Fix javadoc org.eclipse.jgit diff package

Change-Id: I7162d72916abc8533ad37e8b17335ff4a70d6519
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

22 files changed, 333 insertions, 160 deletions

diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/ContentSource.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/ContentSource.java
index 444ab1cb83..5ede3ea6d4 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/ContentSource.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/ContentSource.java
@@ -55,13 +55,13 @@ import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectLoader;
 import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.ObjectStream;
-import org.eclipse.jgit.treewalk.FileTreeIterator;
 import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.jgit.treewalk.WorkingTreeIterator;
 import org.eclipse.jgit.treewalk.filter.PathFilter;
 
 /**
- * Supplies the content of a file for {@link DiffFormatter}.
+ * Supplies the content of a file for
+ * {@link org.eclipse.jgit.diff.DiffFormatter}.
  * <p>
  * A content source is not thread-safe. Sources may contain state, including
  * information about the last ObjectLoader they returned. Callers must be
@@ -83,8 +83,9 @@ public abstract class ContentSource {
 	/**
 	 * Construct a content source for a working directory.
 	 *
-	 * If the iterator is a {@link FileTreeIterator} an optimized version is
-	 * used that doesn't require seeking through a TreeWalk.
+	 * If the iterator is a {@link org.eclipse.jgit.treewalk.FileTreeIterator}
+	 * an optimized version is used that doesn't require seeking through a
+	 * TreeWalk.
 	 *
 	 * @param iterator
 	 *            the iterator to obtain source files through.
@@ -102,7 +103,7 @@ public abstract class ContentSource {
 	 * @param id
 	 *            blob id of the file, if known.
 	 * @return the size in bytes.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the file cannot be accessed.
 	 */
 	public abstract long size(String path, ObjectId id) throws IOException;
@@ -117,7 +118,7 @@ public abstract class ContentSource {
 	 * @return a loader that can supply the content of the file. The loader must
 	 *         be used before another loader can be obtained from this same
 	 *         source.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the file cannot be accessed.
 	 */
 	public abstract ObjectLoader open(String path, ObjectId id)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffAlgorithm.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffAlgorithm.java
index 5f01366c47..19eb39d93c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffAlgorithm.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffAlgorithm.java
@@ -44,7 +44,8 @@
 package org.eclipse.jgit.diff;
 
 /**
- * Compares two {@link Sequence}s to create an {@link EditList} of changes.
+ * Compares two {@link org.eclipse.jgit.diff.Sequence}s to create an
+ * {@link org.eclipse.jgit.diff.EditList} of changes.
  * <p>
  * An algorithm's {@code diff} method must be callable from concurrent threads
  * without data collisions. This permits some algorithms to use a singleton
@@ -69,6 +70,8 @@ public abstract class DiffAlgorithm {
 	}
 
 	/**
+	 * Get diff algorithm
+	 *
 	 * @param alg
 	 *            the diff algorithm for which an implementation should be
 	 *            returned
@@ -88,18 +91,18 @@ public abstract class DiffAlgorithm {
 	/**
 	 * Compare two sequences and identify a list of edits between them.
 	 *
-	 * @param <S>
-	 *            type of sequence being compared.
 	 * @param cmp
 	 *            the comparator supplying the element equivalence function.
 	 * @param a
 	 *            the first (also known as old or pre-image) sequence. Edits
 	 *            returned by this algorithm will reference indexes using the
-	 *            'A' side: {@link Edit#getBeginA()}, {@link Edit#getEndA()}.
+	 *            'A' side: {@link org.eclipse.jgit.diff.Edit#getBeginA()},
+	 *            {@link org.eclipse.jgit.diff.Edit#getEndA()}.
 	 * @param b
 	 *            the second (also known as new or post-image) sequence. Edits
 	 *            returned by this algorithm will reference indexes using the
-	 *            'B' side: {@link Edit#getBeginB()}, {@link Edit#getEndB()}.
+	 *            'B' side: {@link org.eclipse.jgit.diff.Edit#getBeginB()},
+	 *            {@link org.eclipse.jgit.diff.Edit#getEndB()}.
 	 * @return a modifiable edit list comparing the two sequences. If empty, the
 	 *         sequences are identical according to {@code cmp}'s rules. The
 	 *         result list is never null.
@@ -244,20 +247,21 @@ public abstract class DiffAlgorithm {
 	 * proven to have no common starting or ending elements. The expected
 	 * elimination of common starting and ending elements is automatically
 	 * performed by the {@link #diff(SequenceComparator, Sequence, Sequence)}
-	 * method, which invokes this method using {@link Subsequence}s.
+	 * method, which invokes this method using
+	 * {@link org.eclipse.jgit.diff.Subsequence}s.
 	 *
-	 * @param <S>
-	 *            type of sequence being compared.
 	 * @param cmp
 	 *            the comparator supplying the element equivalence function.
 	 * @param a
 	 *            the first (also known as old or pre-image) sequence. Edits
 	 *            returned by this algorithm will reference indexes using the
-	 *            'A' side: {@link Edit#getBeginA()}, {@link Edit#getEndA()}.
+	 *            'A' side: {@link org.eclipse.jgit.diff.Edit#getBeginA()},
+	 *            {@link org.eclipse.jgit.diff.Edit#getEndA()}.
 	 * @param b
 	 *            the second (also known as new or post-image) sequence. Edits
 	 *            returned by this algorithm will reference indexes using the
-	 *            'B' side: {@link Edit#getBeginB()}, {@link Edit#getEndB()}.
+	 *            'B' side: {@link org.eclipse.jgit.diff.Edit#getBeginB()},
+	 *            {@link org.eclipse.jgit.diff.Edit#getEndB()}.
 	 * @return a modifiable edit list comparing the two sequences.
 	 */
 	public abstract <S extends Sequence> EditList diffNonCommon(
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffConfig.java
index ee709495e5..063cefffa6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffConfig.java
@@ -51,7 +51,9 @@ import org.eclipse.jgit.lib.Config.SectionParser;
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.util.StringUtils;
 
-/** Keeps track of diff related configuration options. */
+/**
+ * Keeps track of diff related configuration options.
+ */
 public class DiffConfig {
 	/** Key for {@link Config#get(SectionParser)}. */
 	public static final Config.SectionParser<DiffConfig> KEY = DiffConfig::new;
@@ -83,22 +85,38 @@ public class DiffConfig {
 				ConfigConstants.CONFIG_KEY_RENAMELIMIT, 200);
 	}
 
-	/** @return true if the prefix "a/" and "b/" should be suppressed. */
+	/**
+	 * If prefix should be suppressed
+	 *
+	 * @return true if the prefix "a/" and "b/" should be suppressed
+	 */
 	public boolean isNoPrefix() {
 		return noPrefix;
 	}
 
