Implement similarity based rename detection

Content similarity based rename detection is performed only after
a linear time detection is performed using exact content match on
the ObjectIds.  Any names which were paired up during that exact
match phase are excluded from the inexact similarity based rename,
which reduces the space that must be considered.

During rename detection two entries cannot be marked as a rename
if they are different types of files.  This prevents a symlink from
being renamed to a regular file, even if their blob content appears
to be similar, or is identical.

Efficiently comparing two files is performed by building up two
hash indexes and hashing lines or short blocks from each file,
counting the number of bytes that each line or block represents.

Instead of using a standard java.util.HashMap, we use a custom
open hashing scheme similiar to what we use in ObjecIdSubclassMap.
This permits us to have a very light-weight hash, with very little
memory overhead per cell stored.

As we only need two ints per record in the map (line/block key and
number of bytes), we collapse them into a single long inside of
a long array, making very efficient use of available memory when
we create the index table.  We only need object headers for the
index structure itself, and the index table, but not per-cell.
This offers a massive space savings over using java.util.HashMap.

The score calculation is done by approximating how many bytes are
the same between the two inputs (which for a delta would be how much
is copied from the base into the result).  The score is derived by
dividing the approximate number of bytes in common into the length
of the larger of the two input files.

Right now the SimilarityIndex table should average about 1/2 full,
which means we waste about 50% of our memory on empty entries
after we are done indexing a file and sort the table's contents.
If memory becomes an issue we could discard the table and copy all
records over to a new array that is properly sized.

Building the index requires O(M + N log N) time, where M is the
size of the input file in bytes, and N is the number of unique
lines/blocks in the file.  The N log N time constraint comes
from the sort of the index table that is necessary to perform
linear time matching against another SimilarityIndex created for
a different file.

To actually perform the rename detection, a SxD matrix is created,
placing the sources (aka deletions) along one dimension and the
destinations (aka additions) along the other.  A simple O(S x D)
loop examines every cell in this matrix.

A SimilarityIndex is built along the row and reused for each
column compare along that row, avoiding the costly index rebuild
at the row level.  A future improvement would be to load a smaller
square matrix into SimilarityIndexes and process everything in that
sub-matrix before discarding the column dimension and moving down
to the next sub-matrix block along that same grid of rows.

An optional ProgressMonitor is permitted to be passed in, allowing
applications to see the progress of the detector as it works through
the matrix cells.  This provides some indication of current status
for very long running renames.

The default line/block hash function used by the SimilarityIndex
may not be optimal, and may produce too many collisions.  It is
borrowed from RawText's hash, which is used to quickly skip out of
a longer equality test if two lines have different hash functions.
We may need to refine this hash in the future, in order to minimize
the number of collisions we get on common source files.

Based on a handful of test commits in JGit (especially my own
recent rename repository refactoring series), this rename detector
produces output that is very close to C Git.  The content similarity
scores are sometimes off by 1%, which is most probably caused by
our SimilarityIndex type using a different hash function than C
Git uses when it computes the delta size between any two objects
in the rename matrix.

Bug: 318504
Change-Id: I11dff969e8a2e4cf252636d857d2113053bdd9dc
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

org.eclipse.jgit.test/tst/org/eclipse/jgit/diff/RenameDetectorTest.java

@@ -53,152 +53,237 @@ import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.RepositoryTestCase;
 
 public class RenameDetectorTest extends RepositoryTestCase {
+	private static final String PATH_A = "src/A";
+	private static final String PATH_H = "src/H";
+	private static final String PATH_Q = "src/Q";
 
-	RenameDetector rd;
+	private RenameDetector rd;
 
-	TestRepository testDb;
+	private TestRepository testDb;
 
 	@Override
 	public void setUp() throws Exception {
 		super.setUp();
 		testDb = new TestRepository(db);
-		rd = new RenameDetector();
+		rd = new RenameDetector(db);
 	}
 
-	public void testGetEntriesAddDelete() throws Exception {
-		ObjectId foo = testDb.blob("foo").copy();
+	public void testExactRename_OneRename() throws Exception {
+		ObjectId foo = blob("foo");
 
-		DiffEntry a = new DiffEntry();
-		a.newId = AbbreviatedObjectId.fromObjectId(foo);
-		a.newMode = FileMode.REGULAR_FILE;
-		a.newName = "some/file.c";
-		a.changeType = ChangeType.ADD;
+		DiffEntry a = DiffEntry.add(PATH_A, foo);
+		DiffEntry b = DiffEntry.delete(PATH_Q, foo);
 
-		DiffEntry b = new DiffEntry();
-		b.oldId = AbbreviatedObjectId.fromObjectId(foo);
-		b.oldMode = FileMode.REGULAR_FILE;
-		b.oldName = "some/other_file.c";
-		b.changeType = ChangeType.DELETE;
+		rd.add(a);
+		rd.add(b);
 
-		rd.addDiffEntry(a);
-		rd.addDiffEntry(b);
+		List<DiffEntry> entries = rd.compute();
+		assertEquals(1, entries.size());
+		assertRename(b, a, 100, entries.get(0));
+	}
+
+	public void testExactRename_OneRenameOneModify() throws Exception {
+		ObjectId foo = blob("foo");
+		ObjectId bar = blob("bar");
+
+		DiffEntry a = DiffEntry.add(PATH_A, foo);
+		DiffEntry b = DiffEntry.delete(PATH_Q, foo);
+
+		DiffEntry c = DiffEntry.modify(PATH_H);
+		c.newId = c.oldId = AbbreviatedObjectId.fromObjectId(bar);
+
+		rd.add(a);
+		rd.add(b);
+		rd.add(c);
+
+		List<DiffEntry> entries = rd.compute();
+		assertEquals(2, entries.size());
+		assertRename(b, a, 100, entries.get(0));
+		assertSame(c, entries.get(1));
+	}
+
+	public void testExactRename_ManyRenames() throws Exception {
+		ObjectId foo = blob("foo");
+		ObjectId bar = blob("bar");
+
+		DiffEntry a = DiffEntry.add(PATH_A, foo);
+		DiffEntry b = DiffEntry.delete(PATH_Q, foo);
+
+		DiffEntry c = DiffEntry.add("README", bar);
+		DiffEntry d = DiffEntry.delete("REEDME", bar);
+
+		rd.add(a);
+		rd.add(b);
+		rd.add(c);
+		rd.add(d);
+
+		List<DiffEntry> entries = rd.compute();
+		assertEquals(2, entries.size());
+		assertRename(d, c, 100, entries.get(0));
+		assertRename(b, a, 100, entries.get(1));
+	}
+
+	public void testInexactRename_OnePair() throws Exception {
+		ObjectId aId = blob("foo\nbar\nbaz\n");
+		ObjectId bId = blob("foo\nbar\nblah\n");
+
+		DiffEntry a = DiffEntry.add(PATH_A, aId);
+		DiffEntry b = DiffEntry.delete(PATH_Q, bId);
 
-		List<DiffEntry> entries = rd.getEntries();
+		rd.add(a);
+		rd.add(b);
+
+		List<DiffEntry> entries = rd.compute();
 		assertEquals(1, entries.size());
+		assertRename(b, a, 61, entries.get(0));
+	}
+
+	public void testInexactRename_OneRenameTwoUnrelatedFiles() throws Exception {
+		ObjectId aId = blob("foo\nbar\nbaz\n");
+		ObjectId bId = blob("foo\nbar\nblah\n");
+		DiffEntry a = DiffEntry.add(PATH_A, aId);
+		DiffEntry b = DiffEntry.delete(PATH_Q, bId);
+
+		ObjectId cId = blob("some\nsort\nof\ntext\n");
+		ObjectId dId = blob("completely\nunrelated\ntext\n");
+		DiffEntry c = DiffEntry.add("c", cId);
+		DiffEntry d = DiffEntry.delete("d", dId);
 
