/*
    * Copyright (C) 2012, 2020 Robin Stocker <robin@nibor.org> and others
    *
    * This program and the accompanying materials are made available under the
    * terms of the Eclipse Distribution License v. 1.0 which is available at
    * https://www.eclipse.org/org/documents/edl-v10.php.
    *
    * SPDX-License-Identifier: BSD-3-Clause
    */
  package org.eclipse.jgit.merge;
  
  import static java.nio.charset.StandardCharsets.UTF_8;
  import static java.time.Instant.EPOCH;
  import static org.eclipse.jgit.lib.Constants.OBJ_BLOB;
  import static org.junit.Assert.assertEquals;
  import static org.junit.Assert.assertFalse;
  import static org.junit.Assert.assertNotNull;
  import static org.junit.Assert.assertNull;
  import static org.junit.Assert.assertTrue;
  
  import java.io.ByteArrayOutputStream;
  import java.io.File;
  import java.io.FileInputStream;
  import java.io.IOException;
  import java.time.Instant;
  import java.util.Arrays;
  import java.util.Map;
  
  import org.eclipse.jgit.api.Git;
  import org.eclipse.jgit.api.MergeResult;
  import org.eclipse.jgit.api.MergeResult.MergeStatus;
  import org.eclipse.jgit.api.RebaseResult;
  import org.eclipse.jgit.api.errors.CheckoutConflictException;
  import org.eclipse.jgit.api.errors.GitAPIException;
  import org.eclipse.jgit.api.errors.JGitInternalException;
  import org.eclipse.jgit.diff.RawText;
  import org.eclipse.jgit.dircache.DirCache;
  import org.eclipse.jgit.dircache.DirCacheEditor;
  import org.eclipse.jgit.dircache.DirCacheEntry;
  import org.eclipse.jgit.errors.ConfigInvalidException;
  import org.eclipse.jgit.errors.NoMergeBaseException;
  import org.eclipse.jgit.errors.NoMergeBaseException.MergeBaseFailureReason;
  import org.eclipse.jgit.junit.RepositoryTestCase;
  import org.eclipse.jgit.junit.TestRepository;
  import org.eclipse.jgit.lib.AnyObjectId;
  import org.eclipse.jgit.lib.ConfigConstants;
  import org.eclipse.jgit.lib.Constants;
  import org.eclipse.jgit.lib.FileMode;
  import org.eclipse.jgit.lib.ObjectId;
  import org.eclipse.jgit.lib.ObjectInserter;
  import org.eclipse.jgit.lib.ObjectLoader;
  import org.eclipse.jgit.lib.ObjectReader;
  import org.eclipse.jgit.lib.ObjectStream;
  import org.eclipse.jgit.lib.StoredConfig;
  import org.eclipse.jgit.merge.ResolveMerger.MergeFailureReason;
  import org.eclipse.jgit.revwalk.RevCommit;
  import org.eclipse.jgit.revwalk.RevObject;
  import org.eclipse.jgit.revwalk.RevTree;
  import org.eclipse.jgit.revwalk.RevWalk;
  import org.eclipse.jgit.storage.file.FileBasedConfig;
  import org.eclipse.jgit.treewalk.FileTreeIterator;
  import org.eclipse.jgit.util.FS;
  import org.eclipse.jgit.util.FileUtils;
  import org.junit.Assert;
  import org.junit.experimental.theories.DataPoints;
  import org.junit.experimental.theories.Theories;
  import org.junit.experimental.theories.Theory;
  import org.junit.runner.RunWith;
  
  @RunWith(Theories.class)
  public class MergerTest extends RepositoryTestCase {
  
  	@DataPoints
  	public static MergeStrategy[] strategiesUnderTest = new MergeStrategy[] {
  			MergeStrategy.RECURSIVE, MergeStrategy.RESOLVE };
  
  	@Theory
  	public void failingDeleteOfDirectoryWithUntrackedContent(
  			MergeStrategy strategy) throws Exception {
  		File folder1 = new File(db.getWorkTree(), "folder1");
  		FileUtils.mkdir(folder1);
  		File file = new File(folder1, "file1.txt");
  		write(file, "folder1--file1.txt");
  		file = new File(folder1, "file2.txt");
  		write(file, "folder1--file2.txt");
  
  		try (Git git = new Git(db)) {
  			git.add().addFilepattern(folder1.getName()).call();
  			RevCommit base = git.commit().setMessage("adding folder").call();
  
  			recursiveDelete(folder1);
  			git.rm().addFilepattern("folder1/file1.txt")
  					.addFilepattern("folder1/file2.txt").call();
  			RevCommit other = git.commit()
  					.setMessage("removing folders on 'other'").call();
  
  			git.checkout().setName(base.name()).call();
  
  			file = new File(db.getWorkTree(), "unrelated.txt");
 			write(file, "unrelated");
 
 			git.add().addFilepattern("unrelated.txt").call();
 			RevCommit head = git.commit().setMessage("Adding another file").call();
 
 			// Untracked file to cause failing path for delete() of folder1
 			// but that's ok.
 			file = new File(folder1, "file3.txt");
 			write(file, "folder1--file3.txt");
 
 			ResolveMerger merger = (ResolveMerger) strategy.newMerger(db, false);
 			merger.setCommitNames(new String[] { "BASE", "HEAD", "other" });
 			merger.setWorkingTreeIterator(new FileTreeIterator(db));
 			boolean ok = merger.merge(head.getId(), other.getId());
 			assertTrue(ok);
 			assertTrue(file.exists());
 		}
 	}
 
 	/**
 	 * Merging two conflicting subtrees when the index does not contain any file
 	 * in that subtree should lead to a conflicting state.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkMergeConflictingTreesWithoutIndex(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("d/1", "orig");
 		git.add().addFilepattern("d/1").call();
 		RevCommit first = git.commit().setMessage("added d/1").call();
 
 		writeTrashFile("d/1", "master");
 		RevCommit masterCommit = git.commit().setAll(true)
 				.setMessage("modified d/1 on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("d/1", "side");
 		git.commit().setAll(true).setMessage("modified d/1 on side").call();
 
 		git.rm().addFilepattern("d/1").call();
 		git.rm().addFilepattern("d").call();
 		MergeResult mergeRes = git.merge().setStrategy(strategy)
 				.include(masterCommit).call();
 		assertEquals(MergeStatus.CONFLICTING, mergeRes.getMergeStatus());
 		assertEquals(
 				"[d/1, mode:100644, stage:1, content:orig][d/1, mode:100644, stage:2, content:side][d/1, mode:100644, stage:3, content:master]",
 				indexState(CONTENT));
 	}
 
 	/**
 	 * Merging two different but mergeable subtrees when the index does not
 	 * contain any file in that subtree should lead to a merged state.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkMergeMergeableTreesWithoutIndex(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("d/1", "1\n2\n3");
 		git.add().addFilepattern("d/1").call();
 		RevCommit first = git.commit().setMessage("added d/1").call();
 
 		writeTrashFile("d/1", "1master\n2\n3");
 		RevCommit masterCommit = git.commit().setAll(true)
 				.setMessage("modified d/1 on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("d/1", "1\n2\n3side");
 		git.commit().setAll(true).setMessage("modified d/1 on side").call();
 
 		git.rm().addFilepattern("d/1").call();
 		git.rm().addFilepattern("d").call();
 		MergeResult mergeRes = git.merge().setStrategy(strategy)
 				.include(masterCommit).call();
 		assertEquals(MergeStatus.MERGED, mergeRes.getMergeStatus());
 		assertEquals("[d/1, mode:100644, content:1master\n2\n3side]",
 				indexState(CONTENT));
 	}
 
 	/**
 	 * An existing directory without tracked content should not prevent merging
 	 * a tree where that directory exists.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkUntrackedFolderIsNotAConflict(
 			MergeStrategy strategy) throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("d/1", "1");
 		git.add().addFilepattern("d/1").call();
 		RevCommit first = git.commit().setMessage("added d/1").call();
 
 		writeTrashFile("e/1", "4");
 		git.add().addFilepattern("e/1").call();
 		RevCommit masterCommit = git.commit().setMessage("added e/1").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("f/1", "5");
 		git.add().addFilepattern("f/1").call();
 		git.commit().setAll(true).setMessage("added f/1")
 				.call();
 
 		// Untracked directory e shall not conflict with merged e/1
 		writeTrashFile("e/2", "d two");
 
 		MergeResult mergeRes = git.merge().setStrategy(strategy)
 				.include(masterCommit).call();
 		assertEquals(MergeStatus.MERGED, mergeRes.getMergeStatus());
 		assertEquals(
 				"[d/1, mode:100644, content:1][e/1, mode:100644, content:4][f/1, mode:100644, content:5]",
 				indexState(CONTENT));
 	}
 