-	/** @return true if rename detection is enabled by default. */
+	/**
+	 * If rename detection is enabled
+	 *
+	 * @return true if rename detection is enabled by default
+	 */
 	public boolean isRenameDetectionEnabled() {
 		return renameDetectionType != RenameDetectionType.FALSE;
 	}
 
-	/** @return type of rename detection to perform. */
+	/**
+	 * Get the rename detection type
+	 *
+	 * @return type of rename detection to perform
+	 */
 	public RenameDetectionType getRenameDetectionType() {
 		return renameDetectionType;
 	}
 
-	/** @return limit on number of paths to perform inexact rename detection. */
+	/**
+	 * Get the rename limit
+	 *
+	 * @return limit on number of paths to perform inexact rename detection
+	 */
 	public int getRenameLimit() {
 		return renameLimit;
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffEntry.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffEntry.java
index 5eb1942629..0f5ea76519 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffEntry.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffEntry.java
@@ -58,7 +58,9 @@ import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.jgit.treewalk.filter.TreeFilter;
 import org.eclipse.jgit.treewalk.filter.TreeFilterMarker;
 
-/** A value class representing a change to a file */
+/**
+ * A value class representing a change to a file
+ */
 public class DiffEntry {
 	/** Magical SHA1 used for file adds or deletes */
 	static final AbbreviatedObjectId A_ZERO = AbbreviatedObjectId
@@ -107,9 +109,9 @@ public class DiffEntry {
 	 * @param walk
 	 *            the TreeWalk to walk through. Must have exactly two trees.
 	 * @return headers describing the changed files.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository cannot be accessed.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             When given TreeWalk doesn't have exactly two trees.
 	 */
 	public static List<DiffEntry> scan(TreeWalk walk) throws IOException {
@@ -127,9 +129,9 @@ public class DiffEntry {
 	 * @param includeTrees
 	 *            include tree objects.
 	 * @return headers describing the changed files.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository cannot be accessed.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             when {@code includeTrees} is true and given TreeWalk is
 	 *             recursive. Or when given TreeWalk doesn't have exactly two
 	 *             trees
@@ -155,9 +157,9 @@ public class DiffEntry {
 	 *            queried through {{@link #isMarked(int)} (with the index from
 	 *            this passed array).
 	 * @return headers describing the changed files.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the repository cannot be accessed.
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             when {@code includeTrees} is true and given TreeWalk is
 	 *             recursive. Or when given TreeWalk doesn't have exactly two
 	 *             trees
@@ -392,12 +394,20 @@ public class DiffEntry {
 		return side == Side.OLD ? getOldPath() : getNewPath();
 	}
 
-	/** @return the old file mode, if described in the patch */
+	/**
+	 * Get the old file mode
+	 *
+	 * @return the old file mode, if described in the patch
+	 */
 	public FileMode getOldMode() {
 		return oldMode;
 	}
 
-	/** @return the new file mode, if described in the patch */
+	/**
+	 * Get the new file mode
+	 *
+	 * @return the new file mode, if described in the patch
+	 */
 	public FileMode getNewMode() {
 		return newMode;
 	}
@@ -413,15 +423,22 @@ public class DiffEntry {
 		return side == Side.OLD ? getOldMode() : getNewMode();
 	}
 
-	/** @return the type of change this patch makes on {@link #getNewPath()} */
+	/**
+	 * Get the change type
+	 *
+	 * @return the type of change this patch makes on {@link #getNewPath()}
+	 */
 	public ChangeType getChangeType() {
 		return changeType;
 	}
 
 	/**
+	 * Get similarity score
+	 *
 	 * @return similarity score between {@link #getOldPath()} and
 	 *         {@link #getNewPath()} if {@link #getChangeType()} is
-	 *         {@link ChangeType#COPY} or {@link ChangeType#RENAME}.
+	 *         {@link org.eclipse.jgit.diff.DiffEntry.ChangeType#COPY} or
+	 *         {@link org.eclipse.jgit.diff.DiffEntry.ChangeType#RENAME}.
 	 */
 	public int getScore() {
 		return score;
@@ -466,10 +483,9 @@ public class DiffEntry {
 	 *
 	 * @param index
 	 *            the index of the tree filter to check for (must be between 0
-	 *            and {@link Integer#SIZE}).
-	 *
-	 * @return true, if the tree filter matched; false if not
+	 *            and {@link java.lang.Integer#SIZE}).
 	 * @since 2.3
+	 * @return a boolean.
 	 */
 	public boolean isMarked(int index) {
 		return (treeFilterMarks & (1L << index)) != 0;
@@ -498,6 +514,7 @@ public class DiffEntry {
 		return side == Side.OLD ? getOldId() : getNewId();
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffFormatter.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffFormatter.java
index 22366a6bd2..bf9a27bdc9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffFormatter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffFormatter.java
@@ -84,7 +84,6 @@ import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.patch.FileHeader;
 import org.eclipse.jgit.patch.FileHeader.PatchType;
-import org.eclipse.jgit.patch.HunkHeader;
 import org.eclipse.jgit.revwalk.FollowFilter;
 import org.eclipse.jgit.revwalk.RevTree;
 import org.eclipse.jgit.revwalk.RevWalk;
@@ -100,7 +99,6 @@ import org.eclipse.jgit.treewalk.filter.NotIgnoredFilter;
 import org.eclipse.jgit.treewalk.filter.PathFilter;
 import org.eclipse.jgit.treewalk.filter.TreeFilter;
 import org.eclipse.jgit.util.QuotedString;
-import org.eclipse.jgit.util.io.DisabledOutputStream;
 
 /**
  * Format a Git style patch script.
@@ -155,7 +153,11 @@ public class DiffFormatter implements AutoCloseable {
 		this.out = out;
 	}
 
-	/** @return the stream we are outputting data to. */
+	/**
+	 * Get output stream
+	 *
+	 * @return the stream we are outputting data to
+	 */
 	protected OutputStream getOutputStream() {
 		return out;
 	}
@@ -324,7 +326,11 @@ public class DiffFormatter implements AutoCloseable {
 		return this.newPrefix;
 	}
 
-	/** @return true if rename detection is enabled. */
+	/**
+	 * Get if rename detection is enabled
+	 *
+	 * @return true if rename detection is enabled
+	 */
 	public boolean isDetectRenames() {
 		return renameDetector != null;
 	}
@@ -348,7 +354,11 @@ public class DiffFormatter implements AutoCloseable {
 			renameDetector = null;
 	}
 
