/*
    * Copyright (C) 2007, Dave Watson <dwatson@mimvista.com>
    * Copyright (C) 2008-2011, Shawn O. Pearce <spearce@spearce.org>
    * Copyright (C) 2008-2011, Robin Rosenberg <robin.rosenberg@dewire.com>
    * Copyright (C) 2010-2011, Christian Halstrick <christian.halstrick@sap.com>
    * 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.lib;
  
  import static org.junit.Assert.assertArrayEquals;
  import static org.junit.Assert.assertEquals;
  import static org.junit.Assert.assertFalse;
  import static org.junit.Assert.assertNotNull;
  import static org.junit.Assert.assertTrue;
  import static org.junit.Assert.fail;
  
  import java.io.File;
  import java.io.FileInputStream;
  import java.io.IOException;
  import java.util.Arrays;
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  
  import org.eclipse.jgit.api.CheckoutCommand;
  import org.eclipse.jgit.api.CheckoutResult;
  import org.eclipse.jgit.api.Git;
  import org.eclipse.jgit.api.MergeResult.MergeStatus;
  import org.eclipse.jgit.api.ResetCommand.ResetType;
  import org.eclipse.jgit.api.Status;
  import org.eclipse.jgit.api.errors.GitAPIException;
  import org.eclipse.jgit.api.errors.NoFilepatternException;
  import org.eclipse.jgit.dircache.DirCache;
  import org.eclipse.jgit.dircache.DirCacheCheckout;
  import org.eclipse.jgit.dircache.DirCacheCheckout.CheckoutMetadata;
  import org.eclipse.jgit.dircache.DirCacheEditor;
  import org.eclipse.jgit.dircache.DirCacheEditor.PathEdit;
  import org.eclipse.jgit.dircache.DirCacheEntry;
  import org.eclipse.jgit.errors.CheckoutConflictException;
  import org.eclipse.jgit.errors.CorruptObjectException;
  import org.eclipse.jgit.errors.NoWorkTreeException;
  import org.eclipse.jgit.junit.RepositoryTestCase;
  import org.eclipse.jgit.junit.TestRepository;
  import org.eclipse.jgit.junit.TestRepository.BranchBuilder;
  import org.eclipse.jgit.revwalk.RevCommit;
  import org.eclipse.jgit.treewalk.FileTreeIterator;
  import org.eclipse.jgit.treewalk.TreeWalk;
  import org.eclipse.jgit.util.FS;
  import org.eclipse.jgit.util.FileUtils;
  import org.junit.Assume;
  import org.junit.Test;
  
  public class DirCacheCheckoutTest extends RepositoryTestCase {
  	private DirCacheCheckout dco;
  	protected ObjectId theHead;
  	protected ObjectId theMerge;
  	private DirCache dirCache;
  
  	private void prescanTwoTrees(ObjectId head, ObjectId merge)
  			throws IllegalStateException, IOException {
  		DirCache dc = db.lockDirCache();
  		try {
  			dco = new DirCacheCheckout(db, head, dc, merge);
  			dco.preScanTwoTrees();
  		} finally {
  			dc.unlock();
 		}
 	}
 
 	private void checkout() throws IOException {
 		DirCache dc = db.lockDirCache();
 		try {
 			dco = new DirCacheCheckout(db, theHead, dc, theMerge);
 			dco.checkout();
 		} finally {
 			dc.unlock();
 		}
 	}
 
 	private List<String> getRemoved() {
 		return dco.getRemoved();
 	}
 
 	private Map<String, CheckoutMetadata> getUpdated() {
 		return dco.getUpdated();
 	}
 
 	private List<String> getConflicts() {
 		return dco.getConflicts();
 	}
 
 	private static HashMap<String, String> mk(String a) {
 		return mkmap(a, a);
 	}
 
 	private static HashMap<String, String> mkmap(String... args) {
 		if ((args.length % 2) > 0)
 			throw new IllegalArgumentException("needs to be pairs");
 