-		DiffEntry rename = entries.get(0);
-		assertNotNull(rename);
-		assertTrue(foo.equals(rename.newId.toObjectId()));
-		assertTrue(foo.equals(rename.oldId.toObjectId()));
-		assertEquals(FileMode.REGULAR_FILE, rename.newMode);
-		assertEquals(FileMode.REGULAR_FILE, rename.oldMode);
-		assertEquals(ChangeType.RENAME, rename.changeType);
-		assertEquals("some/file.c", rename.newName);
-		assertEquals("some/other_file.c", rename.oldName);
+		rd.add(a);
+		rd.add(b);
+		rd.add(c);
+		rd.add(d);
+
+		List<DiffEntry> entries = rd.compute();
+		assertEquals(3, entries.size());
+		assertSame(c, entries.get(0));
+		assertSame(d, entries.get(1));
+		assertRename(b, a, 61, entries.get(2));
 	}
 
-	public void testGetEntriesAddDeleteModify() throws Exception {
-		ObjectId foo = testDb.blob("foo").copy();
-		ObjectId bar = testDb.blob("bar").copy();
+	public void testInexactRename_LastByteDifferent() throws Exception {
+		ObjectId aId = blob("foo\nbar\na");
+		ObjectId bId = blob("foo\nbar\nb");
 
-		DiffEntry a = new DiffEntry();
-		a.newId = AbbreviatedObjectId.fromObjectId(foo);
-		a.newMode = FileMode.REGULAR_FILE;
-		a.newName = "some/file.c";
-		a.changeType = ChangeType.ADD;
+		DiffEntry a = DiffEntry.add(PATH_A, aId);
+		DiffEntry b = DiffEntry.delete(PATH_Q, bId);
 
-		DiffEntry b = new DiffEntry();
-		b.oldId = AbbreviatedObjectId.fromObjectId(foo);
-		b.oldMode = FileMode.REGULAR_FILE;
-		b.oldName = "some/other_file.c";
-		b.changeType = ChangeType.DELETE;
+		rd.add(a);
+		rd.add(b);
 
-		DiffEntry c = new DiffEntry();
-		c.newId = c.oldId = AbbreviatedObjectId.fromObjectId(bar);
-		c.newMode = c.oldMode = FileMode.REGULAR_FILE;
-		c.newName = c.oldName = "some/header.h";
-		c.changeType = ChangeType.MODIFY;
+		List<DiffEntry> entries = rd.compute();
+		assertEquals(1, entries.size());
+		assertRename(b, a, 88, entries.get(0));
+	}
+
+	public void testInexactRenames_OnePair2() throws Exception {
+		ObjectId aId = blob("ab\nab\nab\nac\nad\nae\n");
+		ObjectId bId = blob("ac\nab\nab\nab\naa\na0\na1\n");
+
+		DiffEntry a = DiffEntry.add(PATH_A, aId);
+		DiffEntry b = DiffEntry.delete(PATH_Q, bId);
+
+		rd.add(a);
+		rd.add(b);
+		rd.setRenameScore(50);
 
-		rd.addDiffEntry(a);
-		rd.addDiffEntry(b);
-		rd.addDiffEntry(c);
+		List<DiffEntry> entries = rd.compute();
+		assertEquals(1, entries.size());
+		assertRename(b, a, 57, entries.get(0));
+	}
+
+	public void testNoRenames_SingleByteFiles() throws Exception {
+		ObjectId aId = blob("a");
+		ObjectId bId = blob("b");
+
+		DiffEntry a = DiffEntry.add(PATH_A, aId);
+		DiffEntry b = DiffEntry.delete(PATH_Q, bId);
+
+		rd.add(a);
+		rd.add(b);
+
+		List<DiffEntry> entries = rd.compute();
+		assertEquals(2, entries.size());
+		assertSame(a, entries.get(0));
+		assertSame(b, entries.get(1));
+	}
+
+	public void testNoRenames_EmptyFile1() throws Exception {
+		ObjectId aId = blob("");
+		DiffEntry a = DiffEntry.add(PATH_A, aId);
+
+		rd.add(a);
+
+		List<DiffEntry> entries = rd.compute();
+		assertEquals(1, entries.size());
+		assertSame(a, entries.get(0));
+	}
+
+	public void testNoRenames_EmptyFile2() throws Exception {
+		ObjectId aId = blob("");
+		ObjectId bId = blob("blah");
+
+		DiffEntry a = DiffEntry.add(PATH_A, aId);
+		DiffEntry b = DiffEntry.delete(PATH_Q, bId);
 
-		List<DiffEntry> entries = rd.getEntries();
+		rd.add(a);
+		rd.add(b);
+
+		List<DiffEntry> entries = rd.compute();
 		assertEquals(2, entries.size());
+		assertSame(a, entries.get(0));
+		assertSame(b, entries.get(1));
+	}
+
+	public void testNoRenames_SymlinkAndFile() throws Exception {
+		ObjectId aId = blob("src/dest");
+
+		DiffEntry a = DiffEntry.add(PATH_A, aId);
+		DiffEntry b = DiffEntry.delete(PATH_Q, aId);
+		b.oldMode = FileMode.SYMLINK;
 
-		// The renamed change should be first because the output should be
-		// sorted by newName
-		DiffEntry rename = entries.get(0);
-		assertNotNull(rename);
-		assertTrue(foo.equals(rename.newId.toObjectId()));
-		assertTrue(foo.equals(rename.oldId.toObjectId()));
-		assertEquals(FileMode.REGULAR_FILE, rename.newMode);
-		assertEquals(FileMode.REGULAR_FILE, rename.oldMode);
-		assertEquals(ChangeType.RENAME, rename.changeType);
-		assertEquals("some/file.c", rename.newName);
-		assertEquals("some/other_file.c", rename.oldName);
-
-		DiffEntry modify = entries.get(1);
-		assertEquals(c, modify);
+		rd.add(a);
+		rd.add(b);
+
+		List<DiffEntry> entries = rd.compute();
+		assertEquals(2, entries.size());
+		assertSame(a, entries.get(0));
+		assertSame(b, entries.get(1));
 	}
 
-	public void testGetEntriesMultipleRenames() throws Exception {
-		ObjectId foo = testDb.blob("foo").copy();
-		ObjectId bar = testDb.blob("bar").copy();
-
-		DiffEntry a = new DiffEntry();
-		a.newId = AbbreviatedObjectId.fromObjectId(foo);
-		a.newMode = FileMode.REGULAR_FILE;
-		a.newName = "some/file.c";
-		a.changeType = ChangeType.ADD;
-
-		DiffEntry b = new DiffEntry();
-		b.oldId = AbbreviatedObjectId.fromObjectId(foo);
-		b.oldMode = FileMode.REGULAR_FILE;
-		b.oldName = "some/other_file.c";
-		b.changeType = ChangeType.DELETE;
-
-		DiffEntry c = new DiffEntry();
-		c.newId = AbbreviatedObjectId.fromObjectId(bar);
-		c.newMode = FileMode.REGULAR_FILE;
-		c.newName = "README";
-		c.changeType = ChangeType.ADD;
-
-		DiffEntry d = new DiffEntry();
-		d.oldId = AbbreviatedObjectId.fromObjectId(bar);
-		d.oldMode = FileMode.REGULAR_FILE;
-		d.oldName = "REEDME";
-		d.changeType = ChangeType.DELETE;
-
-		rd.addDiffEntry(a);
-		rd.addDiffEntry(b);
-		rd.addDiffEntry(c);
-		rd.addDiffEntry(d);
-
-		List<DiffEntry> entries = rd.getEntries();
+	public void testNoRenames_GitlinkAndFile() throws Exception {
+		ObjectId aId = blob("src/dest");
+
+		DiffEntry a = DiffEntry.add(PATH_A, aId);
+		DiffEntry b = DiffEntry.delete(PATH_Q, aId);
+		b.oldMode = FileMode.GITLINK;
+
+		rd.add(a);
+		rd.add(b);
+
+		List<DiffEntry> entries = rd.compute();
 		assertEquals(2, entries.size());
+		assertSame(a, entries.get(0));
+		assertSame(b, entries.get(1));
+	}
 