-	/** @return the rename detector if rename detection is enabled. */
+	/**
+	 * Get rename detector
+	 *
+	 * @return the rename detector if rename detection is enabled
+	 */
 	public RenameDetector getRenameDetector() {
 		return renameDetector;
 	}
@@ -366,9 +376,10 @@ public class DiffFormatter implements AutoCloseable {
 	/**
 	 * Set the filter to produce only specific paths.
 	 *
-	 * If the filter is an instance of {@link FollowFilter}, the filter path
-	 * will be updated during successive scan or format invocations. The updated
-	 * path can be obtained from {@link #getPathFilter()}.
+	 * If the filter is an instance of
+	 * {@link org.eclipse.jgit.revwalk.FollowFilter}, the filter path will be
+	 * updated during successive scan or format invocations. The updated path
+	 * can be obtained from {@link #getPathFilter()}.
 	 *
 	 * @param filter
 	 *            the tree filter to apply.
@@ -377,7 +388,11 @@ public class DiffFormatter implements AutoCloseable {
 		pathFilter = filter != null ? filter : TreeFilter.ALL;
 	}
 
-	/** @return the current path filter. */
+	/**
+	 * Get path filter
+	 *
+	 * @return the current path filter
+	 */
 	public TreeFilter getPathFilter() {
 		return pathFilter;
 	}
@@ -385,7 +400,7 @@ public class DiffFormatter implements AutoCloseable {
 	/**
 	 * Flush the underlying output stream of this formatter.
 	 *
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream's own flush method threw an exception.
 	 */
 	public void flush() throws IOException {
@@ -393,6 +408,8 @@ public class DiffFormatter implements AutoCloseable {
 	}
 
 	/**
+	 * {@inheritDoc}
+	 * <p>
 	 * Release the internal ObjectReader state.
 	 *
 	 * @since 4.0
@@ -409,8 +426,8 @@ public class DiffFormatter implements AutoCloseable {
 	 *
 	 * No output is created, instead only the file paths that are different are
 	 * returned. Callers may choose to format these paths themselves, or convert
-	 * them into {@link FileHeader} instances with a complete edit list by
-	 * calling {@link #toFileHeader(DiffEntry)}.
+	 * them into {@link org.eclipse.jgit.patch.FileHeader} instances with a
+	 * complete edit list by calling {@link #toFileHeader(DiffEntry)}.
 	 * <p>
 	 * Either side may be null to indicate that the tree has beed added or
 	 * removed. The diff will be computed against nothing.
@@ -420,7 +437,7 @@ public class DiffFormatter implements AutoCloseable {
 	 * @param b
 	 *            the new (or updated) side or null
 	 * @return the paths that are different.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             trees cannot be read or file contents cannot be read.
 	 */
 	public List<DiffEntry> scan(AnyObjectId a, AnyObjectId b)
@@ -439,8 +456,8 @@ public class DiffFormatter implements AutoCloseable {
 	 *
 	 * No output is created, instead only the file paths that are different are
 	 * returned. Callers may choose to format these paths themselves, or convert
-	 * them into {@link FileHeader} instances with a complete edit list by
-	 * calling {@link #toFileHeader(DiffEntry)}.
+	 * them into {@link org.eclipse.jgit.patch.FileHeader} instances with a
+	 * complete edit list by calling {@link #toFileHeader(DiffEntry)}.
 	 * <p>
 	 * Either side may be null to indicate that the tree has beed added or
 	 * removed. The diff will be computed against nothing.
@@ -450,7 +467,7 @@ public class DiffFormatter implements AutoCloseable {
 	 * @param b
 	 *            the new (or updated) side or null
 	 * @return the paths that are different.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             trees cannot be read or file contents cannot be read.
 	 */
 	public List<DiffEntry> scan(RevTree a, RevTree b) throws IOException {
@@ -476,15 +493,15 @@ public class DiffFormatter implements AutoCloseable {
 	 *
 	 * No output is created, instead only the file paths that are different are
 	 * returned. Callers may choose to format these paths themselves, or convert
-	 * them into {@link FileHeader} instances with a complete edit list by
-	 * calling {@link #toFileHeader(DiffEntry)}.
+	 * them into {@link org.eclipse.jgit.patch.FileHeader} instances with a
+	 * complete edit list by calling {@link #toFileHeader(DiffEntry)}.
 	 *
 	 * @param a
 	 *            the old (or previous) side.
 	 * @param b
 	 *            the new (or updated) side.
 	 * @return the paths that are different.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             trees cannot be read or file contents cannot be read.
 	 */
 	public List<DiffEntry> scan(AbstractTreeIterator a, AbstractTreeIterator b)
@@ -596,7 +613,7 @@ public class DiffFormatter implements AutoCloseable {
 	 *            the old (or previous) side or null
 	 * @param b
 	 *            the new (or updated) side or null
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             trees cannot be read, file contents cannot be read, or the
 	 *             patch cannot be output.
 	 */
@@ -618,7 +635,7 @@ public class DiffFormatter implements AutoCloseable {
 	 *            the old (or previous) side or null
 	 * @param b
 	 *            the new (or updated) side or null
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             trees cannot be read, file contents cannot be read, or the
 	 *             patch cannot be output.
 	 */
@@ -639,7 +656,7 @@ public class DiffFormatter implements AutoCloseable {
 	 *            the old (or previous) side or null
 	 * @param b
 	 *            the new (or updated) side or null
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             trees cannot be read, file contents cannot be read, or the
 	 *             patch cannot be output.
 	 */
@@ -655,7 +672,7 @@ public class DiffFormatter implements AutoCloseable {
 	 *
 	 * @param entries
 	 *            entries describing the affected files.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             a file's content cannot be read, or the output stream cannot
 	 *             be written to.
 	 */
@@ -669,7 +686,7 @@ public class DiffFormatter implements AutoCloseable {
 	 *
 	 * @param ent
 	 *            the entry to be formatted.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             a file's content cannot be read, or the output stream cannot
 	 *             be written to.
 	 */
@@ -712,11 +729,13 @@ public class DiffFormatter implements AutoCloseable {
 	 *            existing file header containing the header lines to copy.
 	 * @param a
 	 *            text source for the pre-image version of the content. This
-	 *            must match the content of {@link FileHeader#getOldId()}.
+	 *            must match the content of
+	 *            {@link org.eclipse.jgit.patch.FileHeader#getOldId()}.
 	 * @param b
 	 *            text source for the post-image version of the content. This
-	 *            must match the content of {@link FileHeader#getNewId()}.
-	 * @throws IOException
+	 *            must match the content of
+	 *            {@link org.eclipse.jgit.patch.FileHeader#getNewId()}.
+	 * @throws java.io.IOException
 	 *             writing to the supplied stream failed.
 	 */
 	public void format(final FileHeader head, final RawText a, final RawText b)
@@ -743,7 +762,7 @@ public class DiffFormatter implements AutoCloseable {
 	 *            the text A which was compared
 	 * @param b
 	 *            the text B which was compared
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	public void format(final EditList edits, final RawText a, final RawText b)
 			throws IOException {
@@ -791,7 +810,7 @@ public class DiffFormatter implements AutoCloseable {
 	 *            RawText for accessing raw data
 	 * @param line
 	 *            the line number within text
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	protected void writeContextLine(final RawText text, final int line)
 			throws IOException {
@@ -809,7 +828,7 @@ public class DiffFormatter implements AutoCloseable {
 	 *            RawText for accessing raw data
 	 * @param line
 	 *            the line number within text
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	protected void writeAddedLine(final RawText text, final int line)
 			throws IOException {
@@ -823,7 +842,7 @@ public class DiffFormatter implements AutoCloseable {
 	 *            RawText for accessing raw data
 	 * @param line
 	 *            the line number within text
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	protected void writeRemovedLine(final RawText text, final int line)
 			throws IOException {
@@ -841,7 +860,7 @@ public class DiffFormatter implements AutoCloseable {
 	 *            within second source
 	 * @param bEndLine
 	 *            within second source
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 */
 	protected void writeHunkHeader(int aStartLine, int aEndLine,
 			int bStartLine, int bEndLine) throws IOException {
@@ -894,7 +913,7 @@ public class DiffFormatter implements AutoCloseable {
 	 *            the text object to obtain the line from.
 	 * @param cur
 	 *            line number to output.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream threw an exception while writing to it.
 	 */
 	protected void writeLine(final char prefix, final RawText text,
@@ -905,24 +924,26 @@ public class DiffFormatter implements AutoCloseable {
 	}
 
