessageException,
@@ -224,6 +221,8 @@ public class CherryPickCommand extends GitCommand<CherryPickResult> {
 	}
 
 	/**
+	 * Include a reference to a commit
+	 *
 	 * @param commit
 	 *            a reference to a commit which is cherry-picked to the current
 	 *            head
@@ -236,6 +235,8 @@ public class CherryPickCommand extends GitCommand<CherryPickResult> {
 	}
 
 	/**
+	 * Include a commit
+	 *
 	 * @param commit
 	 *            the Id of a commit which is cherry-picked to the current head
 	 * @return {@code this}
@@ -245,6 +246,8 @@ public class CherryPickCommand extends GitCommand<CherryPickResult> {
 	}
 
 	/**
+	 * Include a commit
+	 *
 	 * @param name
 	 *            a name given to the commit
 	 * @param commit
@@ -257,6 +260,8 @@ public class CherryPickCommand extends GitCommand<CherryPickResult> {
 	}
 
 	/**
+	 * Set the name that should be used in the "OURS" place for conflict markers
+	 *
 	 * @param ourCommitName
 	 *            the name that should be used in the "OURS" place for conflict
 	 *            markers
@@ -284,6 +289,8 @@ public class CherryPickCommand extends GitCommand<CherryPickResult> {
 	}
 
 	/**
+	 * Set the {@code MergeStrategy}
+	 *
 	 * @param strategy
 	 *            The merge strategy to use during this Cherry-pick.
 	 * @return {@code this}
@@ -295,6 +302,8 @@ public class CherryPickCommand extends GitCommand<CherryPickResult> {
 	}
 
 	/**
+	 * Set the (1-based) parent number to diff against
+	 *
 	 * @param mainlineParentNumber
 	 *            the (1-based) parent number to diff against. This allows
 	 *            cherry-picking of merges.
@@ -332,6 +341,7 @@ public class CherryPickCommand extends GitCommand<CherryPickResult> {
 		return headName;
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {

org.eclipse.jgit/src/org/eclipse/jgit/api/CherryPickResult.java

@@ -46,12 +46,11 @@ import java.util.List;
 import java.util.Map;
 
 import org.eclipse.jgit.lib.Ref;
-import org.eclipse.jgit.merge.ResolveMerger;
 import org.eclipse.jgit.merge.ResolveMerger.MergeFailureReason;
 import org.eclipse.jgit.revwalk.RevCommit;
 
 /**
- * Encapsulates the result of a {@link CherryPickCommand}.
+ * Encapsulates the result of a {@link org.eclipse.jgit.api.CherryPickCommand}.
  */
 public class CherryPickResult {
 
@@ -91,6 +90,8 @@ public class CherryPickResult {
 	private final Map<String, MergeFailureReason> failingPaths;
 
 	/**
+	 * Constructor for CherryPickResult
+	 *
 	 * @param newHead
 	 *            commit the head points at after this cherry-pick
 	 * @param cherryPickedRefs
@@ -104,9 +105,12 @@ public class CherryPickResult {
 	}
 
 	/**
+	 * Constructor for CherryPickResult
+	 *
 	 * @param failingPaths
 	 *            list of paths causing this cherry-pick to fail (see
-	 *            {@link ResolveMerger#getFailingPaths()} for details)
+	 *            {@link org.eclipse.jgit.merge.ResolveMerger#getFailingPaths()}
+	 *            for details)
 	 */
 	public CherryPickResult(Map<String, MergeFailureReason> failingPaths) {
 		this.status = CherryPickStatus.FAILED;
@@ -130,6 +134,8 @@ public class CherryPickResult {
 			CherryPickStatus.CONFLICTING);
 
 	/**
+	 * Get status
+	 *
 	 * @return the status this cherry-pick resulted in
 	 */
 	public CherryPickStatus getStatus() {
@@ -137,28 +143,34 @@ public class CherryPickResult {
 	}
 
 	/**
+	 * Get the new head after this cherry-pick
+	 *
 	 * @return the commit the head points at after this cherry-pick,
 	 *         <code>null</code> if {@link #getStatus} is not
-	 *         {@link CherryPickStatus#OK}
+	 *         {@link org.eclipse.jgit.api.CherryPickResult.CherryPickStatus#OK}
 	 */
 	public RevCommit getNewHead() {
 		return newHead;
 	}
 
 	/**
+	 * Get the cherry-picked {@code Ref}s
+	 *
 	 * @return the list of successfully cherry-picked <code>Ref</code>'s,
 	 *         <code>null</code> if {@link #getStatus} is not
-	 *         {@link CherryPickStatus#OK}
+	 *         {@link org.eclipse.jgit.api.CherryPickResult.CherryPickStatus#OK}
 	 */
 	public List<Ref> getCherryPickedRefs() {
 		return cherryPickedRefs;
 	}
 
 	/**
+	 * Get the list of paths causing this cherry-pick to fail
+	 *
 	 * @return the list of paths causing this cherry-pick to fail (see
-	 *         {@link ResolveMerger#getFailingPaths()} for details),
-	 *         <code>null</code> if {@link #getStatus} is not
-	 *         {@link CherryPickStatus#FAILED}
+	 *         {@link org.eclipse.jgit.merge.ResolveMerger#getFailingPaths()}
+	 *         for details), <code>null</code> if {@link #getStatus} is not
+	 *         {@link org.eclipse.jgit.api.CherryPickResult.CherryPickStatus#FAILED}
 	 */
 	public Map<String, MergeFailureReason> getFailingPaths() {
 		return failingPaths;

org.eclipse.jgit/src/org/eclipse/jgit/api/CleanCommand.java

@@ -79,21 +79,22 @@ public class CleanCommand extends GitCommand<Set<String>> {
 	private boolean force = false;
 
 	/**
+	 * Constructor for CleanCommand
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected CleanCommand(Repository repo) {
 		super(repo);
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code clean} command with all the options and parameters
 	 * collected by the setter methods of this class. Each instance of this
 	 * class should only be used for one invocation of the command (means: one
 	 * call to {@link #call()})
-	 *
-	 * @return a set of strings representing each file cleaned.
-	 * @throws GitAPIException
-	 * @throws NoWorkTreeException
 	 */
 	@Override
 	public Set<String> call() throws NoWorkTreeException, GitAPIException {

org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java

@@ -167,6 +167,8 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code Clone} command.
 	 *
 	 * The Git instance returned by this command needs to be closed by the
@@ -174,11 +176,6 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	 * instance. It is recommended to call this method as soon as you don't need
 	 * a reference to this {@link Git} instance and the underlying
 	 * {@link Repository} instance anymore.
-	 *
-	 * @return the newly created {@code Git} object with associated repository
-	 * @throws InvalidRemoteException
-	 * @throws org.eclipse.jgit.api.errors.TransportException
-	 * @throws GitAPIException
 	 */
 	@Override
 	public Git call() throws GitAPIException, InvalidRemoteException,
@@ -450,9 +447,11 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	}
 
 	/**
+	 * Set the URI to clone from
+	 *
 	 * @param uri
-	 *            the URI to clone from, or {@code null} to unset the URI.
-	 *            The URI must be set before {@link #call} is called.
+	 *            the URI to clone from, or {@code null} to unset the URI. The
+	 *            URI must be set before {@link #call} is called.
 	 * @return this instance
 	 */
 	public CloneCommand setURI(String uri) {
@@ -465,12 +464,11 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	 * directory isn't set, a name associated with the source uri will be used.
 	 *
 	 * @see URIish#getHumanishName()
-	 *
 	 * @param directory
 	 *            the directory to clone to, or {@code null} if the directory
 	 *            name should be taken from the source uri
 	 * @return this instance
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             if the combination of directory, gitDir and bare is illegal.
 	 *             E.g. if for a non-bare repository directory and gitDir point
 	 *             to the same directory of if for a bare repository both
@@ -483,11 +481,13 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	}
 
 	/**
+	 * Set the repository meta directory (.git)
+	 *
 	 * @param gitDir
 	 *            the repository meta directory, or {@code null} to choose one
 	 *            automatically at clone time
 	 * @return this instance
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             if the combination of directory, gitDir and bare is illegal.
 	 *             E.g. if for a non-bare repository directory and gitDir point
 	 *             to the same directory of if for a bare repository both
@@ -501,10 +501,12 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	}
 
 	/**
+	 * Set whether the cloned repository shall be bare
+	 *
 	 * @param bare
 	 *            whether the cloned repository is bare or not
 	 * @return this instance
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             if the combination of directory, gitDir and bare is illegal.
 	 *             E.g. if for a non-bare repository directory and gitDir point
 	 *             to the same directory of if for a bare repository both
@@ -536,13 +538,15 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	}
 
 	/**
+	 * Set the initial branch
+	 *
 	 * @param branch
 	 *            the initial branch to check out when cloning the repository.
 	 *            Can be specified as ref name (<code>refs/heads/master</code>),
-	 *            branch name (<code>master</code>) or tag name (<code>v1.2.3</code>).
-	 *            The default is to use the branch pointed to by the cloned
-	 *            repository's HEAD and can be requested by passing {@code null}
-	 *            or <code>HEAD</code>.
+	 *            branch name (<code>master</code>) or tag name
+	 *            (<code>v1.2.3</code>). The default is to use the branch
+	 *            pointed to by the cloned repository's HEAD and can be
+	 *            requested by passing {@code null} or <code>HEAD</code>.
 	 * @return this instance
 	 */
 	public CloneCommand setBranch(String branch) {
@@ -558,8 +562,8 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	 * this is set to <code>NullProgressMonitor</code>
 	 *
 	 * @see NullProgressMonitor
-	 *
 	 * @param monitor
+	 *            a {@link org.eclipse.jgit.lib.ProgressMonitor}
 	 * @return {@code this}
 	 */
 	public CloneCommand setProgressMonitor(ProgressMonitor monitor) {
@@ -571,6 +575,8 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	}
 
 	/**
+	 * Set whether all branches have to be fetched
+	 *
 	 * @param cloneAllBranches
 	 *            true when all branches have to be fetched (indicates wildcard
 	 *            in created fetch refspec), false otherwise.
@@ -582,6 +588,8 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	}
 
 	/**
+	 * Set whether to clone submodules
+	 *
 	 * @param cloneSubmodules
 	 *            true to initialize and update submodules. Ignored when
 	 *            {@link #setBare(boolean)} is set to true.
@@ -593,6 +601,8 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	}
 
 	/**
+	 * Set branches to clone
+	 *
 	 * @param branchesToClone
 	 *            collection of branches to clone. Ignored when allSelected is
 	 *            true. Must be specified as full ref names (e.g.
@@ -605,6 +615,8 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	}
 
 	/**
+	 * Set whether to skip checking out a branch
+	 *
 	 * @param noCheckout
 	 *            if set to <code>true</code> no branch will be checked out
 	 *            after the clone. This enhances performance of the clone

org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java

@@ -140,33 +140,22 @@ public class CommitCommand extends GitCommand<RevCommit> {
 	private Boolean allowEmpty;
 
 	/**
+	 * Constructor for CommitCommand
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected CommitCommand(Repository repo) {
 		super(repo);
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code commit} command with all the options and parameters
 	 * collected by the setter methods of this class. Each instance of this
 	 * class should only be used for one invocation of the command (means: one
 	 * call to {@link #call()})
-	 *
-	 * @return a {@link RevCommit} object representing the successful commit.
-	 * @throws NoHeadException
-	 *             when called on a git repo without a HEAD reference
-	 * @throws NoMessageException
-	 *             when called without specifying a commit message
-	 * @throws UnmergedPathsException
-	 *             when the current index contained unmerged paths (conflicts)
-	 * @throws ConcurrentRefUpdateException
-	 *             when HEAD or branch ref is updated concurrently by someone
-	 *             else
-	 * @throws WrongRepositoryStateException
-	 *             when repository is not in the right state for committing
-	 * @throws AbortedByHookException
-	 *             if there are either pre-commit or commit-msg hooks present in
-	 *             the repository and one of them rejects the commit.
 	 */
 	@Override
 	public RevCommit call() throws GitAPIException, NoHeadException,
@@ -602,6 +591,8 @@ public class CommitCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
+	 * Set the commit message
+	 *
 	 * @param message
 	 *            the commit message used for the {@code commit}
 	 * @return {@code this}
@@ -613,6 +604,8 @@ public class CommitCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
+	 * Set whether to allow to create an empty commit
+	 *
 	 * @param allowEmpty
 	 *            whether it should be allowed to create a commit which has the
 	 *            same tree as it's sole predecessor (a commit which doesn't
@@ -623,8 +616,9 @@ public class CommitCommand extends GitCommand<RevCommit> {
 	 *            <p>
 	 *            By default when creating a commit containing only specified
 	 *            paths an attempt to create an empty commit leads to a
-	 *            {@link JGitInternalException}. By setting this flag to
-	 *            <code>true</code> this exception will not be thrown.
+	 *            {@link org.eclipse.jgit.api.errors.JGitInternalException}. By
+	 *            setting this flag to <code>true</code> this exception will not
+	 *            be thrown.
 	 * @return {@code this}
 	 * @since 4.2
 	 */
@@ -634,6 +628,8 @@ public class CommitCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
+	 * Get the commit message
+	 *
 	 * @return the commit message used for the <code>commit</code>
 	 */
 	public String getMessage() {
@@ -673,10 +669,12 @@ public class CommitCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
+	 * Get the committer
+	 *
 	 * @return the committer used for the {@code commit}. If no committer was
 	 *         specified {@code null} is returned and the default
-	 *         {@link PersonIdent} of this repo is used during execution of the
-	 *         command
+	 *         {@link org.eclipse.jgit.lib.PersonIdent} of this repo is used
+	 *         during execution of the command
 	 */
 	public PersonIdent getCommitter() {
 		return committer;
@@ -715,10 +713,12 @@ public class CommitCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
+	 * Get the author
+	 *
 	 * @return the author used for the {@code commit}. If no author was
 	 *         specified {@code null} is returned and the default
-	 *         {@link PersonIdent} of this repo is used during execution of the
-	 *         command
+	 *         {@link org.eclipse.jgit.lib.PersonIdent} of this repo is used
+	 *         during execution of the command
 	 */
 	public PersonIdent getAuthor() {
 		return author;
@@ -730,6 +730,8 @@ public class CommitCommand extends GitCommand<RevCommit> {
 	 * not affected. This corresponds to the parameter -a on the command line.
 	 *
 	 * @param all
+	 *            whether to auto-stage all files that have been modified and
+	 *            deleted
 	 * @return {@code this}
 	 * @throws JGitInternalException
 	 *             in case of an illegal combination of arguments/ options
@@ -745,11 +747,12 @@ public class CommitCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
-	 * Used to amend the tip of the current branch. If set to true, the previous
-	 * commit will be amended. This is equivalent to --amend on the command
-	 * line.
+	 * Used to amend the tip of the current branch. If set to {@code true}, the
+	 * previous commit will be amended. This is equivalent to --amend on the
+	 * command line.
 	 *
 	 * @param amend
+	 *            whether to ammend the tip of the current branch
 	 * @return {@code this}
 	 */
 	public CommitCommand setAmend(boolean amend) {
@@ -790,7 +793,7 @@ public class CommitCommand extends GitCommand<RevCommit> {
 	 * will be replaced by the change id.
 	 *
 	 * @param insertChangeId
-	 *
+	 *            whether to insert a change id
 	 * @return {@code this}
 	 */
 	public CommitCommand setInsertChangeId(boolean insertChangeId) {

org.eclipse.jgit/src/org/eclipse/jgit/api/CreateBranchCommand.java

@@ -103,23 +103,16 @@ public class CreateBranchCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Constructor for CreateBranchCommand
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected CreateBranchCommand(Repository repo) {
 		super(repo);
 	}
 
-	/**
-	 * @throws RefAlreadyExistsException
-	 *             when trying to create (without force) a branch with a name
-	 *             that already exists
-	 * @throws RefNotFoundException
-	 *             if the start point can not be found
-	 * @throws InvalidRefNameException
-	 *             if the provided name is <code>null</code> or otherwise
-	 *             invalid
-	 * @return the newly created branch
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public Ref call() throws GitAPIException, RefAlreadyExistsException,
 			RefNotFoundException, InvalidRefNameException {
@@ -297,6 +290,8 @@ public class CreateBranchCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Set the name of the new branch
+	 *
 	 * @param name
 	 *            the name of the new branch
 	 * @return this instance
@@ -308,6 +303,8 @@ public class CreateBranchCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Set whether to create the branch forcefully
+	 *
 	 * @param force
 	 *            if <code>true</code> and the branch with the given name
 	 *            already exists, the start-point of an existing branch will be
@@ -322,6 +319,8 @@ public class CreateBranchCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Set the start point
+	 *
 	 * @param startPoint
 	 *            corresponds to the start-point option; if <code>null</code>,
 	 *            the current HEAD will be used
@@ -335,6 +334,8 @@ public class CreateBranchCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Set the start point
+	 *
 	 * @param startPoint
 	 *            corresponds to the start-point option; if <code>null</code>,
 	 *            the current HEAD will be used
@@ -348,6 +349,8 @@ public class CreateBranchCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Set the upstream mode
+	 *
 	 * @param mode
 	 *            corresponds to the --track/--no-track/--set-upstream options;
 	 *            may be <code>null</code>

org.eclipse.jgit/src/org/eclipse/jgit/api/DeleteBranchCommand.java

@@ -84,19 +84,16 @@ public class DeleteBranchCommand extends GitCommand<List<String>> {
 	private boolean force;
 
 	/**
+	 * Constructor for DeleteBranchCommand
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected DeleteBranchCommand(Repository repo) {
 		super(repo);
 	}
 
-	/**
-	 * @throws NotMergedException
-	 *             when trying to delete a branch which has not been merged into
-	 *             the currently checked out branch without force
-	 * @throws CannotDeleteCurrentBranchException
-	 * @return the list with the (full) names of the deleted branches
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public List<String> call() throws GitAPIException,
 			NotMergedException, CannotDeleteCurrentBranchException {
@@ -181,6 +178,8 @@ public class DeleteBranchCommand extends GitCommand<List<String>> {
 	}
 
 	/**
+	 * Set the names of the branches to delete
+	 *
 	 * @param branchnames
 	 *            the names of the branches to delete; if not set, this will do
 	 *            nothing; invalid branch names will simply be ignored
@@ -195,6 +194,8 @@ public class DeleteBranchCommand extends GitCommand<List<String>> {
 	}
 
 	/**
+	 * Set whether to forcefully delete branches
+	 *
 	 * @param force
 	 *            <code>true</code> corresponds to the -D option,
 	 *            <code>false</code> to the -d option (default) <br>

org.eclipse.jgit/src/org/eclipse/jgit/api/DeleteTagCommand.java

@@ -71,15 +71,16 @@ public class DeleteTagCommand extends GitCommand<List<String>> {
 	private final Set<String> tags = new HashSet<>();
 
 	/**
+	 * Constructor for DeleteTagCommand
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected DeleteTagCommand(Repository repo) {
 		super(repo);
 	}
 
-	/**
-	 * @return the list with the full names of the deleted tags
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public List<String> call() throws GitAPIException {
 		checkCallable();
@@ -124,6 +125,8 @@ public class DeleteTagCommand extends GitCommand<List<String>> {
 	}
 
 	/**
+	 * Set names of the tags to delete
+	 *
 	 * @param tags
 	 *            the names of the tags to delete; if not set, this will do
 	 *            nothing; invalid tag names will simply be ignored

org.eclipse.jgit/src/org/eclipse/jgit/api/DescribeCommand.java

@@ -104,8 +104,10 @@ public class DescribeCommand extends GitCommand<String> {
 	private List<IMatcher> matchers = new ArrayList<>();
 
 	/**
+	 * Constructor for DescribeCommand.
 	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected DescribeCommand(Repository repo) {
 		super(repo);
@@ -123,7 +125,7 @@ public class DescribeCommand extends GitCommand<String> {
 	 *             the supplied commit does not exist.
 	 * @throws IncorrectObjectTypeException
 	 *             the supplied id is not a commit or an annotated tag.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             a pack file or loose object could not be read.
 	 */
 	public DescribeCommand setTarget(ObjectId target) throws IOException {
@@ -135,14 +137,15 @@ public class DescribeCommand extends GitCommand<String> {
 	 * Sets the commit to be described.
 	 *
 	 * @param rev
-	 * 		Commit ID, tag, branch, ref, etc.
-	 * 		See {@link Repository#resolve(String)} for allowed syntax.
+	 *            Commit ID, tag, branch, ref, etc. See
+	 *            {@link org.eclipse.jgit.lib.Repository#resolve(String)} for
+	 *            allowed syntax.
 	 * @return {@code this}
 	 * @throws IncorrectObjectTypeException
 	 *             the supplied id is not a commit or an annotated tag.
-	 * @throws RefNotFoundException
+	 * @throws org.eclipse.jgit.api.errors.RefNotFoundException
 	 *             the given rev didn't resolve to any object.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             a pack file or loose object could not be read.
 	 */
 	public DescribeCommand setTarget(String rev) throws IOException,
@@ -160,7 +163,6 @@ public class DescribeCommand extends GitCommand<String> {
 	 * @param longDesc
 	 *            <code>true</code> if always the long format should be used.
 	 * @return {@code this}
-	 *
 	 * @see <a
 	 *      href="https://www.kernel.org/pub/software/scm/git/docs/git-describe.html"
 	 *      >Git documentation about describe</a>
@@ -180,15 +182,17 @@ public class DescribeCommand extends GitCommand<String> {
 	}
 
 	/**
-	 * Sets one or more {@code glob(7)} patterns that tags must match to be considered.
-	 * If multiple patterns are provided, tags only need match one of them.
+	 * Sets one or more {@code glob(7)} patterns that tags must match to be
+	 * considered. If multiple patterns are provided, tags only need match one
+	 * of them.
 	 *
-	 * @param patterns the {@code glob(7)} pattern or patterns
+	 * @param patterns
+	 *            the {@code glob(7)} pattern or patterns
 	 * @return {@code this}
-	 * @throws InvalidPatternException if the pattern passed in was invalid.
-	 *
-	 * @see <a
-	 *      href="https://www.kernel.org/pub/software/scm/git/docs/git-describe.html"
+	 * @throws org.eclipse.jgit.errors.InvalidPatternException
+	 *             if the pattern passed in was invalid.
+	 * @see <a href=
+	 *      "https://www.kernel.org/pub/software/scm/git/docs/git-describe.html"
 	 *      >Git documentation about describe</a>
 	 * @since 4.9
 	 */
@@ -229,16 +233,10 @@ public class DescribeCommand extends GitCommand<String> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Describes the specified commit. Target defaults to HEAD if no commit was
 	 * set explicitly.
-	 *
-	 * @return if there's a tag that points to the commit being described, this
-	 *         tag name is returned. Otherwise additional suffix is added to the
-	 *         nearest tag, just like git-describe(1).
-	 *         <p>
-	 *         If none of the ancestors of the commit being described has any
-	 *         tags at all, then this method returns null, indicating that
-	 *         there's no way to describe this tag.
 	 */
 	@Override
 	public String call() throws GitAPIException {

org.eclipse.jgit/src/org/eclipse/jgit/api/DiffCommand.java

@@ -95,19 +95,22 @@ public class DiffCommand extends GitCommand<List<DiffEntry>> {
 	private ProgressMonitor monitor = NullProgressMonitor.INSTANCE;
 