 		HashMap<String, String> map = new HashMap<>();
 		for (int i = 0; i < args.length; i += 2) {
 			map.put(args[i], args[i + 1]);
 		}
 
 		return map;
 	}
 
 	@Test
 	public void testResetHard() throws IOException, NoFilepatternException,
 			GitAPIException {
 		try (Git git = new Git(db)) {
 			writeTrashFile("f", "f()");
 			writeTrashFile("D/g", "g()");
 			git.add().addFilepattern(".").call();
 			git.commit().setMessage("inital").call();
 			assertIndex(mkmap("f", "f()", "D/g", "g()"));
 
 			git.branchCreate().setName("topic").call();
 
 			writeTrashFile("f", "f()\nmaster");
 			writeTrashFile("D/g", "g()\ng2()");
 			writeTrashFile("E/h", "h()");
 			git.add().addFilepattern(".").call();
 			RevCommit master = git.commit().setMessage("master-1").call();
 			assertIndex(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h", "h()"));
 
 			checkoutBranch("refs/heads/topic");
 			assertIndex(mkmap("f", "f()", "D/g", "g()"));
 
 			writeTrashFile("f", "f()\nside");
 			assertTrue(new File(db.getWorkTree(), "D/g").delete());
 			writeTrashFile("G/i", "i()");
 			git.add().addFilepattern(".").call();
 			git.add().addFilepattern(".").setUpdate(true).call();
 			RevCommit topic = git.commit().setMessage("topic-1").call();
 			assertIndex(mkmap("f", "f()\nside", "G/i", "i()"));
 
 			writeTrashFile("untracked", "untracked");
 
 			resetHard(master);
 			assertIndex(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h", "h()"));
 			resetHard(topic);
 			assertIndex(mkmap("f", "f()\nside", "G/i", "i()"));
 			assertWorkDir(mkmap("f", "f()\nside", "G/i", "i()", "untracked",
 					"untracked"));
 
 			assertEquals(MergeStatus.CONFLICTING, git.merge().include(master)
 					.call().getMergeStatus());
 			assertEquals(
 					"[D/g, mode:100644, stage:1][D/g, mode:100644, stage:3][E/h, mode:100644][G/i, mode:100644][f, mode:100644, stage:1][f, mode:100644, stage:2][f, mode:100644, stage:3]",
 					indexState(0));
 
 			resetHard(master);
 			assertIndex(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h", "h()"));
 			assertWorkDir(mkmap("f", "f()\nmaster", "D/g", "g()\ng2()", "E/h",
 					"h()", "untracked", "untracked"));
 		}
 	}
 
 	/**
 	 * Reset hard from unclean condition.
 	 * <p>
 	 * WorkDir: Empty <br/>
 	 * Index: f/g <br/>
 	 * Merge: x
 	 *
 	 * @throws Exception
 	 */
 	@Test
 	public void testResetHardFromIndexEntryWithoutFileToTreeWithoutFile()
 			throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("x", "x");
 			git.add().addFilepattern("x").call();
 			RevCommit id1 = git.commit().setMessage("c1").call();
 
 			writeTrashFile("f/g", "f/g");
 			git.rm().addFilepattern("x").call();
 			git.add().addFilepattern("f/g").call();
 			git.commit().setMessage("c2").call();
 			deleteTrashFile("f/g");
 			deleteTrashFile("f");
 
 			// The actual test
 			git.reset().setMode(ResetType.HARD).setRef(id1.getName()).call();
 			assertIndex(mkmap("x", "x"));
 		}
 	}
 
 	/**
 	 * Test first checkout in a repo
 	 *
 	 * @throws Exception
 	 */
 	@Test
 	public void testInitialCheckout() throws Exception {
 		try (Git git = new Git(db)) {
 			TestRepository<Repository> db_t = new TestRepository<>(db);
 			BranchBuilder master = db_t.branch("master");
 			master.commit().add("f", "1").message("m0").create();
 			assertFalse(new File(db.getWorkTree(), "f").exists());
 			git.checkout().setName("master").call();
 			assertTrue(new File(db.getWorkTree(), "f").exists());
 		}
 	}
 
 	private DirCacheCheckout resetHard(RevCommit commit)
 			throws NoWorkTreeException,
 			CorruptObjectException, IOException {
 		DirCacheCheckout dc;
 		dc = new DirCacheCheckout(db, null, db.lockDirCache(),
 				commit.getTree());
 		dc.setFailOnConflict(true);
 		assertTrue(dc.checkout());
 		return dc;
 	}
 