 	/**
-	 * Creates a {@link FileHeader} representing the given {@link DiffEntry}
+	 * Creates a {@link org.eclipse.jgit.patch.FileHeader} representing the
+	 * given {@link org.eclipse.jgit.diff.DiffEntry}
 	 * <p>
 	 * This method does not use the OutputStream associated with this
 	 * DiffFormatter instance. It is therefore safe to instantiate this
-	 * DiffFormatter instance with a {@link DisabledOutputStream} if this method
-	 * is the only one that will be used.
+	 * DiffFormatter instance with a
+	 * {@link org.eclipse.jgit.util.io.DisabledOutputStream} if this method is
+	 * the only one that will be used.
 	 *
 	 * @param ent
 	 *            the DiffEntry to create the FileHeader for
 	 * @return a FileHeader representing the DiffEntry. The FileHeader's buffer
 	 *         will contain only the header of the diff output. It will also
-	 *         contain one {@link HunkHeader}.
-	 * @throws IOException
+	 *         contain one {@link org.eclipse.jgit.patch.HunkHeader}.
+	 * @throws java.io.IOException
 	 *             the stream threw an exception while writing to it, or one of
 	 *             the blobs referenced by the DiffEntry could not be read.
-	 * @throws CorruptObjectException
+	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 *             one of the blobs referenced by the DiffEntry is corrupt.
-	 * @throws MissingObjectException
+	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 *             one of the blobs referenced by the DiffEntry is missing.
 	 */
 	public FileHeader toFileHeader(DiffEntry ent) throws IOException,
@@ -1046,12 +1067,12 @@ public class DiffFormatter implements AutoCloseable {
 	 * @param o
 	 *            The stream the formatter will write the first header line to
 	 * @param type
-	 *            The {@link ChangeType}
+	 *            The {@link org.eclipse.jgit.diff.DiffEntry.ChangeType}
 	 * @param oldPath
 	 *            old path to the file
 	 * @param newPath
 	 *            new path to the file
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream threw an exception while writing to it.
 	 */
 	protected void formatGitDiffFirstHeaderLine(ByteArrayOutputStream o,
@@ -1136,11 +1157,13 @@ public class DiffFormatter implements AutoCloseable {
 	}
 
 	/**
+	 * Format index line
+	 *
 	 * @param o
 	 *            the stream the formatter will write line data to
 	 * @param ent
 	 *            the DiffEntry to create the FileHeader for
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             writing to the supplied stream failed.
 	 */
 	protected void formatIndexLine(OutputStream o, DiffEntry ent)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/Edit.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/Edit.java
index a2e167fd20..775d11a46b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/Edit.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/Edit.java
@@ -118,7 +118,11 @@ public class Edit {
 		endB = be;
 	}
 
-	/** @return the type of this region */
+	/**
+	 * Get type
+	 *
+	 * @return the type of this region
+	 */
 	public final Type getType() {
 		if (beginA < endA) {
 			if (beginB < endB)
@@ -134,37 +138,66 @@ public class Edit {
 		}
 	}
 
-	/** @return true if the edit is empty (lengths of both a and b is zero). */
+	/**
+	 * Whether edit is empty
+	 *
+	 * @return {@code true} if the edit is empty (lengths of both a and b is
+	 *         zero)
+	 */
 	public final boolean isEmpty() {
 		return beginA == endA && beginB == endB;
 	}
 
-	/** @return start point in sequence A. */
+	/**
+	 * Get start point in sequence A
+	 *
+	 * @return start point in sequence A
+	 */
 	public final int getBeginA() {
 		return beginA;
 	}
 
-	/** @return end point in sequence A. */
+	/**
+	 * Get end point in sequence A
+	 *
+	 * @return end point in sequence A
+	 */
 	public final int getEndA() {
 		return endA;
 	}
 
-	/** @return start point in sequence B. */
+	/**
+	 * Get start point in sequence B
+	 *
+	 * @return start point in sequence B
+	 */
 	public final int getBeginB() {
 		return beginB;
 	}
 
-	/** @return end point in sequence B. */
+	/**
+	 * Get end point in sequence B
+	 *
+	 * @return end point in sequence B
+	 */
 	public final int getEndB() {
 		return endB;
 	}
 
-	/** @return length of the region in A. */
+	/**
+	 * Get length of the region in A
+	 *
+	 * @return length of the region in A
+	 */
 	public final int getLengthA() {
 		return endA - beginA;
 	}
 
-	/** @return length of the region in B. */
+	/**
+	 * Get length of the region in B
+	 *
+	 * @return return length of the region in B
+	 */
 	public final int getLengthB() {
 		return endB - beginB;
 	}
@@ -210,17 +243,23 @@ public class Edit {
 		return new Edit(cut.endA, endA, cut.endB, endB);
 	}
 