 	/**
 	 * A tracked file is replaced by a folder in THEIRS.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkFileReplacedByFolderInTheirs(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("sub", "file");
 		git.add().addFilepattern("sub").call();
 		RevCommit first = git.commit().setMessage("initial").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 
 		git.rm().addFilepattern("sub").call();
 		writeTrashFile("sub/file", "subfile");
 		git.add().addFilepattern("sub/file").call();
 		RevCommit masterCommit = git.commit().setMessage("file -> folder")
 				.call();
 
 		git.checkout().setName("master").call();
 		writeTrashFile("noop", "other");
 		git.add().addFilepattern("noop").call();
 		git.commit().setAll(true).setMessage("noop").call();
 
 		MergeResult mergeRes = git.merge().setStrategy(strategy)
 				.include(masterCommit).call();
 		assertEquals(MergeStatus.MERGED, mergeRes.getMergeStatus());
 		assertEquals(
 				"[noop, mode:100644, content:other][sub/file, mode:100644, content:subfile]",
 				indexState(CONTENT));
 	}
 
 	/**
 	 * A tracked file is replaced by a folder in OURS.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkFileReplacedByFolderInOurs(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("sub", "file");
 		git.add().addFilepattern("sub").call();
 		RevCommit first = git.commit().setMessage("initial").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("noop", "other");
 		git.add().addFilepattern("noop").call();
 		RevCommit sideCommit = git.commit().setAll(true).setMessage("noop")
 				.call();
 
 		git.checkout().setName("master").call();
 		git.rm().addFilepattern("sub").call();
 		writeTrashFile("sub/file", "subfile");
 		git.add().addFilepattern("sub/file").call();
 		git.commit().setMessage("file -> folder")
 				.call();
 
 		MergeResult mergeRes = git.merge().setStrategy(strategy)
 				.include(sideCommit).call();
 		assertEquals(MergeStatus.MERGED, mergeRes.getMergeStatus());
 		assertEquals(
 				"[noop, mode:100644, content:other][sub/file, mode:100644, content:subfile]",
 				indexState(CONTENT));
 	}
 
 	/**
 	 * An existing directory without tracked content should not prevent merging
 	 * a file with that name.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkUntrackedEmpytFolderIsNotAConflictWithFile(
 			MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("d/1", "1");
 		git.add().addFilepattern("d/1").call();
 		RevCommit first = git.commit().setMessage("added d/1").call();
 
 		writeTrashFile("e", "4");
 		git.add().addFilepattern("e").call();
 		RevCommit masterCommit = git.commit().setMessage("added e").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("f/1", "5");
 		git.add().addFilepattern("f/1").call();
 		git.commit().setAll(true).setMessage("added f/1").call();
 
 		// Untracked empty directory hierarcy e/1 shall not conflict with merged
 		// e/1
 		FileUtils.mkdirs(new File(trash, "e/1"), true);
 
 		MergeResult mergeRes = git.merge().setStrategy(strategy)
 				.include(masterCommit).call();
 		assertEquals(MergeStatus.MERGED, mergeRes.getMergeStatus());
 		assertEquals(
 				"[d/1, mode:100644, content:1][e, mode:100644, content:4][f/1, mode:100644, content:5]",
 				indexState(CONTENT));
 	}
 
 	@Theory
 	public void mergeWithCrlfInWT(MergeStrategy strategy) throws IOException,
 			GitAPIException {
 		Git git = Git.wrap(db);
 		db.getConfig().setString("core", null, "autocrlf", "false");
 		db.getConfig().save();
 		writeTrashFile("crlf.txt", "some\r\ndata\r\n");
 		git.add().addFilepattern("crlf.txt").call();
 		git.commit().setMessage("base").call();
 
 		git.branchCreate().setName("brancha").call();
 
 		writeTrashFile("crlf.txt", "some\r\nmore\r\ndata\r\n");
 		git.add().addFilepattern("crlf.txt").call();
 		git.commit().setMessage("on master").call();
 
 		git.checkout().setName("brancha").call();
 		writeTrashFile("crlf.txt", "some\r\ndata\r\ntoo\r\n");
 		git.add().addFilepattern("crlf.txt").call();
 		git.commit().setMessage("on brancha").call();
 
 		db.getConfig().setString("core", null, "autocrlf", "input");
 		db.getConfig().save();
 
 		MergeResult mergeResult = git.merge().setStrategy(strategy)
 				.include(db.resolve("master"))
 				.call();
 		assertEquals(MergeResult.MergeStatus.MERGED,
 				mergeResult.getMergeStatus());
 	}
 
 	@Theory
 	public void mergeConflictWithCrLfTextAuto(MergeStrategy strategy)
 			throws IOException, GitAPIException {
 		Git git = Git.wrap(db);
 		writeTrashFile("crlf.txt", "a crlf file\r\n");
 		git.add().addFilepattern("crlf.txt").call();
 		git.commit().setMessage("base").call();
 		assertEquals("[crlf.txt, mode:100644, content:a crlf file\r\n]",
 				indexState(CONTENT));
 		writeTrashFile(".gitattributes", "crlf.txt text=auto");
 		git.add().addFilepattern(".gitattributes").call();
 		git.commit().setMessage("attributes").call();
 
 		git.branchCreate().setName("brancha").call();
 
 		writeTrashFile("crlf.txt", "a crlf file\r\na second line\r\n");
 		git.add().addFilepattern("crlf.txt").call();
 		git.commit().setMessage("on master").call();
 		assertEquals(
 				"[.gitattributes, mode:100644, content:crlf.txt text=auto]"
 						+ "[crlf.txt, mode:100644, content:a crlf file\r\na second line\r\n]",
 				indexState(CONTENT));
 
 		git.checkout().setName("brancha").call();
 		File testFile = writeTrashFile("crlf.txt",
 				"a crlf file\r\nanother line\r\n");
 		git.add().addFilepattern("crlf.txt").call();
 		git.commit().setMessage("on brancha").call();
 
 		MergeResult mergeResult = git.merge().setStrategy(strategy)
 				.include(db.resolve("master")).call();
 		assertEquals(MergeResult.MergeStatus.CONFLICTING,
 				mergeResult.getMergeStatus());
 		checkFile(testFile,
 				"a crlf file\r\n" //
 						+ "<<<<<<< HEAD\n" //
 						+ "another line\r\n" //
 						+ "=======\n" //
 						+ "a second line\r\n" //
 						+ ">>>>>>> 8e9e704742f1bc8a41eac88aac4aeefd338b7384\n");
 	}
 
 	@Theory
 	public void mergeWithCrlfAutoCrlfTrue(MergeStrategy strategy)
 			throws IOException, GitAPIException {
 		Git git = Git.wrap(db);
 		db.getConfig().setString("core", null, "autocrlf", "true");
 		db.getConfig().save();
 		writeTrashFile("crlf.txt", "a crlf file\r\n");
 		git.add().addFilepattern("crlf.txt").call();
 		git.commit().setMessage("base").call();
 
 		git.branchCreate().setName("brancha").call();
 
 		writeTrashFile("crlf.txt", "a crlf file\r\na second line\r\n");
 		git.add().addFilepattern("crlf.txt").call();
 		git.commit().setMessage("on master").call();
 
 		git.checkout().setName("brancha").call();
 		File testFile = writeTrashFile("crlf.txt",
 				"a first line\r\na crlf file\r\n");
 		git.add().addFilepattern("crlf.txt").call();
 		git.commit().setMessage("on brancha").call();
 
 		MergeResult mergeResult = git.merge().setStrategy(strategy)
 				.include(db.resolve("master")).call();
 		assertEquals(MergeResult.MergeStatus.MERGED,
 				mergeResult.getMergeStatus());
 		checkFile(testFile, "a first line\r\na crlf file\r\na second line\r\n");
 		assertEquals(
 				"[crlf.txt, mode:100644, content:a first line\na crlf file\na second line\n]",
 				indexState(CONTENT));
 	}
 
 	@Theory
 	public void rebaseWithCrlfAutoCrlfTrue(MergeStrategy strategy)
 			throws IOException, GitAPIException {
 		Git git = Git.wrap(db);
 		db.getConfig().setString("core", null, "autocrlf", "true");
 		db.getConfig().save();
 		writeTrashFile("crlf.txt", "line 1\r\nline 2\r\nline 3\r\n");
 		git.add().addFilepattern("crlf.txt").call();
 		RevCommit first = git.commit().setMessage("base").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("brancha").call();
 
 		File testFile = writeTrashFile("crlf.txt",
 				"line 1\r\nmodified line\r\nline 3\r\n");
 		git.add().addFilepattern("crlf.txt").call();
 		git.commit().setMessage("on brancha").call();
 
 		git.checkout().setName("master").call();
 		File otherFile = writeTrashFile("otherfile.txt", "a line\r\n");
 		git.add().addFilepattern("otherfile.txt").call();
 		git.commit().setMessage("on master").call();
 
 		git.checkout().setName("brancha").call();
 		checkFile(testFile, "line 1\r\nmodified line\r\nline 3\r\n");
 		assertFalse(otherFile.exists());
 