 	private void assertIndex(HashMap<String, String> i)
 			throws CorruptObjectException, IOException {
 		String expectedValue;
 		String path;
 		DirCache read = DirCache.read(db.getIndexFile(), db.getFS());
 
 		assertEquals("Index has not the right size.", i.size(),
 				read.getEntryCount());
 		for (int j = 0; j < read.getEntryCount(); j++) {
 			path = read.getEntry(j).getPathString();
 			expectedValue = i.get(path);
 			assertNotNull("found unexpected entry for path " + path
 					+ " in index", expectedValue);
 			assertTrue("unexpected content for path " + path
 					+ " in index. Expected: <" + expectedValue + ">",
 					Arrays.equals(db.open(read.getEntry(j).getObjectId())
 							.getCachedBytes(), i.get(path).getBytes()));
 		}
 	}
 
 	@Test
 	public void testRules1thru3_NoIndexEntry() throws IOException {
 		ObjectId head = buildTree(mk("foo"));
 		ObjectId merge = db.newObjectInserter().insert(Constants.OBJ_TREE,
 				new byte[0]);
 
 		prescanTwoTrees(head, merge);
 
 		assertTrue(getRemoved().contains("foo"));
 
 		prescanTwoTrees(merge, head);
 
 		assertTrue(getUpdated().containsKey("foo"));
 
 		merge = buildTree(mkmap("foo", "a"));
 
 		prescanTwoTrees(head, merge);
 
 		assertConflict("foo");
 	}
 
 	void setupCase(HashMap<String, String> headEntries, HashMap<String, String> mergeEntries, HashMap<String, String> indexEntries) throws IOException {
 		theHead = buildTree(headEntries);
 		theMerge = buildTree(mergeEntries);
 		buildIndex(indexEntries);
 	}
 
 	private void buildIndex(HashMap<String, String> indexEntries) throws IOException {
 		dirCache = new DirCache(db.getIndexFile(), db.getFS());
 		if (indexEntries != null) {
 			assertTrue(dirCache.lock());
 			DirCacheEditor editor = dirCache.editor();
 			for (java.util.Map.Entry<String,String> e : indexEntries.entrySet()) {
 				writeTrashFile(e.getKey(), e.getValue());
 				ObjectInserter inserter = db.newObjectInserter();
 				final ObjectId id = inserter.insert(Constants.OBJ_BLOB,
 						Constants.encode(e.getValue()));
 				editor.add(new DirCacheEditor.DeletePath(e.getKey()));
 				editor.add(new DirCacheEditor.PathEdit(e.getKey()) {
 					@Override
 					public void apply(DirCacheEntry ent) {
 						ent.setFileMode(FileMode.REGULAR_FILE);
 						ent.setObjectId(id);
 						ent.setUpdateNeeded(false);
 					}
 				});
 			}
 			assertTrue(editor.commit());
 		}
 
 	}
 
 	static final class AddEdit extends PathEdit {
 
 		private final ObjectId data;
 
 		private final long length;
 
 		public AddEdit(String entryPath, ObjectId data, long length) {
 			super(entryPath);
 			this.data = data;
 			this.length = length;
 		}
 
 		@Override
 		public void apply(DirCacheEntry ent) {
 			ent.setFileMode(FileMode.REGULAR_FILE);
 			ent.setLength(length);
 			ent.setObjectId(data);
 		}
 
 	}
 
 	private ObjectId buildTree(HashMap<String, String> headEntries)
 			throws IOException {
 		DirCache lockDirCache = DirCache.newInCore();
 		// assertTrue(lockDirCache.lock());
 		DirCacheEditor editor = lockDirCache.editor();
 		if (headEntries != null) {
 			for (java.util.Map.Entry<String, String> e : headEntries.entrySet()) {
 				AddEdit addEdit = new AddEdit(e.getKey(),
 						genSha1(e.getValue()), e.getValue().length());
 				editor.add(addEdit);
 			}
 		}
 		editor.finish();
 		return lockDirCache.writeTree(db.newObjectInserter());
 	}
 