-	/** Increase {@link #getEndA()} by 1. */
+	/**
+	 * Increase {@link #getEndA()} by 1.
+	 */
 	public void extendA() {
 		endA++;
 	}
 
-	/** Increase {@link #getEndB()} by 1. */
+	/**
+	 * Increase {@link #getEndB()} by 1.
+	 */
 	public void extendB() {
 		endB++;
 	}
 
-	/** Swap A and B, so the edit goes the other direction. */
+	/**
+	 * Swap A and B, so the edit goes the other direction.
+	 */
 	public void swap() {
 		final int sBegin = beginA;
 		final int sEnd = endA;
@@ -232,11 +271,13 @@ public class Edit {
 		endB = sEnd;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int hashCode() {
 		return beginA ^ endA;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean equals(final Object o) {
 		if (o instanceof Edit) {
@@ -247,6 +288,7 @@ public class Edit {
 		return false;
 	}
 
+	/** {@inheritDoc} */
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/EditList.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/EditList.java
index 14f7b4293f..617e0d860f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/EditList.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/EditList.java
@@ -45,7 +45,9 @@ package org.eclipse.jgit.diff;
 
 import java.util.ArrayList;
 
-/** Specialized list of {@link Edit}s in a document. */
+/**
+ * Specialized list of {@link org.eclipse.jgit.diff.Edit}s in a document.
+ */
 public class EditList extends ArrayList<Edit> {
 	private static final long serialVersionUID = 1L;
 
@@ -62,7 +64,9 @@ public class EditList extends ArrayList<Edit> {
 		return res;
 	}
 
-	/** Create a new, empty edit list. */
+	/**
+	 * Create a new, empty edit list.
+	 */
 	public EditList() {
 		super(16);
 	}
@@ -78,6 +82,7 @@ public class EditList extends ArrayList<Edit> {
 		super(capacity);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public String toString() {
 		return "EditList" + super.toString(); //$NON-NLS-1$
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequence.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequence.java
index cb1def620f..04921200c2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequence.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequence.java
@@ -44,13 +44,15 @@
 package org.eclipse.jgit.diff;
 
 /**
- * Wraps a {@link Sequence} to assign hash codes to elements.
+ * Wraps a {@link org.eclipse.jgit.diff.Sequence} to assign hash codes to
+ * elements.
  * <p>
  * This sequence acts as a proxy for the real sequence, caching element hash
  * codes so they don't need to be recomputed each time. Sequences of this type
- * must be used with a {@link HashedSequenceComparator}.
+ * must be used with a {@link org.eclipse.jgit.diff.HashedSequenceComparator}.
  * <p>
- * To construct an instance of this type use {@link HashedSequencePair}.
+ * To construct an instance of this type use
+ * {@link org.eclipse.jgit.diff.HashedSequencePair}.
  *
  * @param <S>
  *            the base sequence type.
@@ -65,6 +67,7 @@ public final class HashedSequence<S extends Sequence> extends Sequence {
 		this.hashes = hashes;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int size() {
 		return base.size();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequenceComparator.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequenceComparator.java
index 1ca7fdd9d4..bd9618e0bf 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequenceComparator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequenceComparator.java
@@ -44,13 +44,16 @@
 package org.eclipse.jgit.diff;
 
 /**
- * Wrap another comparator for use with {@link HashedSequence}.
+ * Wrap another comparator for use with
+ * {@link org.eclipse.jgit.diff.HashedSequence}.
  * <p>
  * This comparator acts as a proxy for the real comparator, evaluating the
  * cached hash code before testing the underlying comparator's equality.
- * Comparators of this type must be used with a {@link HashedSequence}.
+ * Comparators of this type must be used with a
+ * {@link org.eclipse.jgit.diff.HashedSequence}.
  * <p>
- * To construct an instance of this type use {@link HashedSequencePair}.
+ * To construct an instance of this type use
+ * {@link org.eclipse.jgit.diff.HashedSequencePair}.
  *
  * @param <S>
  *            the base sequence type.
@@ -63,6 +66,7 @@ public final class HashedSequenceComparator<S extends Sequence> extends
 		this.cmp = cmp;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean equals(HashedSequence<S> a, int ai, //
 			HashedSequence<S> b, int bi) {
@@ -70,6 +74,7 @@ public final class HashedSequenceComparator<S extends Sequence> extends
 				&& cmp.equals(a.base, ai, b.base, bi);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int hash(HashedSequence<S> seq, int ptr) {
 		return seq.hashes[ptr];
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequencePair.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequencePair.java
index bf6d967c50..8d120155ac 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequencePair.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/HashedSequencePair.java
@@ -44,7 +44,8 @@
 package org.eclipse.jgit.diff;
 
 /**
- * Wraps two {@link Sequence} instances to cache their element hash codes.
+ * Wraps two {@link org.eclipse.jgit.diff.Sequence} instances to cache their
+ * element hash codes.
  * <p>
  * This pair wraps two sequences that contain cached hash codes for the input
  * sequences.
@@ -79,19 +80,31 @@ public class HashedSequencePair<S extends Sequence> {
 		this.baseB = b;
 	}
 
-	/** @return obtain a comparator that uses the cached hash codes. */
+	/**
+	 * Get comparator
+	 *
+	 * @return obtain a comparator that uses the cached hash codes
+	 */
 	public HashedSequenceComparator<S> getComparator() {
 		return new HashedSequenceComparator<>(cmp);
 	}
 
-	/** @return wrapper around A that includes cached hash codes. */
+	/**
+	 * Get A
+	 *
+	 * @return wrapper around A that includes cached hash codes
+	 */
 	public HashedSequence<S> getA() {
 		if (cachedA == null)
 			cachedA = wrap(baseA);
 		return cachedA;
 	}
 
-	/** @return wrapper around B that includes cached hash codes. */
+	/**
+	 * Get B
+	 *
+	 * @return wrapper around B that includes cached hash codes
+	 */
 	public HashedSequence<S> getB() {
 		if (cachedB == null)
 			cachedB = wrap(baseB);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/HistogramDiff.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/HistogramDiff.java
index 4ef58455a7..c1c6e9a6eb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/HistogramDiff.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/HistogramDiff.java
@@ -85,8 +85,9 @@ import java.util.List;
  * So long as {@link #setMaxChainLength(int)} is a small constant (such as 64),
  * the algorithm runs in O(N * D) time, where N is the sum of the input lengths
  * and D is the number of edits in the resulting EditList. If the supplied
- * {@link SequenceComparator} has a good hash function, this implementation
- * typically out-performs {@link MyersDiff}, even though its theoretical running
+ * {@link org.eclipse.jgit.diff.SequenceComparator} has a good hash function,
+ * this implementation typically out-performs
+ * {@link org.eclipse.jgit.diff.MyersDiff}, even though its theoretical running
  * time is the same.
  * <p>
  * This implementation has an internal limitation that prevents it from handling
@@ -130,6 +131,7 @@ public class HistogramDiff extends LowLevelDiffAlgorithm {
 		maxChainLength = maxLen;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public <S extends Sequence> void diffNonCommon(EditList edits,
 			HashedSequenceComparator<S> cmp, HashedSequence<S> a,
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/LowLevelDiffAlgorithm.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/LowLevelDiffAlgorithm.java
index 55ceec8012..9e5ff25558 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/LowLevelDiffAlgorithm.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/LowLevelDiffAlgorithm.java
@@ -43,8 +43,11 @@
 
 package org.eclipse.jgit.diff;
 