-		// The REEDME -> README renamed change should be first because the
-		// output should be sorted by newName
-		DiffEntry readme = entries.get(0);
-		assertNotNull(readme);
-		assertTrue(bar.equals(readme.newId.toObjectId()));
-		assertTrue(bar.equals(readme.oldId.toObjectId()));
-		assertEquals(FileMode.REGULAR_FILE, readme.newMode);
-		assertEquals(FileMode.REGULAR_FILE, readme.oldMode);
-		assertEquals(ChangeType.RENAME, readme.changeType);
-		assertEquals("README", readme.newName);
-		assertEquals("REEDME", readme.oldName);
-
-		DiffEntry somefile = entries.get(1);
-		assertNotNull(somefile);
-		assertTrue(foo.equals(somefile.newId.toObjectId()));
-		assertTrue(foo.equals(somefile.oldId.toObjectId()));
-		assertEquals(FileMode.REGULAR_FILE, somefile.newMode);
-		assertEquals(FileMode.REGULAR_FILE, somefile.oldMode);
-		assertEquals(ChangeType.RENAME, somefile.changeType);
-		assertEquals("some/file.c", somefile.newName);
-		assertEquals("some/other_file.c", somefile.oldName);
+	private ObjectId blob(String content) throws Exception {
+		return testDb.blob(content).copy();
 	}
 
+	private static void assertRename(DiffEntry o, DiffEntry n, int score,
+			DiffEntry rename) {
+		assertEquals(ChangeType.RENAME, rename.getChangeType());
+
+		assertEquals(o.getOldName(), rename.getOldName());
+		assertEquals(n.getNewName(), rename.getNewName());
+
+		assertEquals(o.getOldMode(), rename.getOldMode());
+		assertEquals(n.getNewMode(), rename.getNewMode());
+
+		assertEquals(o.getOldId(), rename.getOldId());
+		assertEquals(n.getNewId(), rename.getNewId());
+
+		assertEquals(score, rename.getScore());
+	}
 }

org.eclipse.jgit.test/tst/org/eclipse/jgit/diff/SimilarityIndexTest.java

@@ -0,0 +1,137 @@
+/*
+ * Copyright (C) 2010, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.diff;
+
+import junit.framework.TestCase;
+
+import org.eclipse.jgit.lib.Constants;
+
+public class SimilarityIndexTest extends TestCase {
+	public void testIndexing() {
+		SimilarityIndex si = hash("" //
+				+ "A\n" //
+				+ "B\n" //
+				+ "D\n" //
+				+ "B\n" //
+		);
+
+		int key_A = keyFor("A\n");
+		int key_B = keyFor("B\n");
+		int key_D = keyFor("D\n");
+		assertTrue(key_A != key_B && key_A != key_D && key_B != key_D);
+
+		assertEquals(3, si.size());
+		assertEquals(2, si.count(si.findIndex(key_A)));
+		assertEquals(4, si.count(si.findIndex(key_B)));
+		assertEquals(2, si.count(si.findIndex(key_D)));
+	}
+
+	public void testCommonScore_SameFiles() {
+		String text = "" //
+				+ "A\n" //
+				+ "B\n" //
+				+ "D\n" //
+				+ "B\n";
+		SimilarityIndex src = hash(text);
+		SimilarityIndex dst = hash(text);
+		assertEquals(8, src.common(dst));
+		assertEquals(8, dst.common(src));
+
+		assertEquals(100, src.score(dst));
+		assertEquals(100, dst.score(src));
+	}
+
+	public void testCommonScore_EmptyFiles() {
+		SimilarityIndex src = hash("");
+		SimilarityIndex dst = hash("");
+		assertEquals(0, src.common(dst));
+		assertEquals(0, dst.common(src));
+	}
+
+	public void testCommonScore_TotallyDifferentFiles() {
+		SimilarityIndex src = hash("A\n");
+		SimilarityIndex dst = hash("D\n");
+		assertEquals(0, src.common(dst));
+		assertEquals(0, dst.common(src));
+	}
+
+	public void testCommonScore_SimiliarBy75() {
+		SimilarityIndex src = hash("A\nB\nC\nD\n");
+		SimilarityIndex dst = hash("A\nB\nC\nQ\n");
+		assertEquals(6, src.common(dst));
+		assertEquals(6, dst.common(src));
+
+		assertEquals(75, src.score(dst));
+		assertEquals(75, dst.score(src));
+	}
+
+	private static SimilarityIndex hash(String text) {
+		SimilarityIndex src = new SimilarityIndex() {
+			@Override
+			void hash(byte[] raw, int ptr, final int end) {
+				while (ptr < end) {
+					int hash = raw[ptr] & 0xff;
+					int start = ptr;
+					do {
+						int c = raw[ptr++] & 0xff;
+						if (c == '\n')
+							break;
+					} while (ptr < end && ptr - start < 64);
+					add(hash, ptr - start);
+				}
+			}
+		};
+		byte[] raw = Constants.encode(text);
+		src.setFileSize(raw.length);
+		src.hash(raw, 0, raw.length);
+		src.sort();
+		return src;
+	}
+
+	private static int keyFor(String line) {
+		SimilarityIndex si = hash(line);
+		assertEquals("single line scored", 1, si.size());
+		return si.key(0);
+	}
+}

org.eclipse.jgit.test/tst/org/eclipse/jgit/patch/FileHeaderTest.java

@@ -45,6 +45,7 @@ package org.eclipse.jgit.patch;
 
 import junit.framework.TestCase;
 
+import org.eclipse.jgit.diff.DiffEntry;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
@@ -153,7 +154,7 @@ public class FileHeaderTest extends TestCase {
 		assertParse(fh);
 
 		assertEquals("/dev/null", fh.getOldName());
-		assertSame(FileHeader.DEV_NULL, fh.getOldName());
+		assertSame(DiffEntry.DEV_NULL, fh.getOldName());
 		assertEquals("\u00c5ngstr\u00f6m", fh.getNewName());
 
 		assertSame(FileHeader.ChangeType.ADD, fh.getChangeType());
@@ -179,7 +180,7 @@ public class FileHeaderTest extends TestCase {
 
 		assertEquals("\u00c5ngstr\u00f6m", fh.getOldName());
 		assertEquals("/dev/null", fh.getNewName());
-		assertSame(FileHeader.DEV_NULL, fh.getNewName());
+		assertSame(DiffEntry.DEV_NULL, fh.getNewName());
 
 		assertSame(FileHeader.ChangeType.DELETE, fh.getChangeType());
 		assertSame(FileHeader.PatchType.UNIFIED, fh.getPatchType());

org.eclipse.jgit.test/tst/org/eclipse/jgit/patch/PatchCcTest.java

@@ -46,10 +46,11 @@ package org.eclipse.jgit.patch;
 import java.io.IOException;
 import java.io.InputStream;
 
-import org.eclipse.jgit.lib.FileMode;
-
 import junit.framework.TestCase;
 
+import org.eclipse.jgit.diff.DiffEntry;
+import org.eclipse.jgit.lib.FileMode;
+
 public class PatchCcTest extends TestCase {
 	public void testParse_OneFileCc() throws IOException {
 		final Patch p = parseTestPatchFile();
@@ -113,7 +114,7 @@ public class PatchCcTest extends TestCase {
 
 		final CombinedFileHeader cfh = (CombinedFileHeader) p.getFiles().get(0);
 
-		assertSame(FileHeader.DEV_NULL, cfh.getOldName());
+		assertSame(DiffEntry.DEV_NULL, cfh.getOldName());
 		assertEquals("d", cfh.getNewName());
 
 		assertEquals(187, cfh.startOffset);
@@ -168,7 +169,7 @@ public class PatchCcTest extends TestCase {
 		final CombinedFileHeader cfh = (CombinedFileHeader) p.getFiles().get(0);
 
 		assertEquals("a", cfh.getOldName());
-		assertSame(FileHeader.DEV_NULL, cfh.getNewName());
+		assertSame(DiffEntry.DEV_NULL, cfh.getNewName());
 
 		assertEquals(187, cfh.startOffset);
 

org.eclipse.jgit/resources/org/eclipse/jgit/JGitText.properties

@@ -298,6 +298,8 @@ remoteDoesNotSupportSmartHTTPPush=remote does not support smart HTTP push
 remoteHungUpUnexpectedly=remote hung up unexpectedly
 remoteNameCantBeNull=Remote name can't be null.
 renamesAlreadyFound=Renames have already been found.
+renamesFindingByContent=Finding renames by content similarity
+renamesFindingExact=Finding exact renames
 repositoryAlreadyExists=Repository already exists: {0}
 repositoryNotFound=repository not found: {0}
 requiredHashFunctionNotAvailable=Required hash function {0} not available.
@@ -307,6 +309,7 @@ shortCompressedStreamAt=Short compressed stream at {0}
 shortReadOfBlock=Short read of block.
 shortReadOfOptionalDIRCExtensionExpectedAnotherBytes=Short read of optional DIRC extension {0}; expected another {1} bytes within the section.
 shortSkipOfBlock=Short skip of block.
+similarityScoreMustBeWithinBounds=Similarity score must be between 0 and 100.
 smartHTTPPushDisabled=smart HTTP push disabled
 sourceDestinationMustMatch=Source/Destination must match.
 sourceIsNotAWildcard=Source is not a wildcard.