 	/**
+	 * Constructor for DiffCommand
+	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	protected DiffCommand(Repository repo) {
 		super(repo);
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code Diff} command with all the options and parameters
 	 * collected by the setter methods (e.g. {@link #setCached(boolean)} of this
 	 * class. Each instance of this class should only be used for one invocation
 	 * of the command. Don't call this method twice on an instance.
-	 *
-	 * @return a DiffEntry for each path which is different
 	 */
 	@Override
 	public List<DiffEntry> call() throws GitAPIException {
@@ -162,9 +165,10 @@ public class DiffCommand extends GitCommand<List<DiffEntry>> {
 	}
 
 	/**
+	 * Whether to view the changes staged for the next commit
 	 *
 	 * @param cached
-	 *            whether to view the changes you staged for the next commit
+	 *            whether to view the changes staged for the next commit
 	 * @return this instance
 	 */
 	public DiffCommand setCached(boolean cached) {
@@ -173,6 +177,8 @@ public class DiffCommand extends GitCommand<List<DiffEntry>> {
 	}
 
 	/**
+	 * Set path filter
+	 *
 	 * @param pathFilter
 	 *            parameter, used to limit the diff to the named path
 	 * @return this instance
@@ -183,6 +189,8 @@ public class DiffCommand extends GitCommand<List<DiffEntry>> {
 	}
 
 	/**
+	 * Set old tree
+	 *
 	 * @param oldTree
 	 *            the previous state
 	 * @return this instance
@@ -193,6 +201,8 @@ public class DiffCommand extends GitCommand<List<DiffEntry>> {
 	}
 
 	/**
+	 * Set new tree
+	 *
 	 * @param newTree
 	 *            the updated state
 	 * @return this instance
@@ -203,6 +213,8 @@ public class DiffCommand extends GitCommand<List<DiffEntry>> {
 	}
 
 	/**
+	 * Set whether to return only names and status of changed files
+	 *
 	 * @param showNameAndStatusOnly
 	 *            whether to return only names and status of changed files
 	 * @return this instance
@@ -213,6 +225,8 @@ public class DiffCommand extends GitCommand<List<DiffEntry>> {
 	}
 
 	/**
+	 * Set output stream
+	 *
 	 * @param out
 	 *            the stream to write line data
 	 * @return this instance
@@ -263,7 +277,6 @@ public class DiffCommand extends GitCommand<List<DiffEntry>> {
 	 * is set to <code>NullProgressMonitor</code>
 	 *
 	 * @see NullProgressMonitor
-	 *
 	 * @param monitor
 	 *            a progress monitor
 	 * @return this instance

org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java

@@ -122,7 +122,10 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	}
 
 	/**
+	 * Constructor for FetchCommand.
+	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	protected FetchCommand(Repository repo) {
 		super(repo);
@@ -210,17 +213,12 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	}
 
 	/**
-	 * Executes the {@code fetch} command with all the options and parameters
+	 * {@inheritDoc}
+	 * <p>
+	 * Execute the {@code fetch} command with all the options and parameters
 	 * collected by the setter methods of this class. Each instance of this
 	 * class should only be used for one invocation of the command (means: one
 	 * call to {@link #call()})
-	 *
-	 * @return a {@link FetchResult} object representing the successful fetch
-	 *         result
-	 * @throws InvalidRemoteException
-	 *             when called with an invalid remote uri
-	 * @throws org.eclipse.jgit.api.errors.TransportException
-	 *             when an error occurs during transport
 	 */
 	@Override
 	public FetchResult call() throws GitAPIException, InvalidRemoteException,
@@ -288,6 +286,7 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	 *
 	 * @see Constants#DEFAULT_REMOTE_NAME
 	 * @param remote
+	 *            name of a remote
 	 * @return {@code this}
 	 */
 	public FetchCommand setRemote(String remote) {
@@ -297,6 +296,8 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	}
 
 	/**
+	 * Get the remote
+	 *
 	 * @return the remote used for the remote operation
 	 */
 	public String getRemote() {
@@ -304,6 +305,8 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	}
 
 	/**
+	 * Get timeout
+	 *
 	 * @return the timeout used for the fetch operation
 	 */
 	public int getTimeout() {
@@ -311,16 +314,19 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	}
 
 	/**
-	 * @return whether to check received objects checked for validity
+	 * Whether to check received objects for validity
+	 *
+	 * @return whether to check received objects for validity
 	 */
 	public boolean isCheckFetchedObjects() {
 		return checkFetchedObjects;
 	}
 
 	/**
-	 * If set to true, objects received will be checked for validity
+	 * If set to {@code true}, objects received will be checked for validity
 	 *
 	 * @param checkFetchedObjects
+	 *            whether to check objects for validity
 	 * @return {@code this}
 	 */
 	public FetchCommand setCheckFetchedObjects(boolean checkFetchedObjects) {
@@ -330,7 +336,9 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	}
 
 	/**
-	 * @return whether or not to remove refs which no longer exist in the source
+	 * Whether to remove refs which no longer exist in the source
+	 *
+	 * @return whether to remove refs which no longer exist in the source
 	 */
 	public boolean isRemoveDeletedRefs() {
 		if (removeDeletedRefs != null)
@@ -347,9 +355,11 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	}
 
 	/**
-	 * If set to true, refs are removed which no longer exist in the source
+	 * If set to {@code true}, refs are removed which no longer exist in the
+	 * source
 	 *
 	 * @param removeDeletedRefs
+	 *            whether to remove deleted {@code Ref}s
 	 * @return {@code this}
 	 */
 	public FetchCommand setRemoveDeletedRefs(boolean removeDeletedRefs) {
@@ -359,6 +369,8 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	}
 
 	/**
+	 * Get progress monitor
+	 *
 	 * @return the progress monitor for the fetch operation
 	 */
 	public ProgressMonitor getProgressMonitor() {
@@ -370,8 +382,8 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	 * this is set to <code>NullProgressMonitor</code>
 	 *
 	 * @see NullProgressMonitor
-	 *
 	 * @param monitor
+	 *            a {@link org.eclipse.jgit.lib.ProgressMonitor}
 	 * @return {@code this}
 	 */
 	public FetchCommand setProgressMonitor(ProgressMonitor monitor) {
@@ -384,6 +396,8 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	}
 
 	/**
+	 * Get list of {@code RefSpec}s
+	 *
 	 * @return the ref specs
 	 */
 	public List<RefSpec> getRefSpecs() {
@@ -394,6 +408,7 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	 * The ref specs to be used in the fetch operation
 	 *
 	 * @param specs
+	 *            String representation of {@code RefSpec}s
 	 * @return {@code this}
 	 * @since 4.9
 	 */
@@ -406,6 +421,7 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	 * The ref specs to be used in the fetch operation
 	 *
 	 * @param specs
+	 *            one or multiple {@link org.eclipse.jgit.transport.RefSpec}s
 	 * @return {@code this}
 	 */
 	public FetchCommand setRefSpecs(RefSpec... specs) {
@@ -416,6 +432,7 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	 * The ref specs to be used in the fetch operation
 	 *
 	 * @param specs
+	 *            list of {@link org.eclipse.jgit.transport.RefSpec}s
 	 * @return {@code this}
 	 */
 	public FetchCommand setRefSpecs(List<RefSpec> specs) {
@@ -426,6 +443,8 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	}
 
 	/**
+	 * Whether to do a dry run
+	 *
 	 * @return the dry run preference for the fetch operation
 	 */
 	public boolean isDryRun() {
@@ -436,6 +455,7 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	 * Sets whether the fetch operation should be a dry run
 	 *
 	 * @param dryRun
+	 *            whether to do a dry run
 	 * @return {@code this}
 	 */
 	public FetchCommand setDryRun(boolean dryRun) {
@@ -445,6 +465,8 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	}
 
 	/**
+	 * Get thin-pack preference
+	 *
 	 * @return the thin-pack preference for fetch operation
 	 */
 	public boolean isThin() {
@@ -457,6 +479,7 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	 * Default setting is Transport.DEFAULT_FETCH_THIN
 	 *
 	 * @param thin
+	 *            the thin-pack preference
 	 * @return {@code this}
 	 */
 	public FetchCommand setThin(boolean thin) {
@@ -469,6 +492,7 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	 * Sets the specification of annotated tag behavior during fetch
 	 *
 	 * @param tagOpt
+	 *            the {@link org.eclipse.jgit.transport.TagOpt}
 	 * @return {@code this}
 	 */
 	public FetchCommand setTagOpt(TagOpt tagOpt) {

org.eclipse.jgit/src/org/eclipse/jgit/api/GarbageCollectCommand.java

@@ -61,7 +61,6 @@ import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.storage.pack.PackConfig;
-import org.eclipse.jgit.util.GitDateParser;
 
 /**
  * A class used to execute a {@code gc} command. It has setters for all
@@ -97,7 +96,10 @@ public class GarbageCollectCommand extends GitCommand<Properties> {
 	private PackConfig pconfig;
 
 	/**
+	 * Constructor for GarbageCollectCommand.
+	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	protected GarbageCollectCommand(Repository repo) {
 		super(repo);
@@ -105,6 +107,8 @@ public class GarbageCollectCommand extends GitCommand<Properties> {
 	}
 
 	/**
+	 * Set progress monitor
+	 *
 	 * @param monitor
 	 *            a progress monitor
 	 * @return this instance
@@ -118,8 +122,8 @@ public class GarbageCollectCommand extends GitCommand<Properties> {
 	 * During gc() or prune() each unreferenced, loose object which has been
 	 * created or modified after <code>expire</code> will not be pruned. Only
 	 * older objects may be pruned. If set to null then every object is a
-	 * candidate for pruning. Use {@link GitDateParser} to parse time formats
-	 * used by git gc.
+	 * candidate for pruning. Use {@link org.eclipse.jgit.util.GitDateParser} to
+	 * parse time formats used by git gc.
 	 *
 	 * @param expire
 	 *            minimal age of objects to be pruned.
@@ -191,6 +195,7 @@ public class GarbageCollectCommand extends GitCommand<Properties> {
 		return this;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Properties call() throws GitAPIException {
 		checkCallable();
@@ -229,7 +234,7 @@ public class GarbageCollectCommand extends GitCommand<Properties> {
 	 * Computes and returns the repository statistics.
 	 *
 	 * @return the repository statistics
-	 * @throws GitAPIException
+	 * @throws org.eclipse.jgit.api.errors.GitAPIException
 	 *             thrown if the repository statistics cannot be computed
 	 * @since 3.0
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/api/Git.java

@@ -89,25 +89,30 @@ public class Git implements AutoCloseable {
 	private final boolean closeRepo;
 
 	/**
+	 * Open repository
+	 *
 	 * @param dir
 	 *            the repository to open. May be either the GIT_DIR, or the
 	 *            working tree directory that contains {@code .git}.
-	 * @return a {@link Git} object for the existing git repository
-	 * @throws IOException
+	 * @return a {@link org.eclipse.jgit.api.Git} object for the existing git
+	 *         repository
+	 * @throws java.io.IOException
 	 */
 	public static Git open(File dir) throws IOException {
 		return open(dir, FS.DETECTED);
 	}
 
 	/**
+	 * Open repository
+	 *
 	 * @param dir
 	 *            the repository to open. May be either the GIT_DIR, or the
 	 *            working tree directory that contains {@code .git}.
 	 * @param fs
 	 *            filesystem abstraction to use when accessing the repository.
-	 * @return a {@link Git} object for the existing git repository. Closing this
-	 *         instance will close the repo.
-	 * @throws IOException
+	 * @return a {@link org.eclipse.jgit.api.Git} object for the existing git
+	 *         repository. Closing this instance will close the repo.
+	 * @throws java.io.IOException
 	 */
 	public static Git open(File dir, FS fs) throws IOException {
 		RepositoryCache.FileKey key;
@@ -119,31 +124,36 @@ public class Git implements AutoCloseable {
 	}
 
 	/**
+	 * Wrap repository
+	 *
 	 * @param repo
 	 *            the git repository this class is interacting with;
 	 *            {@code null} is not allowed.
-	 * @return a {@link Git} object for the existing git repository. The caller is
-	 *         responsible for closing the repository; {@link #close()} on this
-	 *         instance does not close the repo.
+	 * @return a {@link org.eclipse.jgit.api.Git} object for the existing git
+	 *         repository. The caller is responsible for closing the repository;
+	 *         {@link #close()} on this instance does not close the repo.
 	 */
 	public static Git wrap(Repository repo) {
 		return new Git(repo);
 	}
 
 	/**
-	 * Frees resources associated with this instance.
+	 * {@inheritDoc}
+	 * <p>
+	 * Free resources associated with this instance.
 	 * <p>
-	 * If the repository was opened by a static factory method in this class, then
-	 * this method calls {@link Repository#close()} on the underlying repository
-	 * instance. (Whether this actually releases underlying resources, such as
-	 * file handles, may vary; see {@link Repository} for more details.)
+	 * If the repository was opened by a static factory method in this class,
+	 * then this method calls {@link Repository#close()} on the underlying
+	 * repository instance. (Whether this actually releases underlying
+	 * resources, such as file handles, may vary; see {@link Repository} for
+	 * more details.)
 	 * <p>
-	 * If the repository was created by a caller and passed into {@link
-	 * #Git(Repository)} or a static factory method in this class, then this
-	 * method does not call close on the underlying repository.
+	 * If the repository was created by a caller and passed into
+	 * {@link #Git(Repository)} or a static factory method in this class, then
+	 * this method does not call close on the underlying repository.
 	 * <p>
-	 * In all cases, after calling this method you should not use this {@link Git}
-	 * instance anymore.
+	 * In all cases, after calling this method you should not use this
+	 * {@link Git} instance anymore.
 	 *
 	 * @since 3.2
 	 */
@@ -154,23 +164,23 @@ public class Git implements AutoCloseable {
 	}
 
 	/**
-	 * Returns a command object to execute a {@code clone} command
+	 * Return a command object to execute a {@code clone} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-clone.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-clone.html"
 	 *      >Git documentation about clone</a>
-	 * @return a {@link CloneCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code clone} command
+	 * @return a {@link org.eclipse.jgit.api.CloneCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code clone}
+	 *         command
 	 */
 	public static CloneCommand cloneRepository() {
 		return new CloneCommand();
 	}
 
 	/**
-	 * Returns a command to list remote branches/tags without a local
-	 * repository.
+	 * Return a command to list remote branches/tags without a local repository.
 	 *
-	 * @return a {@link LsRemoteCommand}
+	 * @return a {@link org.eclipse.jgit.api.LsRemoteCommand}
 	 * @since 3.1
 	 */
 	public static LsRemoteCommand lsRemoteRepository() {
@@ -178,24 +188,25 @@ public class Git implements AutoCloseable {
 	}
 
 	/**
-	 * Returns a command object to execute a {@code init} command
+	 * Return a command object to execute a {@code init} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-init.html"
-	 *      >Git documentation about init</a>
-	 * @return a {@link InitCommand} used to collect all optional parameters and
-	 *         to finally execute the {@code init} command
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-init.html" >Git
+	 *      documentation about init</a>
+	 * @return a {@link org.eclipse.jgit.api.InitCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code init}
+	 *         command
 	 */
 	public static InitCommand init() {
 		return new InitCommand();
 	}
 
 	/**
-	 * Constructs a new {@link Git} object which can interact with the specified
-	 * git repository.
+	 * Construct a new {@link org.eclipse.jgit.api.Git} object which can
+	 * interact with the specified git repository.
 	 * <p>
-	 * All command classes returned by methods of this class will always interact
-	 * with this git repository.
+	 * All command classes returned by methods of this class will always
+	 * interact with this git repository.
 	 * <p>
 	 * The caller is responsible for closing the repository; {@link #close()} on
 	 * this instance does not close the repo.
@@ -216,75 +227,78 @@ public class Git implements AutoCloseable {
 	}
 
 	/**
-	 * Returns a command object to execute a {@code Commit} command
+	 * Return a command object to execute a {@code Commit} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-commit.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-commit.html"
 	 *      >Git documentation about Commit</a>
-	 * @return a {@link CommitCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code Commit} command
+	 * @return a {@link org.eclipse.jgit.api.CommitCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code Commit}
+	 *         command
 	 */
 	public CommitCommand commit() {
 		return new CommitCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code Log} command
+	 * Return a command object to execute a {@code Log} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-log.html"
-	 *      >Git documentation about Log</a>
-	 * @return a {@link LogCommand} used to collect all optional parameters and
-	 *         to finally execute the {@code Log} command
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-log.html" >Git
+	 *      documentation about Log</a>
+	 * @return a {@link org.eclipse.jgit.api.LogCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code Log}
+	 *         command
 	 */
 	public LogCommand log() {
 		return new LogCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code Merge} command
+	 * Return a command object to execute a {@code Merge} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-merge.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-merge.html"
 	 *      >Git documentation about Merge</a>
-	 * @return a {@link MergeCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code Merge} command
+	 * @return a {@link org.eclipse.jgit.api.MergeCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code Merge}
+	 *         command
 	 */
 	public MergeCommand merge() {
 		return new MergeCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code Pull} command
+	 * Return a command object to execute a {@code Pull} command
 	 *
-	 * @return a {@link PullCommand}
+	 * @return a {@link org.eclipse.jgit.api.PullCommand}
 	 */
 	public PullCommand pull() {
 		return new PullCommand(repo);
 	}
 
 	/**
-	 * Returns a command object used to create branches
+	 * Return a command object used to create branches
 	 *
-	 * @return a {@link CreateBranchCommand}
+	 * @return a {@link org.eclipse.jgit.api.CreateBranchCommand}
 	 */
 	public CreateBranchCommand branchCreate() {
 		return new CreateBranchCommand(repo);
 	}
 
 	/**
-	 * Returns a command object used to delete branches
+	 * Return a command object used to delete branches
 	 *
-	 * @return a {@link DeleteBranchCommand}
+	 * @return a {@link org.eclipse.jgit.api.DeleteBranchCommand}
 	 */
 	public DeleteBranchCommand branchDelete() {
 		return new DeleteBranchCommand(repo);
 	}
 
 	/**
-	 * Returns a command object used to list branches
+	 * Return a command object used to list branches
 	 *
-	 * @return a {@link ListBranchCommand}
+	 * @return a {@link org.eclipse.jgit.api.ListBranchCommand}
 	 */
 	public ListBranchCommand branchList() {
 		return new ListBranchCommand(repo);
@@ -292,170 +306,180 @@ public class Git implements AutoCloseable {
 
 	/**
 	 *
-	 * Returns a command object used to list tags
+	 * Return a command object used to list tags
 	 *
-	 * @return a {@link ListTagCommand}
+	 * @return a {@link org.eclipse.jgit.api.ListTagCommand}
 	 */
 	public ListTagCommand tagList() {
 		return new ListTagCommand(repo);
 	}
 
 	/**
-	 * Returns a command object used to rename branches
+	 * Return a command object used to rename branches
 	 *
-	 * @return a {@link RenameBranchCommand}
+	 * @return a {@link org.eclipse.jgit.api.RenameBranchCommand}
 	 */
 	public RenameBranchCommand branchRename() {
 		return new RenameBranchCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code Add} command
+	 * Return a command object to execute a {@code Add} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-add.html"
-	 *      >Git documentation about Add</a>
-	 * @return a {@link AddCommand} used to collect all optional parameters and
-	 *         to finally execute the {@code Add} command
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-add.html" >Git
+	 *      documentation about Add</a>
+	 * @return a {@link org.eclipse.jgit.api.AddCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code Add}
+	 *         command
 	 */
 	public AddCommand add() {
 		return new AddCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code Tag} command
+	 * Return a command object to execute a {@code Tag} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-tag.html"
-	 *      >Git documentation about Tag</a>
-	 * @return a {@link TagCommand} used to collect all optional parameters and
-	 *         to finally execute the {@code Tag} command
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-tag.html" >Git
+	 *      documentation about Tag</a>
+	 * @return a {@link org.eclipse.jgit.api.TagCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code Tag}
+	 *         command
 	 */
 	public TagCommand tag() {
 		return new TagCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code Fetch} command
+	 * Return a command object to execute a {@code Fetch} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-fetch.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-fetch.html"
 	 *      >Git documentation about Fetch</a>
-	 * @return a {@link FetchCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code Fetch} command
+	 * @return a {@link org.eclipse.jgit.api.FetchCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code Fetch}
+	 *         command
 	 */
 	public FetchCommand fetch() {
 		return new FetchCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code Push} command
+	 * Return a command object to execute a {@code Push} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-push.html"
-	 *      >Git documentation about Push</a>
-	 * @return a {@link PushCommand} used to collect all optional parameters and
-	 *         to finally execute the {@code Push} command
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-push.html" >Git
+	 *      documentation about Push</a>
+	 * @return a {@link org.eclipse.jgit.api.PushCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code Push}
+	 *         command
 	 */
 	public PushCommand push() {
 		return new PushCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code cherry-pick} command
+	 * Return a command object to execute a {@code cherry-pick} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-cherry-pick.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-cherry-pick.html"
 	 *      >Git documentation about cherry-pick</a>
-	 * @return a {@link CherryPickCommand} used to collect all optional
-	 *         parameters and to finally execute the {@code cherry-pick} command
+	 * @return a {@link org.eclipse.jgit.api.CherryPickCommand} used to collect
+	 *         all optional parameters and to finally execute the
+	 *         {@code cherry-pick} command
 	 */
 	public CherryPickCommand cherryPick() {
 		return new CherryPickCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code revert} command
+	 * Return a command object to execute a {@code revert} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-revert.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-revert.html"
 	 *      >Git documentation about reverting changes</a>
-	 * @return a {@link RevertCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code cherry-pick} command
+	 * @return a {@link org.eclipse.jgit.api.RevertCommand} used to collect all
+	 *         optional parameters and to finally execute the
+	 *         {@code cherry-pick} command
 	 */
 	public RevertCommand revert() {
 		return new RevertCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code Rebase} command
+	 * Return a command object to execute a {@code Rebase} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-rebase.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-rebase.html"
 	 *      >Git documentation about rebase</a>
-	 * @return a {@link RebaseCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code rebase} command
+	 * @return a {@link org.eclipse.jgit.api.RebaseCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code rebase}
+	 *         command
 	 */
 	public RebaseCommand rebase() {
 		return new RebaseCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code rm} command
+	 * Return a command object to execute a {@code rm} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-rm.html"
-	 *      >Git documentation about rm</a>
-	 * @return a {@link RmCommand} used to collect all optional parameters and
-	 *         to finally execute the {@code rm} command
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-rm.html" >Git
+	 *      documentation about rm</a>
+	 * @return a {@link org.eclipse.jgit.api.RmCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code rm} command
 	 */
 	public RmCommand rm() {
 		return new RmCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code checkout} command
+	 * Return a command object to execute a {@code checkout} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-checkout.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-checkout.html"
 	 *      >Git documentation about checkout</a>
-	 * @return a {@link CheckoutCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code checkout} command
+	 * @return a {@link org.eclipse.jgit.api.CheckoutCommand} used to collect
+	 *         all optional parameters and to finally execute the
+	 *         {@code checkout} command
 	 */
 	public CheckoutCommand checkout() {
 		return new CheckoutCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code reset} command
+	 * Return a command object to execute a {@code reset} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-reset.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-reset.html"
 	 *      >Git documentation about reset</a>
-	 * @return a {@link ResetCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code reset} command
+	 * @return a {@link org.eclipse.jgit.api.ResetCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code reset}
+	 *         command
 	 */
 	public ResetCommand reset() {
 		return new ResetCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code status} command
+	 * Return a command object to execute a {@code status} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-status.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-status.html"
 	 *      >Git documentation about status</a>
-	 * @return a {@link StatusCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code status} command
+	 * @return a {@link org.eclipse.jgit.api.StatusCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code status}
+	 *         command
 	 */
 	public StatusCommand status() {
 		return new StatusCommand(repo);
 	}
 