-/** Compares two sequences primarily based upon hash codes. */
+/**
+ * Compares two sequences primarily based upon hash codes.
+ */
 public abstract class LowLevelDiffAlgorithm extends DiffAlgorithm {
+	/** {@inheritDoc} */
 	@Override
 	public <S extends Sequence> EditList diffNonCommon(
 			SequenceComparator<? super S> cmp, S a, S b) {
@@ -67,10 +70,9 @@ public abstract class LowLevelDiffAlgorithm extends DiffAlgorithm {
 	 * proven to have no common starting or ending elements. The expected
 	 * elimination of common starting and ending elements is automatically
 	 * performed by the {@link #diff(SequenceComparator, Sequence, Sequence)}
-	 * method, which invokes this method using {@link Subsequence}s.
+	 * method, which invokes this method using
+	 * {@link org.eclipse.jgit.diff.Subsequence}s.
 	 *
-	 * @param <S>
-	 *            type of sequence being compared.
 	 * @param edits
 	 *            result list to append the region's edits onto.
 	 * @param cmp
@@ -78,11 +80,13 @@ public abstract class LowLevelDiffAlgorithm extends DiffAlgorithm {
 	 * @param a
 	 *            the first (also known as old or pre-image) sequence. Edits
 	 *            returned by this algorithm will reference indexes using the
-	 *            'A' side: {@link Edit#getBeginA()}, {@link Edit#getEndA()}.
+	 *            'A' side: {@link org.eclipse.jgit.diff.Edit#getBeginA()},
+	 *            {@link org.eclipse.jgit.diff.Edit#getEndA()}.
 	 * @param b
 	 *            the second (also known as new or post-image) sequence. Edits
 	 *            returned by this algorithm will reference indexes using the
-	 *            'B' side: {@link Edit#getBeginB()}, {@link Edit#getEndB()}.
+	 *            'B' side: {@link org.eclipse.jgit.diff.Edit#getBeginB()},
+	 *            {@link org.eclipse.jgit.diff.Edit#getEndB()}.
 	 * @param region
 	 *            the region being compared within the two sequences.
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/MyersDiff.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/MyersDiff.java
index a3860de04c..646f264e09 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/MyersDiff.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/MyersDiff.java
@@ -557,7 +557,10 @@ if (k < beginK || k > endK)
 	}
 
 	/**
-	 * @param args two filenames specifying the contents to be diffed
+	 * Main method
+	 *
+	 * @param args
+	 *            two filenames specifying the contents to be diffed
 	 */
 	public static void main(String[] args) {
 		if (args.length != 2) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/PatchIdDiffFormatter.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/PatchIdDiffFormatter.java
index 146b910401..7f6aa9ab05 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/PatchIdDiffFormatter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/PatchIdDiffFormatter.java
@@ -58,7 +58,9 @@ public class PatchIdDiffFormatter extends DiffFormatter {
 
 	private final MessageDigest digest;
 
-	/** Initialize a formatter to compute a patch id. */
+	/**
+	 * Initialize a formatter to compute a patch id.
+	 */
 	public PatchIdDiffFormatter() {
 		super(new DigestOutputStream(NullOutputStream.INSTANCE,
 				Constants.newMessageDigest()));
@@ -74,12 +76,14 @@ public class PatchIdDiffFormatter extends DiffFormatter {
 		return ObjectId.fromRaw(digest.digest());
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void writeHunkHeader(int aStartLine, int aEndLine,
 			int bStartLine, int bEndLine) throws IOException {
 		// The hunk header is not taken into account for patch id calculation
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	protected void formatIndexLine(OutputStream o, DiffEntry ent)
 			throws IOException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/RawText.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/RawText.java
index 656319dd7c..7be1659105 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/RawText.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/RawText.java
@@ -103,7 +103,7 @@ public class RawText extends Sequence {
 	 *
 	 * @param file
 	 *            the text file.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if Exceptions occur while reading the file
 	 */
 	public RawText(File file) throws IOException {
@@ -111,6 +111,7 @@ public class RawText extends Sequence {
 	}
 
 	/** @return total number of items in the sequence. */
+	/** {@inheritDoc} */
 	@Override
 	public int size() {
 		// The line map is always 2 entries larger than the number of lines in
@@ -135,7 +136,7 @@ public class RawText extends Sequence {
 	 * @param i
 	 *            index of the line to extract. Note this is 0-based, so line
 	 *            number 1 is actually index 0.
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             the stream write operation failed.
 	 */
 	public void writeLine(final OutputStream out, final int i)
@@ -244,7 +245,7 @@ public class RawText extends Sequence {
 	 * @param raw
 	 *            input stream containing the raw file content.
 	 * @return true if raw is likely to be a binary file, false otherwise
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             if input stream could not be read
 	 */
 	public static boolean isBinary(InputStream raw) throws IOException {
@@ -301,17 +302,20 @@ public class RawText extends Sequence {
 	}
 
 	/**
-	 * Read a blob object into RawText, or throw BinaryBlobException if
-	 * the blob is binary.
+	 * Read a blob object into RawText, or throw BinaryBlobException if the blob
+	 * is binary.
 	 *
 	 * @param ldr
-	 *   the ObjectLoader for the blob
+	 *            the ObjectLoader for the blob
 	 * @param threshold
-	 *   if the blob is larger than this size, it is always assumed to be binary.
+	 *            if the blob is larger than this size, it is always assumed to
+	 *            be binary.
 	 * @since 4.10
 	 * @return the RawText representing the blob.
-	 * @throws BinaryBlobException if the blob contains binary data.
-	 * @throws IOException if the input could not be read.
+	 * @throws org.eclipse.jgit.errors.BinaryBlobException
+	 *             if the blob contains binary data.
+	 * @throws java.io.IOException
+	 *             if the input could not be read.
 	 */
 	public static RawText load(ObjectLoader ldr, int threshold) throws IOException, BinaryBlobException {
 		long sz = ldr.getSize();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/RawTextComparator.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/RawTextComparator.java
index 2793fa2e8c..ed2eebb858 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/RawTextComparator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/RawTextComparator.java
@@ -50,7 +50,9 @@ import static org.eclipse.jgit.util.RawCharUtil.trimTrailingWhitespace;
 
 import org.eclipse.jgit.util.IntList;
 