 		RebaseResult rebaseResult = git.rebase().setStrategy(strategy)
 				.setUpstream(db.resolve("master")).call();
 		assertEquals(RebaseResult.Status.OK, rebaseResult.getStatus());
 		checkFile(testFile, "line 1\r\nmodified line\r\nline 3\r\n");
 		checkFile(otherFile, "a line\r\n");
 		assertEquals(
 				"[crlf.txt, mode:100644, content:line 1\nmodified line\nline 3\n]"
 						+ "[otherfile.txt, mode:100644, content:a line\n]",
 				indexState(CONTENT));
 	}
 
 	/**
 	 * Merging two equal subtrees when the index does not contain any file in
 	 * that subtree should lead to a merged state.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkMergeEqualTreesWithoutIndex(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("d/1", "orig");
 		git.add().addFilepattern("d/1").call();
 		RevCommit first = git.commit().setMessage("added d/1").call();
 
 		writeTrashFile("d/1", "modified");
 		RevCommit masterCommit = git.commit().setAll(true)
 				.setMessage("modified d/1 on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("d/1", "modified");
 		git.commit().setAll(true).setMessage("modified d/1 on side").call();
 
 		git.rm().addFilepattern("d/1").call();
 		git.rm().addFilepattern("d").call();
 		MergeResult mergeRes = git.merge().setStrategy(strategy)
 				.include(masterCommit).call();
 		assertEquals(MergeStatus.MERGED, mergeRes.getMergeStatus());
 		assertEquals("[d/1, mode:100644, content:modified]",
 				indexState(CONTENT));
 	}
 
 	/**
 	 * Merging two equal subtrees with an incore merger should lead to a merged
 	 * state.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkMergeEqualTreesInCore(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("d/1", "orig");
 		git.add().addFilepattern("d/1").call();
 		RevCommit first = git.commit().setMessage("added d/1").call();
 
 		writeTrashFile("d/1", "modified");
 		RevCommit masterCommit = git.commit().setAll(true)
 				.setMessage("modified d/1 on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("d/1", "modified");
 		RevCommit sideCommit = git.commit().setAll(true)
 				.setMessage("modified d/1 on side").call();
 
 		git.rm().addFilepattern("d/1").call();
 		git.rm().addFilepattern("d").call();
 
 		ThreeWayMerger resolveMerger = (ThreeWayMerger) strategy.newMerger(db,
 				true);
 		boolean noProblems = resolveMerger.merge(masterCommit, sideCommit);
 		assertTrue(noProblems);
 	}
 
 	/**
 	 * Merging two equal subtrees with an incore merger should lead to a merged
 	 * state, without using a Repository (the 'Gerrit' use case).
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkMergeEqualTreesInCore_noRepo(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("d/1", "orig");
 		git.add().addFilepattern("d/1").call();
 		RevCommit first = git.commit().setMessage("added d/1").call();
 
 		writeTrashFile("d/1", "modified");
 		RevCommit masterCommit = git.commit().setAll(true)
 				.setMessage("modified d/1 on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("d/1", "modified");
 		RevCommit sideCommit = git.commit().setAll(true)
 				.setMessage("modified d/1 on side").call();
 
 		git.rm().addFilepattern("d/1").call();
 		git.rm().addFilepattern("d").call();
 
 		try (ObjectInserter ins = db.newObjectInserter()) {
 			ThreeWayMerger resolveMerger =
 					(ThreeWayMerger) strategy.newMerger(ins, db.getConfig());
 			boolean noProblems = resolveMerger.merge(masterCommit, sideCommit);
 			assertTrue(noProblems);
 		}
 	}
 
 	/**
 	 * Merging two equal subtrees when the index and HEAD does not contain any
 	 * file in that subtree should lead to a merged state.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkMergeEqualNewTrees(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("2", "orig");
 		git.add().addFilepattern("2").call();
 		RevCommit first = git.commit().setMessage("added 2").call();
 
 		writeTrashFile("d/1", "orig");
 		git.add().addFilepattern("d/1").call();
 		RevCommit masterCommit = git.commit().setAll(true)
 				.setMessage("added d/1 on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("d/1", "orig");
 		git.add().addFilepattern("d/1").call();
 		git.commit().setAll(true).setMessage("added d/1 on side").call();
 
 		git.rm().addFilepattern("d/1").call();
 		git.rm().addFilepattern("d").call();
 		MergeResult mergeRes = git.merge().setStrategy(strategy)
 				.include(masterCommit).call();
 		assertEquals(MergeStatus.MERGED, mergeRes.getMergeStatus());
 		assertEquals(
 				"[2, mode:100644, content:orig][d/1, mode:100644, content:orig]",
 				indexState(CONTENT));
 	}
 
 	/**
 	 * Merging two conflicting subtrees when the index and HEAD does not contain
 	 * any file in that subtree should lead to a conflicting state.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkMergeConflictingNewTrees(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("2", "orig");
 		git.add().addFilepattern("2").call();
 		RevCommit first = git.commit().setMessage("added 2").call();
 
 		writeTrashFile("d/1", "master");
 		git.add().addFilepattern("d/1").call();
 		RevCommit masterCommit = git.commit().setAll(true)
 				.setMessage("added d/1 on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("d/1", "side");
 		git.add().addFilepattern("d/1").call();
 		git.commit().setAll(true).setMessage("added d/1 on side").call();
 
 		git.rm().addFilepattern("d/1").call();
 		git.rm().addFilepattern("d").call();
 		MergeResult mergeRes = git.merge().setStrategy(strategy)
 				.include(masterCommit).call();
 		assertEquals(MergeStatus.CONFLICTING, mergeRes.getMergeStatus());
 		assertEquals(
 				"[2, mode:100644, content:orig][d/1, mode:100644, stage:2, content:side][d/1, mode:100644, stage:3, content:master]",
 				indexState(CONTENT));
 	}
 
 	/**
 	 * Merging two conflicting files when the index contains a tree for that
 	 * path should lead to a failed state.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkMergeConflictingFilesWithTreeInIndex(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("0", "orig");
 		git.add().addFilepattern("0").call();
 		RevCommit first = git.commit().setMessage("added 0").call();
 
 		writeTrashFile("0", "master");
 		RevCommit masterCommit = git.commit().setAll(true)
 				.setMessage("modified 0 on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("0", "side");
 		git.commit().setAll(true).setMessage("modified 0 on side").call();
 
 		git.rm().addFilepattern("0").call();
 		writeTrashFile("0/0", "side");
 		git.add().addFilepattern("0/0").call();
 		MergeResult mergeRes = git.merge().setStrategy(strategy)
 				.include(masterCommit).call();
 		assertEquals(MergeStatus.FAILED, mergeRes.getMergeStatus());
 	}
 
 	/**
 	 * Merging two equal files when the index contains a tree for that path
 	 * should lead to a failed state.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkMergeMergeableFilesWithTreeInIndex(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("0", "orig");
 		writeTrashFile("1", "1\n2\n3");
 		git.add().addFilepattern("0").addFilepattern("1").call();
 		RevCommit first = git.commit().setMessage("added 0, 1").call();
 
 		writeTrashFile("1", "1master\n2\n3");
 		RevCommit masterCommit = git.commit().setAll(true)
 				.setMessage("modified 1 on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("1", "1\n2\n3side");
 		git.commit().setAll(true).setMessage("modified 1 on side").call();
 
 		git.rm().addFilepattern("0").call();
 		writeTrashFile("0/0", "modified");
 		git.add().addFilepattern("0/0").call();
 		try {
 			git.merge().setStrategy(strategy).include(masterCommit).call();
 			Assert.fail("Didn't get the expected exception");
 		} catch (CheckoutConflictException e) {
 			assertEquals(1, e.getConflictingPaths().size());
 			assertEquals("0/0", e.getConflictingPaths().get(0));
 		}
 	}
 
 	@Theory
 	public void checkContentMergeNoConflict(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("file", "1\n2\n3");
 		git.add().addFilepattern("file").call();
 		RevCommit first = git.commit().setMessage("added file").call();
 
 		writeTrashFile("file", "1master\n2\n3");
 		git.commit().setAll(true).setMessage("modified file on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("file", "1\n2\n3side");
 		RevCommit sideCommit = git.commit().setAll(true)
 				.setMessage("modified file on side").call();
 
 		git.checkout().setName("master").call();
 		MergeResult result =
 				git.merge().setStrategy(strategy).include(sideCommit).call();
 		assertEquals(MergeStatus.MERGED, result.getMergeStatus());
 		String expected = "1master\n2\n3side";
 		assertEquals(expected, read("file"));
 	}
 
 	@Theory
 	public void checkContentMergeNoConflict_noRepo(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("file", "1\n2\n3");
 		git.add().addFilepattern("file").call();
 		RevCommit first = git.commit().setMessage("added file").call();
 
 		writeTrashFile("file", "1master\n2\n3");
 		RevCommit masterCommit = git.commit().setAll(true)
 				.setMessage("modified file on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("file", "1\n2\n3side");
 		RevCommit sideCommit = git.commit().setAll(true)
 				.setMessage("modified file on side").call();
 
 		try (ObjectInserter ins = db.newObjectInserter()) {
 			ResolveMerger merger =
 					(ResolveMerger) strategy.newMerger(ins, db.getConfig());
 			boolean noProblems = merger.merge(masterCommit, sideCommit);
 			assertTrue(noProblems);
 			assertEquals("1master\n2\n3side",
 					readBlob(merger.getResultTreeId(), "file"));
 		}
 	}
 