 	/**
-	 * Returns a command to create an archive from a tree
+	 * Return a command to create an archive from a tree
 	 *
-	 * @return a {@link ArchiveCommand}
+	 * @return a {@link org.eclipse.jgit.api.ArchiveCommand}
 	 * @since 3.1
 	 */
 	public ArchiveCommand archive() {
@@ -463,179 +487,185 @@ public class Git implements AutoCloseable {
 	}
 
 	/**
-	 * Returns a command to add notes to an object
+	 * Return a command to add notes to an object
 	 *
-	 * @return a {@link AddNoteCommand}
+	 * @return a {@link org.eclipse.jgit.api.AddNoteCommand}
 	 */
 	public AddNoteCommand notesAdd() {
 		return new AddNoteCommand(repo);
 	}
 
 	/**
-	 * Returns a command to remove notes on an object
+	 * Return a command to remove notes on an object
 	 *
-	 * @return a {@link RemoveNoteCommand}
+	 * @return a {@link org.eclipse.jgit.api.RemoveNoteCommand}
 	 */
 	public RemoveNoteCommand notesRemove() {
 		return new RemoveNoteCommand(repo);
 	}
 
 	/**
-	 * Returns a command to list all notes
+	 * Return a command to list all notes
 	 *
-	 * @return a {@link ListNotesCommand}
+	 * @return a {@link org.eclipse.jgit.api.ListNotesCommand}
 	 */
 	public ListNotesCommand notesList() {
 		return new ListNotesCommand(repo);
 	}
 
 	/**
-	 * Returns a command to show notes on an object
+	 * Return a command to show notes on an object
 	 *
-	 * @return a {@link ShowNoteCommand}
+	 * @return a {@link org.eclipse.jgit.api.ShowNoteCommand}
 	 */
 	public ShowNoteCommand notesShow() {
 		return new ShowNoteCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code ls-remote} command
+	 * Return a command object to execute a {@code ls-remote} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-ls-remote.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-ls-remote.html"
 	 *      >Git documentation about ls-remote</a>
-	 * @return a {@link LsRemoteCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code status} command
+	 * @return a {@link org.eclipse.jgit.api.LsRemoteCommand} used to collect
+	 *         all optional parameters and to finally execute the {@code status}
+	 *         command
 	 */
 	public LsRemoteCommand lsRemote() {
 		return new LsRemoteCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code clean} command
+	 * Return a command object to execute a {@code clean} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-clean.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-clean.html"
 	 *      >Git documentation about Clean</a>
-	 * @return a {@link CleanCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code clean} command
+	 * @return a {@link org.eclipse.jgit.api.CleanCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code clean}
+	 *         command
 	 */
 	public CleanCommand clean() {
 		return new CleanCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code blame} command
+	 * Return a command object to execute a {@code blame} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-blame.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-blame.html"
 	 *      >Git documentation about Blame</a>
-	 * @return a {@link BlameCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code blame} command
+	 * @return a {@link org.eclipse.jgit.api.BlameCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code blame}
+	 *         command
 	 */
 	public BlameCommand blame() {
 		return new BlameCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code reflog} command
+	 * Return a command object to execute a {@code reflog} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-reflog.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-reflog.html"
 	 *      >Git documentation about reflog</a>
-	 * @return a {@link ReflogCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code reflog} command
+	 * @return a {@link org.eclipse.jgit.api.ReflogCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code reflog}
+	 *         command
 	 */
 	public ReflogCommand reflog() {
 		return new ReflogCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code diff} command
+	 * Return a command object to execute a {@code diff} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-diff.html"
-	 *      >Git documentation about diff</a>
-	 * @return a {@link DiffCommand} used to collect all optional parameters and
-	 *         to finally execute the {@code diff} command
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-diff.html" >Git
+	 *      documentation about diff</a>
+	 * @return a {@link org.eclipse.jgit.api.DiffCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code diff}
+	 *         command
 	 */
 	public DiffCommand diff() {
 		return new DiffCommand(repo);
 	}
 
 	/**
-	 * Returns a command object used to delete tags
+	 * Return a command object used to delete tags
 	 *
-	 * @return a {@link DeleteTagCommand}
+	 * @return a {@link org.eclipse.jgit.api.DeleteTagCommand}
 	 */
 	public DeleteTagCommand tagDelete() {
 		return new DeleteTagCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code submodule add} command
+	 * Return a command object to execute a {@code submodule add} command
 	 *
-	 * @return a {@link SubmoduleAddCommand} used to add a new submodule to a
-	 *         parent repository
+	 * @return a {@link org.eclipse.jgit.api.SubmoduleAddCommand} used to add a
+	 *         new submodule to a parent repository
 	 */
 	public SubmoduleAddCommand submoduleAdd() {
 		return new SubmoduleAddCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code submodule init} command
+	 * Return a command object to execute a {@code submodule init} command
 	 *
-	 * @return a {@link SubmoduleInitCommand} used to initialize the
-	 *         repository's config with settings from the .gitmodules file in
-	 *         the working tree
+	 * @return a {@link org.eclipse.jgit.api.SubmoduleInitCommand} used to
+	 *         initialize the repository's config with settings from the
+	 *         .gitmodules file in the working tree
 	 */
 	public SubmoduleInitCommand submoduleInit() {
 		return new SubmoduleInitCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code submodule status} command
+	 * Return a command object to execute a {@code submodule status} command
 	 *
-	 * @return a {@link SubmoduleStatusCommand} used to report the status of a
-	 *         repository's configured submodules
+	 * @return a {@link org.eclipse.jgit.api.SubmoduleStatusCommand} used to
+	 *         report the status of a repository's configured submodules
 	 */
 	public SubmoduleStatusCommand submoduleStatus() {
 		return new SubmoduleStatusCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code submodule sync} command
+	 * Return a command object to execute a {@code submodule sync} command
 	 *
-	 * @return a {@link SubmoduleSyncCommand} used to update the URL of a
-	 *         submodule from the parent repository's .gitmodules file
+	 * @return a {@link org.eclipse.jgit.api.SubmoduleSyncCommand} used to
+	 *         update the URL of a submodule from the parent repository's
+	 *         .gitmodules file
 	 */
 	public SubmoduleSyncCommand submoduleSync() {
 		return new SubmoduleSyncCommand(repo);
 	}
 
 	/**
-	 * Returns a command object to execute a {@code submodule update} command
+	 * Return a command object to execute a {@code submodule update} command
 	 *
-	 * @return a {@link SubmoduleUpdateCommand} used to update the submodules in
-	 *         a repository to the configured revision
+	 * @return a {@link org.eclipse.jgit.api.SubmoduleUpdateCommand} used to
+	 *         update the submodules in a repository to the configured revision
 	 */
 	public SubmoduleUpdateCommand submoduleUpdate() {
 		return new SubmoduleUpdateCommand(repo);
 	}
 
 	/**
-	 * Returns a command object used to list stashed commits
+	 * Return a command object used to list stashed commits
 	 *
-	 * @return a {@link StashListCommand}
+	 * @return a {@link org.eclipse.jgit.api.StashListCommand}
 	 */
 	public StashListCommand stashList() {
 		return new StashListCommand(repo);
 	}
 
 	/**
-	 * Returns a command object used to create a stashed commit
+	 * Return a command object used to create a stashed commit
 	 *
-	 * @return a {@link StashCreateCommand}
+	 * @return a {@link org.eclipse.jgit.api.StashCreateCommand}
 	 * @since 2.0
 	 */
 	public StashCreateCommand stashCreate() {
@@ -643,9 +673,9 @@ public class Git implements AutoCloseable {
 	}
 
 	/**
-	 * Returns a command object used to apply a stashed commit
+	 * Returs a command object used to apply a stashed commit
 	 *
-	 * @return a {@link StashApplyCommand}
+	 * @return a {@link org.eclipse.jgit.api.StashApplyCommand}
 	 * @since 2.0
 	 */
 	public StashApplyCommand stashApply() {
@@ -653,9 +683,9 @@ public class Git implements AutoCloseable {
 	}
 
 	/**
-	 * Returns a command object used to drop a stashed commit
+	 * Return a command object used to drop a stashed commit
 	 *
-	 * @return a {@link StashDropCommand}
+	 * @return a {@link org.eclipse.jgit.api.StashDropCommand}
 	 * @since 2.0
 	 */
 	public StashDropCommand stashDrop() {
@@ -663,14 +693,14 @@ public class Git implements AutoCloseable {
 	}
 
 	/**
-	 * Returns a command object to execute a {@code apply} command
+	 * Return a command object to execute a {@code apply} command
 	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-apply.html"
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-apply.html"
 	 *      >Git documentation about apply</a>
-	 *
-	 * @return a {@link ApplyCommand} used to collect all optional parameters
-	 *         and to finally execute the {@code apply} command
+	 * @return a {@link org.eclipse.jgit.api.ApplyCommand} used to collect all
+	 *         optional parameters and to finally execute the {@code apply}
+	 *         command
 	 * @since 2.0
 	 */
 	public ApplyCommand apply() {
@@ -678,14 +708,14 @@ public class Git implements AutoCloseable {
 	}
 
 	/**
-	 * Returns a command object to execute a {@code gc} command
-	 *
-	 * @see <a
-	 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-gc.html"
-	 *      >Git documentation about gc</a>
+	 * Return a command object to execute a {@code gc} command
 	 *
-	 * @return a {@link GarbageCollectCommand} used to collect all optional
-	 *         parameters and to finally execute the {@code gc} command
+	 * @see <a href=
+	 *      "http://www.kernel.org/pub/software/scm/git/docs/git-gc.html" >Git
+	 *      documentation about gc</a>
+	 * @return a {@link org.eclipse.jgit.api.GarbageCollectCommand} used to
+	 *         collect all optional parameters and to finally execute the
+	 *         {@code gc} command
 	 * @since 2.2
 	 */
 	public GarbageCollectCommand gc() {
@@ -693,9 +723,9 @@ public class Git implements AutoCloseable {
 	}
 
 	/**
-	 * Returns a command object to find human-readable names of revisions.
+	 * Return a command object to find human-readable names of revisions.
 	 *
-	 * @return a {@link NameRevCommand}.
+	 * @return a {@link org.eclipse.jgit.api.NameRevCommand}.
 	 * @since 3.0
 	 */
 	public NameRevCommand nameRev() {
@@ -703,10 +733,10 @@ public class Git implements AutoCloseable {
 	}
 
 	/**
-	 * Returns a command object to come up with a short name that describes a
+	 * Return a command object to come up with a short name that describes a
 	 * commit in terms of the nearest git tag.
 	 *
-	 * @return a {@link DescribeCommand}.
+	 * @return a {@link org.eclipse.jgit.api.DescribeCommand}.
 	 * @since 3.2
 	 */
 	public DescribeCommand describe() {
@@ -716,7 +746,7 @@ public class Git implements AutoCloseable {
 	/**
 	 * Return a command used to list the available remotes.
 	 *
-	 * @return a {@link RemoteListCommand}
+	 * @return a {@link org.eclipse.jgit.api.RemoteListCommand}
 	 * @since 4.2
 	 */
 	public RemoteListCommand remoteList() {
@@ -726,7 +756,7 @@ public class Git implements AutoCloseable {
 	/**
 	 * Return a command used to add a new remote.
 	 *
-	 * @return a {@link RemoteAddCommand}
+	 * @return a {@link org.eclipse.jgit.api.RemoteAddCommand}
 	 * @since 4.2
 	 */
 	public RemoteAddCommand remoteAdd() {
@@ -736,7 +766,7 @@ public class Git implements AutoCloseable {
 	/**
 	 * Return a command used to remove an existing remote.
 	 *
-	 * @return a {@link RemoteRemoveCommand}
+	 * @return a {@link org.eclipse.jgit.api.RemoteRemoveCommand}
 	 * @since 4.2
 	 */
 	public RemoteRemoveCommand remoteRemove() {
@@ -746,7 +776,7 @@ public class Git implements AutoCloseable {
 	/**
 	 * Return a command used to change the URL of an existing remote.
 	 *
-	 * @return a {@link RemoteSetUrlCommand}
+	 * @return a {@link org.eclipse.jgit.api.RemoteSetUrlCommand}
 	 * @since 4.2
 	 */
 	public RemoteSetUrlCommand remoteSetUrl() {
@@ -754,6 +784,8 @@ public class Git implements AutoCloseable {
 	}
 
 	/**
+	 * Get repository
+	 *
 	 * @return the git repository this class is interacting with; see
 	 *         {@link #close()} for notes on closing this repository.
 	 */
@@ -761,6 +793,7 @@ public class Git implements AutoCloseable {
 		return repo;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		return "Git[" + repo + "]"; //$NON-NLS-1$//$NON-NLS-2$

org.eclipse.jgit/src/org/eclipse/jgit/api/GitCommand.java

@@ -48,18 +48,20 @@ import org.eclipse.jgit.lib.Repository;
 /**
  * Common superclass of all commands in the package {@code org.eclipse.jgit.api}
  * <p>
- * This class ensures that all commands fulfill the {@link Callable} interface.
- * It also has a property {@link #repo} holding a reference to the git
- * {@link Repository} this command should work with.
+ * This class ensures that all commands fulfill the
+ * {@link java.util.concurrent.Callable} interface. It also has a property
+ * {@link #repo} holding a reference to the git
+ * {@link org.eclipse.jgit.lib.Repository} this command should work with.
  * <p>
  * Finally this class stores a state telling whether it is allowed to call
- * {@link #call()} on this instance. Instances of {@link GitCommand} can only be
- * used for one single successful call to {@link #call()}. Afterwards this
- * instance may not be used anymore to set/modify any properties or to call
- * {@link #call()} again. This is achieved by setting the {@link #callable}
- * property to false after the successful execution of {@link #call()} and to
- * check the state (by calling {@link #checkCallable()}) before setting of
- * properties and inside {@link #call()}.
+ * {@link #call()} on this instance. Instances of
+ * {@link org.eclipse.jgit.api.GitCommand} can only be used for one single
+ * successful call to {@link #call()}. Afterwards this instance may not be used
+ * anymore to set/modify any properties or to call {@link #call()} again. This
+ * is achieved by setting the {@link #callable} property to false after the
+ * successful execution of {@link #call()} and to check the state (by calling
+ * {@link #checkCallable()}) before setting of properties and inside
+ * {@link #call()}.
  *
  * @param <T>
  *            the return type which is expected from {@link #call()}
@@ -78,14 +80,18 @@ public abstract class GitCommand<T> implements Callable<T> {
 	 * Creates a new command which interacts with a single repository
 	 *
 	 * @param repo
-	 *            the {@link Repository} this command should interact with
+	 *            the {@link org.eclipse.jgit.lib.Repository} this command
+	 *            should interact with
 	 */
 	protected GitCommand(Repository repo) {
 		this.repo = repo;
 	}
 
 	/**
-	 * @return the {@link Repository} this command is interacting with
+	 * Get repository this command is working on
+	 *
+	 * @return the {@link org.eclipse.jgit.lib.Repository} this command is
+	 *         interacting with
 	 */
 	public Repository getRepository() {
 		return repo;
@@ -106,9 +112,9 @@ public abstract class GitCommand<T> implements Callable<T> {
 
 	/**
 	 * Checks that the property {@link #callable} is {@code true}. If not then
-	 * an {@link IllegalStateException} is thrown
+	 * an {@link java.lang.IllegalStateException} is thrown
 	 *
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             when this method is called and the property {@link #callable}
 	 *             is {@code false}
 	 */
@@ -120,11 +126,9 @@ public abstract class GitCommand<T> implements Callable<T> {
 	}
 
 	/**
-	 * Executes the command
-	 *
-	 * @return T a result. Each command has its own return type
-	 * @throws GitAPIException
-	 *             or subclass thereof when an error occurs
+	 * {@inheritDoc}
+	 * <p>
+	 * Execute the command
 	 */
 	@Override
 	public abstract T call() throws GitAPIException;

org.eclipse.jgit/src/org/eclipse/jgit/api/InitCommand.java

@@ -69,9 +69,9 @@ public class InitCommand implements Callable<Git> {
 	private boolean bare;
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code Init} command.
-	 *
-	 * @return the newly created {@code Git} object with associated repository
 	 */
 	@Override
 	public Git call() throws GitAPIException {
@@ -127,7 +127,7 @@ public class InitCommand implements Callable<Git> {
 	 * @param directory
 	 *            the directory to init to
 	 * @return this instance
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             if the combination of directory, gitDir and bare is illegal.
 	 *             E.g. if for a non-bare repository directory and gitDir point
 	 *             to the same directory of if for a bare repository both
@@ -141,10 +141,12 @@ public class InitCommand implements Callable<Git> {
 	}
 
 	/**
+	 * Set the repository meta directory (.git)
+	 *
 	 * @param gitDir
 	 *            the repository meta directory
 	 * @return this instance
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             if the combination of directory, gitDir and bare is illegal.
 	 *             E.g. if for a non-bare repository directory and gitDir point
 	 *             to the same directory of if for a bare repository both
@@ -176,9 +178,11 @@ public class InitCommand implements Callable<Git> {
 	}
 
 	/**
+	 * Set whether the repository is bare or not
+	 *
 	 * @param bare
 	 *            whether the repository is bare or not
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             if the combination of directory, gitDir and bare is illegal.
 	 *             E.g. if for a non-bare repository directory and gitDir point
 	 *             to the same directory of if for a bare repository both

org.eclipse.jgit/src/org/eclipse/jgit/api/ListBranchCommand.java

@@ -95,12 +95,16 @@ public class ListBranchCommand extends GitCommand<List<Ref>> {
 	}
 
 	/**
+	 * Constructor for ListBranchCommand.
+	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	protected ListBranchCommand(Repository repo) {
 		super(repo);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public List<Ref> call() throws GitAPIException {
 		checkCallable();
@@ -154,6 +158,8 @@ public class ListBranchCommand extends GitCommand<List<Ref>> {
 	}
 
 	/**
+	 * Set the list mode
+	 *
 	 * @param listMode
 	 *            optional: corresponds to the -r/-a options; by default, only
 	 *            local branches will be listed

org.eclipse.jgit/src/org/eclipse/jgit/api/ListNotesCommand.java

@@ -68,15 +68,16 @@ public class ListNotesCommand extends GitCommand<List<Note>> {
 	private String notesRef = Constants.R_NOTES_COMMITS;
 
 	/**
+	 * Constructor for ListNotesCommand.
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected ListNotesCommand(Repository repo) {
 		super(repo);
 	}
 
-	/**
-	 * @return the requested notes
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public List<Note> call() throws GitAPIException {
 		checkCallable();
@@ -101,12 +102,14 @@ public class ListNotesCommand extends GitCommand<List<Note>> {
 	}
 
 	/**
+	 * Set the {@code Ref} to read notes from
+	 *
 	 * @param notesRef
-	 *            the ref to read notes from. Note, the default value of
-	 *            {@link Constants#R_NOTES_COMMITS} will be used if nothing is
-	 *            set
+	 *            the name of the {@code Ref} to read notes from. Note, the
+	 *            default value of
+	 *            {@link org.eclipse.jgit.lib.Constants#R_NOTES_COMMITS} will be
+	 *            used if nothing is set
 	 * @return {@code this}
-	 *
 	 * @see Constants#R_NOTES_COMMITS
 	 */
 	public ListNotesCommand setNotesRef(String notesRef) {

org.eclipse.jgit/src/org/eclipse/jgit/api/ListTagCommand.java

@@ -65,15 +65,16 @@ import org.eclipse.jgit.revwalk.RevWalk;
 public class ListTagCommand extends GitCommand<List<Ref>> {
 
 	/**
+	 * Constructor for ListTagCommand.
+	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	protected ListTagCommand(Repository repo) {
 		super(repo);
 	}
 
-	/**
-	 * @return the tags available
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public List<Ref> call() throws GitAPIException {
 		checkCallable();

org.eclipse.jgit/src/org/eclipse/jgit/api/LogCommand.java

@@ -78,7 +78,7 @@ import org.eclipse.jgit.treewalk.filter.TreeFilter;
  * to finally execute the command. Each instance of this class should only be
  * used for one invocation of the command (means: one call to {@link #call()})
  * <p>
- * Examples (<code>git</code> is a {@link Git} instance):
+ * Examples (<code>git</code> is a {@link org.eclipse.jgit.api.Git} instance):
  * <p>
  * Get newest 10 commits, starting from the current branch:
  *
@@ -114,7 +114,10 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 	private int skip = -1;
 