-/** Equivalence function for {@link RawText}. */
+/**
+ * Equivalence function for {@link org.eclipse.jgit.diff.RawText}.
+ */
 public abstract class RawTextComparator extends SequenceComparator<RawText> {
 	/** No special treatment. */
 	public static final RawTextComparator DEFAULT = new RawTextComparator() {
@@ -134,7 +136,9 @@ public abstract class RawTextComparator extends SequenceComparator<RawText> {
 		}
 	};
 
-	/** Ignores leading whitespace. */
+	/**
+	 * Ignore leading whitespace.
+	 **/
 	public static final RawTextComparator WS_IGNORE_LEADING = new RawTextComparator() {
 		@Override
 		public boolean equals(RawText a, int ai, RawText b, int bi) {
@@ -262,6 +266,7 @@ public abstract class RawTextComparator extends SequenceComparator<RawText> {
 		return hashRegion(seq.content, begin, end);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public Edit reduceCommonStartEnd(RawText a, RawText b, Edit e) {
 		// This is a faster exact match based form that tries to improve
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/RenameDetector.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/RenameDetector.java
index d899429c3b..7bb217d04d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/RenameDetector.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/RenameDetector.java
@@ -65,7 +65,9 @@ import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.lib.Repository;
 
-/** Detect and resolve object renames. */
+/**
+ * Detect and resolve object renames.
+ */
 public class RenameDetector {
 	private static final int EXACT_RENAME_SCORE = 100;
 
@@ -156,6 +158,8 @@ public class RenameDetector {
 	}
 
 	/**
+	 * Get rename score
+	 *
 	 * @return minimum score required to pair an add/delete as a rename. The
 	 *         score ranges are within the bounds of (0, 100).
 	 */
@@ -173,7 +177,7 @@ public class RenameDetector {
 	 *
 	 * @param score
 	 *            new rename score, must be within [0, 100].
-	 * @throws IllegalArgumentException
+	 * @throws java.lang.IllegalArgumentException
 	 *             the score was not within [0, 100].
 	 */
 	public void setRenameScore(int score) {
@@ -184,6 +188,8 @@ public class RenameDetector {
 	}
 
 	/**
+	 * Get break score
+	 *
 	 * @return the similarity score required to keep modified file pairs
 	 *         together. Any modify pairs that score below this will be broken
 	 *         apart into separate add/deletes. Values less than or equal to
@@ -195,6 +201,8 @@ public class RenameDetector {
 	}
 
 	/**
+	 * Set break score
+	 *
 	 * @param breakScore
 	 *            the similarity score required to keep modified file pairs
 	 *            together. Any modify pairs that score below this will be
@@ -206,7 +214,11 @@ public class RenameDetector {
 		this.breakScore = breakScore;
 	}
 
-	/** @return limit on number of paths to perform inexact rename detection. */
+	/**
+	 * Get rename limit
+	 *
+	 * @return limit on number of paths to perform inexact rename detection
+	 */
 	public int getRenameLimit() {
 		return renameLimit;
 	}
@@ -250,7 +262,7 @@ public class RenameDetector {
 	 *
 	 * @param entriesToAdd
 	 *            one or more entries to add.
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             if {@code getEntries} was already invoked.
 	 */
 	public void addAll(Collection<DiffEntry> entriesToAdd) {
@@ -290,7 +302,7 @@ public class RenameDetector {
 	 *
 	 * @param entry
 	 *            to add.
-	 * @throws IllegalStateException
+	 * @throws java.lang.IllegalStateException
 	 *             if {@code getEntries} was already invoked.
 	 */
 	public void add(DiffEntry entry) {
@@ -302,9 +314,9 @@ public class RenameDetector {
 	 * <p>
 	 * This convenience function runs without a progress monitor.
 	 *
-	 * @return an unmodifiable list of {@link DiffEntry}s representing all files
-	 *         that have been changed.
-	 * @throws IOException
+	 * @return an unmodifiable list of {@link org.eclipse.jgit.diff.DiffEntry}s
+	 *         representing all files that have been changed.
+	 * @throws java.io.IOException
 	 *             file contents cannot be read from the repository.
 	 */
 	public List<DiffEntry> compute() throws IOException {
@@ -316,9 +328,9 @@ public class RenameDetector {
 	 *
 	 * @param pm
 	 *            report progress during the detection phases.
-	 * @return an unmodifiable list of {@link DiffEntry}s representing all files
-	 *         that have been changed.
-	 * @throws IOException
+	 * @return an unmodifiable list of {@link org.eclipse.jgit.diff.DiffEntry}s
+	 *         representing all files that have been changed.
+	 * @throws java.io.IOException
 	 *             file contents cannot be read from the repository.
 	 */
 	public List<DiffEntry> compute(ProgressMonitor pm) throws IOException {
@@ -339,9 +351,9 @@ public class RenameDetector {
 	 *            reader to obtain objects from the repository with.
 	 * @param pm
 	 *            report progress during the detection phases.
-	 * @return an unmodifiable list of {@link DiffEntry}s representing all files
-	 *         that have been changed.
-	 * @throws IOException
+	 * @return an unmodifiable list of {@link org.eclipse.jgit.diff.DiffEntry}s
+	 *         representing all files that have been changed.
+	 * @throws java.io.IOException
 	 *             file contents cannot be read from the repository.
 	 */
 	public List<DiffEntry> compute(ObjectReader reader, ProgressMonitor pm)
@@ -357,9 +369,9 @@ public class RenameDetector {
 	 *            reader to obtain objects from the repository with.
 	 * @param pm
 	 *            report progress during the detection phases.
-	 * @return an unmodifiable list of {@link DiffEntry}s representing all files
-	 *         that have been changed.
-	 * @throws IOException
+	 * @return an unmodifiable list of {@link org.eclipse.jgit.diff.DiffEntry}s
+	 *         representing all files that have been changed.
+	 * @throws java.io.IOException
 	 *             file contents cannot be read from the repository.
 	 */
 	public List<DiffEntry> compute(ContentSource.Pair reader, ProgressMonitor pm)
@@ -393,7 +405,9 @@ public class RenameDetector {
 		return Collections.unmodifiableList(entries);
 	}
 