 
 	/**
 	 * Merging a change involving large binary files should short-circuit reads.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkContentMergeLargeBinaries(MergeStrategy strategy) throws Exception {
 		Git git = Git.wrap(db);
 		final int LINELEN = 72;
 
 		// setup a merge that would work correctly if we disconsider the stray '\0'
 		// that the file contains near the start.
 		byte[] binary = new byte[LINELEN * 2000];
 		for (int i = 0; i < binary.length; i++) {
 			binary[i] = (byte)((i % LINELEN) == 0 ? '\n' : 'x');
 		}
 		binary[50] = '\0';
 
 		writeTrashFile("file", new String(binary, UTF_8));
 		git.add().addFilepattern("file").call();
 		RevCommit first = git.commit().setMessage("added file").call();
 
 		// Generate an edit in a single line.
 		int idx = LINELEN * 1200 + 1;
 		byte save = binary[idx];
 		binary[idx] = '@';
 		writeTrashFile("file", new String(binary, UTF_8));
 
 		binary[idx] = save;
 		git.add().addFilepattern("file").call();
 		RevCommit masterCommit = git.commit().setAll(true)
 			.setMessage("modified file l 1200").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first).setName("side").call();
 		binary[LINELEN * 1500 + 1] = '!';
 		writeTrashFile("file", new String(binary, UTF_8));
 		git.add().addFilepattern("file").call();
 		RevCommit sideCommit = git.commit().setAll(true)
 			.setMessage("modified file l 1500").call();
 
 		int originalBufferSize = RawText.getBufferSize();
 		int smallBufferSize = RawText.setBufferSize(8000);
 		try (ObjectInserter ins = db.newObjectInserter()) {
 			// Check that we don't read the large blobs.
 			ObjectInserter forbidInserter = new ObjectInserter.Filter() {
 				@Override
 				protected ObjectInserter delegate() {
 					return ins;
 				}
 
 				@Override
 				public ObjectReader newReader() {
 					return new BigReadForbiddenReader(super.newReader(),
 							smallBufferSize);
 				}
 			};
 
 			ResolveMerger merger =
 				(ResolveMerger) strategy.newMerger(forbidInserter, db.getConfig());
 			boolean noProblems = merger.merge(masterCommit, sideCommit);
 			assertFalse(noProblems);
 		} finally {
 			RawText.setBufferSize(originalBufferSize);
 		}
 	}
 
 	/**
 	 * Throws an exception if reading beyond limit.
 	 */
 	static class BigReadForbiddenStream extends ObjectStream.Filter {
 		long limit;
 
 		BigReadForbiddenStream(ObjectStream orig, long limit) {
 			super(orig.getType(), orig.getSize(), orig);
 			this.limit = limit;
 		}
 
 		@Override
 		public long skip(long n) throws IOException {
 			limit -= n;
 			if (limit < 0) {
 				throw new IllegalStateException();
 			}
 
 			return super.skip(n);
 		}
 
 		@Override
 		public int read() throws IOException {
 			int r = super.read();
 			limit--;
 			if (limit < 0) {
 				throw new IllegalStateException();
 			}
 			return r;
 		}
 
 		@Override
 		public int read(byte[] b, int off, int len) throws IOException {
 			int n = super.read(b, off, len);
 			limit -= n;
 			if (limit < 0) {
 				throw new IllegalStateException();
 			}
 			return n;
 		}
 	}
 
 	static class BigReadForbiddenReader extends ObjectReader.Filter {
 		ObjectReader delegate;
 		int limit;
 
 		@Override
 		protected ObjectReader delegate() {
 			return delegate;
 		}
 
 		BigReadForbiddenReader(ObjectReader delegate, int limit) {
 			this.delegate = delegate;
 			this.limit = limit;
 		}
 
 		@Override
 		public ObjectLoader open(AnyObjectId objectId, int typeHint) throws IOException {
 			ObjectLoader orig = super.open(objectId, typeHint);
 			return new ObjectLoader.Filter() {
 				@Override
 				protected ObjectLoader delegate() {
 					return orig;
 				}
 
 				@Override
 				public ObjectStream openStream() throws IOException {
 					ObjectStream os = orig.openStream();
 					return new BigReadForbiddenStream(os, limit);
 				}
 			};
 		}
 	}
 
 	@Theory
 	public void checkContentMergeConflict(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("file", "1\n2\n3");
 		git.add().addFilepattern("file").call();
 		RevCommit first = git.commit().setMessage("added file").call();
 
 		writeTrashFile("file", "1master\n2\n3");
 		git.commit().setAll(true).setMessage("modified file on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("file", "1side\n2\n3");
 		RevCommit sideCommit = git.commit().setAll(true)
 				.setMessage("modified file on side").call();
 
 		git.checkout().setName("master").call();
 		MergeResult result =
 				git.merge().setStrategy(strategy).include(sideCommit).call();
 		assertEquals(MergeStatus.CONFLICTING, result.getMergeStatus());
 		String expected = "<<<<<<< HEAD\n"
 				+ "1master\n"
 				+ "=======\n"
 				+ "1side\n"
 				+ ">>>>>>> " + sideCommit.name() + "\n"
 				+ "2\n"
 				+ "3";
 		assertEquals(expected, read("file"));
 	}
 
 	@Theory
 	public void checkContentMergeConflict_noTree(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("file", "1\n2\n3");
 		git.add().addFilepattern("file").call();
 		RevCommit first = git.commit().setMessage("added file").call();
 
 		writeTrashFile("file", "1master\n2\n3");
 		RevCommit masterCommit = git.commit().setAll(true)
 				.setMessage("modified file on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("file", "1side\n2\n3");
 		RevCommit sideCommit = git.commit().setAll(true)
 				.setMessage("modified file on side").call();
 
 		try (ObjectInserter ins = db.newObjectInserter()) {
 			ResolveMerger merger =
 					(ResolveMerger) strategy.newMerger(ins, db.getConfig());
 			boolean noProblems = merger.merge(masterCommit, sideCommit);
 			assertFalse(noProblems);
 			assertEquals(Arrays.asList("file"), merger.getUnmergedPaths());
 
 			MergeFormatter fmt = new MergeFormatter();
 			merger.getMergeResults().get("file");
 			try (ByteArrayOutputStream out = new ByteArrayOutputStream()) {
 				fmt.formatMerge(out, merger.getMergeResults().get("file"),
 						"BASE", "OURS", "THEIRS", UTF_8);
 				String expected = "<<<<<<< OURS\n"
 						+ "1master\n"
 						+ "=======\n"
 						+ "1side\n"
 						+ ">>>>>>> THEIRS\n"
 						+ "2\n"
 						+ "3";
 				assertEquals(expected, new String(out.toByteArray(), UTF_8));
 			}
 		}
 	}
 
 	@Theory
 	public void fileBecomesDir_noTree(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("file", "1\n2\n3");
 		writeTrashFile("side", "1\n2\n3");
 		git.add().addFilepattern("file").addFilepattern("side").call();
 		RevCommit first = git.commit().setMessage("base").call();
 
 		writeTrashFile("side", "our changed");
 		RevCommit ours = git.commit().setAll(true)
 				.setMessage("ours").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("theirs").call();
 		deleteTrashFile("file");
 		writeTrashFile("file/file", "in subdir");
 		git.add().addFilepattern("file/file").call();
 
 		RevCommit theirs = git.commit().setAll(true)
 				.setMessage("theirs").call();
 
 		// Exercise inCore flavor of the merge.
 		try (ObjectInserter ins = db.newObjectInserter()) {
 			ResolveMerger merger =
 					(ResolveMerger) strategy.newMerger(ins, db.getConfig());
 			boolean success = merger.merge(ours, theirs);
 			assertTrue(success);
 			assertTrue(merger.getModifiedFiles().isEmpty());
 		}
 	}
 
 	/**
 	 * This is a high-level test for https://bugs.eclipse.org/bugs/show_bug.cgi?id=535919
 	 *
 	 * The actual fix was made in {@link org.eclipse.jgit.treewalk.NameConflictTreeWalk}
 	 * and tested in {@link org.eclipse.jgit.treewalk.NameConflictTreeWalkTest#tesdDF_LastItemsInTreeHasDFConflictAndSpecialNames}.
 	 */
 	@Theory
 	public void checkMergeDoesntCrashWithSpecialFileNames(
 			MergeStrategy strategy) throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("subtree", "");
 		writeTrashFile("subtree-0", "");
 		git.add().addFilepattern("subtree").call();
 		git.add().addFilepattern("subtree-0").call();
 		RevCommit toMerge = git.commit().setMessage("commit-1").call();
 
 		git.rm().addFilepattern("subtree").call();
 		writeTrashFile("subtree/file", "");
 		git.add().addFilepattern("subtree").call();
 		RevCommit mergeTip = git.commit().setMessage("commit2").call();
 