 	/**
+	 * Constructor for LogCommand.
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected LogCommand(Repository repo) {
 		super(repo);
@@ -122,15 +125,13 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code Log} command with all the options and parameters
 	 * collected by the setter methods (e.g. {@link #add(AnyObjectId)},
 	 * {@link #not(AnyObjectId)}, ..) of this class. Each instance of this class
 	 * should only be used for one invocation of the command. Don't call this
 	 * method twice on an instance.
-	 *
-	 * @return an iteration over RevCommits
-	 * @throws NoHeadException
-	 *             of the references ref cannot be resolved
 	 */
 	@Override
 	public Iterable<RevCommit> call() throws GitAPIException, NoHeadException {
@@ -174,23 +175,26 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 	 *
 	 * @see RevWalk#markStart(RevCommit)
 	 * @param start
+	 *            the id of the commit to start from
 	 * @return {@code this}
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the commit supplied is not available from the object
 	 *             database. This usually indicates the supplied commit is
 	 *             invalid, but the reference was constructed during an earlier
-	 *             invocation to {@link RevWalk#lookupCommit(AnyObjectId)}.
-	 * @throws IncorrectObjectTypeException
+	 *             invocation to
+	 *             {@link org.eclipse.jgit.revwalk.RevWalk#lookupCommit(AnyObjectId)}.
+	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
 	 *             the object was not parsed yet and it was discovered during
 	 *             parsing that it is not actually a commit. This usually
 	 *             indicates the caller supplied a non-commit SHA-1 to
-	 *             {@link RevWalk#lookupCommit(AnyObjectId)}.
+	 *             {@link org.eclipse.jgit.revwalk.RevWalk#lookupCommit(AnyObjectId)}.
 	 * @throws JGitInternalException
 	 *             a low-level exception of JGit has occurred. The original
 	 *             exception can be retrieved by calling
-	 *             {@link Exception#getCause()}. Expect only
+	 *             {@link java.lang.Exception#getCause()}. Expect only
 	 *             {@code IOException's} to be wrapped. Subclasses of
-	 *             {@link IOException} (e.g. {@link MissingObjectException}) are
+	 *             {@link java.io.IOException} (e.g.
+	 *             {@link org.eclipse.jgit.errors.MissingObjectException}) are
 	 *             typically not wrapped here but thrown as original exception
 	 */
 	public LogCommand add(AnyObjectId start) throws MissingObjectException,
@@ -202,23 +206,26 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 	 * Same as {@code --not start}, or {@code ^start}
 	 *
 	 * @param start
+	 *            a {@link org.eclipse.jgit.lib.AnyObjectId}
 	 * @return {@code this}
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the commit supplied is not available from the object
 	 *             database. This usually indicates the supplied commit is
 	 *             invalid, but the reference was constructed during an earlier
-	 *             invocation to {@link RevWalk#lookupCommit(AnyObjectId)}.
-	 * @throws IncorrectObjectTypeException
+	 *             invocation to
+	 *             {@link org.eclipse.jgit.revwalk.RevWalk#lookupCommit(AnyObjectId)}.
+	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
 	 *             the object was not parsed yet and it was discovered during
 	 *             parsing that it is not actually a commit. This usually
 	 *             indicates the caller supplied a non-commit SHA-1 to
-	 *             {@link RevWalk#lookupCommit(AnyObjectId)}.
+	 *             {@link org.eclipse.jgit.revwalk.RevWalk#lookupCommit(AnyObjectId)}.
 	 * @throws JGitInternalException
 	 *             a low-level exception of JGit has occurred. The original
 	 *             exception can be retrieved by calling
-	 *             {@link Exception#getCause()}. Expect only
+	 *             {@link java.lang.Exception#getCause()}. Expect only
 	 *             {@code IOException's} to be wrapped. Subclasses of
-	 *             {@link IOException} (e.g. {@link MissingObjectException}) are
+	 *             {@link java.io.IOException} (e.g.
+	 *             {@link org.eclipse.jgit.errors.MissingObjectException}) are
 	 *             typically not wrapped here but thrown as original exception
 	 */
 	public LogCommand not(AnyObjectId start) throws MissingObjectException,
@@ -230,24 +237,28 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 	 * Adds the range {@code since..until}
 	 *
 	 * @param since
+	 *            a {@link org.eclipse.jgit.lib.AnyObjectId} object.
 	 * @param until
+	 *            a {@link org.eclipse.jgit.lib.AnyObjectId} object.
 	 * @return {@code this}
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the commit supplied is not available from the object
 	 *             database. This usually indicates the supplied commit is
 	 *             invalid, but the reference was constructed during an earlier
-	 *             invocation to {@link RevWalk#lookupCommit(AnyObjectId)}.
-	 * @throws IncorrectObjectTypeException
+	 *             invocation to
+	 *             {@link org.eclipse.jgit.revwalk.RevWalk#lookupCommit(AnyObjectId)}.
+	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
 	 *             the object was not parsed yet and it was discovered during
 	 *             parsing that it is not actually a commit. This usually
 	 *             indicates the caller supplied a non-commit SHA-1 to
-	 *             {@link RevWalk#lookupCommit(AnyObjectId)}.
+	 *             {@link org.eclipse.jgit.revwalk.RevWalk#lookupCommit(AnyObjectId)}.
 	 * @throws JGitInternalException
 	 *             a low-level exception of JGit has occurred. The original
 	 *             exception can be retrieved by calling
-	 *             {@link Exception#getCause()}. Expect only
+	 *             {@link java.lang.Exception#getCause()}. Expect only
 	 *             {@code IOException's} to be wrapped. Subclasses of
-	 *             {@link IOException} (e.g. {@link MissingObjectException}) are
+	 *             {@link java.io.IOException} (e.g.
+	 *             {@link org.eclipse.jgit.errors.MissingObjectException}) are
 	 *             typically not wrapped here but thrown as original exception
 	 */
 	public LogCommand addRange(AnyObjectId since, AnyObjectId until)
@@ -260,7 +271,7 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 	 *
 	 * @see #add(AnyObjectId)
 	 * @return {@code this}
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the references could not be accessed
 	 */
 	public LogCommand all() throws IOException {
@@ -354,8 +365,7 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 
 
 	/**
-	 * Sets a filter for the <code>LogCommand</code>.
-	 *
+	 * Set a filter for the <code>LogCommand</code>.
 	 *
 	 * @param aFilter
 	 *            the filter that this instance of <code>LogCommand</code>

org.eclipse.jgit/src/org/eclipse/jgit/api/LsRemoteCommand.java

@@ -83,6 +83,8 @@ public class LsRemoteCommand extends
 	private String uploadPack;
 
 	/**
+	 * Constructor for LsRemoteCommand
+	 *
 	 * @param repo
 	 *            local repository or null for operation without local
 	 *            repository
@@ -98,6 +100,7 @@ public class LsRemoteCommand extends
 	 *
 	 * @see Constants#DEFAULT_REMOTE_NAME
 	 * @param remote
+	 *            a {@link java.lang.String} object.
 	 * @return {@code this}
 	 */
 	public LsRemoteCommand setRemote(String remote) {
@@ -110,6 +113,7 @@ public class LsRemoteCommand extends
 	 * Include refs/heads in references results
 	 *
 	 * @param heads
+	 *            whether to include refs/heads
 	 * @return {@code this}
 	 */
 	public LsRemoteCommand setHeads(boolean heads) {
@@ -121,6 +125,7 @@ public class LsRemoteCommand extends
 	 * Include refs/tags in references results
 	 *
 	 * @param tags
+	 *            whether to include tags
 	 * @return {@code this}
 	 */
 	public LsRemoteCommand setTags(boolean tags) {
@@ -132,6 +137,8 @@ public class LsRemoteCommand extends
 	 * The full path of git-upload-pack on the remote host
 	 *
 	 * @param uploadPack
+	 *            the full path of executable providing the git-upload-pack
+	 *            service on remote host
 	 * @return {@code this}
 	 */
 	public LsRemoteCommand setUploadPack(String uploadPack) {
@@ -140,18 +147,12 @@ public class LsRemoteCommand extends
 	}
 
 	/**
-	 * Executes the {@code LsRemote} command with all the options and parameters
+	 * {@inheritDoc}
+	 * <p>
+	 * Execute the {@code LsRemote} command with all the options and parameters
 	 * collected by the setter methods (e.g. {@link #setHeads(boolean)}) of this
 	 * class. Each instance of this class should only be used for one invocation
 	 * of the command. Don't call this method twice on an instance.
-	 *
-	 * @return a collection of references in the remote repository
-	 * @throws GitAPIException
-	 *             or subclass thereof when an error occurs
-	 * @throws InvalidRemoteException
-	 *             when called with an invalid remote uri
-	 * @throws org.eclipse.jgit.api.errors.TransportException
-	 *             for errors that occurs during transport
 	 */
 	@Override
 	public Collection<Ref> call() throws GitAPIException,
@@ -164,9 +165,9 @@ public class LsRemoteCommand extends
 	 * Same as {@link #call()}, but return Map instead of Collection.
 	 *
 	 * @return a map from names to references in the remote repository
-	 * @throws GitAPIException
+	 * @throws org.eclipse.jgit.api.errors.GitAPIException
 	 *             or subclass thereof when an error occurs
-	 * @throws InvalidRemoteException
+	 * @throws org.eclipse.jgit.api.errors.InvalidRemoteException
 	 *             when called with an invalid remote uri
 	 * @throws org.eclipse.jgit.api.errors.TransportException
 	 *             for errors that occurs during transport

org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java

@@ -211,19 +211,22 @@ public class MergeCommand extends GitCommand<MergeResult> {
 	private Boolean commit;
 
 	/**
+	 * Constructor for MergeCommand.
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected MergeCommand(Repository repo) {
 		super(repo);
 	}
 
 	/**
-	 * Executes the {@code Merge} command with all the options and parameters
+	 * {@inheritDoc}
+	 * <p>
+	 * Execute the {@code Merge} command with all the options and parameters
 	 * collected by the setter methods (e.g. {@link #include(Ref)}) of this
 	 * class. Each instance of this class should only be used for one invocation
 	 * of the command. Don't call this method twice on an instance.
-	 *
-	 * @return the result of the merge
 	 */
 	@Override
 	@SuppressWarnings("boxing")
@@ -492,9 +495,10 @@ public class MergeCommand extends GitCommand<MergeResult> {
 	}
 
 	/**
+	 * Set merge strategy
 	 *
 	 * @param mergeStrategy
-	 *            the {@link MergeStrategy} to be used
+	 *            the {@link org.eclipse.jgit.merge.MergeStrategy} to be used
 	 * @return {@code this}
 	 */
 	public MergeCommand setStrategy(MergeStrategy mergeStrategy) {
@@ -504,6 +508,8 @@ public class MergeCommand extends GitCommand<MergeResult> {
 	}
 
 	/**
+	 * Reference to a commit to be merged with the current head
+	 *
 	 * @param aCommit
 	 *            a reference to a commit which is merged with the current head
 	 * @return {@code this}
@@ -515,6 +521,8 @@ public class MergeCommand extends GitCommand<MergeResult> {
 	}
 
 	/**
+	 * Id of a commit which is to be merged with the current head
+	 *
 	 * @param aCommit
 	 *            the Id of a commit which is merged with the current head
 	 * @return {@code this}
@@ -524,8 +532,10 @@ public class MergeCommand extends GitCommand<MergeResult> {
 	}
 
 	/**
+	 * Include a commit
+	 *
 	 * @param name
-	 *            a name given to the commit
+	 *            a name of a {@code Ref} pointing to the commit
 	 * @param aCommit
 	 *            the Id of a commit which is merged with the current head
 	 * @return {@code this}
@@ -541,9 +551,10 @@ public class MergeCommand extends GitCommand<MergeResult> {
 	 * HEAD. Otherwise, perform the merge and commit the result.
 	 * <p>
 	 * In case the merge was successful but this flag was set to
-	 * <code>true</code> a {@link MergeResult} with status
-	 * {@link MergeStatus#MERGED_SQUASHED} or
-	 * {@link MergeStatus#FAST_FORWARD_SQUASHED} is returned.
+	 * <code>true</code> a {@link org.eclipse.jgit.api.MergeResult} with status
+	 * {@link org.eclipse.jgit.api.MergeResult.MergeStatus#MERGED_SQUASHED} or
+	 * {@link org.eclipse.jgit.api.MergeResult.MergeStatus#FAST_FORWARD_SQUASHED}
+	 * is returned.
 	 *
 	 * @param squash
 	 *            whether to squash commits or not
@@ -582,9 +593,11 @@ public class MergeCommand extends GitCommand<MergeResult> {
 	 *            <code>true</code> if this command should commit (this is the
 	 *            default behavior). <code>false</code> if this command should
 	 *            not commit. In case the merge was successful but this flag was
-	 *            set to <code>false</code> a {@link MergeResult} with type
-	 *            {@link MergeResult} with status
-	 *            {@link MergeStatus#MERGED_NOT_COMMITTED} is returned
+	 *            set to <code>false</code> a
+	 *            {@link org.eclipse.jgit.api.MergeResult} with type
+	 *            {@link org.eclipse.jgit.api.MergeResult} with status
+	 *            {@link org.eclipse.jgit.api.MergeResult.MergeStatus#MERGED_NOT_COMMITTED}
+	 *            is returned
 	 * @return {@code this}
 	 * @since 3.0
 	 */
@@ -612,7 +625,6 @@ public class MergeCommand extends GitCommand<MergeResult> {
 	 * is set to <code>NullProgressMonitor</code>
 	 *
 	 * @see NullProgressMonitor
-	 *
 	 * @param monitor
 	 *            A progress monitor
 	 * @return this instance

org.eclipse.jgit/src/org/eclipse/jgit/api/MergeResult.java

@@ -53,11 +53,10 @@ import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.merge.MergeChunk;
 import org.eclipse.jgit.merge.MergeChunk.ConflictState;
 import org.eclipse.jgit.merge.MergeStrategy;
-import org.eclipse.jgit.merge.ResolveMerger;
 import org.eclipse.jgit.merge.ResolveMerger.MergeFailureReason;
 
 /**
- * Encapsulates the result of a {@link MergeCommand}.
+ * Encapsulates the result of a {@link org.eclipse.jgit.api.MergeCommand}.
  */
 public class MergeResult {
 
@@ -249,6 +248,8 @@ public class MergeResult {
 	private List<String> checkoutConflicts;
 
 	/**
+	 * Constructor for MergeResult.
+	 *
 	 * @param newHead
 	 *            the object the head points at after the merge
 	 * @param base
@@ -260,10 +261,10 @@ public class MergeResult {
 	 * @param mergeStatus
 	 *            the status the merge resulted in
 	 * @param mergeStrategy
-	 *            the used {@link MergeStrategy}
+	 *            the used {@link org.eclipse.jgit.merge.MergeStrategy}
 	 * @param lowLevelResults
 	 *            merge results as returned by
-	 *            {@link ResolveMerger#getMergeResults()}
+	 *            {@link org.eclipse.jgit.merge.ResolveMerger#getMergeResults()}
 	 * @since 2.0
 	 */
 	public MergeResult(ObjectId newHead, ObjectId base,
@@ -275,6 +276,8 @@ public class MergeResult {
 	}
 
 	/**
+	 * Constructor for MergeResult.
+	 *
 	 * @param newHead
 	 *            the object the head points at after the merge
 	 * @param base
@@ -286,9 +289,10 @@ public class MergeResult {
 	 * @param mergeStatus
 	 *            the status the merge resulted in
 	 * @param mergeStrategy
-	 *            the used {@link MergeStrategy}
+	 *            the used {@link org.eclipse.jgit.merge.MergeStrategy}
 	 * @param lowLevelResults
-	 *            merge results as returned by {@link ResolveMerger#getMergeResults()}
+	 *            merge results as returned by
+	 *            {@link org.eclipse.jgit.merge.ResolveMerger#getMergeResults()}
 	 * @param description
 	 *            a user friendly description of the merge result
 	 */
@@ -302,6 +306,8 @@ public class MergeResult {
 	}
 
 	/**
+	 * Constructor for MergeResult.
+	 *
 	 * @param newHead
 	 *            the object the head points at after the merge
 	 * @param base
@@ -313,13 +319,13 @@ public class MergeResult {
 	 * @param mergeStatus
 	 *            the status the merge resulted in
 	 * @param mergeStrategy
-	 *            the used {@link MergeStrategy}
+	 *            the used {@link org.eclipse.jgit.merge.MergeStrategy}
 	 * @param lowLevelResults
 	 *            merge results as returned by
-	 *            {@link ResolveMerger#getMergeResults()}
+	 *            {@link org.eclipse.jgit.merge.ResolveMerger#getMergeResults()}
 	 * @param failingPaths
 	 *            list of paths causing this merge to fail as returned by
-	 *            {@link ResolveMerger#getFailingPaths()}
+	 *            {@link org.eclipse.jgit.merge.ResolveMerger#getFailingPaths()}
 	 * @param description
 	 *            a user friendly description of the merge result
 	 */
@@ -354,6 +360,8 @@ public class MergeResult {
 	}
 
 	/**
+	 * Get the object the head points at after the merge
+	 *
 	 * @return the object the head points at after the merge
 	 */
 	public ObjectId getNewHead() {
@@ -361,6 +369,8 @@ public class MergeResult {
 	}
 
 	/**
+	 * Get the merge status
+	 *
 	 * @return the status the merge resulted in
 	 */
 	public MergeStatus getMergeStatus() {
@@ -368,6 +378,8 @@ public class MergeResult {
 	}
 
 	/**
+	 * Get the commits which have been merged
+	 *
 	 * @return all the commits which have been merged together
 	 */
 	public ObjectId[] getMergedCommits() {
@@ -375,6 +387,8 @@ public class MergeResult {
 	}
 
 	/**
+	 * Get the common base
+	 *
 	 * @return base the common base which was used to produce a content-merge.
 	 *         May be <code>null</code> if the merge-result was produced without
 	 *         computing a common base
@@ -383,6 +397,7 @@ public class MergeResult {
 		return base;
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
@@ -402,6 +417,8 @@ public class MergeResult {
 	}
 
 	/**
+	 * Set conflicts
+	 *
 	 * @param conflicts
 	 *            the conflicts to set
 	 */
@@ -410,7 +427,10 @@ public class MergeResult {
 	}
 
 	/**
+	 * Add a conflict
+	 *
 	 * @param path
+	 *            path of the file to add a conflict for
 	 * @param conflictingRanges
 	 *            the conflicts to set
 	 */
@@ -421,8 +441,12 @@ public class MergeResult {
 	}
 
 	/**
+	 * Add a conflict
+	 *
 	 * @param path
+	 *            path of the file to add a conflict for
 	 * @param lowLevelResult
+	 *            a {@link org.eclipse.jgit.merge.MergeResult}
 	 */
 	public void addConflict(String path, org.eclipse.jgit.merge.MergeResult<?> lowLevelResult) {
 		if (!lowLevelResult.containsConflicts())
@@ -462,9 +486,10 @@ public class MergeResult {
 
 	/**
 	 * Returns information about the conflicts which occurred during a
-	 * {@link MergeCommand}. The returned value maps the path of a conflicting
-	 * file to a two-dimensional int-array of line-numbers telling where in the
-	 * file conflict markers for which merged commit can be found.
+	 * {@link org.eclipse.jgit.api.MergeCommand}. The returned value maps the
+	 * path of a conflicting file to a two-dimensional int-array of line-numbers
+	 * telling where in the file conflict markers for which merged commit can be
+	 * found.
 	 * <p>
 	 * If the returned value contains a mapping "path"-&gt;[x][y]=z then this
 	 * means
@@ -505,7 +530,7 @@ public class MergeResult {
 
 	/**
 	 * Returns a list of paths causing this merge to fail as returned by
-	 * {@link ResolveMerger#getFailingPaths()}
+	 * {@link org.eclipse.jgit.merge.ResolveMerger#getFailingPaths()}
 	 *
 	 * @return the list of paths causing this merge to fail or <code>null</code>
 	 *         if no failure occurred

org.eclipse.jgit/src/org/eclipse/jgit/api/NameRevCommand.java

@@ -57,7 +57,6 @@ import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
-import org.eclipse.jgit.lib.RefDatabase;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.FIFORevQueue;
 import org.eclipse.jgit.revwalk.RevCommit;
@@ -120,6 +119,7 @@ public class NameRevCommand extends GitCommand<Map<ObjectId, String>> {
 	 * Create a new name-rev command.
 	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected NameRevCommand(Repository repo) {
 		super(repo);
@@ -134,6 +134,7 @@ public class NameRevCommand extends GitCommand<Map<ObjectId, String>> {
 		};
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Map<ObjectId, String> call() throws GitAPIException {
 		try {
@@ -199,13 +200,13 @@ public class NameRevCommand extends GitCommand<Map<ObjectId, String>> {
 	 * @param id
 	 *            object ID to add.
 	 * @return {@code this}
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object supplied is not available from the object
 	 *             database.
-	 * @throws JGitInternalException
+	 * @throws org.eclipse.jgit.api.errors.JGitInternalException
 	 *             a low-level exception of JGit has occurred. The original
 	 *             exception can be retrieved by calling
-	 *             {@link Exception#getCause()}.
+	 *             {@link java.lang.Exception#getCause()}.
 	 */
 	public NameRevCommand add(ObjectId id) throws MissingObjectException,
 			JGitInternalException {
@@ -227,13 +228,13 @@ public class NameRevCommand extends GitCommand<Map<ObjectId, String>> {
 	 * @param ids
 	 *            object IDs to add.
 	 * @return {@code this}
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             the object supplied is not available from the object
 	 *             database.
-	 * @throws JGitInternalException
+	 * @throws org.eclipse.jgit.api.errors.JGitInternalException
 	 *             a low-level exception of JGit has occurred. The original
 	 *             exception can be retrieved by calling
-	 *             {@link Exception#getCause()}.
+	 *             {@link java.lang.Exception#getCause()}.
 	 */
 	public NameRevCommand add(Iterable<ObjectId> ids)
 			throws MissingObjectException, JGitInternalException {
@@ -250,7 +251,8 @@ public class NameRevCommand extends GitCommand<Map<ObjectId, String>> {
 	 * prefix added by {@link #addPrefix(String)}.
 	 *
 	 * @param prefix
-	 *            prefix to add; see {@link RefDatabase#getRefs(String)}
+	 *            prefix to add; see
+	 *            {@link org.eclipse.jgit.lib.RefDatabase#getRefs(String)}
 	 * @return {@code this}
 	 */
 	public NameRevCommand addPrefix(String prefix) {
@@ -260,8 +262,8 @@ public class NameRevCommand extends GitCommand<Map<ObjectId, String>> {
 	}
 