org.eclipse.jgit/src/org/eclipse/jgit/JGitText.java

@@ -357,6 +357,8 @@ public class JGitText extends TranslationBundle {
 	/***/ public String remoteHungUpUnexpectedly;
 	/***/ public String remoteNameCantBeNull;
 	/***/ public String renamesAlreadyFound;
+	/***/ public String renamesFindingByContent;
+	/***/ public String renamesFindingExact;
 	/***/ public String repositoryAlreadyExists;
 	/***/ public String repositoryNotFound;
 	/***/ public String requiredHashFunctionNotAvailable;
@@ -366,6 +368,7 @@ public class JGitText extends TranslationBundle {
 	/***/ public String shortReadOfBlock;
 	/***/ public String shortReadOfOptionalDIRCExtensionExpectedAnotherBytes;
 	/***/ public String shortSkipOfBlock;
+	/***/ public String similarityScoreMustBeWithinBounds;
 	/***/ public String smartHTTPPushDisabled;
 	/***/ public String sourceDestinationMustMatch;
 	/***/ public String sourceIsNotAWildcard;

org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffEntry.java

@@ -43,11 +43,25 @@
 
 package org.eclipse.jgit.diff;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
 import org.eclipse.jgit.lib.AbbreviatedObjectId;
+import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.FileMode;
+import org.eclipse.jgit.lib.MutableObjectId;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.treewalk.TreeWalk;
 
 /** A value class representing a change to a file */
 public class DiffEntry {
+	private static final AbbreviatedObjectId A_ZERO = AbbreviatedObjectId
+			.fromObjectId(ObjectId.zeroId());
+
+	/** Magical file name used for file adds or deletes. */
+	public static final String DEV_NULL = "/dev/null";
 
 	/** General type of change a single file-level patch describes. */
 	public static enum ChangeType {
@@ -67,6 +81,130 @@ public class DiffEntry {
 		COPY;
 	}
 
+	/**
+	 * Convert the TreeWalk into DiffEntry headers.
+	 *
+	 * @param walk
+	 *            the TreeWalk to walk through. Must have exactly two trees.
+	 * @return headers describing the changed files.
+	 * @throws IOException
+	 *             the repository cannot be accessed.
+	 */
+	public static List<DiffEntry> scan(TreeWalk walk) throws IOException {
+		List<DiffEntry> r = new ArrayList<DiffEntry>();
+		MutableObjectId idBuf = new MutableObjectId();
+		while (walk.next()) {
+			DiffEntry entry = new DiffEntry();
+
+			walk.getObjectId(idBuf, 0);
+			entry.oldId = AbbreviatedObjectId.fromObjectId(idBuf);
+
+			walk.getObjectId(idBuf, 1);
+			entry.newId = AbbreviatedObjectId.fromObjectId(idBuf);
+
+			entry.oldMode = walk.getFileMode(0);
+			entry.newMode = walk.getFileMode(1);
+			entry.newName = entry.oldName = walk.getPathString();
+
+			if (entry.oldMode == FileMode.MISSING) {
+				entry.oldName = DiffEntry.DEV_NULL;
+				entry.changeType = ChangeType.ADD;
+				r.add(entry);
+
+			} else if (entry.newMode == FileMode.MISSING) {
+				entry.newName = DiffEntry.DEV_NULL;
+				entry.changeType = ChangeType.DELETE;
+				r.add(entry);
+
+			} else {
+				entry.changeType = ChangeType.MODIFY;
+				if (RenameDetector.sameType(entry.oldMode, entry.newMode))
+					r.add(entry);
+				else
+					r.addAll(breakModify(entry));
+			}
+		}
+		return r;
+	}
+
+	static DiffEntry add(String path, AnyObjectId id) {
+		DiffEntry e = new DiffEntry();
+		e.oldId = A_ZERO;
+		e.oldMode = FileMode.MISSING;
+		e.oldName = DEV_NULL;
+
+		e.newId = AbbreviatedObjectId.fromObjectId(id);
+		e.newMode = FileMode.REGULAR_FILE;
+		e.newName = path;
+		e.changeType = ChangeType.ADD;
+		return e;
+	}
+
+	static DiffEntry delete(String path, AnyObjectId id) {
+		DiffEntry e = new DiffEntry();
+		e.oldId = AbbreviatedObjectId.fromObjectId(id);
+		e.oldMode = FileMode.REGULAR_FILE;
+		e.oldName = path;
+
+		e.newId = A_ZERO;
+		e.newMode = FileMode.MISSING;
+		e.newName = DEV_NULL;
+		e.changeType = ChangeType.DELETE;
+		return e;
+	}
+
+	static DiffEntry modify(String path) {
+		DiffEntry e = new DiffEntry();
+		e.oldMode = FileMode.REGULAR_FILE;
+		e.oldName = path;
+
+		e.newMode = FileMode.REGULAR_FILE;
+		e.newName = path;
+		e.changeType = ChangeType.MODIFY;
+		return e;
+	}
+
+	static List<DiffEntry> breakModify(DiffEntry entry) {
+		DiffEntry del = new DiffEntry();
+		del.oldId = entry.getOldId();
+		del.oldMode = entry.getOldMode();
+		del.oldName = entry.getOldName();
+
+		del.newId = A_ZERO;
+		del.newMode = FileMode.MISSING;
+		del.newName = DiffEntry.DEV_NULL;
+		del.changeType = ChangeType.DELETE;
+
+		DiffEntry add = new DiffEntry();
+		add.oldId = A_ZERO;
+		add.oldMode = FileMode.MISSING;
+		add.oldName = DiffEntry.DEV_NULL;
+
+		add.newId = entry.getNewId();
+		add.newMode = entry.getNewMode();
+		add.newName = entry.getNewName();
+		add.changeType = ChangeType.ADD;
+		return Arrays.asList(del, add);
+	}
+
+	static DiffEntry pair(ChangeType changeType, DiffEntry src, DiffEntry dst,
+			int score) {
+		DiffEntry r = new DiffEntry();
+
+		r.oldId = src.oldId;
+		r.oldMode = src.oldMode;
+		r.oldName = src.oldName;
+
+		r.newId = dst.newId;
+		r.newMode = dst.newMode;
+		r.newName = dst.newName;
+
+		r.changeType = changeType;
+		r.score = score;
+
+		return r;
+	}
+
 	/** File name of the old (pre-image). */
 	protected String oldName;
 
@@ -170,5 +308,4 @@ public class DiffEntry {
 	public AbbreviatedObjectId getNewId() {
 		return newId;
 	}
-
 }

org.eclipse.jgit/src/org/eclipse/jgit/diff/RenameDetector.java

@@ -53,22 +53,48 @@ import java.util.List;
 
 import org.eclipse.jgit.JGitText;
 import org.eclipse.jgit.diff.DiffEntry.ChangeType;
-import org.eclipse.jgit.errors.CorruptObjectException;
-import org.eclipse.jgit.errors.IncorrectObjectTypeException;
-import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.lib.AbbreviatedObjectId;
+import org.eclipse.jgit.lib.Config;
 import org.eclipse.jgit.lib.FileMode;
-import org.eclipse.jgit.lib.MutableObjectId;
-import org.eclipse.jgit.treewalk.TreeWalk;
+import org.eclipse.jgit.lib.NullProgressMonitor;
+import org.eclipse.jgit.lib.ProgressMonitor;
+import org.eclipse.jgit.lib.Repository;
 