 		ResolveMerger merger = (ResolveMerger) strategy.newMerger(db, false);
 		assertTrue(merger.merge(mergeTip, toMerge));
 	}
 
 	/**
 	 * Merging after criss-cross merges. In this case we merge together two
 	 * commits which have two equally good common ancestors
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkMergeCrissCross(MergeStrategy strategy) throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("1", "1\n2\n3");
 		git.add().addFilepattern("1").call();
 		RevCommit first = git.commit().setMessage("added 1").call();
 
 		writeTrashFile("1", "1master\n2\n3");
 		RevCommit masterCommit = git.commit().setAll(true)
 				.setMessage("modified 1 on master").call();
 
 		writeTrashFile("1", "1master2\n2\n3");
 		git.commit().setAll(true)
 				.setMessage("modified 1 on master again").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("1", "1\n2\na\nb\nc\n3side");
 		RevCommit sideCommit = git.commit().setAll(true)
 				.setMessage("modified 1 on side").call();
 
 		writeTrashFile("1", "1\n2\n3side2");
 		git.commit().setAll(true)
 				.setMessage("modified 1 on side again").call();
 
 		MergeResult result = git.merge().setStrategy(strategy)
 				.include(masterCommit).call();
 		assertEquals(MergeStatus.MERGED, result.getMergeStatus());
 		result.getNewHead();
 		git.checkout().setName("master").call();
 		result = git.merge().setStrategy(strategy).include(sideCommit).call();
 		assertEquals(MergeStatus.MERGED, result.getMergeStatus());
 
 		// we have two branches which are criss-cross merged. Try to merge the
 		// tips. This should succeed with RecursiveMerge and fail with
 		// ResolveMerge
 		try {
 			MergeResult mergeResult = git.merge().setStrategy(strategy)
 					.include(git.getRepository().exactRef("refs/heads/side"))
 					.call();
 			assertEquals(MergeStrategy.RECURSIVE, strategy);
 			assertEquals(MergeResult.MergeStatus.MERGED,
 					mergeResult.getMergeStatus());
 			assertEquals("1master2\n2\n3side2", read("1"));
 		} catch (JGitInternalException e) {
 			assertEquals(MergeStrategy.RESOLVE, strategy);
 			assertTrue(e.getCause() instanceof NoMergeBaseException);
 			assertEquals(((NoMergeBaseException) e.getCause()).getReason(),
 					MergeBaseFailureReason.MULTIPLE_MERGE_BASES_NOT_SUPPORTED);
 		}
 	}
 
 	@Theory
 	public void checkLockedFilesToBeDeleted(MergeStrategy strategy)
 			throws Exception {
 		Git git = Git.wrap(db);
 
 		writeTrashFile("a.txt", "orig");
 		writeTrashFile("b.txt", "orig");
 		git.add().addFilepattern("a.txt").addFilepattern("b.txt").call();
 		RevCommit first = git.commit().setMessage("added a.txt, b.txt").call();
 
 		// modify and delete files on the master branch
 		writeTrashFile("a.txt", "master");
 		git.rm().addFilepattern("b.txt").call();
 		RevCommit masterCommit = git.commit()
 				.setMessage("modified a.txt, deleted b.txt").setAll(true)
 				.call();
 
 		// switch back to a side branch
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("side").call();
 		writeTrashFile("c.txt", "side");
 		git.add().addFilepattern("c.txt").call();
 		git.commit().setMessage("added c.txt").call();
 
 		// Get a handle to the file so on windows it can't be deleted.
 		try (FileInputStream fis = new FileInputStream(
 				new File(db.getWorkTree(), "b.txt"))) {
 			MergeResult mergeRes = git.merge().setStrategy(strategy)
 					.include(masterCommit).call();
 			if (mergeRes.getMergeStatus().equals(MergeStatus.FAILED)) {
 				// probably windows
 				assertEquals(1, mergeRes.getFailingPaths().size());
 				assertEquals(MergeFailureReason.COULD_NOT_DELETE,
 						mergeRes.getFailingPaths().get("b.txt"));
 			}
 			assertEquals(
 					"[a.txt, mode:100644, content:master]"
 							+ "[c.txt, mode:100644, content:side]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Theory
 	public void checkForCorrectIndex(MergeStrategy strategy) throws Exception {
 		File f;
 		Instant lastTs4, lastTsIndex;
 		Git git = Git.wrap(db);
 		File indexFile = db.getIndexFile();
 
 		// Create initial content and remember when the last file was written.
 		f = writeTrashFiles(false, "orig", "orig", "1\n2\n3", "orig", "orig");
 		lastTs4 = FS.DETECTED.lastModifiedInstant(f);
 
 		// add all files, commit and check this doesn't update any working tree
 		// files and that the index is in a new file system timer tick. Make
 		// sure to wait long enough before adding so the index doesn't contain
 		// racily clean entries
 		fsTick(f);
 		git.add().addFilepattern(".").call();
 		RevCommit firstCommit = git.commit().setMessage("initial commit")
 				.call();
 		checkConsistentLastModified("0", "1", "2", "3", "4");
 		checkModificationTimeStampOrder("1", "2", "3", "4", "<.git/index");
 		assertEquals("Commit should not touch working tree file 4", lastTs4,
 				FS.DETECTED
 						.lastModifiedInstant(new File(db.getWorkTree(), "4")));
 		lastTsIndex = FS.DETECTED.lastModifiedInstant(indexFile);
 
 		// Do modifications on the master branch. Then add and commit. This
 		// should touch only "0", "2 and "3"
 		fsTick(indexFile);
 		f = writeTrashFiles(false, "master", null, "1master\n2\n3", "master",
 				null);
 		fsTick(f);
 		git.add().addFilepattern(".").call();
 		RevCommit masterCommit = git.commit().setMessage("master commit")
 				.call();
 		checkConsistentLastModified("0", "1", "2", "3", "4");
 		checkModificationTimeStampOrder("1", "4", "*" + lastTs4, "<*"
 				+ lastTsIndex, "<0", "2", "3", "<.git/index");
 		lastTsIndex = FS.DETECTED.lastModifiedInstant(indexFile);
 
 		// Checkout a side branch. This should touch only "0", "2 and "3"
 		fsTick(indexFile);
 		git.checkout().setCreateBranch(true).setStartPoint(firstCommit)
 				.setName("side").call();
 		checkConsistentLastModified("0", "1", "2", "3", "4");
 		checkModificationTimeStampOrder("1", "4", "*" + lastTs4, "<*"
 				+ lastTsIndex, "<0", "2", "3", ".git/index");
 		lastTsIndex = FS.DETECTED.lastModifiedInstant(indexFile);
 
 		// This checkout may have populated worktree and index so fast that we
 		// may have smudged entries now. Check that we have the right content
 		// and then rewrite the index to get rid of smudged state
 		assertEquals("[0, mode:100644, content:orig]" //
 				+ "[1, mode:100644, content:orig]" //
 				+ "[2, mode:100644, content:1\n2\n3]" //
 				+ "[3, mode:100644, content:orig]" //
 				+ "[4, mode:100644, content:orig]", //
 				indexState(CONTENT));
 		fsTick(indexFile);
 		f = writeTrashFiles(false, "orig", "orig", "1\n2\n3", "orig", "orig");
 		lastTs4 = FS.DETECTED.lastModifiedInstant(f);
 		fsTick(f);
 		git.add().addFilepattern(".").call();
 		checkConsistentLastModified("0", "1", "2", "3", "4");
 		checkModificationTimeStampOrder("*" + lastTsIndex, "<0", "1", "2", "3",
 				"4", "<.git/index");
 		lastTsIndex = FS.DETECTED.lastModifiedInstant(indexFile);
 
 		// Do modifications on the side branch. Touch only "1", "2 and "3"
 		fsTick(indexFile);
 		f = writeTrashFiles(false, null, "side", "1\n2\n3side", "side", null);
 		fsTick(f);
 		git.add().addFilepattern(".").call();
 		git.commit().setMessage("side commit").call();
 		checkConsistentLastModified("0", "1", "2", "3", "4");
 		checkModificationTimeStampOrder("0", "4", "*" + lastTs4, "<*"
 				+ lastTsIndex, "<1", "2", "3", "<.git/index");
 		lastTsIndex = FS.DETECTED.lastModifiedInstant(indexFile);
 
 		// merge master and side. Should only touch "0," "2" and "3"
 		fsTick(indexFile);
 		git.merge().setStrategy(strategy).include(masterCommit).call();
 		checkConsistentLastModified("0", "1", "2", "4");
 		checkModificationTimeStampOrder("4", "*" + lastTs4, "<1", "<*"
 				+ lastTsIndex, "<0", "2", "3", ".git/index");
 		assertEquals(
 				"[0, mode:100644, content:master]" //
 						+ "[1, mode:100644, content:side]" //
 						+ "[2, mode:100644, content:1master\n2\n3side]" //
 						+ "[3, mode:100644, stage:1, content:orig][3, mode:100644, stage:2, content:side][3, mode:100644, stage:3, content:master]" //
 						+ "[4, mode:100644, content:orig]", //
 				indexState(CONTENT));
 	}
 