 	/**
-	 * Add all annotated tags under {@code refs/tags/} to the set that all results
-	 * must match.
+	 * Add all annotated tags under {@code refs/tags/} to the set that all
+	 * results must match.
 	 * <p>
 	 * Calls {@link #addRef(Ref)}; see that method for a note on matching
 	 * priority.
@@ -270,7 +272,7 @@ public class NameRevCommand extends GitCommand<Map<ObjectId, String>> {
 	 * @throws JGitInternalException
 	 *             a low-level exception of JGit has occurred. The original
 	 *             exception can be retrieved by calling
-	 *             {@link Exception#getCause()}.
+	 *             {@link java.lang.Exception#getCause()}.
 	 */
 	public NameRevCommand addAnnotatedTags() {
 		checkCallable();

org.eclipse.jgit/src/org/eclipse/jgit/api/PullCommand.java

@@ -52,7 +52,6 @@ import org.eclipse.jgit.api.MergeCommand.FastForwardMode;
 import org.eclipse.jgit.api.MergeCommand.FastForwardMode.Merge;
 import org.eclipse.jgit.api.RebaseCommand.Operation;
 import org.eclipse.jgit.api.errors.CanceledException;
-import org.eclipse.jgit.api.errors.DetachedHeadException;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidConfigurationException;
 import org.eclipse.jgit.api.errors.InvalidRemoteException;
@@ -104,13 +103,18 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	private FetchRecurseSubmodulesMode submoduleRecurseMode = null;
 
 	/**
+	 * Constructor for PullCommand.
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected PullCommand(Repository repo) {
 		super(repo);
 	}
 
 	/**
+	 * Set progress monitor
+	 *
 	 * @param monitor
 	 *            a progress monitor
 	 * @return this instance
@@ -139,6 +143,7 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	 * branch.[name].rebase and branch.autosetuprebase.
 	 *
 	 * @param useRebase
+	 *            whether to use rebase after fetching
 	 * @return {@code this}
 	 */
 	public PullCommand setRebase(boolean useRebase) {
@@ -149,7 +154,8 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	}
 
 	/**
-	 * Sets the {@link BranchRebaseMode} to use after fetching.
+	 * Sets the {@link org.eclipse.jgit.lib.BranchConfig.BranchRebaseMode} to
+	 * use after fetching.
 	 *
 	 * <dl>
 	 * <dt>BranchRebaseMode.REBASE</dt>
@@ -176,7 +182,8 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	 * {@code pull.rebase}.
 	 *
 	 * @param rebaseMode
-	 *            the {@link BranchRebaseMode} to use
+	 *            the {@link org.eclipse.jgit.lib.BranchConfig.BranchRebaseMode}
+	 *            to use
 	 * @return {@code this}
 	 * @since 4.5
 	 */
@@ -187,23 +194,13 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	}
 
 	/**
-	 * Executes the {@code Pull} command with all the options and parameters
+	 * {@inheritDoc}
+	 * <p>
+	 * Execute the {@code Pull} command with all the options and parameters
 	 * collected by the setter methods (e.g.
 	 * {@link #setProgressMonitor(ProgressMonitor)}) of this class. Each
 	 * instance of this class should only be used for one invocation of the
 	 * command. Don't call this method twice on an instance.
-	 *
-	 * @return the result of the pull
-	 * @throws WrongRepositoryStateException
-	 * @throws InvalidConfigurationException
-	 * @throws DetachedHeadException
-	 * @throws InvalidRemoteException
-	 * @throws CanceledException
-	 * @throws RefNotFoundException
-	 * @throws RefNotAdvertisedException
-	 * @throws NoHeadException
-	 * @throws org.eclipse.jgit.api.errors.TransportException
-	 * @throws GitAPIException
 	 */
 	@Override
 	public PullResult call() throws GitAPIException,
@@ -370,6 +367,7 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	 *
 	 * @see Constants#DEFAULT_REMOTE_NAME
 	 * @param remote
+	 *            name of the remote to pull from
 	 * @return {@code this}
 	 * @since 3.3
 	 */
@@ -386,6 +384,7 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	 * the current branch is used.
 	 *
 	 * @param remoteBranchName
+	 *            remote branch name to be used for pull operation
 	 * @return {@code this}
 	 * @since 3.3
 	 */
@@ -396,6 +395,8 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	}
 
 	/**
+	 * Get the remote name used for pull operation
+	 *
 	 * @return the remote used for the pull operation if it was set explicitly
 	 * @since 3.3
 	 */
@@ -404,6 +405,8 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	}
 
 	/**
+	 * Get the remote branch name for the pull operation
+	 *
 	 * @return the remote branch name used for the pull operation if it was set
 	 *         explicitly
 	 * @since 3.3
@@ -413,6 +416,8 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	}
 
 	/**
+	 * Set the @{code MergeStrategy}
+	 *
 	 * @param strategy
 	 *            The merge strategy to use during this pull operation.
 	 * @return {@code this}
@@ -424,9 +429,10 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	}
 
 	/**
-	 * Sets the specification of annotated tag behavior during fetch
+	 * Set the specification of annotated tag behavior during fetch
 	 *
 	 * @param tagOpt
+	 *            the {@link org.eclipse.jgit.transport.TagOpt}
 	 * @return {@code this}
 	 * @since 4.7
 	 */
@@ -437,8 +443,8 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	}
 
 	/**
-	 * Sets the fast forward mode. It is used if pull is configured to do a
-	 * merge as opposed to rebase. If non-{@code null} takes precedence over the
+	 * Set the fast forward mode. It is used if pull is configured to do a merge
+	 * as opposed to rebase. If non-{@code null} takes precedence over the
 	 * fast-forward mode configured in git config.
 	 *
 	 * @param fastForwardMode
@@ -461,6 +467,9 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	 * Set the mode to be used for recursing into submodules.
 	 *
 	 * @param recurse
+	 *            the
+	 *            {@link org.eclipse.jgit.lib.SubmoduleConfig.FetchRecurseSubmodulesMode}
+	 *            to be used for recursing into submodules
 	 * @return {@code this}
 	 * @since 4.7
 	 * @see FetchCommand#setRecurseSubmodules(FetchRecurseSubmodulesMode)
@@ -475,13 +484,14 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	 * Reads the rebase mode to use for a pull command from the repository
 	 * configuration. This is the value defined for the configurations
 	 * {@code branch.[branchName].rebase}, or,if not set, {@code pull.rebase}.
-	 * If neither is set, yields {@link BranchRebaseMode#NONE}.
+	 * If neither is set, yields
+	 * {@link org.eclipse.jgit.lib.BranchConfig.BranchRebaseMode#NONE}.
 	 *
 	 * @param branchName
 	 *            name of the local branch
 	 * @param config
-	 *            the {@link Config} to read the value from
-	 * @return the {@link BranchRebaseMode}
+	 *            the {@link org.eclipse.jgit.lib.Config} to read the value from
+	 * @return the {@link org.eclipse.jgit.lib.BranchConfig.BranchRebaseMode}
 	 * @since 4.5
 	 */
 	public static BranchRebaseMode getRebaseMode(String branchName,

org.eclipse.jgit/src/org/eclipse/jgit/api/PullResult.java

@@ -45,7 +45,7 @@ package org.eclipse.jgit.api;
 import org.eclipse.jgit.transport.FetchResult;
 
 /**
- * Encapsulates the result of a {@link PullCommand}
+ * Encapsulates the result of a {@link org.eclipse.jgit.api.PullCommand}
  */
 public class PullResult {
 	private final FetchResult fetchResult;
@@ -73,6 +73,8 @@ public class PullResult {
 	}
 
 	/**
+	 * Get fetch result
+	 *
 	 * @return the fetch result, or <code>null</code>
 	 */
 	public FetchResult getFetchResult() {
@@ -80,6 +82,8 @@ public class PullResult {
 	}
 
 	/**
+	 * Get merge result
+	 *
 	 * @return the merge result, or <code>null</code>
 	 */
 	public MergeResult getMergeResult() {
@@ -87,6 +91,8 @@ public class PullResult {
 	}
 
 	/**
+	 * Get rebase result
+	 *
 	 * @return the rebase result, or <code>null</code>
 	 */
 	public RebaseResult getRebaseResult() {
@@ -94,6 +100,8 @@ public class PullResult {
 	}
 
 	/**
+	 * Get name of the remote configuration from which fetch was tried
+	 *
 	 * @return the name of the remote configuration from which fetch was tried,
 	 *         or <code>null</code>
 	 */
@@ -102,6 +110,8 @@ public class PullResult {
 	}
 
 	/**
+	 * Whether the pull was successful
+	 *
 	 * @return whether the pull was successful
 	 */
 	public boolean isSuccessful() {
@@ -112,6 +122,7 @@ public class PullResult {
 		return true;
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {

org.eclipse.jgit/src/org/eclipse/jgit/api/PushCommand.java

@@ -105,7 +105,12 @@ public class PushCommand extends
 	private List<String> pushOptions;
 
 	/**
+	 * <p>
+	 * Constructor for PushCommand.
+	 * </p>
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected PushCommand(Repository repo) {
 		super(repo);
@@ -114,17 +119,12 @@ public class PushCommand extends
 	}
 
 	/**
-	 * Executes the {@code push} command with all the options and parameters
+	 * {@inheritDoc}
+	 * <p>
+	 * Execute the {@code push} command with all the options and parameters
 	 * collected by the setter methods of this class. Each instance of this
 	 * class should only be used for one invocation of the command (means: one
 	 * call to {@link #call()})
-	 *
-	 * @return an iteration over {@link PushResult} objects
-	 * @throws InvalidRemoteException
-	 *             when called with an invalid remote uri
-	 * @throws org.eclipse.jgit.api.errors.TransportException
-	 *             when an error occurs with the transport
-	 * @throws GitAPIException
 	 */
 	@Override
 	public Iterable<PushResult> call() throws GitAPIException,
@@ -209,6 +209,7 @@ public class PushCommand extends
 	 *
 	 * @see Constants#DEFAULT_REMOTE_NAME
 	 * @param remote
+	 *            the remote name
 	 * @return {@code this}
 	 */
 	public PushCommand setRemote(String remote) {
@@ -218,6 +219,8 @@ public class PushCommand extends
 	}
 
 	/**
+	 * Get remote name
+	 *
 	 * @return the remote used for the remote operation
 	 */
 	public String getRemote() {
@@ -231,6 +234,8 @@ public class PushCommand extends
 	 *
 	 * @see RemoteConfig#DEFAULT_RECEIVE_PACK
 	 * @param receivePack
+	 *            name of the remote executable providing the receive-pack
+	 *            service
 	 * @return {@code this}
 	 */
 	public PushCommand setReceivePack(String receivePack) {
@@ -240,6 +245,8 @@ public class PushCommand extends
 	}
 
 	/**
+	 * Get the name of the remote executable providing the receive-pack service
+	 *
 	 * @return the receive-pack used for the remote operation
 	 */
 	public String getReceivePack() {
@@ -247,6 +254,8 @@ public class PushCommand extends
 	}
 
 	/**
+	 * Get timeout used for push operation
+	 *
 	 * @return the timeout used for the push operation
 	 */
 	public int getTimeout() {
@@ -254,6 +263,8 @@ public class PushCommand extends
 	}
 
 	/**
+	 * Get the progress monitor
+	 *
 	 * @return the progress monitor for the push operation
 	 */
 	public ProgressMonitor getProgressMonitor() {
@@ -265,8 +276,8 @@ public class PushCommand extends
 	 * is set to <code>NullProgressMonitor</code>
 	 *
 	 * @see NullProgressMonitor
-	 *
 	 * @param monitor
+	 *            a {@link org.eclipse.jgit.lib.ProgressMonitor}
 	 * @return {@code this}
 	 */
 	public PushCommand setProgressMonitor(ProgressMonitor monitor) {
@@ -279,7 +290,9 @@ public class PushCommand extends
 	}
 
 	/**
-	 * @return the ref lease specs
+	 * Get the <code>RefLeaseSpec</code>s.
+	 *
+	 * @return the <code>RefLeaseSpec</code>s
 	 * @since 4.7
 	 */
 	public List<RefLeaseSpec> getRefLeaseSpecs() {
@@ -287,10 +300,11 @@ public class PushCommand extends
 	}
 
 	/**
-	 * The ref lease specs to be used in the push operation,
-	 * for a force-with-lease push operation.
+	 * The ref lease specs to be used in the push operation, for a
+	 * force-with-lease push operation.
 	 *
 	 * @param specs
+	 *            a {@link org.eclipse.jgit.transport.RefLeaseSpec} object.
 	 * @return {@code this}
 	 * @since 4.7
 	 */
@@ -299,10 +313,11 @@ public class PushCommand extends
 	}
 
 	/**
-	 * The ref lease specs to be used in the push operation,
-	 * for a force-with-lease push operation.
+	 * The ref lease specs to be used in the push operation, for a
+	 * force-with-lease push operation.
 	 *
 	 * @param specs
+	 *            list of {@code RefLeaseSpec}s
 	 * @return {@code this}
 	 * @since 4.7
 	 */
@@ -316,6 +331,9 @@ public class PushCommand extends
 	}
 
 	/**
+	 * Get <code>RefSpec</code>s.
+	 * </p>
+	 *
 	 * @return the ref specs
 	 */
 	public List<RefSpec> getRefSpecs() {
@@ -325,7 +343,7 @@ public class PushCommand extends
 	/**
 	 * The ref specs to be used in the push operation
 	 *
-	 * @param specs
+	 * @param specs a {@link org.eclipse.jgit.transport.RefSpec} object.
 	 * @return {@code this}
 	 */
 	public PushCommand setRefSpecs(RefSpec... specs) {
@@ -339,6 +357,7 @@ public class PushCommand extends
 	 * The ref specs to be used in the push operation
 	 *
 	 * @param specs
+	 *            list of {@link org.eclipse.jgit.transport.RefSpec}s
 	 * @return {@code this}
 	 */
 	public PushCommand setRefSpecs(List<RefSpec> specs) {
@@ -408,6 +427,8 @@ public class PushCommand extends
 	}
 
 	/**
+	 * Whether to run the push operation as a dry run
+	 *
 	 * @return the dry run preference for the push operation
 	 */
 	public boolean isDryRun() {
@@ -417,7 +438,7 @@ public class PushCommand extends
 	/**
 	 * Sets whether the push operation should be a dry run
 	 *
-	 * @param dryRun
+	 * @param dryRun a boolean.
 	 * @return {@code this}
 	 */
 	public PushCommand setDryRun(boolean dryRun) {
@@ -427,6 +448,8 @@ public class PushCommand extends
 	}
 
 	/**
+	 * Get the thin-pack preference
+	 *
 	 * @return the thin-pack preference for push operation
 	 */
 	public boolean isThin() {
@@ -434,11 +457,12 @@ public class PushCommand extends
 	}
 
 	/**
-	 * Sets the thin-pack preference for push operation.
+	 * Set the thin-pack preference for push operation.
 	 *
 	 * Default setting is Transport.DEFAULT_PUSH_THIN
 	 *
 	 * @param thin
+	 *            the thin-pack preference value
 	 * @return {@code this}
 	 */
 	public PushCommand setThin(boolean thin) {
@@ -448,6 +472,9 @@ public class PushCommand extends
 	}
 
 	/**
+	 * Whether this push should be executed atomically (all references updated,
+	 * or none)
+	 *
 	 * @return true if all-or-nothing behavior is requested.
 	 * @since 4.2
 	 */
@@ -461,6 +488,7 @@ public class PushCommand extends
 	 * Default setting is false.
 	 *
 	 * @param atomic
+	 *            whether to run the push atomically
 	 * @return {@code this}
 	 * @since 4.2
 	 */
@@ -471,6 +499,8 @@ public class PushCommand extends
 	}
 
 	/**
+	 * Whether to push forcefully
+	 *
 	 * @return the force preference for push operation
 	 */
 	public boolean isForce() {
@@ -481,6 +511,7 @@ public class PushCommand extends
 	 * Sets the force preference for push operation.
 	 *
 	 * @param force
+	 *            whether to push forcefully
 	 * @return {@code this}
 	 */
 	public PushCommand setForce(boolean force) {
@@ -493,6 +524,7 @@ public class PushCommand extends
 	 * Sets the output stream to write sideband messages to
 	 *
 	 * @param out
+	 *            an {@link java.io.OutputStream}
 	 * @return {@code this}
 	 * @since 3.0
 	 */
@@ -502,6 +534,8 @@ public class PushCommand extends
 	}
 
 	/**
+	 * Get push options
+	 *
 	 * @return the option strings associated with the push operation
 	 * @since 4.5
 	 */
@@ -510,9 +544,10 @@ public class PushCommand extends
 	}
 
 	/**
-	 * Sets the option strings associated with the push operation.
+	 * Set the option strings associated with the push operation.
 	 *
 	 * @param pushOptions
+	 *            a {@link java.util.List} of push option strings
 	 * @return {@code this}
 	 * @since 4.5
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java

@@ -238,7 +238,12 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	private boolean preserveMerges = false;
 
 	/**
+	 * <p>
+	 * Constructor for RebaseCommand.
+	 * </p>
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected RebaseCommand(Repository repo) {
 		super(repo);
@@ -247,16 +252,12 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code Rebase} command with all the options and parameters
 	 * collected by the setter methods of this class. Each instance of this
 	 * class should only be used for one invocation of the command. Don't call
 	 * this method twice on an instance.
-	 *
-	 * @return an object describing the result of this command
-	 * @throws GitAPIException
-	 * @throws WrongRepositoryStateException
-	 * @throws NoHeadException
-	 * @throws RefNotFoundException
 	 */
 	@Override
 	public RebaseResult call() throws GitAPIException, NoHeadException,
@@ -1228,12 +1229,14 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	}
 
 	/**
-	 * checks if we can fast-forward and returns the new head if it is possible
+	 * Check if we can fast-forward and returns the new head if it is possible
 	 *
 	 * @param newCommit
+	 *            a {@link org.eclipse.jgit.revwalk.RevCommit} object to check
+	 *            if we can fast-forward to.
 	 * @return the new head, or null
-	 * @throws IOException
-	 * @throws GitAPIException
+	 * @throws java.io.IOException
+	 * @throws org.eclipse.jgit.api.errors.GitAPIException
 	 */
 	public RevCommit tryFastForward(RevCommit newCommit) throws IOException,
 			GitAPIException {
@@ -1436,6 +1439,8 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 
 
 	/**
+	 * Set upstream {@code RevCommit}
+	 *
 	 * @param upstream
 	 *            the upstream commit
 	 * @return {@code this}
@@ -1447,6 +1452,8 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	}
 
 	/**
+	 * Set the upstream commit
+	 *
 	 * @param upstream
 	 *            id of the upstream commit
 	 * @return {@code this}
@@ -1464,10 +1471,12 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	}
 
 	/**
+	 * Set the upstream branch
+	 *
 	 * @param upstream
-	 *            the upstream branch
+	 *            the name of the upstream branch
 	 * @return {@code this}
-	 * @throws RefNotFoundException
+	 * @throws org.eclipse.jgit.api.errors.RefNotFoundException
 	 */
 	public RebaseCommand setUpstream(String upstream)
 			throws RefNotFoundException {
@@ -1502,6 +1511,8 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	}
 
 	/**
+	 * Set the operation to execute during rebase
+	 *
 	 * @param operation
 	 *            the operation to perform
 	 * @return {@code this}
@@ -1512,6 +1523,8 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	}
 
 	/**
+	 * Set progress monitor
+	 *
 	 * @param monitor
 	 *            a progress monitor
 	 * @return this instance
@@ -1525,15 +1538,18 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	}
 
 	/**
-	 * Enables interactive rebase
+	 * Enable interactive rebase
 	 * <p>
 	 * Does not stop after initialization of interactive rebase. This is
 	 * equivalent to
-	 * {@link RebaseCommand#runInteractively(InteractiveHandler, boolean)
+	 * {@link org.eclipse.jgit.api.RebaseCommand#runInteractively(InteractiveHandler, boolean)
 	 * runInteractively(handler, false)};
 	 * </p>
 	 *
 	 * @param handler
+	 *            the
+	 *            {@link org.eclipse.jgit.api.RebaseCommand.InteractiveHandler}
+	 *            to use
 	 * @return this
 	 */
 	public RebaseCommand runInteractively(InteractiveHandler handler) {
@@ -1541,14 +1557,17 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	}
 
 	/**
-	 * Enables interactive rebase
+	 * Enable interactive rebase
 	 * <p>
 	 * If stopAfterRebaseInteractiveInitialization is {@code true} the rebase
 	 * stops after initialization of interactive rebase returning
-	 * {@link RebaseResult#INTERACTIVE_PREPARED_RESULT}
+	 * {@link org.eclipse.jgit.api.RebaseResult#INTERACTIVE_PREPARED_RESULT}
 	 * </p>
 	 *
 	 * @param handler
+	 *            the
+	 *            {@link org.eclipse.jgit.api.RebaseCommand.InteractiveHandler}
+	 *            to use
 	 * @param stopAfterRebaseInteractiveInitialization
 	 *            if {@code true} the rebase stops after initialization
 	 * @return this instance
@@ -1562,6 +1581,8 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	}
 
 	/**
+	 * Set the <code>MergeStrategy</code>.
+	 *
 	 * @param strategy
 	 *            The merge strategy to use during this rebase operation.
 	 * @return {@code this}
@@ -1573,9 +1594,11 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	}
 
 	/**
+	 * Whether to preserve merges during rebase
+	 *
 	 * @param preserve
-	 *            True to re-create merges during rebase. Defaults to false, a
-	 *            flattening rebase.
+	 *            {@code true} to re-create merges during rebase. Defaults to
+	 *            {@code false}, a flattening rebase.
 	 * @return {@code this}
 	 * @since 3.5
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseResult.java

@@ -45,12 +45,11 @@ package org.eclipse.jgit.api;
 import java.util.List;
 import java.util.Map;
 
-import org.eclipse.jgit.merge.ResolveMerger;
 import org.eclipse.jgit.merge.ResolveMerger.MergeFailureReason;
 import org.eclipse.jgit.revwalk.RevCommit;
 