-	/** Reset this rename detector for another rename detection pass. */
+	/**
+	 * Reset this rename detector for another rename detection pass.
+	 */
 	public void reset() {
 		entries = new ArrayList<>();
 		deleted = new ArrayList<>();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/Sequence.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/Sequence.java
index 53ab2f96ea..c475132c2b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/Sequence.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/Sequence.java
@@ -52,13 +52,19 @@ package org.eclipse.jgit.diff;
  * Unlike a List, the members of the sequence are not directly obtainable.
  * <p>
  * Implementations of Sequence are primarily intended for use in content
- * difference detection algorithms, to produce an {@link EditList} of
- * {@link Edit} instances describing how two Sequence instances differ.
+ * difference detection algorithms, to produce an
+ * {@link org.eclipse.jgit.diff.EditList} of {@link org.eclipse.jgit.diff.Edit}
+ * instances describing how two Sequence instances differ.
  * <p>
  * To be compared against another Sequence of the same type, a supporting
- * {@link SequenceComparator} must also be supplied.
+ * {@link org.eclipse.jgit.diff.SequenceComparator} must also be supplied.
  */
 public abstract class Sequence {
 	/** @return total number of items in the sequence. */
+	/**
+	 * Get size
+	 *
+	 * @return size
+	 */
 	public abstract int size();
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SequenceComparator.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SequenceComparator.java
index cc38d4b5c0..ccd0055585 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SequenceComparator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SequenceComparator.java
@@ -44,7 +44,8 @@
 package org.eclipse.jgit.diff;
 
 /**
- * Equivalence function for a {@link Sequence} compared by difference algorithm.
+ * Equivalence function for a {@link org.eclipse.jgit.diff.Sequence} compared by
+ * difference algorithm.
  * <p>
  * Difference algorithms can use a comparator to compare portions of two
  * sequences and discover the minimal edits required to transform from one
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java
index 1c40d7fcbf..8b4d2ec8fc 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java
@@ -56,8 +56,9 @@ import org.eclipse.jgit.lib.ObjectStream;
  * Index structure of lines/blocks in one file.
  * <p>
  * This structure can be used to compute an approximation of the similarity
- * between two files. The index is used by {@link SimilarityRenameDetector} to
- * compute scores between files.
+ * between two files. The index is used by
+ * {@link org.eclipse.jgit.diff.SimilarityRenameDetector} to compute scores
+ * between files.
  * <p>
  * To save space in memory, this index uses a space efficient encoding which
  * will not exceed 1 MiB per instance. The index starts out at a smaller size
@@ -114,9 +115,9 @@ public class SimilarityIndex {
 	 * @param obj
 	 *            the object to hash
 	 * @return similarity index for this object
-	 * @throws IOException
+	 * @throws java.io.IOException
 	 *             file contents cannot be read from the repository.
-	 * @throws TableFullException
+	 * @throws org.eclipse.jgit.diff.SimilarityIndex.TableFullException
 	 *             object hashing overflowed the storage capacity of the
 	 *             SimilarityIndex.
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/Subsequence.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/Subsequence.java
index 50ca613cca..aa10f6c9ba 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/Subsequence.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/Subsequence.java
@@ -44,11 +44,12 @@
 package org.eclipse.jgit.diff;
 
 /**
- * Wraps a {@link Sequence} to have a narrower range of elements.
+ * Wraps a {@link org.eclipse.jgit.diff.Sequence} to have a narrower range of
+ * elements.
  * <p>
  * This sequence acts as a proxy for the real sequence, translating element
  * indexes on the fly by adding {@code begin} to them. Sequences of this type
- * must be used with a {@link SubsequenceComparator}.
+ * must be used with a {@link org.eclipse.jgit.diff.SubsequenceComparator}.
  *
  * @param <S>
  *            the base sequence type.
@@ -57,8 +58,6 @@ public final class Subsequence<S extends Sequence> extends Sequence {
 	/**
 	 * Construct a subsequence around the A region/base sequence.
 	 *
-	 * @param <S>
-	 *            the base sequence type.
 	 * @param a
 	 *            the A sequence.
 	 * @param region
@@ -72,8 +71,6 @@ public final class Subsequence<S extends Sequence> extends Sequence {
 	/**
 	 * Construct a subsequence around the B region/base sequence.
 	 *
-	 * @param <S>
-	 *            the base sequence type.
 	 * @param b
 	 *            the B sequence.
 	 * @param region
@@ -87,8 +84,6 @@ public final class Subsequence<S extends Sequence> extends Sequence {
 	/**
 	 * Adjust the Edit to reflect positions in the base sequence.
 	 *
-	 * @param <S>
-	 *            the base sequence type.
 	 * @param e
 	 *            edit to adjust in-place. Prior to invocation the indexes are
 	 *            in terms of the two subsequences; after invocation the indexes
@@ -110,8 +105,6 @@ public final class Subsequence<S extends Sequence> extends Sequence {
 	/**
 	 * Adjust the Edits to reflect positions in the base sequence.
 	 *
-	 * @param <S>
-	 *            the base sequence type.
 	 * @param edits
 	 *            edits to adjust in-place. Prior to invocation the indexes are
 	 *            in terms of the two subsequences; after invocation the indexes
@@ -156,6 +149,7 @@ public final class Subsequence<S extends Sequence> extends Sequence {
 		this.size = end - begin;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int size() {
 		return size;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SubsequenceComparator.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SubsequenceComparator.java
index dff2a429e1..9b3889b305 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SubsequenceComparator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SubsequenceComparator.java
@@ -44,11 +44,13 @@
 package org.eclipse.jgit.diff;
 
 /**
- * Wrap another comparator for use with {@link Subsequence}.
+ * Wrap another comparator for use with
+ * {@link org.eclipse.jgit.diff.Subsequence}.
  * <p>
  * This comparator acts as a proxy for the real comparator, translating element
  * indexes on the fly by adding the subsequence's begin offset to them.
- * Comparators of this type must be used with a {@link Subsequence}.
+ * Comparators of this type must be used with a
+ * {@link org.eclipse.jgit.diff.Subsequence}.
  *
  * @param <S>
  *            the base sequence type.
@@ -67,11 +69,13 @@ public final class SubsequenceComparator<S extends Sequence> extends
 		this.cmp = cmp;
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public boolean equals(Subsequence<S> a, int ai, Subsequence<S> b, int bi) {
 		return cmp.equals(a.base, ai + a.begin, b.base, bi + b.begin);
 	}
 
+	/** {@inheritDoc} */
 	@Override
 	public int hash(Subsequence<S> seq, int ptr) {
 		return cmp.hash(seq.base, ptr + seq.begin);