 	/**
 	 * Merging two conflicting submodules when the index does not contain any
 	 * entry for that submodule.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkMergeConflictingSubmodulesWithoutIndex(
 			MergeStrategy strategy) throws Exception {
 		Git git = Git.wrap(db);
 		writeTrashFile("initial", "initial");
 		git.add().addFilepattern("initial").call();
 		RevCommit initial = git.commit().setMessage("initial").call();
 
 		writeSubmodule("one", ObjectId
 				.fromString("1000000000000000000000000000000000000000"));
 		git.add().addFilepattern(Constants.DOT_GIT_MODULES).call();
 		RevCommit right = git.commit().setMessage("added one").call();
 
 		// a second commit in the submodule
 
 		git.checkout().setStartPoint(initial).setName("left")
 				.setCreateBranch(true).call();
 		writeSubmodule("one", ObjectId
 				.fromString("2000000000000000000000000000000000000000"));
 
 		git.add().addFilepattern(Constants.DOT_GIT_MODULES).call();
 		git.commit().setMessage("a different one").call();
 
 		MergeResult result = git.merge().setStrategy(strategy).include(right)
 				.call();
 
 		assertEquals(MergeStatus.CONFLICTING, result.getMergeStatus());
 		Map<String, int[][]> conflicts = result.getConflicts();
 		assertEquals(1, conflicts.size());
 		assertNotNull(conflicts.get("one"));
 	}
 
 	/**
 	 * Merging two non-conflicting submodules when the index does not contain
 	 * any entry for either submodule.
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkMergeNonConflictingSubmodulesWithoutIndex(
 			MergeStrategy strategy) throws Exception {
 		Git git = Git.wrap(db);
 		writeTrashFile("initial", "initial");
 		git.add().addFilepattern("initial").call();
 
 		writeSubmodule("one", ObjectId
 				.fromString("1000000000000000000000000000000000000000"));
 
 		// Our initial commit should include a .gitmodules with a bunch of
 		// comment lines, so that
 		// we don't have a content merge issue when we add a new submodule at
 		// the top and a different
 		// one at the bottom. This is sort of a hack, but it should allow
 		// add/add submodule merges
 		String existing = read(Constants.DOT_GIT_MODULES);
 		String context = "\n# context\n# more context\n# yet more context\n";
 		write(new File(db.getWorkTree(), Constants.DOT_GIT_MODULES),
 				existing + context + context + context);
 
 		git.add().addFilepattern(Constants.DOT_GIT_MODULES).call();
 		RevCommit initial = git.commit().setMessage("initial").call();
 
 		writeSubmodule("two", ObjectId
 				.fromString("1000000000000000000000000000000000000000"));
 		git.add().addFilepattern(Constants.DOT_GIT_MODULES).call();
 
 		RevCommit right = git.commit().setMessage("added two").call();
 
 		git.checkout().setStartPoint(initial).setName("left")
 				.setCreateBranch(true).call();
 
 		// we need to manually create the submodule for three for the
 		// .gitmodules hackery
 		addSubmoduleToIndex("three", ObjectId
 				.fromString("1000000000000000000000000000000000000000"));
 		new File(db.getWorkTree(), "three").mkdir();
 
 		existing = read(Constants.DOT_GIT_MODULES);
 		String three = "[submodule \"three\"]\n\tpath = three\n\turl = "
 				+ db.getDirectory().toURI() + "\n";
 		write(new File(db.getWorkTree(), Constants.DOT_GIT_MODULES),
 				three + existing);
 
 		git.add().addFilepattern(Constants.DOT_GIT_MODULES).call();
 		git.commit().setMessage("a different one").call();
 
 		MergeResult result = git.merge().setStrategy(strategy).include(right)
 				.call();
 
 		assertNull(result.getCheckoutConflicts());
 		assertNull(result.getFailingPaths());
 		for (String dir : Arrays.asList("one", "two", "three")) {
 			assertTrue(new File(db.getWorkTree(), dir).isDirectory());
 		}
 	}
 
 	/**
 	 * Merging two commits with a conflict in the virtual ancestor.
 	 *
 	 * Content conflicts while merging the virtual ancestor must be ignored.
 	 *
 	 * In the following tree, while merging A and B, the recursive algorithm
 	 * finds as base commits X and Y and tries to merge them: X deletes file "a"
 	 * and Y modifies it.
 	 *
 	 * Note: we delete "a" in (master) and (second-branch) to make avoid manual
 	 * merges. The situation is the same without those deletions and fixing
 	 * manually the merge of (merge-both-sides) on both branches.
 	 *
 	 * <pre>
 	 * A  (second-branch) Merge branch 'merge-both-sides' into second-branch
 	 * |\
 	 * o | Delete modified a
 	 * | |
 	 * | | B (master) Merge branch 'merge-both-sides' (into master)
 	 * | |/|
 	 * | X | (merge-both-sides) Delete original a
 	 * | | |
 	 * | | o Delete modified a
 	 * | |/
 	 * |/|
 	 * Y | Modify a
 	 * |/
 	 * o Initial commit
 	 * </pre>
 	 *
 	 * @param strategy
 	 * @throws Exception
 	 */
 	@Theory
 	public void checkMergeConflictInVirtualAncestor(
 			MergeStrategy strategy) throws Exception {
 		if (!strategy.equals(MergeStrategy.RECURSIVE)) {
 			return;
 		}
 
 		Git git = Git.wrap(db);
 
 		// master
 		writeTrashFile("a", "aaaaaaaa");
 		writeTrashFile("b", "bbbbbbbb");
 		git.add().addFilepattern("a").addFilepattern("b").call();
 		RevCommit first = git.commit().setMessage("Initial commit").call();
 
 		writeTrashFile("a", "aaaaaaaaaaaaaaa");
 		git.add().addFilepattern("a").call();
 		RevCommit commitY = git.commit().setMessage("Modify a").call();
 
 		git.rm().addFilepattern("a").call();
 		// Do more in this commits, so it is not identical to the deletion in
 		// second-branch
 		writeTrashFile("c", "cccccccc");
 		git.add().addFilepattern("c").call();
 		git.commit().setMessage("Delete modified a").call();
 
 		// merge-both-sides: starts before "a" is modified and deletes it
 		git.checkout().setCreateBranch(true).setStartPoint(first)
 				.setName("merge-both-sides").call();
 		git.rm().addFilepattern("a").call();
 		RevCommit commitX = git.commit().setMessage("Delete original a").call();
 
 		// second branch
 		git.checkout().setCreateBranch(true).setStartPoint(commitY)
 				.setName("second-branch").call();
 		git.rm().addFilepattern("a").call();
 		git.commit().setMessage("Delete modified a").call();
 
 		// Merge merge-both-sides into second-branch
 		MergeResult mergeResult = git.merge().include(commitX)
 				.setStrategy(strategy)
 				.call();
 		ObjectId commitB = mergeResult.getNewHead();
 
 		// Merge merge-both-sides into master
 		git.checkout().setName("master").call();
 		mergeResult = git.merge().include(commitX).setStrategy(strategy)
 				.call();
 
 		// Now, merge commit A and B (i.e. "master" and "second-branch").
 		// None of them have the file "a", so there is no conflict, BUT while
 		// building the virtual ancestor it will find a conflict between Y and X
 		git.merge().include(commitB).call();
 	}
 
 	/**
 	 * Merging two commits with a file/dir conflict in the virtual ancestor.
 	 *
 	 * <p>
 	 * Those conflicts should be ignored, otherwise the found base can not be used by the
 	 * RecursiveMerger.
 	 * <pre>
 	 *  --------------
 	 * |              \
 	 * |         C1 - C4 --- ?     master
 	 * |        /          /
 	 * |  I - A1 - C2 - C3         second-branch
 	 * |   \            /
 	 * \    \          /
 	 *  ----A2--------             branch-to-merge
 	 *  </pre>
 	 * <p>
 	 * <p>
 	 * Path "a" is initially a file in I and A1. It is changed to a directory in A2
 	 * ("branch-to-merge").
 	 * <p>
 	 * A2 is merged into "master" and "second-branch". The dir/file merge conflict is resolved
 	 * manually, results in C4 and C3.
 	 * <p>
 	 * While merging C3 and C4, A1 and A2 are the base commits found by the recursive merge that
 	 * have the dir/file conflict.
 	 */
 	@Theory
 	public void checkFileDirMergeConflictInVirtualAncestor_NoConflictInChildren(
 			MergeStrategy strategy)
 			throws Exception {
 		if (!strategy.equals(MergeStrategy.RECURSIVE)) {
 			return;
 		}
 
 		Git git = Git.wrap(db);
 