 /**
- * The result of a {@link RebaseCommand} execution
+ * The result of a {@link org.eclipse.jgit.api.RebaseCommand} execution
  */
 public class RebaseResult {
 	/**
@@ -279,6 +278,8 @@ public class RebaseResult {
 	}
 
 	/**
+	 * Get the status
+	 *
 	 * @return the overall status
 	 */
 	public Status getStatus() {
@@ -286,33 +287,46 @@ public class RebaseResult {
 	}
 
 	/**
-	 * @return the current commit if status is {@link Status#STOPPED}, otherwise
+	 * Get the current commit if status is
+	 * {@link org.eclipse.jgit.api.RebaseResult.Status#STOPPED}, otherwise
 	 * <code>null</code>
+	 *
+	 * @return the current commit if status is
+	 *         {@link org.eclipse.jgit.api.RebaseResult.Status#STOPPED},
+	 *         otherwise <code>null</code>
 	 */
 	public RevCommit getCurrentCommit() {
 		return currentCommit;
 	}
 
 	/**
+	 * Get the list of paths causing this rebase to fail
+	 *
 	 * @return the list of paths causing this rebase to fail (see
-	 *         {@link ResolveMerger#getFailingPaths()} for details) if status is
-	 *         {@link Status#FAILED}, otherwise <code>null</code>
+	 *         {@link org.eclipse.jgit.merge.ResolveMerger#getFailingPaths()}
+	 *         for details) if status is
+	 *         {@link org.eclipse.jgit.api.RebaseResult.Status#FAILED},
+	 *         otherwise <code>null</code>
 	 */
 	public Map<String, MergeFailureReason> getFailingPaths() {
 		return failingPaths;
 	}
 
 	/**
-	 * @return the list of conflicts if status is {@link Status#CONFLICTS}
+	 * Get the list of conflicts
+	 *
+	 * @return the list of conflicts if status is
+	 *         {@link org.eclipse.jgit.api.RebaseResult.Status#CONFLICTS}
 	 */
 	public List<String> getConflicts() {
 		return conflicts;
 	}
 
 	/**
-	 * @return the list of uncommitted changes if status is
-	 *         {@link Status#UNCOMMITTED_CHANGES}
+	 * <p>Getter for the field <code>uncommittedChanges</code>.</p>
 	 *
+	 * @return the list of uncommitted changes if status is
+	 *         {@link org.eclipse.jgit.api.RebaseResult.Status#UNCOMMITTED_CHANGES}
 	 * @since 3.2
 	 */
 	public List<String> getUncommittedChanges() {

org.eclipse.jgit/src/org/eclipse/jgit/api/ReflogCommand.java

@@ -67,7 +67,10 @@ public class ReflogCommand extends GitCommand<Collection<ReflogEntry>> {
 	private String ref = Constants.HEAD;
 
 	/**
+	 * Constructor for ReflogCommand.
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	public ReflogCommand(Repository repo) {
 		super(repo);
@@ -78,6 +81,7 @@ public class ReflogCommand extends GitCommand<Collection<ReflogEntry>> {
 	 * value of HEAD will be used.
 	 *
 	 * @param ref
+	 *            the name of the {@code Ref} to log
 	 * @return {@code this}
 	 */
 	public ReflogCommand setRef(String ref) {
@@ -87,10 +91,9 @@ public class ReflogCommand extends GitCommand<Collection<ReflogEntry>> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Run the reflog command
-	 *
-	 * @throws GitAPIException
-	 * @throws InvalidRefNameException
 	 */
 	@Override
 	public Collection<ReflogEntry> call() throws GitAPIException,

org.eclipse.jgit/src/org/eclipse/jgit/api/RemoteAddCommand.java

@@ -63,7 +63,6 @@ import org.eclipse.jgit.transport.URIish;
  * @see <a href=
  *      "http://www.kernel.org/pub/software/scm/git/docs/git-remote.html" > Git
  *      documentation about Remote</a>
- *
  * @since 4.2
  */
 public class RemoteAddCommand extends GitCommand<RemoteConfig> {
@@ -73,7 +72,10 @@ public class RemoteAddCommand extends GitCommand<RemoteConfig> {
 	private URIish uri;
 
 	/**
+	 * Constructor for RemoteAddCommand.
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected RemoteAddCommand(Repository repo) {
 		super(repo);
@@ -100,10 +102,10 @@ public class RemoteAddCommand extends GitCommand<RemoteConfig> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code remote add} command with all the options and
 	 * parameters collected by the setter methods of this class.
-	 *
-	 * @return the {@link RemoteConfig} object of the added remote
 	 */
 	@Override
 	public RemoteConfig call() throws GitAPIException {

org.eclipse.jgit/src/org/eclipse/jgit/api/RemoteListCommand.java

@@ -59,23 +59,27 @@ import org.eclipse.jgit.transport.RemoteConfig;
  * @see <a href=
  *      "http://www.kernel.org/pub/software/scm/git/docs/git-remote.html" > Git
  *      documentation about Remote</a>
- *
  * @since 4.2
  */
 public class RemoteListCommand extends GitCommand<List<RemoteConfig>> {
 
 	/**
+	 * <p>
+	 * Constructor for RemoteListCommand.
+	 * </p>
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected RemoteListCommand(Repository repo) {
 		super(repo);
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code remote} command with all the options and parameters
 	 * collected by the setter methods of this class.
-	 *
-	 * @return a list of {@link RemoteConfig} objects.
 	 */
 	@Override
 	public List<RemoteConfig> call() throws GitAPIException {

org.eclipse.jgit/src/org/eclipse/jgit/api/RemoteRemoveCommand.java

@@ -61,7 +61,6 @@ import org.eclipse.jgit.transport.RemoteConfig;
  * @see <a href=
  *      "http://www.kernel.org/pub/software/scm/git/docs/git-remote.html" > Git
  *      documentation about Remote</a>
- *
  * @since 4.2
  */
 public class RemoteRemoveCommand extends GitCommand<RemoteConfig> {
@@ -69,7 +68,12 @@ public class RemoteRemoveCommand extends GitCommand<RemoteConfig> {
 	private String name;
 
 	/**
+	 * <p>
+	 * Constructor for RemoteRemoveCommand.
+	 * </p>
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected RemoteRemoveCommand(Repository repo) {
 		super(repo);
@@ -86,10 +90,10 @@ public class RemoteRemoveCommand extends GitCommand<RemoteConfig> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code remote} command with all the options and parameters
 	 * collected by the setter methods of this class.
-	 *
-	 * @return the {@link RemoteConfig} object of the removed remote
 	 */
 	@Override
 	public RemoteConfig call() throws GitAPIException {

org.eclipse.jgit/src/org/eclipse/jgit/api/RemoteSetUrlCommand.java

@@ -62,7 +62,6 @@ import org.eclipse.jgit.transport.URIish;
  * @see <a href=
  *      "http://www.kernel.org/pub/software/scm/git/docs/git-remote.html" > Git
  *      documentation about Remote</a>
- *
  * @since 4.2
  */
 public class RemoteSetUrlCommand extends GitCommand<RemoteConfig> {
@@ -74,7 +73,12 @@ public class RemoteSetUrlCommand extends GitCommand<RemoteConfig> {
 	private boolean push;
 
 	/**
+	 * <p>
+	 * Constructor for RemoteSetUrlCommand.
+	 * </p>
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected RemoteSetUrlCommand(Repository repo) {
 		super(repo);
@@ -112,10 +116,10 @@ public class RemoteSetUrlCommand extends GitCommand<RemoteConfig> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code remote} command with all the options and parameters
 	 * collected by the setter methods of this class.
-	 *
-	 * @return the {@link RemoteConfig} object of the modified remote
 	 */
 	@Override
 	public RemoteConfig call() throws GitAPIException {

org.eclipse.jgit/src/org/eclipse/jgit/api/RemoveNoteCommand.java

@@ -73,12 +73,18 @@ public class RemoveNoteCommand extends GitCommand<Note> {
 	private String notesRef = Constants.R_NOTES_COMMITS;
 
 	/**
+	 * <p>
+	 * Constructor for RemoveNoteCommand.
+	 * </p>
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected RemoveNoteCommand(Repository repo) {
 		super(repo);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Note call() throws GitAPIException {
 		checkCallable();
@@ -105,6 +111,8 @@ public class RemoveNoteCommand extends GitCommand<Note> {
 	 * Sets the object id of object you want to remove a note
 	 *
 	 * @param id
+	 *            the {@link org.eclipse.jgit.revwalk.RevObject} to remove a
+	 *            note from.
 	 * @return {@code this}
 	 */
 	public RemoveNoteCommand setObjectId(RevObject id) {
@@ -138,12 +146,13 @@ public class RemoveNoteCommand extends GitCommand<Note> {
 	}
 
 	/**
+	 * Set the name of the <code>Ref</code> to remove a note from.
+	 *
 	 * @param notesRef
-	 *            the ref to read notes from. Note, the default value of
-	 *            {@link Constants#R_NOTES_COMMITS} will be used if nothing is
-	 *            set
+	 *            the {@code Ref} to read notes from. Note, the default value of
+	 *            {@link org.eclipse.jgit.lib.Constants#R_NOTES_COMMITS} will be
+	 *            used if nothing is set
 	 * @return {@code this}
-	 *
 	 * @see Constants#R_NOTES_COMMITS
 	 */
 	public RemoveNoteCommand setNotesRef(String notesRef) {

org.eclipse.jgit/src/org/eclipse/jgit/api/RenameBranchCommand.java

@@ -77,25 +77,18 @@ public class RenameBranchCommand extends GitCommand<Ref> {
 	private String newName;
 
 	/**
+	 * <p>
+	 * Constructor for RenameBranchCommand.
+	 * </p>
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected RenameBranchCommand(Repository repo) {
 		super(repo);
 	}
 
-	/**
-	 * @throws RefNotFoundException
-	 *             if the old branch can not be found (branch with provided old
-	 *             name does not exist or old name resolves to a tag)
-	 * @throws InvalidRefNameException
-	 *             if the provided new name is <code>null</code> or otherwise
-	 *             invalid
-	 * @throws RefAlreadyExistsException
-	 *             if a branch with the new name already exists
-	 * @throws DetachedHeadException
-	 *             if rename is tried without specifying the old name and HEAD
-	 *             is detached
-	 */
+	/** {@inheritDoc} */
 	@Override
 	public Ref call() throws GitAPIException, RefNotFoundException, InvalidRefNameException,
 			RefAlreadyExistsException, DetachedHeadException {
@@ -198,6 +191,8 @@ public class RenameBranchCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Set the new name of the branch
+	 *
 	 * @param newName
 	 *            the new name
 	 * @return this instance
@@ -209,6 +204,8 @@ public class RenameBranchCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Set the old name of the branch
+	 *
 	 * @param oldName
 	 *            the name of the branch to rename; if not set, the currently
 	 *            checked out branch (if any) will be renamed

org.eclipse.jgit/src/org/eclipse/jgit/api/ResetCommand.java

@@ -126,20 +126,23 @@ public class ResetCommand extends GitCommand<Ref> {
 	private boolean isReflogDisabled;
 
 	/**
+	 * <p>
+	 * Constructor for ResetCommand.
+	 * </p>
 	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	public ResetCommand(Repository repo) {
 		super(repo);
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code Reset} command. Each instance of this class should
 	 * only be used for one invocation of the command. Don't call this method
 	 * twice on an instance.
-	 *
-	 * @return the Ref after reset
-	 * @throws GitAPIException
 	 */
 	@Override
 	public Ref call() throws GitAPIException, CheckoutConflictException {
@@ -258,6 +261,8 @@ public class ResetCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Set the name of the <code>Ref</code> to reset to
+	 *
 	 * @param ref
 	 *            the ref to reset to, defaults to HEAD if not specified
 	 * @return this instance
@@ -268,6 +273,8 @@ public class ResetCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Set the reset mode
+	 *
 	 * @param mode
 	 *            the mode of the reset command
 	 * @return this instance
@@ -282,6 +289,8 @@ public class ResetCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Repository relative path of file or directory to reset
+	 *
 	 * @param path
 	 *            repository-relative path of file/directory to reset (with
 	 *            <code>/</code> as separator)
@@ -297,6 +306,8 @@ public class ResetCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Whether to disable reflog
+	 *
 	 * @param disable
 	 *            if {@code true} disables writing a reflog entry for this reset
 	 *            command
@@ -309,6 +320,8 @@ public class ResetCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Whether reflog is disabled
+	 *
 	 * @return {@code true} if writing reflog is disabled for this reset command
 	 * @since 4.5
 	 */
@@ -433,6 +446,7 @@ public class ResetCommand extends GitCommand<Ref> {
 		repo.writeMergeCommitMsg(null);
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {

org.eclipse.jgit/src/org/eclipse/jgit/api/RevertCommand.java

@@ -98,27 +98,24 @@ public class RevertCommand extends GitCommand<RevCommit> {
 	private MergeStrategy strategy = MergeStrategy.RECURSIVE;
 
 	/**
+	 * <p>
+	 * Constructor for RevertCommand.
+	 * </p>
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected RevertCommand(Repository repo) {
 		super(repo);
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code revert} command with all the options and parameters
 	 * collected by the setter methods (e.g. {@link #include(Ref)} of this
 	 * class. Each instance of this class should only be used for one invocation
 	 * of the command. Don't call this method twice on an instance.
-	 *
-	 * @return on success the {@link RevCommit} pointed to by the new HEAD is
-	 *         returned. If a failure occurred during revert <code>null</code>
-	 *         is returned. The list of successfully reverted {@link Ref}'s can
-	 *         be obtained by calling {@link #getRevertedRefs()}
-	 * @throws GitAPIException
-	 * @throws WrongRepositoryStateException
-	 * @throws ConcurrentRefUpdateException
-	 * @throws UnmergedPathsException
-	 * @throws NoMessageException
 	 */
 	@Override
 	public RevCommit call() throws NoMessageException, UnmergedPathsException,
@@ -227,9 +224,10 @@ public class RevertCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
+	 * Include a {@code Ref} to a commit to be reverted
+	 *
 	 * @param commit
-	 *            a reference to a commit which is reverted into the current
-	 *            head
+	 *            a reference to a commit to be reverted into the current head
 	 * @return {@code this}
 	 */
 	public RevertCommand include(Ref commit) {
@@ -239,8 +237,10 @@ public class RevertCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
+	 * Include a commit to be reverted
+	 *
 	 * @param commit
-	 *            the Id of a commit which is reverted into the current head
+	 *            the Id of a commit to be reverted into the current head
 	 * @return {@code this}
 	 */
 	public RevertCommand include(AnyObjectId commit) {
@@ -248,8 +248,10 @@ public class RevertCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
+	 * Include a commit to be reverted
+	 *
 	 * @param name
-	 *            a name given to the commit
+	 *            name of a {@code Ref} referring to the commit
 	 * @param commit
 	 *            the Id of a commit which is reverted into the current head
 	 * @return {@code this}
@@ -260,6 +262,8 @@ public class RevertCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
+	 * Set the name to be used in the "OURS" place for conflict markers
+	 *
 	 * @param ourCommitName
 	 *            the name that should be used in the "OURS" place for conflict
 	 *            markers
@@ -280,16 +284,20 @@ public class RevertCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
-	 * @return the list of successfully reverted {@link Ref}'s. Never
-	 *         <code>null</code> but maybe an empty list if no commit was
-	 *         successfully cherry-picked
+	 * Get the list of successfully reverted {@link org.eclipse.jgit.lib.Ref}'s.
+	 *
+	 * @return the list of successfully reverted
+	 *         {@link org.eclipse.jgit.lib.Ref}'s. Never <code>null</code> but
+	 *         maybe an empty list if no commit was successfully cherry-picked
 	 */
 	public List<Ref> getRevertedRefs() {
 		return revertedRefs;
 	}
 
 	/**
-	 * @return the result of the merge failure, <code>null</code> if no merge
+	 * Get the result of a merge failure
+	 *
+	 * @return the result of a merge failure, <code>null</code> if no merge
 	 *         failure occurred during the revert
 	 */
 	public MergeResult getFailingResult() {
@@ -297,6 +305,8 @@ public class RevertCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
+	 * Get unmerged paths
+	 *
 	 * @return the unmerged paths, will be null if no merge conflicts
 	 */
 	public List<String> getUnmergedPaths() {
@@ -304,8 +314,10 @@ public class RevertCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
+	 * Set the merge strategy to use for this revert command
+	 *
 	 * @param strategy
-	 *            The merge strategy to use during this revert command.
+	 *            The merge strategy to use for this revert command.
 	 * @return {@code this}
 	 * @since 3.4
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/api/RmCommand.java

@@ -72,7 +72,7 @@ import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
  * class should only be used for one invocation of the command (means: one call
  * to {@link #call()}).
  * <p>
- * Examples (<code>git</code> is a {@link Git} instance):
+ * Examples (<code>git</code> is a {@link org.eclipse.jgit.api.Git} instance):
  * <p>
  * Remove file "test.txt" from both index and working directory:
  *
@@ -97,8 +97,10 @@ public class RmCommand extends GitCommand<DirCache> {
 	private boolean cached = false;
 
 	/**
+	 * Constructor for RmCommand.
 	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	public RmCommand(Repository repo) {
 		super(repo);
@@ -106,6 +108,8 @@ public class RmCommand extends GitCommand<DirCache> {
 	}
 
 	/**
+	 * Add file name pattern of files to be removed
+	 *
 	 * @param filepattern
 	 *            repository-relative path of file to remove (with
 	 *            <code>/</code> as separator)
@@ -121,8 +125,9 @@ public class RmCommand extends GitCommand<DirCache> {
 	 * Only remove the specified files from the index.
 	 *
 	 * @param cached
-	 *            true if files should only be removed from index, false if
-	 *            files should also be deleted from the working directory
+	 *            {@code true} if files should only be removed from index,
+	 *            {@code false} if files should also be deleted from the working
+	 *            directory
 	 * @return {@code this}
 	 * @since 2.2
 	 */
@@ -133,11 +138,11 @@ public class RmCommand extends GitCommand<DirCache> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code Rm} command. Each instance of this class should only
 	 * be used for one invocation of the command. Don't call this method twice
 	 * on an instance.
-	 *
-	 * @return the DirCache after Rm
 	 */
 	@Override
 	public DirCache call() throws GitAPIException,

org.eclipse.jgit/src/org/eclipse/jgit/api/ShowNoteCommand.java

@@ -68,12 +68,16 @@ public class ShowNoteCommand extends GitCommand<Note> {
 	private String notesRef = Constants.R_NOTES_COMMITS;
 
 	/**
+	 * Constructor for ShowNoteCommand.
+	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	protected ShowNoteCommand(Repository repo) {
 		super(repo);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Note call() throws GitAPIException {
 		checkCallable();
@@ -96,6 +100,8 @@ public class ShowNoteCommand extends GitCommand<Note> {
 	 * Sets the object id of object you want a note on
 	 *
 	 * @param id
+	 *            the {@link org.eclipse.jgit.revwalk.RevObject} to show notes
+	 *            for.
 	 * @return {@code this}
 	 */
 	public ShowNoteCommand setObjectId(RevObject id) {
@@ -105,12 +111,13 @@ public class ShowNoteCommand extends GitCommand<Note> {
 	}
 
 	/**
+	 * Set the {@code Ref} to read notes from.
+	 *
 	 * @param notesRef
 	 *            the ref to read notes from. Note, the default value of
-	 *            {@link Constants#R_NOTES_COMMITS} will be used if nothing is
-	 *            set
+	 *            {@link org.eclipse.jgit.lib.Constants#R_NOTES_COMMITS} will be
+	 *            used if nothing is set
 	 * @return {@code this}
-	 *
 	 * @see Constants#R_NOTES_COMMITS
 	 */
 	public ShowNoteCommand setNotesRef(String notesRef) {

org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java

@@ -88,7 +88,6 @@ import org.eclipse.jgit.treewalk.TreeWalk;
  *
  * @see <a href="http://www.kernel.org/pub/software/scm/git/docs/git-stash.html"
  *      >Git documentation about Stash</a>
- *
  * @since 2.0
  */
 public class StashApplyCommand extends GitCommand<ObjectId> {
@@ -109,6 +108,8 @@ public class StashApplyCommand extends GitCommand<ObjectId> {
 	 * Create command to apply the changes of a stashed commit
 	 *
 	 * @param repo
+	 *            the {@link org.eclipse.jgit.lib.Repository} to apply the stash
+	 *            to
 	 */
 	public StashApplyCommand(final Repository repo) {
 		super(repo);
@@ -121,6 +122,7 @@ public class StashApplyCommand extends GitCommand<ObjectId> {
 	 * unspecified
 	 *
 	 * @param stashRef
+	 *            name of the stash {@code Ref} to apply
 	 * @return {@code this}
 	 */
 	public StashApplyCommand setStashRef(final String stashRef) {
@@ -129,7 +131,10 @@ public class StashApplyCommand extends GitCommand<ObjectId> {
 	}
 
 	/**
+	 * Whether to ignore the repository state when applying the stash
+	 *
 	 * @param willIgnoreRepositoryState
+	 *            whether to ignore the repository state when applying the stash
 	 * @return {@code this}
 	 * @since 3.2
 	 */
@@ -154,14 +159,9 @@ public class StashApplyCommand extends GitCommand<ObjectId> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Apply the changes in a stashed commit to the working directory and index
-	 *
-	 * @return id of stashed commit that was applied TODO: Does anyone depend on
-	 *         this, or could we make it more like Merge/CherryPick/Revert?
-	 * @throws GitAPIException
-	 * @throws WrongRepositoryStateException
-	 * @throws NoHeadException
-	 * @throws StashApplyFailureException
 	 */
 	@Override
 	public ObjectId call() throws GitAPIException,
@@ -273,6 +273,8 @@ public class StashApplyCommand extends GitCommand<ObjectId> {
 	}
 
 	/**
+	 * Whether to restore the index state
+	 *
 	 * @param applyIndex
 	 *            true (default) if the command should restore the index state
 	 */
@@ -281,6 +283,8 @@ public class StashApplyCommand extends GitCommand<ObjectId> {
 	}
 
 	/**
+	 * Set the <code>MergeStrategy</code> to use.
+	 *
 	 * @param strategy
 	 *            The merge strategy to use in order to merge during this
 	 *            command execution.
@@ -293,6 +297,8 @@ public class StashApplyCommand extends GitCommand<ObjectId> {
 	}
 