 /** Detect and resolve object renames. */
 public class RenameDetector {
-
 	private static final int EXACT_RENAME_SCORE = 100;
 
 	private static final Comparator<DiffEntry> DIFF_COMPARATOR = new Comparator<DiffEntry>() {
-		public int compare(DiffEntry o1, DiffEntry o2) {
-			return o1.newName.compareTo(o2.newName);
+		public int compare(DiffEntry a, DiffEntry b) {
+			int cmp = nameOf(a).compareTo(nameOf(b));
+			if (cmp == 0)
+				cmp = sortOf(a.getChangeType()) - sortOf(b.getChangeType());
+			return cmp;
+		}
+
+		private String nameOf(DiffEntry ent) {
+			// Sort by the new name, unless the change is a delete. On
+			// deletes the new name is /dev/null, so we sort instead by
+			// the old name.
+			//
+			if (ent.changeType == ChangeType.DELETE)
+				return ent.oldName;
+			return ent.newName;
+		}
+
+		private int sortOf(ChangeType changeType) {
+			// Sort deletes before adds so that a major type change for
+			// a file path (such as symlink to regular file) will first
+			// remove the path, then add it back with the new type.
+			//
+			switch (changeType) {
+			case DELETE:
+				return 1;
+			case ADD:
+				return 2;
+			default:
+				return 10;
+			}
 		}
 	};
 
@@ -78,181 +104,305 @@ public class RenameDetector {
 
 	private List<DiffEntry> added = new ArrayList<DiffEntry>();
 
-	private boolean done = false;
+	private boolean done;
+
+	private final Repository repo;
+
+	/** Similarity score required to pair an add/delete as a rename. */
+	private int renameScore = 60;
+
+	/** Limit in the number of files to consider for renames. */
+	private int renameLimit;
+
+	/** Set if the number of adds or deletes was over the limit. */
+	private boolean overRenameLimit;
+
+	/**
+	 * Create a new rename detector for the given repository
+	 *
+	 * @param repo
+	 *            the repository to use for rename detection
+	 */
+	public RenameDetector(Repository repo) {
+		this.repo = repo;
+
+		Config cfg = repo.getConfig();
+		renameLimit = cfg.getInt("diff", "renamelimit", 200);
+	}
 
 	/**
-	 * Walk through a given tree walk with exactly two trees and add all
-	 * differing files to the list of object to run rename detection on.
+	 * @return minimum score required to pair an add/delete as a rename. The
+	 *         score ranges are within the bounds of (0, 100).
+	 */
+	public int getRenameScore() {
+		return renameScore;
+	}
+
+	/**
+	 * Set the minimum score required to pair an add/delete as a rename.
 	 * <p>
-	 * The tree walk must have two trees attached to it, as well as a filter.
-	 * Calling this method after calling {@link #getEntries()} will result in an
-	 * {@link IllegalStateException}.
+	 * When comparing two files together their score must be greater than or
+	 * equal to the rename score for them to be considered a rename match. The
+	 * score is computed based on content similarity, so a score of 60 implies
+	 * that approximately 60% of the bytes in the files are identical.
 	 *
-	 * @param walk
-	 *            the TreeWalk to walk through. Must have exactly two trees.
+	 * @param score
+	 *            new rename score, must be within (0, 100).
+	 */
+	public void setRenameScore(int score) {
+		if (score < 0 || score > 100)
+			throw new IllegalArgumentException(
+					JGitText.get().similarityScoreMustBeWithinBounds);
+		renameScore = score;
+	}
+
+	/** @return limit on number of paths to perform inexact rename detection. */
+	public int getRenameLimit() {
+		return renameLimit;
+	}
+
+	/**
+	 * Set the limit on the number of files to perform inexact rename detection.
+	 * <p>
+	 * The rename detector has to build a square matrix of the rename limit on
+	 * each side, then perform that many file compares to determine similarity.
+	 * If 1000 files are added, and 1000 files are deleted, a 1000*1000 matrix
+	 * must be allocated, and 1,000,000 file compares may need to be performed.
+	 *
+	 * @param limit
+	 *            new file limit.
+	 */
+	public void setRenameLimit(int limit) {
+		renameLimit = limit;
+	}
+
+	/**
+	 * Check if the detector is over the rename limit.
+	 * <p>
+	 * This method can be invoked either before or after {@code getEntries} has
+	 * been used to perform rename detection.
+	 *
+	 * @return true if the detector has more file additions or removals than the
+	 *         rename limit is currently set to. In such configurations the
+	 *         detector will skip expensive computation.
+	 */
+	public boolean isOverRenameLimit() {
+		if (done)
+			return overRenameLimit;
+		int cnt = Math.max(added.size(), deleted.size());
+		return getRenameLimit() != 0 && getRenameLimit() < cnt;
+	}
+
+	/**
+	 * Add entries to be considered for rename detection.
+	 *
+	 * @param entriesToAdd
+	 *            one or more entries to add.
 	 * @throws IllegalStateException
-	 *             the {@link #getEntries()} method has already been called for
-	 *             this instance.
-	 * @throws MissingObjectException
-	 *             {@link TreeWalk#isRecursive()} was enabled on the tree, a
-	 *             subtree was found, but the subtree object does not exist in
-	 *             this repository. The repository may be missing objects.
-	 * @throws IncorrectObjectTypeException
-	 *             {@link TreeWalk#isRecursive()} was enabled on the tree, a
-	 *             subtree was found, and the subtree id does not denote a tree,
-	 *             but instead names some other non-tree type of object. The
-	 *             repository may have data corruption.
-	 * @throws CorruptObjectException
-	 *             the contents of a tree did not appear to be a tree. The
-	 *             repository may have data corruption.
-	 * @throws IOException
-	 *             a loose object or pack file could not be read.
+	 *             if {@code getEntries} was already invoked.
 	 */
-	public void addTreeWalk(TreeWalk walk) throws MissingObjectException,
-			IncorrectObjectTypeException, CorruptObjectException, IOException {
+	public void addAll(Collection<DiffEntry> entriesToAdd) {
 		if (done)
 			throw new IllegalStateException(JGitText.get().renamesAlreadyFound);
-		MutableObjectId idBuf = new MutableObjectId();
-		while (walk.next()) {
-			DiffEntry entry = new DiffEntry();
-			walk.getObjectId(idBuf, 0);
-			entry.oldId = AbbreviatedObjectId.fromObjectId(idBuf);
-			walk.getObjectId(idBuf, 1);
-			entry.newId = AbbreviatedObjectId.fromObjectId(idBuf);
-			entry.oldMode = walk.getFileMode(0);
-			entry.newMode = walk.getFileMode(1);
-			entry.newName = entry.oldName = walk.getPathString();
-			if (entry.oldMode == FileMode.MISSING) {
-				entry.changeType = ChangeType.ADD;
+
+		for (DiffEntry entry : entriesToAdd) {
+			switch (entry.getChangeType()) {
+			case ADD:
 				added.add(entry);
-			} else if (entry.newMode == FileMode.MISSING) {
-				entry.changeType = ChangeType.DELETE;
+				break;
+
+			case DELETE:
 				deleted.add(entry);
-			} else {
-				entry.changeType = ChangeType.MODIFY;
-				entries.add(entry);
+				break;
+
+			case MODIFY:
+				if (sameType(entry.getOldMode(), entry.getNewMode()))
+					entries.add(entry);
+				else
+					entries.addAll(DiffEntry.breakModify(entry));
+				break;
+
+			case COPY:
+			case RENAME:
+			default:
+				entriesToAdd.add(entry);
 			}
 		}
 	}
 
 	/**
-	 * Add a DiffEntry to the list of items to run rename detection on. Calling
-	 * this method after calling {@link #getEntries()} will result in an
-	 * {@link IllegalStateException}.
+	 * Add an entry to be considered for rename detection.
 	 *
 	 * @param entry
-	 *            the {@link DiffEntry} to add
-	 *
+	 *            to add.
 	 * @throws IllegalStateException
-	 *             the {@link #getEntries()} method has already been called for
-	 *             this instance
+	 *             if {@code getEntries} was already invoked.
 	 */
-	public void addDiffEntry(DiffEntry entry) {
-		if (done)
-			throw new IllegalStateException(JGitText.get().renamesAlreadyFound);
-		switch (entry.changeType) {
-		case ADD:
-			added.add(entry);
-			break;
-		case DELETE:
-			deleted.add(entry);
-			break;
-		case COPY:
-		case MODIFY:
-		case RENAME:
-		default:
-			entries.add(entry);
-		}
+	public void add(DiffEntry entry) {
+		addAll(Collections.singletonList(entry));
 	}
 