 		// master
 		writeTrashFile("a", "initial content");
 		git.add().addFilepattern("a").call();
 		RevCommit commitI = git.commit().setMessage("Initial commit").call();
 
 		writeTrashFile("a", "content in Ancestor 1");
 		git.add().addFilepattern("a").call();
 		RevCommit commitA1 = git.commit().setMessage("Ancestor 1").call();
 
 		writeTrashFile("a", "content in Child 1 (commited on master)");
 		git.add().addFilepattern("a").call();
 		// commit C1M
 		git.commit().setMessage("Child 1 on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(commitI).setName("branch-to-merge").call();
 		// "a" becomes a directory in A2
 		git.rm().addFilepattern("a").call();
 		writeTrashFile("a/content", "content in Ancestor 2 (commited on branch-to-merge)");
 		git.add().addFilepattern("a/content").call();
 		RevCommit commitA2 = git.commit().setMessage("Ancestor 2").call();
 
 		// second branch
 		git.checkout().setCreateBranch(true).setStartPoint(commitA1).setName("second-branch").call();
 		writeTrashFile("a", "content in Child 2 (commited on second-branch)");
 		git.add().addFilepattern("a").call();
 		// commit C2S
 		git.commit().setMessage("Child 2 on second-branch").call();
 
 		// Merge branch-to-merge into second-branch
 		MergeResult mergeResult = git.merge().include(commitA2).setStrategy(strategy).call();
 		assertEquals(mergeResult.getNewHead(), null);
 		assertEquals(mergeResult.getMergeStatus(), MergeStatus.CONFLICTING);
 		// Resolve the conflict manually, merge "a" as a file
 		git.rm().addFilepattern("a").call();
 		git.rm().addFilepattern("a/content").call();
 		writeTrashFile("a", "merge conflict resolution");
 		git.add().addFilepattern("a").call();
 		RevCommit commitC3S = git.commit().setMessage("Child 3 on second bug - resolve merge conflict")
 				.call();
 
 		// Merge branch-to-merge into master
 		git.checkout().setName("master").call();
 		mergeResult = git.merge().include(commitA2).setStrategy(strategy).call();
 		assertEquals(mergeResult.getNewHead(), null);
 		assertEquals(mergeResult.getMergeStatus(), MergeStatus.CONFLICTING);
 
 		// Resolve the conflict manually - merge "a" as a file
 		git.rm().addFilepattern("a").call();
 		git.rm().addFilepattern("a/content").call();
 		writeTrashFile("a", "merge conflict resolution");
 		git.add().addFilepattern("a").call();
 		// commit C4M
 		git.commit().setMessage("Child 4 on master - resolve merge conflict").call();
 
 		// Merge C4M (second-branch) into master (C3S)
 		// Conflict in virtual base should be here, but there are no conflicts in
 		// children
 		mergeResult = git.merge().include(commitC3S).call();
 		assertEquals(mergeResult.getMergeStatus(), MergeStatus.MERGED);
 
 	}
 
 	@Theory
 	public void checkFileDirMergeConflictInVirtualAncestor_ConflictInChildren_FileDir(MergeStrategy strategy)
 			throws Exception {
 		if (!strategy.equals(MergeStrategy.RECURSIVE)) {
 			return;
 		}
 
 		Git git = Git.wrap(db);
 
 		// master
 		writeTrashFile("a", "initial content");
 		git.add().addFilepattern("a").call();
 		RevCommit commitI = git.commit().setMessage("Initial commit").call();
 
 		writeTrashFile("a", "content in Ancestor 1");
 		git.add().addFilepattern("a").call();
 		RevCommit commitA1 = git.commit().setMessage("Ancestor 1").call();
 
 		writeTrashFile("a", "content in Child 1 (commited on master)");
 		git.add().addFilepattern("a").call();
 		// commit C1M
 		git.commit().setMessage("Child 1 on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(commitI).setName("branch-to-merge").call();
 
 		// "a" becomes a directory in A2
 		git.rm().addFilepattern("a").call();
 		writeTrashFile("a/content", "content in Ancestor 2 (commited on branch-to-merge)");
 		git.add().addFilepattern("a/content").call();
 		RevCommit commitA2 = git.commit().setMessage("Ancestor 2").call();
 
 		// second branch
 		git.checkout().setCreateBranch(true).setStartPoint(commitA1).setName("second-branch").call();
 		writeTrashFile("a", "content in Child 2 (commited on second-branch)");
 		git.add().addFilepattern("a").call();
 		// commit C2S
 		git.commit().setMessage("Child 2 on second-branch").call();
 
 		// Merge branch-to-merge into second-branch
 		MergeResult mergeResult = git.merge().include(commitA2).setStrategy(strategy).call();
 		assertEquals(mergeResult.getNewHead(), null);
 		assertEquals(mergeResult.getMergeStatus(), MergeStatus.CONFLICTING);
 		// Resolve the conflict manually - write a file
 		git.rm().addFilepattern("a").call();
 		git.rm().addFilepattern("a/content").call();
 		writeTrashFile("a",
 				"content in Child 3 (commited on second-branch) - merge conflict resolution");
 		git.add().addFilepattern("a").call();
 		RevCommit commitC3S = git.commit().setMessage("Child 3 on second bug - resolve merge conflict")
 				.call();
 
 		// Merge branch-to-merge into master
 		git.checkout().setName("master").call();
 		mergeResult = git.merge().include(commitA2).setStrategy(strategy).call();
 		assertEquals(mergeResult.getNewHead(), null);
 		assertEquals(mergeResult.getMergeStatus(), MergeStatus.CONFLICTING);
 
 		// Resolve the conflict manually - write a file
 		git.rm().addFilepattern("a").call();
 		git.rm().addFilepattern("a/content").call();
 		writeTrashFile("a", "content in Child 4 (commited on master) - merge conflict resolution");
 		git.add().addFilepattern("a").call();
 		// commit C4M
 		git.commit().setMessage("Child 4 on master - resolve merge conflict").call();
 
 		// Merge C4M (second-branch) into master (C3S)
 		// Conflict in virtual base should be here
 		mergeResult = git.merge().include(commitC3S).call();
 		assertEquals(mergeResult.getMergeStatus(), MergeStatus.CONFLICTING);
 		String expected =
 				"<<<<<<< HEAD\n" + "content in Child 4 (commited on master) - merge conflict resolution\n"
 						+ "=======\n"
 						+ "content in Child 3 (commited on second-branch) - merge conflict resolution\n"
 						+ ">>>>>>> " + commitC3S.name() + "\n";
 		assertEquals(expected, read("a"));
 		// Nothing was populated from the ancestors.
 		assertEquals(
 				"[a, mode:100644, stage:2, content:content in Child 4 (commited on master) - merge conflict resolution][a, mode:100644, stage:3, content:content in Child 3 (commited on second-branch) - merge conflict resolution]",
 				indexState(CONTENT));
 	}
 
 	/**
 	 * Same test as above, but "a" is a dir in A1 and a file in A2
 	 */
 	@Theory
 	public void checkFileDirMergeConflictInVirtualAncestor_ConflictInChildren_DirFile(MergeStrategy strategy)
 			throws Exception {
 		if (!strategy.equals(MergeStrategy.RECURSIVE)) {
 			return;
 		}
 
 		Git git = Git.wrap(db);
 
 		// master
 		writeTrashFile("a/content", "initial content");
 		git.add().addFilepattern("a/content").call();
 		RevCommit commitI = git.commit().setMessage("Initial commit").call();
 
 		writeTrashFile("a/content", "content in Ancestor 1");
 		git.add().addFilepattern("a/content").call();
 		RevCommit commitA1 = git.commit().setMessage("Ancestor 1").call();
 
 		writeTrashFile("a/content", "content in Child 1 (commited on master)");
 		git.add().addFilepattern("a/content").call();
 		// commit C1M
 		git.commit().setMessage("Child 1 on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(commitI).setName("branch-to-merge").call();
 
 		// "a" becomes a file in A2
 		git.rm().addFilepattern("a/content").call();
 		writeTrashFile("a", "content in Ancestor 2 (commited on branch-to-merge)");
 		git.add().addFilepattern("a").call();
 		RevCommit commitA2 = git.commit().setMessage("Ancestor 2").call();
 
 		// second branch
 		git.checkout().setCreateBranch(true).setStartPoint(commitA1).setName("second-branch").call();
 		writeTrashFile("a/content", "content in Child 2 (commited on second-branch)");
 		git.add().addFilepattern("a/content").call();
 		// commit C2S
 		git.commit().setMessage("Child 2 on second-branch").call();
 
 		// Merge branch-to-merge into second-branch
 		MergeResult mergeResult = git.merge().include(commitA2).setStrategy(strategy).call();
 		assertEquals(mergeResult.getNewHead(), null);
 		assertEquals(mergeResult.getMergeStatus(), MergeStatus.CONFLICTING);
 		// Resolve the conflict manually - write a file
 		git.rm().addFilepattern("a").call();
 		git.rm().addFilepattern("a/content").call();
 		deleteTrashFile("a/content");
 		deleteTrashFile("a");
 		writeTrashFile("a", "content in Child 3 (commited on second-branch) - merge conflict resolution");
 		git.add().addFilepattern("a").call();
 		RevCommit commitC3S = git.commit().setMessage("Child 3 on second bug - resolve merge conflict").call();
 