 	/**
+	 * Whether the command should restore untracked files
+	 *
 	 * @param applyUntracked
 	 *            true (default) if the command should restore untracked files
 	 * @since 3.4

org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java

@@ -115,6 +115,7 @@ public class StashCreateCommand extends GitCommand<RevCommit> {
 	 * Create a command to stash changes in the working directory and index
 	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	public StashCreateCommand(Repository repo) {
 		super(repo);
@@ -128,6 +129,7 @@ public class StashCreateCommand extends GitCommand<RevCommit> {
 	 * id, and short commit message when used.
 	 *
 	 * @param message
+	 *            the stash message
 	 * @return {@code this}
 	 */
 	public StashCreateCommand setIndexMessage(String message) {
@@ -142,6 +144,7 @@ public class StashCreateCommand extends GitCommand<RevCommit> {
 	 * id, and short commit message when used.
 	 *
 	 * @param message
+	 *            the working directory message
 	 * @return {@code this}
 	 */
 	public StashCreateCommand setWorkingDirectoryMessage(String message) {
@@ -153,6 +156,8 @@ public class StashCreateCommand extends GitCommand<RevCommit> {
 	 * Set the person to use as the author and committer in the commits made
 	 *
 	 * @param person
+	 *            the {@link org.eclipse.jgit.lib.PersonIdent} of the person who
+	 *            creates the stash.
 	 * @return {@code this}
 	 */
 	public StashCreateCommand setPerson(PersonIdent person) {
@@ -161,12 +166,13 @@ public class StashCreateCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
-	 * Set the reference to update with the stashed commit id
-	 * If null, no reference is updated
+	 * Set the reference to update with the stashed commit id If null, no
+	 * reference is updated
 	 * <p>
-	 * This value defaults to {@link Constants#R_STASH}
+	 * This value defaults to {@link org.eclipse.jgit.lib.Constants#R_STASH}
 	 *
 	 * @param ref
+	 *            the name of the {@code Ref} to update
 	 * @return {@code this}
 	 */
 	public StashCreateCommand setRef(String ref) {
@@ -178,6 +184,7 @@ public class StashCreateCommand extends GitCommand<RevCommit> {
 	 * Whether to include untracked files in the stash.
 	 *
 	 * @param includeUntracked
+	 *            whether to include untracked files in the stash
 	 * @return {@code this}
 	 * @since 3.4
 	 */
@@ -232,11 +239,10 @@ public class StashCreateCommand extends GitCommand<RevCommit> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Stash the contents on the working directory and index in separate commits
 	 * and reset to the current HEAD commit.
-	 *
-	 * @return stashed commit or null if no changes to stash
-	 * @throws GitAPIException
 	 */
 	@Override
 	public RevCommit call() throws GitAPIException {

org.eclipse.jgit/src/org/eclipse/jgit/api/StashDropCommand.java

@@ -84,7 +84,10 @@ public class StashDropCommand extends GitCommand<ObjectId> {
 	private boolean all;
 
 	/**
+	 * Constructor for StashDropCommand.
+	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	public StashDropCommand(Repository repo) {
 		super(repo);
@@ -101,6 +104,7 @@ public class StashDropCommand extends GitCommand<ObjectId> {
 	 * unspecified
 	 *
 	 * @param stashRef
+	 *            the 0-based index of the stash reference
 	 * @return {@code this}
 	 */
 	public StashDropCommand setStashRef(final int stashRef) {
@@ -112,11 +116,12 @@ public class StashDropCommand extends GitCommand<ObjectId> {
 	}
 
 	/**
-	 * Set wheter drop all stashed commits
+	 * Set whether to drop all stashed commits
 	 *
 	 * @param all
-	 *            true to drop all stashed commits, false to drop only the
-	 *            stashed commit set via calling {@link #setStashRef(int)}
+	 *            {@code true} to drop all stashed commits, {@code false} to
+	 *            drop only the stashed commit set via calling
+	 *            {@link #setStashRef(int)}
 	 * @return {@code this}
 	 */
 	public StashDropCommand setAll(final boolean all) {
@@ -173,11 +178,10 @@ public class StashDropCommand extends GitCommand<ObjectId> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Drop the configured entry from the stash reflog and return value of the
 	 * stash reference after the drop occurs
-	 *
-	 * @return commit id of stash reference or null if no more stashed changes
-	 * @throws GitAPIException
 	 */
 	@Override
 	public ObjectId call() throws GitAPIException {

org.eclipse.jgit/src/org/eclipse/jgit/api/StashListCommand.java

@@ -70,12 +70,13 @@ public class StashListCommand extends GitCommand<Collection<RevCommit>> {
 	/**
 	 * Create a new stash list command
 	 *
-	 * @param repo
+	 * @param repo a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	public StashListCommand(final Repository repo) {
 		super(repo);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Collection<RevCommit> call() throws GitAPIException,
 			InvalidRefNameException {

org.eclipse.jgit/src/org/eclipse/jgit/api/Status.java

@@ -70,7 +70,10 @@ public class Status {
 	private final boolean hasUncommittedChanges;
 
 	/**
+	 * Constructor for Status.
+	 *
 	 * @param diff
+	 *            the {@link org.eclipse.jgit.lib.IndexDiff} having the status
 	 */
 	public Status(IndexDiff diff) {
 		super();
@@ -86,16 +89,20 @@ public class Status {
 	}
 
 	/**
-	 * @return true if no differences exist between the working-tree, the index,
-	 *         and the current HEAD, false if differences do exist
+	 * Whether the status is clean
+	 *
+	 * @return {@code true} if no differences exist between the working-tree,
+	 *         the index, and the current HEAD, {@code false} if differences do
+	 *         exist
 	 */
 	public boolean isClean() {
 		return clean;
 	}
 
 	/**
-	 * @return true if any tracked file is changed
+	 * Whether there are uncommitted changes
 	 *
+	 * @return {@code true} if any tracked file is changed
 	 * @since 3.2
 	 */
 	public boolean hasUncommittedChanges() {
@@ -103,14 +110,18 @@ public class Status {
 	}
 
 	/**
+	 * Get files added to the index
+	 *
 	 * @return list of files added to the index, not in HEAD (e.g. what you get
-	 *         if you call 'git add ...' on a newly created file)
+	 *         if you call {@code git add ...} on a newly created file)
 	 */
 	public Set<String> getAdded() {
 		return Collections.unmodifiableSet(diff.getAdded());
 	}
 
 	/**
+	 * Get changed files from HEAD to index
+	 *
 	 * @return list of files changed from HEAD to index (e.g. what you get if
 	 *         you modify an existing file and call 'git add ...' on it)
 	 */
@@ -119,6 +130,8 @@ public class Status {
 	}
 
 	/**
+	 * Get removed files
+	 *
 	 * @return list of files removed from index, but in HEAD (e.g. what you get
 	 *         if you call 'git rm ...' on a existing file)
 	 */
@@ -127,6 +140,8 @@ public class Status {
 	}
 
 	/**
+	 * Get missing files
+	 *
 	 * @return list of files in index, but not filesystem (e.g. what you get if
 	 *         you call 'rm ...' on a existing file)
 	 */
@@ -135,6 +150,8 @@ public class Status {
 	}
 
 	/**
+	 * Get modified files relative to the index
+	 *
 	 * @return list of files modified on disk relative to the index (e.g. what
 	 *         you get if you modify an existing file without adding it to the
 	 *         index)
@@ -144,6 +161,8 @@ public class Status {
 	}
 
 	/**
+	 * Get untracked files
+	 *
 	 * @return list of files that are not ignored, and not in the index. (e.g.
 	 *         what you get if you create a new file without adding it to the
 	 *         index)
@@ -153,6 +172,8 @@ public class Status {
 	}
 
 	/**
+	 * Get untracked folders
+	 *
 	 * @return set of directories that are not ignored, and not in the index.
 	 */
 	public Set<String> getUntrackedFolders() {
@@ -160,6 +181,8 @@ public class Status {
 	}
 
 	/**
+	 * Get conflicting files
+	 *
 	 * @return list of files that are in conflict. (e.g what you get if you
 	 *         modify file that was modified by someone else in the meantime)
 	 */
@@ -168,7 +191,10 @@ public class Status {
 	}
 
 	/**
-	 * @return a map from conflicting path to its {@link StageState}.
+	 * Get StageState of conflicting files
+	 *
+	 * @return a map from conflicting path to its
+	 *         {@link org.eclipse.jgit.lib.IndexDiff.StageState}.
 	 * @since 3.0
 	 */
 	public Map<String, StageState> getConflictingStageState() {
@@ -176,6 +202,8 @@ public class Status {
 	}
 
 	/**
+	 * Get ignored files which are not in the index
+	 *
 	 * @return set of files and folders that are ignored and not in the index.
 	 */
 	public Set<String> getIgnoredNotInIndex() {
@@ -183,9 +211,11 @@ public class Status {
 	}
 
 	/**
+	 * Get uncommitted changes, i.e. all files changed in the index or working
+	 * tree
+	 *
 	 * @return set of files and folders that are known to the repo and changed
 	 *         either in the index or in the working tree.
-	 *
 	 * @since 3.2
 	 */
 	public Set<String> getUncommittedChanges() {

org.eclipse.jgit/src/org/eclipse/jgit/api/StatusCommand.java

@@ -64,9 +64,9 @@ import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
  * to finally execute the command. Each instance of this class should only be
  * used for one invocation of the command (means: one call to {@link #call()})
  *
- * @see <a
- *      href="http://www.kernel.org/pub/software/scm/git/docs/git-status.html"
- *      >Git documentation about Status</a>
+ * @see <a href=
+ *      "http://www.kernel.org/pub/software/scm/git/docs/git-status.html" >Git
+ *      documentation about Status</a>
  */
 public class StatusCommand extends GitCommand<Status> {
 	private WorkingTreeIterator workingTreeIt;
@@ -76,14 +76,21 @@ public class StatusCommand extends GitCommand<Status> {
 	private IgnoreSubmoduleMode ignoreSubmoduleMode = null;
 
 	/**
+	 * Constructor for StatusCommand.
+	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	protected StatusCommand(Repository repo) {
 		super(repo);
 	}
 
 	/**
+	 * Whether to ignore submodules
+	 *
 	 * @param mode
+	 *            the
+	 *            {@link org.eclipse.jgit.submodule.SubmoduleWalk.IgnoreSubmoduleMode}
 	 * @return {@code this}
 	 * @since 3.6
 	 */
@@ -126,13 +133,12 @@ public class StatusCommand extends GitCommand<Status> {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code Status} command with all the options and parameters
 	 * collected by the setter methods of this class. Each instance of this
 	 * class should only be used for one invocation of the command. Don't call
 	 * this method twice on an instance.
-	 *
-	 * @return a {@link Status} object telling about each path where working
-	 *         tree, index or HEAD differ from each other.
 	 */
 	@Override
 	public Status call() throws GitAPIException, NoWorkTreeException {
@@ -157,8 +163,9 @@ public class StatusCommand extends GitCommand<Status> {
 	}
 
 	/**
-	 * To set the {@link WorkingTreeIterator} which should be used. If this
-	 * method is not called a standard {@link FileTreeIterator} is used.
+	 * To set the {@link org.eclipse.jgit.treewalk.WorkingTreeIterator} which
+	 * should be used. If this method is not called a standard
+	 * {@link org.eclipse.jgit.treewalk.FileTreeIterator} is used.
 	 *
 	 * @param workingTreeIt
 	 *            a working tree iterator
@@ -170,10 +177,11 @@ public class StatusCommand extends GitCommand<Status> {
 	}
 
 	/**
-	 * To set the {@link ProgressMonitor} which contains callback methods to
-	 * inform you about the progress of this command.
+	 * To set the {@link org.eclipse.jgit.lib.ProgressMonitor} which contains
+	 * callback methods to inform you about the progress of this command.
 	 *
 	 * @param progressMonitor
+	 *            a {@link org.eclipse.jgit.lib.ProgressMonitor} object.
 	 * @return {@code this}
 	 * @since 3.1
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleAddCommand.java

@@ -69,8 +69,8 @@ import org.eclipse.jgit.treewalk.filter.TreeFilter;
  * .gitmodules file and the repository config file, and also add the submodule
  * and .gitmodules file to the index.
  *
- * @see <a
- *      href="http://www.kernel.org/pub/software/scm/git/docs/git-submodule.html"
+ * @see <a href=
+ *      "http://www.kernel.org/pub/software/scm/git/docs/git-submodule.html"
  *      >Git documentation about submodules</a>
  */
 public class SubmoduleAddCommand extends
@@ -83,7 +83,10 @@ public class SubmoduleAddCommand extends
 	private ProgressMonitor monitor;
 
 	/**
+	 * Constructor for SubmoduleAddCommand.
+	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	public SubmoduleAddCommand(final Repository repo) {
 		super(repo);
@@ -105,6 +108,7 @@ public class SubmoduleAddCommand extends
 	 * Set URI to clone submodule from
 	 *
 	 * @param uri
+	 *            a {@link java.lang.String} object.
 	 * @return this command
 	 */
 	public SubmoduleAddCommand setURI(final String uri) {
@@ -118,6 +122,7 @@ public class SubmoduleAddCommand extends
 	 *
 	 * @see NullProgressMonitor
 	 * @param monitor
+	 *            a {@link org.eclipse.jgit.lib.ProgressMonitor} object.
 	 * @return this command
 	 */
 	public SubmoduleAddCommand setProgressMonitor(final ProgressMonitor monitor) {
@@ -129,7 +134,7 @@ public class SubmoduleAddCommand extends
 	 * Is the configured already a submodule in the index?
 	 *
 	 * @return true if submodule exists in index, false otherwise
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	protected boolean submoduleExists() throws IOException {
 		TreeFilter filter = PathFilter.create(path);
@@ -139,15 +144,14 @@ public class SubmoduleAddCommand extends
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code SubmoduleAddCommand}
 	 *
 	 * The {@code Repository} instance returned by this command needs to be
 	 * closed by the caller to free resources held by the {@code Repository}
 	 * instance. It is recommended to call this method as soon as you don't need
 	 * a reference to this {@code Repository} instance anymore.
-	 *
-	 * @return the newly created {@link Repository}
-	 * @throws GitAPIException
 	 */
 	@Override
 	public Repository call() throws GitAPIException {

org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleInitCommand.java

@@ -63,8 +63,8 @@ import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
  * .gitmodules file to a repository's config file for each submodule not
  * currently present in the repository's config file.
  *
- * @see <a
- *      href="http://www.kernel.org/pub/software/scm/git/docs/git-submodule.html"
+ * @see <a href=
+ *      "http://www.kernel.org/pub/software/scm/git/docs/git-submodule.html"
  *      >Git documentation about submodules</a>
  */
 public class SubmoduleInitCommand extends GitCommand<Collection<String>> {
@@ -72,7 +72,10 @@ public class SubmoduleInitCommand extends GitCommand<Collection<String>> {
 	private final Collection<String> paths;
 
 	/**
+	 * Constructor for SubmoduleInitCommand.
+	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	public SubmoduleInitCommand(final Repository repo) {
 		super(repo);
@@ -91,6 +94,7 @@ public class SubmoduleInitCommand extends GitCommand<Collection<String>> {
 		return this;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Collection<String> call() throws GitAPIException {
 		checkCallable();

org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleStatusCommand.java

@@ -62,8 +62,8 @@ import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
 /**
  * A class used to execute a submodule status command.
  *
- * @see <a
- *      href="http://www.kernel.org/pub/software/scm/git/docs/git-submodule.html"
+ * @see <a href=
+ *      "http://www.kernel.org/pub/software/scm/git/docs/git-submodule.html"
  *      >Git documentation about submodules</a>
  */
 public class SubmoduleStatusCommand extends
@@ -72,7 +72,10 @@ public class SubmoduleStatusCommand extends
 	private final Collection<String> paths;
 
 	/**
+	 * Constructor for SubmoduleStatusCommand.
+	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	public SubmoduleStatusCommand(final Repository repo) {
 		super(repo);
@@ -91,6 +94,7 @@ public class SubmoduleStatusCommand extends
 		return this;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Map<String, SubmoduleStatus> call() throws GitAPIException {
 		checkCallable();

org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleSyncCommand.java

@@ -65,8 +65,8 @@ import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
  * This will set the remote URL in a submodule's repository to the current value
  * in the .gitmodules file.
  *
- * @see <a
- *      href="http://www.kernel.org/pub/software/scm/git/docs/git-submodule.html"
+ * @see <a href=
+ *      "http://www.kernel.org/pub/software/scm/git/docs/git-submodule.html"
  *      >Git documentation about submodules</a>
  */
 public class SubmoduleSyncCommand extends GitCommand<Map<String, String>> {
@@ -74,7 +74,10 @@ public class SubmoduleSyncCommand extends GitCommand<Map<String, String>> {
 	private final Collection<String> paths;
 
 	/**
+	 * Constructor for SubmoduleSyncCommand.
+	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	public SubmoduleSyncCommand(final Repository repo) {
 		super(repo);
@@ -97,8 +100,9 @@ public class SubmoduleSyncCommand extends GitCommand<Map<String, String>> {
 	 * Get branch that HEAD currently points to
 	 *
 	 * @param subRepo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 * @return shortened branch name, null on failures
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	protected String getHeadBranch(final Repository subRepo) throws IOException {
 		Ref head = subRepo.exactRef(Constants.HEAD);
@@ -108,6 +112,7 @@ public class SubmoduleSyncCommand extends GitCommand<Map<String, String>> {
 			return null;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Map<String, String> call() throws GitAPIException {
 		checkCallable();

org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleUpdateCommand.java

@@ -96,7 +96,12 @@ public class SubmoduleUpdateCommand extends
 	private boolean fetch = false;
 
 	/**
+	 * <p>
+	 * Constructor for SubmoduleUpdateCommand.
+	 * </p>
+	 *
 	 * @param repo
+	 *            a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	public SubmoduleUpdateCommand(final Repository repo) {
 		super(repo);
@@ -109,6 +114,7 @@ public class SubmoduleUpdateCommand extends
 	 *
 	 * @see NullProgressMonitor
 	 * @param monitor
+	 *            a {@link org.eclipse.jgit.lib.ProgressMonitor} object.
 	 * @return this command
 	 */
 	public SubmoduleUpdateCommand setProgressMonitor(
@@ -122,6 +128,7 @@ public class SubmoduleUpdateCommand extends
 	 * is set to <code>false</code>
 	 *
 	 * @param fetch
+	 *            whether to fetch the submodules before we update them
 	 * @return this command
 	 * @since 4.9
 	 */
@@ -143,18 +150,9 @@ public class SubmoduleUpdateCommand extends
 	}
 
 	/**
-	 * Execute the SubmoduleUpdateCommand command.
+	 * {@inheritDoc}
 	 *
-	 * @return a collection of updated submodule paths
-	 * @throws ConcurrentRefUpdateException
-	 * @throws CheckoutConflictException
-	 * @throws InvalidMergeHeadsException
-	 * @throws InvalidConfigurationException
-	 * @throws NoHeadException
-	 * @throws NoMessageException
-	 * @throws RefNotFoundException
-	 * @throws WrongRepositoryStateException
-	 * @throws GitAPIException
+	 * Execute the SubmoduleUpdateCommand command.
 	 */
 	@Override
 	public Collection<String> call() throws InvalidConfigurationException,
@@ -252,6 +250,8 @@ public class SubmoduleUpdateCommand extends
 	}
 
 	/**
+	 * Setter for the field <code>strategy</code>.
+	 *
 	 * @param strategy
 	 *            The merge strategy to use during this update operation.
 	 * @return {@code this}

org.eclipse.jgit/src/org/eclipse/jgit/api/TagCommand.java

@@ -68,7 +68,7 @@ import org.eclipse.jgit.revwalk.RevWalk;
 /**
  * Create/update an annotated tag object or a simple unannotated tag
  * <p>
- * Examples (<code>git</code> is a {@link Git} instance):
+ * Examples (<code>git</code> is a {@link org.eclipse.jgit.api.Git} instance):
  * <p>
  * Create a new tag for the current commit:
  *
@@ -104,21 +104,22 @@ public class TagCommand extends GitCommand<Ref> {
 	private boolean annotated = true;
 
 	/**
-	 * @param repo
+	 * <p>Constructor for TagCommand.</p>
+	 *
+	 * @param repo a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	protected TagCommand(Repository repo) {
 		super(repo);
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Executes the {@code tag} command with all the options and parameters
 	 * collected by the setter methods of this class. Each instance of this
 	 * class should only be used for one invocation of the command (means: one
 	 * call to {@link #call()})
 	 *
-	 * @return a {@link Ref} a ref pointing to a tag
-	 * @throws NoHeadException
-	 *             when called on a git repo without a HEAD reference
 	 * @since 2.0
 	 */
 	@Override
@@ -226,6 +227,8 @@ public class TagCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Set the tag <code>name</code>.
+	 *
 	 * @param name
 	 *            the tag name used for the {@code tag}
 	 * @return {@code this}
@@ -237,6 +240,8 @@ public class TagCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Get the tag <code>name</code>.
+	 *
 	 * @return the tag name used for the <code>tag</code>
 	 */
 	public String getName() {
@@ -244,6 +249,8 @@ public class TagCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Get the tag <code>message</code>.
+	 *
 	 * @return the tag message used for the <code>tag</code>
 	 */
 	public String getMessage() {
@@ -251,6 +258,8 @@ public class TagCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Set the tag <code>message</code>.
+	 *
 	 * @param message
 	 *            the tag message used for the {@code tag}
 	 * @return {@code this}
@@ -262,6 +271,8 @@ public class TagCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Whether this tag is signed
+	 *
 	 * @return whether the tag is signed
 	 */
 	public boolean isSigned() {
@@ -273,6 +284,7 @@ public class TagCommand extends GitCommand<Ref> {
 	 * corresponds to the parameter -s on the command line.
 	 *
 	 * @param signed
+	 *            a boolean.
 	 * @return {@code this}
 	 */
 	public TagCommand setSigned(boolean signed) {
@@ -285,6 +297,7 @@ public class TagCommand extends GitCommand<Ref> {
 	 * created from the info in the repository.
 	 *
 	 * @param tagger
+	 *            a {@link org.eclipse.jgit.lib.PersonIdent} object.
 	 * @return {@code this}
 	 */
 	public TagCommand setTagger(PersonIdent tagger) {
@@ -293,6 +306,8 @@ public class TagCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Get the <code>tagger</code> who created the tag.
+	 *
 	 * @return the tagger of the tag
 	 */
 	public PersonIdent getTagger() {
@@ -300,6 +315,8 @@ public class TagCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Get the tag's object id
+	 *
 	 * @return the object id of the tag
 	 */
 	public RevObject getObjectId() {
@@ -311,6 +328,7 @@ public class TagCommand extends GitCommand<Ref> {
 	 * pointed to from HEAD will be used.
 	 *
 	 * @param id
+	 *            a {@link org.eclipse.jgit.revwalk.RevObject} object.
 	 * @return {@code this}
 	 */
 	public TagCommand setObjectId(RevObject id) {
@@ -319,6 +337,8 @@ public class TagCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Whether this is a forced update
+	 *
 	 * @return is this a force update
 	 */
 	public boolean isForceUpdate() {
@@ -330,6 +350,7 @@ public class TagCommand extends GitCommand<Ref> {
 	 * corresponds to the parameter -f on the command line.
 	 *
 	 * @param forceUpdate
+	 *            whether this is a forced update
 	 * @return {@code this}
 	 */
 	public TagCommand setForceUpdate(boolean forceUpdate) {
@@ -338,7 +359,10 @@ public class TagCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Configure this tag to be created as an annotated tag
+	 *
 	 * @param annotated
+	 *            whether this shall be an annotated tag
 	 * @return {@code this}
 	 * @since 3.0
 	 */
@@ -348,6 +372,8 @@ public class TagCommand extends GitCommand<Ref> {
 	}
 