 	/**
-	 * Determines which files, if any, are renames, and returns an unmodifiable
-	 * list of {@link DiffEntry}s representing all files that have been changed
-	 * in some way. The list will contain all modified files first
+	 * Detect renames in the current file set.
+	 * <p>
+	 * This convenience function runs without a progress monitor.
 	 *
 	 * @return an unmodifiable list of {@link DiffEntry}s representing all files
-	 *         that have been changed
+	 *         that have been changed.
 	 * @throws IOException
+	 *             file contents cannot be read from the repository.
 	 */
-	public List<DiffEntry> getEntries() throws IOException {
+	public List<DiffEntry> compute() throws IOException {
+		return compute(NullProgressMonitor.INSTANCE);
+	}
+
+	/**
+	 * Detect renames in the current file set.
+	 *
+	 * @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
+	 *             file contents cannot be read from the repository.
+	 */
+	public List<DiffEntry> compute(ProgressMonitor pm) throws IOException {
 		if (!done) {
 			done = true;
-			findExactRenames();
+
+			if (pm == null)
+				pm = NullProgressMonitor.INSTANCE;
+			findExactRenames(pm);
+			findContentRenames(pm);
+
 			entries.addAll(added);
-			entries.addAll(deleted);
 			added = null;
+
+			entries.addAll(deleted);
 			deleted = null;
+
 			Collections.sort(entries, DIFF_COMPARATOR);
 		}
 		return Collections.unmodifiableList(entries);
 	}
 
+	private void findContentRenames(ProgressMonitor pm) throws IOException {
+		int cnt = Math.max(added.size(), deleted.size());
+		if (cnt == 0)
+			return;
+
+		if (getRenameLimit() == 0 || cnt <= getRenameLimit()) {
+			SimilarityRenameDetector d;
+
+			d = new SimilarityRenameDetector(repo, deleted, added);
+			d.setRenameScore(getRenameScore());
+			d.compute(pm);
+			deleted = d.getLeftOverSources();
+			added = d.getLeftOverDestinations();
+			entries.addAll(d.getMatches());
+		} else {
+			overRenameLimit = true;
+		}
+	}
+
 	@SuppressWarnings("unchecked")
-	private void findExactRenames() {
-		HashMap<AbbreviatedObjectId, Object> map = new HashMap<AbbreviatedObjectId, Object>();
+	private void findExactRenames(ProgressMonitor pm) {
+		if (added.isEmpty() || deleted.isEmpty())
+			return;
 
+		pm.beginTask(JGitText.get().renamesFindingExact, //
+				added.size() + deleted.size());
+
+		HashMap<AbbreviatedObjectId, Object> map = new HashMap<AbbreviatedObjectId, Object>();
 		for (DiffEntry del : deleted) {
 			Object old = map.put(del.oldId, del);
-			if (old != null) {
-				if (old instanceof DiffEntry) {
-					ArrayList<DiffEntry> tmp = new ArrayList<DiffEntry>(2);
-					tmp.add((DiffEntry) old);
-					tmp.add(del);
-					map.put(del.oldId, tmp);
-				} else {
-					// Must be a list of DiffEntrys
-					((List) old).add(del);
-					map.put(del.oldId, old);
-				}
+			if (old instanceof DiffEntry) {
+				ArrayList<DiffEntry> list = new ArrayList<DiffEntry>(2);
+				list.add((DiffEntry) old);
+				list.add(del);
+				map.put(del.oldId, list);
+
+			} else if (old != null) {
+				// Must be a list of DiffEntries
+				((List) old).add(del);
+				map.put(del.oldId, old);
 			}
+			pm.update(1);
 		}
 
-		ArrayList<DiffEntry> tempAdded = new ArrayList<DiffEntry>(added.size());
+		ArrayList<DiffEntry> left = new ArrayList<DiffEntry>(added.size());
+		for (DiffEntry dst : added) {
+			Object del = map.get(dst.newId);
+			if (del instanceof DiffEntry) {
+				DiffEntry e = (DiffEntry) del;
+				if (sameType(e.oldMode, dst.newMode)) {
+					if (e.changeType == ChangeType.DELETE) {
+						e.changeType = ChangeType.RENAME;
+						entries.add(exactRename(e, dst));
+					} else {
+						entries.add(exactCopy(e, dst));
+					}
+				} else {
+					left.add(dst);
+				}
 
-		for (DiffEntry add : added) {
-			Object del = map.remove(add.newId);
-			if (del != null) {
-				if (del instanceof DiffEntry) {
-					entries.add(resolveRename(add, (DiffEntry) del,
-							EXACT_RENAME_SCORE));
+			} else if (del != null) {
+				List<DiffEntry> list = (List<DiffEntry>) del;
+				DiffEntry best = null;
+				for (DiffEntry e : list) {
+					if (best == null && sameType(e.oldMode, dst.newMode))
+						best = e;
+				}
+				if (best != null) {
+					if (best.changeType == ChangeType.DELETE) {
+						best.changeType = ChangeType.RENAME;
+						entries.add(exactRename(best, dst));
+					} else {
+						entries.add(exactCopy(best, dst));
+					}
 				} else {
-					// Must be a list of DiffEntrys
-					List<DiffEntry> tmp = (List<DiffEntry>) del;
-					entries.add(resolveRename(add, tmp.remove(0),
-							EXACT_RENAME_SCORE));
-					if (!tmp.isEmpty())
-						map.put(add.newId, del);
+					left.add(dst);
 				}
+
 			} else {
-				tempAdded.add(add);
+				left.add(dst);
 			}
+			pm.update(1);
 		}
-		added = tempAdded;
-
-		Collection<Object> values = map.values();
-		ArrayList<DiffEntry> tempDeleted = new ArrayList<DiffEntry>(values
-				.size());
-		for (Object o : values) {
-			if (o instanceof DiffEntry)
-				tempDeleted.add((DiffEntry) o);
-			else
-				tempDeleted.addAll((List<DiffEntry>) o);
+		added = left;
+
+		deleted = new ArrayList<DiffEntry>(map.size());
+		for (Object o : map.values()) {
+			if (o instanceof DiffEntry) {
+				DiffEntry e = (DiffEntry) o;
+				if (e.changeType == ChangeType.DELETE)
+					deleted.add(e);
+			} else {
+				List<DiffEntry> list = (List<DiffEntry>) o;
+				for (DiffEntry e : list) {
+					if (e.changeType == ChangeType.DELETE)
+						deleted.add(e);
+				}
+			}
 		}
-		deleted = tempDeleted;
+		pm.endTask();
 	}
 
-	private DiffEntry resolveRename(DiffEntry add, DiffEntry del, int score) {
-		DiffEntry renamed = new DiffEntry();
+	static boolean sameType(FileMode a, FileMode b) {
+		// Files have to be of the same type in order to rename them.
+		// We would never want to rename a file to a gitlink, or a
+		// symlink to a file.
+		//
+		int aType = a.getBits() & FileMode.TYPE_MASK;
+		int bType = b.getBits() & FileMode.TYPE_MASK;
+		return aType == bType;
+	}
 
-		renamed.oldId = del.oldId;
-		renamed.oldMode = del.oldMode;
-		renamed.oldName = del.oldName;
-		renamed.newId = add.newId;
-		renamed.newMode = add.newMode;
-		renamed.newName = add.newName;
-		renamed.changeType = ChangeType.RENAME;
-		renamed.score = score;
+	private static DiffEntry exactRename(DiffEntry src, DiffEntry dst) {
+		return DiffEntry.pair(ChangeType.RENAME, src, dst, EXACT_RENAME_SCORE);
+	}
 