 		// Merge branch-to-merge into master
 		git.checkout().setName("master").call();
 		mergeResult = git.merge().include(commitA2).setStrategy(strategy).call();
 		assertEquals(mergeResult.getNewHead(), null);
 		assertEquals(mergeResult.getMergeStatus(), MergeStatus.CONFLICTING);
 
 		// Resolve the conflict manually - write a file
 		git.rm().addFilepattern("a").call();
 		git.rm().addFilepattern("a/content").call();
 		deleteTrashFile("a/content");
 		deleteTrashFile("a");
 		writeTrashFile("a", "content in Child 4 (commited on master) - merge conflict resolution");
 		git.add().addFilepattern("a").call();
 		// commit C4M
 		git.commit().setMessage("Child 4 on master - resolve merge conflict").call();
 
 		// Merge C4M (second-branch) into master (C3S)
 		// Conflict in virtual base should be here
 		mergeResult = git.merge().include(commitC3S).call();
 		assertEquals(mergeResult.getMergeStatus(), MergeStatus.CONFLICTING);
 		String expected = "<<<<<<< HEAD\n" + "content in Child 4 (commited on master) - merge conflict resolution\n"
 				+ "=======\n" + "content in Child 3 (commited on second-branch) - merge conflict resolution\n"
 				+ ">>>>>>> " + commitC3S.name() + "\n";
 		assertEquals(expected, read("a"));
 		// Nothing was populated from the ancestors.
 		assertEquals(
 				"[a, mode:100644, stage:2, content:content in Child 4 (commited on master) - merge conflict resolution][a, mode:100644, stage:3, content:content in Child 3 (commited on second-branch) - merge conflict resolution]",
 				indexState(CONTENT));
 	}
 
 	/**
 	 * Merging two commits when files have equal content, but conflicting file mode
 	 * in the virtual ancestor.
 	 *
 	 * <p>
 	 * This test has the same set up as
 	 * {@code checkFileDirMergeConflictInVirtualAncestor_NoConflictInChildren}, only
 	 * with the mode conflict in A1 and A2.
 	 */
 	@Theory
 	public void checkModeMergeConflictInVirtualAncestor(MergeStrategy strategy) throws Exception {
 		if (!strategy.equals(MergeStrategy.RECURSIVE)) {
 			return;
 		}
 
 		Git git = Git.wrap(db);
 
 		// master
 		writeTrashFile("c", "initial file");
 		git.add().addFilepattern("c").call();
 		RevCommit commitI = git.commit().setMessage("Initial commit").call();
 
 		File a = writeTrashFile("a", "content in Ancestor");
 		git.add().addFilepattern("a").call();
 		RevCommit commitA1 = git.commit().setMessage("Ancestor 1").call();
 
 		a = writeTrashFile("a", "content in Child 1 (commited on master)");
 		git.add().addFilepattern("a").call();
 		// commit C1M
 		git.commit().setMessage("Child 1 on master").call();
 
 		git.checkout().setCreateBranch(true).setStartPoint(commitI).setName("branch-to-merge").call();
 		// "a" becomes executable in A2
 		a = writeTrashFile("a", "content in Ancestor");
 		a.setExecutable(true);
 		git.add().addFilepattern("a").call();
 		RevCommit commitA2 = git.commit().setMessage("Ancestor 2").call();
 
 		// second branch
 		git.checkout().setCreateBranch(true).setStartPoint(commitA1).setName("second-branch").call();
 		a = writeTrashFile("a", "content in Child 2 (commited on second-branch)");
 		git.add().addFilepattern("a").call();
 		// commit C2S
 		git.commit().setMessage("Child 2 on second-branch").call();
 
 		// Merge branch-to-merge into second-branch
 		MergeResult mergeResult = git.merge().include(commitA2).setStrategy(strategy).call();
 		assertEquals(mergeResult.getNewHead(), null);
 		assertEquals(mergeResult.getMergeStatus(), MergeStatus.CONFLICTING);
 		// Resolve the conflict manually, merge "a" as non-executable
 		a = writeTrashFile("a", "merge conflict resolution");
 		a.setExecutable(false);
 		git.add().addFilepattern("a").call();
 		RevCommit commitC3S = git.commit().setMessage("Child 3 on second bug - resolve merge conflict").call();
 
 		// Merge branch-to-merge into master
 		git.checkout().setName("master").call();
 		mergeResult = git.merge().include(commitA2).setStrategy(strategy).call();
 		assertEquals(mergeResult.getNewHead(), null);
 		assertEquals(mergeResult.getMergeStatus(), MergeStatus.CONFLICTING);
 
 		// Resolve the conflict manually - merge "a" as non-executable
 		a = writeTrashFile("a", "merge conflict resolution");
 		a.setExecutable(false);
 		git.add().addFilepattern("a").call();
 		// commit C4M
 		git.commit().setMessage("Child 4 on master - resolve merge conflict").call();
 
 		// Merge C4M (second-branch) into master (C3S)
 		// Conflict in virtual base should be here, but there are no conflicts in
 		// children
 		mergeResult = git.merge().include(commitC3S).call();
 		assertEquals(mergeResult.getMergeStatus(), MergeStatus.MERGED);
 
 	}
 
 	private void writeSubmodule(String path, ObjectId commit)
 			throws IOException, ConfigInvalidException {
 		addSubmoduleToIndex(path, commit);
 		new File(db.getWorkTree(), path).mkdir();
 
 		StoredConfig config = db.getConfig();
 		config.setString(ConfigConstants.CONFIG_SUBMODULE_SECTION, path,
 				ConfigConstants.CONFIG_KEY_URL,
 				db.getDirectory().toURI().toString());
 		config.save();
 
 		FileBasedConfig modulesConfig = new FileBasedConfig(
 				new File(db.getWorkTree(), Constants.DOT_GIT_MODULES),
 				db.getFS());
 		modulesConfig.load();
 		modulesConfig.setString(ConfigConstants.CONFIG_SUBMODULE_SECTION, path,
 				ConfigConstants.CONFIG_KEY_PATH, path);
 		modulesConfig.save();
 
 	}
 
 	private void addSubmoduleToIndex(String path, ObjectId commit)
 			throws IOException {
 		DirCache cache = db.lockDirCache();
 		DirCacheEditor editor = cache.editor();
 		editor.add(new DirCacheEditor.PathEdit(path) {
 
 			@Override
 			public void apply(DirCacheEntry ent) {
 				ent.setFileMode(FileMode.GITLINK);
 				ent.setObjectId(commit);
 			}
 		});
 		editor.commit();
 	}
 
 	// Assert that every specified index entry has the same last modification
 	// timestamp as the associated file
 	private void checkConsistentLastModified(String... pathes)
 			throws IOException {
 		DirCache dc = db.readDirCache();
 		File workTree = db.getWorkTree();
 		for (String path : pathes)
 			assertEquals(
 					"IndexEntry with path "
 							+ path
 							+ " has lastmodified which is different from the worktree file",
 					FS.DETECTED.lastModifiedInstant(new File(workTree, path)),
 					dc.getEntry(path)
 							.getLastModifiedInstant());
 	}
 
 	// Assert that modification timestamps of working tree files are as
 	// expected. You may specify n files. It is asserted that every file
 	// i+1 is not older than file i. If a path of file i+1 is prefixed with "<"
 	// then this file must be younger then file i. A path "*<modtime>"
 	// represents a file with a modification time of <modtime>
 	// E.g. ("a", "b", "<c", "f/a.txt") means: a<=b<c<=f/a.txt
 	private void checkModificationTimeStampOrder(String... pathes) {
 		Instant lastMod = EPOCH;
 		for (String p : pathes) {
 			boolean strong = p.startsWith("<");
 			boolean fixed = p.charAt(strong ? 1 : 0) == '*';
 			p = p.substring((strong ? 1 : 0) + (fixed ? 1 : 0));
 			Instant curMod = fixed ? Instant.parse(p)
 					: FS.DETECTED
 							.lastModifiedInstant(new File(db.getWorkTree(), p));
 			if (strong) {
 				assertTrue("path " + p + " is not younger than predecesssor",
 						curMod.compareTo(lastMod) > 0);
 			} else {
 				assertTrue("path " + p + " is older than predecesssor",
 						curMod.compareTo(lastMod) >= 0);
 			}
 		}
 	}
 
 	private String readBlob(ObjectId treeish, String path) throws Exception {
 		try (TestRepository<?> tr = new TestRepository<>(db);
 				RevWalk rw = tr.getRevWalk()) {
 			db.incrementOpen();
 			RevTree tree = rw.parseTree(treeish);
 			RevObject obj = tr.get(tree, path);
 			if (obj == null) {
 				return null;
 			}
 			return new String(
 					rw.getObjectReader().open(obj, OBJ_BLOB).getBytes(), UTF_8);
 		}
 	}
 }