 	/**
+	 * Whether this will create an annotated command
+	 *
 	 * @return true if this command will create an annotated tag (default is
 	 *         true)
 	 * @since 3.0

org.eclipse.jgit/src/org/eclipse/jgit/api/TransportCommand.java

@@ -47,11 +47,12 @@ import org.eclipse.jgit.transport.CredentialsProvider;
 import org.eclipse.jgit.transport.Transport;
 
 /**
- * Base class for commands that use a {@link Transport} during execution.
+ * Base class for commands that use a
+ * {@link org.eclipse.jgit.transport.Transport} during execution.
  * <p>
  * This class provides standard configuration of a transport for options such as
- * a {@link CredentialsProvider}, a timeout, and a
- * {@link TransportConfigCallback}.
+ * a {@link org.eclipse.jgit.transport.CredentialsProvider}, a timeout, and a
+ * {@link org.eclipse.jgit.api.TransportConfigCallback}.
  *
  * @param <C>
  * @param <T>
@@ -75,7 +76,9 @@ public abstract class TransportCommand<C extends GitCommand, T> extends
 	protected TransportConfigCallback transportConfigCallback;
 
 	/**
-	 * @param repo
+	 * <p>Constructor for TransportCommand.</p>
+	 *
+	 * @param repo a {@link org.eclipse.jgit.lib.Repository} object.
 	 */
 	protected TransportCommand(final Repository repo) {
 		super(repo);
@@ -83,8 +86,11 @@ public abstract class TransportCommand<C extends GitCommand, T> extends
 	}
 
 	/**
+	 * Set the <code>credentialsProvider</code>.
+	 *
 	 * @param credentialsProvider
-	 *            the {@link CredentialsProvider} to use
+	 *            the {@link org.eclipse.jgit.transport.CredentialsProvider} to
+	 *            use
 	 * @return {@code this}
 	 */
 	public C setCredentialsProvider(
@@ -94,6 +100,8 @@ public abstract class TransportCommand<C extends GitCommand, T> extends
 	}
 
 	/**
+	 * Set <code>timeout</code>.
+	 *
 	 * @param timeout
 	 *            the timeout (in seconds) used for the transport step
 	 * @return {@code this}
@@ -104,12 +112,15 @@ public abstract class TransportCommand<C extends GitCommand, T> extends
 	}
 
 	/**
+	 * Set the <code>TransportConfigCallback</code>.
+	 *
 	 * @param transportConfigCallback
 	 *            if set, the callback will be invoked after the
-	 *            {@link Transport} has created, but before the
-	 *            {@link Transport} is used. The callback can use this
-	 *            opportunity to set additional type-specific configuration on
-	 *            the {@link Transport} instance.
+	 *            {@link org.eclipse.jgit.transport.Transport} has created, but
+	 *            before the {@link org.eclipse.jgit.transport.Transport} is
+	 *            used. The callback can use this opportunity to set additional
+	 *            type-specific configuration on the
+	 *            {@link org.eclipse.jgit.transport.Transport} instance.
 	 * @return {@code this}
 	 */
 	public C setTransportConfigCallback(
@@ -119,6 +130,11 @@ public abstract class TransportCommand<C extends GitCommand, T> extends
 	}
 
 	/** @return {@code this} */
+	/**
+	 * Return this command
+	 *
+	 * @return this command
+	 */
 	@SuppressWarnings("unchecked")
 	protected final C self() {
 		return (C) this;
@@ -129,6 +145,7 @@ public abstract class TransportCommand<C extends GitCommand, T> extends
 	 * callback
 	 *
 	 * @param transport
+	 *            a {@link org.eclipse.jgit.transport.Transport} object.
 	 * @return {@code this}
 	 */
 	protected C configure(final Transport transport) {
@@ -145,6 +162,7 @@ public abstract class TransportCommand<C extends GitCommand, T> extends
 	 * {@code this} command
 	 *
 	 * @param childCommand
+	 *            a {@link org.eclipse.jgit.api.TransportCommand} object.
 	 * @return {@code this}
 	 */
 	protected C configure(final TransportCommand childCommand) {

org.eclipse.jgit/src/org/eclipse/jgit/api/TransportConfigCallback.java

@@ -64,7 +64,9 @@ public interface TransportConfigCallback {
 
 	/**
 	 * Add any additional transport-specific configuration required.
+	 *
 	 * @param transport
+	 *            a {@link org.eclipse.jgit.transport.Transport} object.
 	 */
 	public void configure(Transport transport);
 }

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/AbortedByHookException.java

@@ -67,6 +67,8 @@ public class AbortedByHookException extends GitAPIException {
 	private final int returnCode;
 
 	/**
+	 * Constructor for AbortedByHookException
+	 *
 	 * @param message
 	 *            The error details.
 	 * @param hookName
@@ -83,6 +85,8 @@ public class AbortedByHookException extends GitAPIException {
 	}
 
 	/**
+	 * Get hook name
+	 *
 	 * @return the type of the hook that interrupted the git command.
 	 */
 	public String getHookName() {
@@ -90,12 +94,15 @@ public class AbortedByHookException extends GitAPIException {
 	}
 
 	/**
+	 * Get return code
+	 *
 	 * @return the hook process result.
 	 */
 	public int getReturnCode() {
 		return returnCode;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String getMessage() {
 		return MessageFormat.format(JGitText.get().commandRejectedByHook,

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/CanceledException.java

@@ -45,7 +45,9 @@ public class CanceledException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
-	 * @param message
+	 * <p>Constructor for CanceledException.</p>
+	 *
+	 * @param message a {@link java.lang.String} object.
 	 */
 	public CanceledException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/CannotDeleteCurrentBranchException.java

@@ -44,8 +44,10 @@ public class CannotDeleteCurrentBranchException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for CannotDeleteCurrentBranchException
+	 *
 	 * @param message
-	 *            the message
+	 *            error message
 	 */
 	public CannotDeleteCurrentBranchException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/CheckoutConflictException.java

@@ -53,7 +53,6 @@ public class CheckoutConflictException extends GitAPIException {
 	 *
 	 * @param conflictingPaths
 	 *            list of conflicting paths
-	 *
 	 * @param e
 	 *            a {@link org.eclipse.jgit.errors.CheckoutConflictException}
 	 *            exception
@@ -82,7 +81,11 @@ public class CheckoutConflictException extends GitAPIException {
 		this.conflictingPaths = conflictingPaths;
 	}
 
-	/** @return all the paths where unresolved conflicts have been detected */
+	/**
+	 * Get conflicting paths
+	 *
+	 * @return all the paths where unresolved conflicts have been detected
+	 */
 	public List<String> getConflictingPaths() {
 		return conflictingPaths;
 	}

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/ConcurrentRefUpdateException.java

@@ -55,10 +55,16 @@ public class ConcurrentRefUpdateException extends GitAPIException {
 	private Ref ref;
 
 	/**
+	 * Constructor for ConcurrentRefUpdateException.
+	 *
 	 * @param message
+	 *            error message
 	 * @param ref
+	 *            a {@link org.eclipse.jgit.lib.Ref}
 	 * @param rc
+	 *            a {@link org.eclipse.jgit.lib.RefUpdate.Result}
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 */
 	public ConcurrentRefUpdateException(String message, Ref ref,
 			RefUpdate.Result rc, Throwable cause) {
@@ -69,9 +75,14 @@ public class ConcurrentRefUpdateException extends GitAPIException {
 	}
 
 	/**
+	 * Constructor for ConcurrentRefUpdateException.
+	 *
 	 * @param message
+	 *            error message
 	 * @param ref
+	 *            a {@link org.eclipse.jgit.lib.Ref}
 	 * @param rc
+	 *            a {@link org.eclipse.jgit.lib.RefUpdate.Result}
 	 */
 	public ConcurrentRefUpdateException(String message, Ref ref,
 			RefUpdate.Result rc) {
@@ -82,15 +93,21 @@ public class ConcurrentRefUpdateException extends GitAPIException {
 	}
 
 	/**
-	 * @return the {@link Ref} which was tried to by updated
+	 * Get <code>Ref</code>
+	 *
+	 * @return the {@link org.eclipse.jgit.lib.Ref} which was tried to by
+	 *         updated
 	 */
 	public Ref getRef() {
 		return ref;
 	}
 
 	/**
-	 * @return the result which was returned by {@link RefUpdate#update()} and
-	 *         which caused this error
+	 * Get result
+	 *
+	 * @return the result which was returned by
+	 *         {@link org.eclipse.jgit.lib.RefUpdate#update()} and which caused
+	 *         this error
 	 */
 	public RefUpdate.Result getResult() {
 		return rc;

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/DetachedHeadException.java

@@ -55,15 +55,22 @@ public class DetachedHeadException extends GitAPIException {
 	}
 
 	/**
+	 * Constructor for DetachedHeadException.
+	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable} object.
 	 */
 	public DetachedHeadException(String message, Throwable cause) {
 		super(message, cause);
 	}
 
 	/**
+	 * Constructor for DetachedHeadException.
+	 *
 	 * @param message
+	 *            error message
 	 */
 	public DetachedHeadException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/EmtpyCommitException.java

@@ -46,15 +46,22 @@ public class EmtpyCommitException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for EmtpyCommitException
+	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 */
 	public EmtpyCommitException(String message, Throwable cause) {
 		super(message, cause);
 	}
 
 	/**
+	 * Constructor for EmtpyCommitException.
+	 *
 	 * @param message
+	 *            error message
 	 */
 	public EmtpyCommitException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/FilterFailedException.java

@@ -106,6 +106,8 @@ public class FilterFailedException extends GitAPIException {
 	}
 
 	/**
+	 * Get filter command
+	 *
 	 * @return the filterCommand
 	 */
 	public String getFilterCommand() {
@@ -113,6 +115,8 @@ public class FilterFailedException extends GitAPIException {
 	}
 
 	/**
+	 * Get path
+	 *
 	 * @return the path of the file processed by the filter command
 	 */
 	public String getPath() {
@@ -120,6 +124,8 @@ public class FilterFailedException extends GitAPIException {
 	}
 
 	/**
+	 * Get output
+	 *
 	 * @return the output generated by the filter command. Might be truncated to
 	 *         limit memory consumption.
 	 */
@@ -128,6 +134,8 @@ public class FilterFailedException extends GitAPIException {
 	}
 
 	/**
+	 * Get error
+	 *
 	 * @return the error output returned by the filter command
 	 */
 	public String getError() {
@@ -135,6 +143,8 @@ public class FilterFailedException extends GitAPIException {
 	}
 
 	/**
+	 * Get return code
+	 *
 	 * @return the return code returned by the filter command
 	 */
 	public int getReturnCode() {

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/GitAPIException.java

@@ -40,7 +40,6 @@ package org.eclipse.jgit.api.errors;
 /**
  * Superclass of all exceptions thrown by the API classes in
  * {@code org.eclipse.jgit.api}
- *
  */
 public abstract class GitAPIException extends Exception {
 	private static final long serialVersionUID = 1L;

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/InvalidConfigurationException.java

@@ -45,15 +45,22 @@ public class InvalidConfigurationException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for InvalidConfigurationException
+	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 */
 	public InvalidConfigurationException(String message, Throwable cause) {
 		super(message, cause);
 	}
 
 	/**
+	 * Constructor for InvalidConfigurationException.
+	 *
 	 * @param message
+	 *            error message
 	 */
 	public InvalidConfigurationException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/InvalidMergeHeadsException.java

@@ -47,7 +47,10 @@ public class InvalidMergeHeadsException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for InvalidMergeHeadsException.
+	 *
 	 * @param msg
+	 *            error message
 	 */
 	public InvalidMergeHeadsException(String msg) {
 		super(msg);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/InvalidRebaseStepException.java

@@ -45,16 +45,24 @@ package org.eclipse.jgit.api.errors;
  */
 public class InvalidRebaseStepException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
+
 	/**
+	 * Constructor for InvalidRebaseStepException.
+	 *
 	 * @param msg
+	 *            error message
 	 */
 	public InvalidRebaseStepException(String msg) {
 		super(msg);
 	}
 
 	/**
+	 * Constructor for InvalidRebaseStepException.
+	 *
 	 * @param msg
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 */
 	public InvalidRebaseStepException(String msg, Throwable cause) {
 		super(msg, cause);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/InvalidRefNameException.java

@@ -44,15 +44,22 @@ public class InvalidRefNameException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for InvalidRefNameException
+	 *
 	 * @param msg
+	 *            error message
 	 */
 	public InvalidRefNameException(String msg) {
 		super(msg);
 	}
 
 	/**
+	 * Constructor for InvalidRefNameException.
+	 *
 	 * @param msg
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 */
 	public InvalidRefNameException(String msg, Throwable cause) {
 		super(msg, cause);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/InvalidRemoteException.java

@@ -44,15 +44,22 @@ public class InvalidRemoteException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
-	 * @param msg message describing the invalid remote.
+	 * Constructor for InvalidRemoteException
+	 *
+	 * @param msg
+	 *            message describing the invalid remote.
 	 */
 	public InvalidRemoteException(String msg) {
 		super(msg);
 	}
 
 	/**
-	 * @param msg message describing the invalid remote.
-	 * @param cause why the remote is invalid.
+	 * Constructor for InvalidRemoteException
+	 *
+	 * @param msg
+	 *            message describing the invalid remote.
+	 * @param cause
+	 *            why the remote is invalid.
 	 */
 	public InvalidRemoteException(String msg, Throwable cause) {
 		super(msg, cause);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/InvalidTagNameException.java

@@ -45,7 +45,10 @@ public class InvalidTagNameException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for InvalidTagNameException.
+	 *
 	 * @param msg
+	 *            error message
 	 */
 	public InvalidTagNameException(String msg) {
 		super(msg);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/JGitInternalException.java

@@ -63,7 +63,9 @@ public class JGitInternalException extends RuntimeException {
 	 * Construct an exception for low-level internal exceptions
 	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 */
 	public JGitInternalException(String message, Throwable cause) {
 		super(message, cause);
@@ -73,6 +75,7 @@ public class JGitInternalException extends RuntimeException {
 	 * Construct an exception for low-level internal exceptions
 	 *
 	 * @param message
+	 *            error message
 	 */
 	public JGitInternalException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/MultipleParentsNotAllowedException.java

@@ -49,15 +49,22 @@ public class MultipleParentsNotAllowedException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for MultipleParentsNotAllowedException.
+	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 */
 	public MultipleParentsNotAllowedException(String message, Throwable cause) {
 		super(message, cause);
 	}
 
 	/**
+	 * Constructor for MultipleParentsNotAllowedException.
+	 *
 	 * @param message
+	 *            error message
 	 */
 	public MultipleParentsNotAllowedException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/NoFilepatternException.java

@@ -48,15 +48,22 @@ public class NoFilepatternException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for NoFilepatternException.
+	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 */
 	public NoFilepatternException(String message, Throwable cause) {
 		super(message, cause);
 	}
 
 	/**
+	 * Constructor for NoFilepatternException.
+	 *
 	 * @param message
+	 *            error message
 	 */
 	public NoFilepatternException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/NoHeadException.java

@@ -45,15 +45,22 @@ public class NoHeadException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for NoHeadException
+	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 */
 	public NoHeadException(String message, Throwable cause) {
 		super(message, cause);
 	}
 
 	/**
+	 * Constructor for NoHeadException
+	 *
 	 * @param message
+	 *            error message
 	 */
 	public NoHeadException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/NoMessageException.java

@@ -47,15 +47,22 @@ public class NoMessageException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for NoMessageException
+	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 */
 	public NoMessageException(String message, Throwable cause) {
 		super(message, cause);
 	}
 
 	/**
+	 * Constructor for NoMessageException
+	 *
 	 * @param message
+	 *            error message
 	 */
 	public NoMessageException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/PatchApplyException.java

@@ -46,21 +46,27 @@ package org.eclipse.jgit.api.errors;
  * Exception thrown when applying a patch fails
  *
  * @since 2.0
- *
  */
 public class PatchApplyException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for PatchApplyException
+	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 */
 	public PatchApplyException(String message, Throwable cause) {
 		super(message, cause);
 	}
 
 	/**
+	 * Constructor for PatchApplyException
+	 *
 	 * @param message
+	 *            error message
 	 */
 	public PatchApplyException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/PatchFormatException.java

@@ -52,7 +52,6 @@ import org.eclipse.jgit.patch.FormatError;
  * Exception thrown when applying a patch fails due to an invalid format
  *
  * @since 2.0
- *
  */
 public class PatchFormatException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
@@ -60,7 +59,10 @@ public class PatchFormatException extends GitAPIException {
 	private List<FormatError> errors;
 
 	/**
+	 * Constructor for PatchFormatException
+	 *
 	 * @param errors
+	 *            a {@link java.util.List} of {@link FormatError}s
 	 */
 	public PatchFormatException(List<FormatError> errors) {
 		super(MessageFormat.format(JGitText.get().patchFormatException, errors));
@@ -68,6 +70,8 @@ public class PatchFormatException extends GitAPIException {
 	}
 
 	/**
+	 * Get list of errors
+	 *
 	 * @return all the errors where unresolved conflicts have been detected
 	 */
 	public List<FormatError> getErrors() {

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/RefAlreadyExistsException.java

@@ -37,17 +37,18 @@
  */
 package org.eclipse.jgit.api.errors;
 
-import org.eclipse.jgit.lib.Ref;
-
 /**
- * Thrown when trying to create a {@link Ref} with the same name as an existing
- * one
+ * Thrown when trying to create a {@link org.eclipse.jgit.lib.Ref} with the same
+ * name as an existing one
  */
 public class RefAlreadyExistsException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for RefAlreadyExistsException
+	 *
 	 * @param message
+	 *            error message
 	 */
 	public RefAlreadyExistsException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/RefNotAdvertisedException.java

@@ -46,7 +46,10 @@ public class RefNotAdvertisedException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for RefNotAdvertisedException
+	 *
 	 * @param message
+	 *            error message
 	 */
 	public RefNotAdvertisedException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/RefNotFoundException.java

@@ -44,8 +44,12 @@ public class RefNotFoundException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for RefNotFoundException
+	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 * @since 4.1
 	 */
 	public RefNotFoundException(String message, Throwable cause) {
@@ -53,7 +57,10 @@ public class RefNotFoundException extends GitAPIException {
 	}
 
 	/**
+	 * Constructor for RefNotFoundException
+	 *
 	 * @param message
+	 *            error message
 	 */
 	public RefNotFoundException(String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/StashApplyFailureException.java

@@ -8,8 +8,12 @@ public class StashApplyFailureException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for StashApplyFailureException
+	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 * @since 4.1
 	 */
 	public StashApplyFailureException(String message, Throwable cause) {
@@ -20,6 +24,7 @@ public class StashApplyFailureException extends GitAPIException {
 	 * Create a StashApplyFailedException
 	 *
 	 * @param message
+	 *            error message
 	 */
 	public StashApplyFailureException(final String message) {
 		super(message);

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/TooLargeObjectInPackException.java

@@ -47,6 +47,8 @@ public class TooLargeObjectInPackException extends TransportException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for TooLargeObjectInPackException
+	 *
 	 * @param msg
 	 *            message describing the transport failure.
 	 */
@@ -55,6 +57,8 @@ public class TooLargeObjectInPackException extends TransportException {
 	}
 
 	/**
+	 * Constructor for TooLargeObjectInPackException
+	 *
 	 * @param msg
 	 *            message describing the transport exception.
 	 * @param cause

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/TooLargePackException.java

@@ -46,6 +46,8 @@ public class TooLargePackException extends TransportException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for TooLargePackException
+	 *
 	 * @param msg
 	 *            message describing the transport failure.
 	 */
@@ -54,6 +56,8 @@ public class TooLargePackException extends TransportException {
 	}
 
 	/**
+	 * Constructor for TooLargePackException
+	 *
 	 * @param msg
 	 *            message describing the transport exception.
 	 * @param cause

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/TransportException.java

@@ -44,6 +44,8 @@ public class TransportException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for TransportException
+	 *
 	 * @param msg
 	 *            message describing the transport failure.
 	 */
@@ -52,6 +54,8 @@ public class TransportException extends GitAPIException {
 	}
 
 	/**
+	 * Constructor for TransportException
+	 *
 	 * @param msg
 	 *            message describing the transport exception.
 	 * @param cause

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/UnmergedPathsException.java

@@ -63,8 +63,12 @@ public class UnmergedPathsException extends GitAPIException {
 	}
 
 	/**
+	 * Constructor for UnmergedPathsException
+	 *
 	 * @param message
+	 *            the message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 * @since 4.1
 	 */
 	public UnmergedPathsException(String message, Throwable cause) {

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/WrongRepositoryStateException.java

@@ -46,15 +46,22 @@ public class WrongRepositoryStateException extends GitAPIException {
 	private static final long serialVersionUID = 1L;
 
 	/**
+	 * Constructor for WrongRepositoryStateException.
+	 *
 	 * @param message
+	 *            error message
 	 * @param cause
+	 *            a {@link java.lang.Throwable}
 	 */
 	public WrongRepositoryStateException(String message, Throwable cause) {
 		super(message, cause);
 	}
 
 	/**
+	 * Constructor for WrongRepositoryStateException.
+	 *
 	 * @param message
+	 *            error message
 	 */
 	public WrongRepositoryStateException(String message) {
 		super(message);