-		return renamed;
+	private static DiffEntry exactCopy(DiffEntry src, DiffEntry dst) {
+		return DiffEntry.pair(ChangeType.COPY, src, dst, EXACT_RENAME_SCORE);
 	}
 }

org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java

@@ -0,0 +1,295 @@
+/*
+ * Copyright (C) 2010, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.diff;
+
+import java.util.Arrays;
+
+import org.eclipse.jgit.lib.ObjectLoader;
+
+/**
+ * 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.
+ * <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
+ * (closer to 2 KiB), but may grow as more distinct blocks within the scanned
+ * file are discovered.
+ */
+class SimilarityIndex {
+	/** The {@link #idHash} table stops growing at {@code 1 << MAX_HASH_BITS}. */
+	private static final int MAX_HASH_BITS = 17;
+
+	/** The {@link #idHash} table will not grow bigger than this, ever. */
+	private static final int MAX_HASH_SIZE = 1 << MAX_HASH_BITS;
+
+	/** Prime just before {@link #MAX_HASH_SIZE}. */
+	private static final int P = 131071;
+
+	/**
+	 * Shift to apply before storing a key.
+	 * <p>
+	 * Within the 64 bit table record space, we leave the highest bit unset so
+	 * all values are positive, and we need {@link #MAX_HASH_BITS} bits for the
+	 * keys. The lower 32 bits are used to count bytes impacted.
+	 */
+	private static final int KEY_SHIFT = 64 - 1 - MAX_HASH_BITS;
+
+	/** Total size of the file we hashed into the structure. */
+	private long fileSize;
+
+	/** Number of non-zero entries in {@link #idHash}. */
+	private int idSize;
+
+	/**
+	 * Pairings of content keys and counters.
+	 * <p>
+	 * Slots in the table are actually two ints wedged into a single long. The
+	 * upper {@link #MAX_HASH_BITS} bits stores the content key, and the
+	 * remaining lower bits stores the number of bytes associated with that key.
+	 * Empty slots are denoted by 0, which cannot occur because the count cannot
+	 * be 0. Values can only be positive, which we enforce during key addition.
+	 */
+	private long[] idHash;
+
+	SimilarityIndex() {
+		idHash = new long[256];
+	}
+
+	long getFileSize() {
+		return fileSize;
+	}
+
+	void setFileSize(long size) {
+		fileSize = size;
+	}
+
+	void hash(ObjectLoader obj) {
+		byte[] raw = obj.getCachedBytes();
+		setFileSize(raw.length);
+		hash(raw, 0, raw.length);
+	}
+
+	void hash(byte[] raw, int ptr, final int end) {
+		while (ptr < end) {
+			int hash = 5381;
+			int start = ptr;
+
+			// Hash one line, or one block, whichever occurs first.
+			do {
+				int c = raw[ptr++] & 0xff;
+				if (c == '\n')
+					break;
+				hash = (hash << 5) ^ c;
+			} while (ptr < end && ptr - start < 64);
+			add(hash, ptr - start);
+		}
+	}
+
+	/**
+	 * Sort the internal table so it can be used for efficient scoring.
+	 * <p>
+	 * Once sorted, additional lines/blocks cannot be added to the index.
+	 */
+	void sort() {
+		// Sort the array. All of the empty space will wind up at the front,
+		// because we forced all of the keys to always be positive. Later
+		// we only work with the back half of the array.
+		//
+		Arrays.sort(idHash);
+	}
+
+	int score(SimilarityIndex dst) {
+		long max = Math.max(fileSize, dst.fileSize);
+		return (int) ((common(dst) * 100L) / max);
+	}
+
+	int common(SimilarityIndex dst) {
+		return common(this, dst);
+	}
+
+	private static int common(SimilarityIndex src, SimilarityIndex dst) {
+		int srcIdx = src.packedIndex(0);
+		int dstIdx = dst.packedIndex(0);
+		long[] srcHash = src.idHash;
+		long[] dstHash = dst.idHash;
+		return common(srcHash, srcIdx, dstHash, dstIdx);
+	}
+
+	private static int common(long[] srcHash, int srcIdx, //
+			long[] dstHash, int dstIdx) {
+		if (srcIdx == srcHash.length || dstIdx == dstHash.length)
+			return 0;
+
+		int common = 0;
+		int srcKey = keyOf(srcHash[srcIdx]);
+		int dstKey = keyOf(dstHash[dstIdx]);
+
+		for (;;) {
+			if (srcKey == dstKey) {
+				common += countOf(dstHash[dstIdx]);
+
+				if (++srcIdx == srcHash.length)
+					break;
+				srcKey = keyOf(srcHash[srcIdx]);
+
+				if (++dstIdx == dstHash.length)
+					break;
+				dstKey = keyOf(dstHash[dstIdx]);
+
+			} else if (srcKey < dstKey) {
+				// Regions of src which do not appear in dst.
+				if (++srcIdx == srcHash.length)
+					break;
+				srcKey = keyOf(srcHash[srcIdx]);
+
+			} else /* if (srcKey > dstKey) */{
+				// Regions of dst which do not appear in dst.
+				if (++dstIdx == dstHash.length)
+					break;
+				dstKey = keyOf(dstHash[dstIdx]);
+			}
+		}
+
+		return common;
+	}
+
+	// Testing only
+	int size() {
+		return idSize;
+	}
+
+	// Testing only
+	int key(int idx) {
+		return keyOf(idHash[packedIndex(idx)]);
+	}
+
+	// Testing only
+	long count(int idx) {
+		return countOf(idHash[packedIndex(idx)]);
+	}
+
+	// Brute force approach only for testing.
+	int findIndex(int key) {
+		for (int i = 0; i < idSize; i++)
+			if (key(i) == key)
+				return i;
+		return -1;
+	}
+
+	private int packedIndex(int idx) {
+		return (idHash.length - idSize) + idx;
+	}
+
+	void add(int key, int cnt) {
+		key = hash(key);
+		int j = slot(key);
+		for (;;) {
+			long v = idHash[j];
+			if (v == 0) {
+				// Empty slot in the table, store here.
+				if (shouldGrow()) {
+					grow();
+					j = slot(key);
+					continue;
+				}
+				idHash[j] = (((long) key) << KEY_SHIFT) | cnt;
+				idSize++;
+				return;
+
+			} else if (keyOf(v) == key) {
+				// Same key, increment the counter.
+				idHash[j] = v + cnt;
+				return;
+
+			} else if (++j >= idHash.length) {
+				j = 0;
+			}
+		}
+	}
+
+	private static int hash(int key) {
+		// Make the key fit into our table. Since we have a maximum size
+		// that we cap the table at, all keys get squashed before going
+		// into the table. This prevents overflow.
+		//
+		return (key >>> 1) % P;
+	}
+
+	private int slot(int key) {
+		return key % idHash.length;
+	}
+
+	private boolean shouldGrow() {
+		int n = idHash.length;
+		return n < MAX_HASH_SIZE && n <= idSize * 2;
+	}
+
+	private void grow() {
+		long[] oldHash = idHash;
+		int oldSize = idHash.length;
+
+		idHash = new long[2 * oldSize];
+		for (int i = 0; i < oldSize; i++) {
+			long v = oldHash[i];
+			if (v != 0) {
+				int j = slot(keyOf(v));
+				while (idHash[j] != 0)
+					if (++j >= idHash.length)
+						j = 0;
+				idHash[j] = v;
+			}
+		}
+	}
+
+	private static int keyOf(long v) {
+		return (int) (v >>> KEY_SHIFT);
+	}
+
+	private static int countOf(long v) {
+		return (int) v;
+	}
+}

org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityRenameDetector.java

@@ -0,0 +1,295 @@
+/*
+ * Copyright (C) 2010, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.diff;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.eclipse.jgit.JGitText;
+import org.eclipse.jgit.diff.DiffEntry.ChangeType;
+import org.eclipse.jgit.lib.FileMode;
+import org.eclipse.jgit.lib.NullProgressMonitor;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ProgressMonitor;
+import org.eclipse.jgit.lib.Repository;
+
+class SimilarityRenameDetector {
+	/**
+	 * Number of bits we need to express an index into src or dst list.
+	 * <p>
+	 * This must be 28, giving us a limit of 2^28 entries in either list, which
+	 * is an insane limit of 536,870,912 file names being considered in a single
+	 * rename pass. The other 8 bits are used to store the score, while staying
+	 * under 127 so the long doesn't go negative.
+	 */
+	private static final int BITS_PER_INDEX = 28;
+
+	private static final int INDEX_MASK = (1 << BITS_PER_INDEX) - 1;
+
+	private static final int SCORE_SHIFT = 2 * BITS_PER_INDEX;
+
+	private final Repository repo;
+
+	/**
+	 * All sources to consider for copies or renames.
+	 * <p>
+	 * A source is typically a {@link ChangeType#DELETE} change, but could be
+	 * another type when trying to perform copy detection concurrently with
+	 * rename detection.
+	 */
+	private List<DiffEntry> srcs;
+
+	/**
+	 * All destinations to consider looking for a rename.
+	 * <p>
+	 * A destination is typically an {@link ChangeType#ADD}, as the name has
+	 * just come into existence, and we want to discover where its initial
+	 * content came from.
+	 */
+	private List<DiffEntry> dsts;
+
+	/**
+	 * Matrix of all examined file pairs, and their scores.
+	 * <p>
+	 * The upper 8 bits of each long stores the score, but the score is bounded
+	 * to be in the range (0, 128] so that the highest bit is never set, and all
+	 * entries are therefore positive.
+	 * <p>
+	 * List indexes to an element of {@link #srcs} and {@link #dsts} are encoded
+	 * as the lower two groups of 28 bits, respectively, but the encoding is
+	 * inverted, so that 0 is expressed as {@code (1 << 28) - 1}. This sorts
+	 * lower list indices later in the matrix, giving precedence to files whose
+	 * names sort earlier in the tree.
+	 */
+	private long[] matrix;
+
+	/** Score a pair must exceed to be considered a rename. */
+	private int renameScore = 60;
+
+	private List<DiffEntry> out;
+
+	SimilarityRenameDetector(Repository repo, List<DiffEntry> srcs,
+			List<DiffEntry> dsts) {
+		this.repo = repo;
+		this.srcs = srcs;
+		this.dsts = dsts;
+	}
+
+	void setRenameScore(int score) {
+		renameScore = score;
+	}
+
+	void compute(ProgressMonitor pm) throws IOException {
+		if (pm == null)
+			pm = NullProgressMonitor.INSTANCE;
+
+		pm.beginTask(JGitText.get().renamesFindingByContent, //
+				2 * srcs.size() * dsts.size());
+
+		int mNext = buildMatrix(pm);
+		out = new ArrayList<DiffEntry>(Math.min(mNext, dsts.size()));
+
+		// Match rename pairs on a first come, first serve basis until
+		// we have looked at everything that is above our minimum score.
+		//
+		for (--mNext; mNext >= 0; mNext--) {
+			long ent = matrix[mNext];
+			int sIdx = srcFile(ent);
+			int dIdx = dstFile(ent);
+			DiffEntry s = srcs.get(sIdx);
+			DiffEntry d = dsts.get(dIdx);
+
+			if (d == null) {
+				pm.update(1);
+				continue; // was already matched earlier
+			}
+
+			ChangeType type;
+			if (s.changeType == ChangeType.DELETE) {
+				// First use of this source file. Tag it as a rename so we
+				// later know it is already been used as a rename, other
+				// matches (if any) will claim themselves as copies instead.
+				//
+				s.changeType = ChangeType.RENAME;
+				type = ChangeType.RENAME;
+			} else {
+				type = ChangeType.COPY;
+			}
+
+			out.add(DiffEntry.pair(type, s, d, score(ent)));
+			dsts.set(dIdx, null); // Claim the destination was matched.
+			pm.update(1);
+		}
+
+		srcs = compactSrcList(srcs);
+		dsts = compactDstList(dsts);
+		pm.endTask();
+	}
+
+	List<DiffEntry> getMatches() {
+		return out;
+	}
+
+	List<DiffEntry> getLeftOverSources() {
+		return srcs;
+	}
+
+	List<DiffEntry> getLeftOverDestinations() {
+		return dsts;
+	}
+
+	private static List<DiffEntry> compactSrcList(List<DiffEntry> in) {
+		ArrayList<DiffEntry> r = new ArrayList<DiffEntry>(in.size());
+		for (DiffEntry e : in) {
+			if (e.changeType == ChangeType.DELETE)
+				r.add(e);
+		}
+		return r;
+	}
+
+	private static List<DiffEntry> compactDstList(List<DiffEntry> in) {
+		ArrayList<DiffEntry> r = new ArrayList<DiffEntry>(in.size());
+		for (DiffEntry e : in) {
+			if (e != null)
+				r.add(e);
+		}
+		return r;
+	}
+
+	private int buildMatrix(ProgressMonitor pm) throws IOException {
+		// Allocate for the worst-case scenario where every pair has a
+		// score that we need to consider. We might not need that many.
+		//
+		matrix = new long[srcs.size() * dsts.size()];
+
+		// Consider each pair of files, if the score is above the minimum
+		// threshold we need record that scoring in the matrix so we can
+		// later find the best matches.
+		//
+		int mNext = 0;
+		for (int srcIdx = 0; srcIdx < srcs.size(); srcIdx++) {
+			DiffEntry srcEnt = srcs.get(srcIdx);
+			if (!isFile(srcEnt.oldMode)) {
+				pm.update(dsts.size());
+				continue;
+			}
+
+			SimilarityIndex s = hash(srcEnt.oldId.toObjectId());
+			for (int dstIdx = 0; dstIdx < dsts.size(); dstIdx++) {
+				DiffEntry dstEnt = dsts.get(dstIdx);
+
+				if (!isFile(dstEnt.newMode)) {
+					pm.update(1);
+					continue;
+				}
+
+				if (!RenameDetector.sameType(srcEnt.oldMode, dstEnt.newMode)) {
+					pm.update(1);
+					continue;
+				}
+
+				SimilarityIndex d = hash(dstEnt.newId.toObjectId());
+				int score = s.score(d);
+
+				if (score < renameScore) {
+					pm.update(1);
+					continue;
+				}
+
+				matrix[mNext++] = encode(score, srcIdx, dstIdx);
+				pm.update(1);
+			}
+		}
+
+		// Sort everything in the range we populated, which might be the
+		// entire matrix, or just a smaller slice if we had some bad low
+		// scoring pairs.
+		//
+		Arrays.sort(matrix, 0, mNext);
+		return mNext;
+	}
+
+	private SimilarityIndex hash(ObjectId objectId) throws IOException {
+		SimilarityIndex r = new SimilarityIndex();
+		r.hash(repo.openObject(objectId));
+		r.sort();
+		return r;
+	}
+
+	private static int score(long value) {
+		return (int) (value >>> SCORE_SHIFT);
+	}
+
+	private static int srcFile(long value) {
+		return decodeFile(((int) (value >>> BITS_PER_INDEX)) & INDEX_MASK);
+	}
+
+	private static int dstFile(long value) {
+		return decodeFile(((int) value) & INDEX_MASK);
+	}
+
+	private static long encode(int score, int srcIdx, int dstIdx) {
+		return (((long) score) << SCORE_SHIFT) //
+				| (encodeFile(srcIdx) << BITS_PER_INDEX) //
+				| encodeFile(dstIdx);
+	}
+
+	private static long encodeFile(int idx) {
+		// We invert the index so that the first file in the list sorts
+		// later in the table. This permits us to break ties favoring
+		// earlier names over later ones.
+		//
+		return INDEX_MASK - idx;
+	}
+
+	private static int decodeFile(int v) {
+		return INDEX_MASK - v;
+	}
+
+	private static boolean isFile(FileMode mode) {
+		return (mode.getBits() & FileMode.TYPE_MASK) == FileMode.TYPE_FILE;
+	}
+}

org.eclipse.jgit/src/org/eclipse/jgit/patch/FileHeader.java

@@ -71,9 +71,6 @@ import org.eclipse.jgit.util.TemporaryBuffer;
 
 /** Patch header describing an action for a single file path. */
 public class FileHeader extends DiffEntry {
-	/** Magical file name used for file adds or deletes. */
-	public static final String DEV_NULL = "/dev/null";
-
 	private static final byte[] OLD_MODE = encodeASCII("old mode ");
 
 	private static final byte[] NEW_MODE = encodeASCII("new mode ");