 	ObjectId genSha1(String data) {
 		try (ObjectInserter w = db.newObjectInserter()) {
 			ObjectId id = w.insert(Constants.OBJ_BLOB, data.getBytes());
 			w.flush();
 			return id;
 		} catch (IOException e) {
 			fail(e.toString());
 		}
 		return null;
 	}
 
 	protected void go() throws IllegalStateException, IOException {
 		prescanTwoTrees(theHead, theMerge);
 	}
 
 	@Test
 	public void testRules4thru13_IndexEntryNotInHead() throws IOException {
 		// rules 4 and 5
 		HashMap<String, String> idxMap;
 
 		idxMap = new HashMap<>();
 		idxMap.put("foo", "foo");
 		setupCase(null, null, idxMap);
 		go();
 
 		assertTrue(getUpdated().isEmpty());
 		assertTrue(getRemoved().isEmpty());
 		assertTrue(getConflicts().isEmpty());
 
 		// rules 6 and 7
 		idxMap = new HashMap<>();
 		idxMap.put("foo", "foo");
 		setupCase(null, idxMap, idxMap);
 		go();
 
 		assertAllEmpty();
 
 		// rules 8 and 9
 		HashMap<String, String> mergeMap;
 		mergeMap = new HashMap<>();
 
 		mergeMap.put("foo", "merge");
 		setupCase(null, mergeMap, idxMap);
 		go();
 
 		assertTrue(getUpdated().isEmpty());
 		assertTrue(getRemoved().isEmpty());
 		assertTrue(getConflicts().contains("foo"));
 
 		// rule 10
 
 		HashMap<String, String> headMap = new HashMap<>();
 		headMap.put("foo", "foo");
 		setupCase(headMap, null, idxMap);
 		go();
 
 		assertTrue(getRemoved().contains("foo"));
 		assertTrue(getUpdated().isEmpty());
 		assertTrue(getConflicts().isEmpty());
 
 		// rule 11
 		setupCase(headMap, null, idxMap);
 		assertTrue(new File(trash, "foo").delete());
 		writeTrashFile("foo", "bar");
 		db.readDirCache().getEntry(0).setUpdateNeeded(true);
 		go();
 
 		assertTrue(getRemoved().isEmpty());
 		assertTrue(getUpdated().isEmpty());
 		assertTrue(getConflicts().contains("foo"));
 
 		// rule 12 & 13
 		headMap.put("foo", "head");
 		setupCase(headMap, null, idxMap);
 		go();
 
 		assertTrue(getRemoved().isEmpty());
 		assertTrue(getUpdated().isEmpty());
 		assertTrue(getConflicts().contains("foo"));
 
 		// rules 14 & 15
 		setupCase(headMap, headMap, idxMap);
 		go();
 
 		assertAllEmpty();
 
 		// rules 16 & 17
 		setupCase(headMap, mergeMap, idxMap); go();
 		assertTrue(getConflicts().contains("foo"));
 
 		// rules 18 & 19
 		setupCase(headMap, idxMap, idxMap); go();
 		assertAllEmpty();
 
 		// rule 20
 		setupCase(idxMap, mergeMap, idxMap); go();
 		assertTrue(getUpdated().containsKey("foo"));
 
 		// rules 21
 		setupCase(idxMap, mergeMap, idxMap);
 		assertTrue(new File(trash, "foo").delete());
 		writeTrashFile("foo", "bar");
 		db.readDirCache().getEntry(0).setUpdateNeeded(true);
 		go();
 		assertTrue(getConflicts().contains("foo"));
 	}
 
 	private void assertAllEmpty() {
 		assertTrue(getRemoved().isEmpty());
 		assertTrue(getUpdated().isEmpty());
 		assertTrue(getConflicts().isEmpty());
 	}
 
 	/*-
 	 * Directory/File Conflict cases:
 	 * It's entirely possible that in practice a number of these may be equivalent
 	 * to the cases described in git-read-tree.txt. As long as it does the right thing,
 	 * that's all I care about. These are basically reverse-engineered from
 	 * what git currently does. If there are tests for these in git, it's kind of
 	 * hard to track them all down...
 	 *
 	 *     H        I       M     Clean     H==M     H==I    I==M         Result
 	 *     ------------------------------------------------------------------
 	 *1    D        D       F       Y         N       Y       N           Update
 	 *2    D        D       F       N         N       Y       N           Conflict
 	 *3    D        F       D                 Y       N       N           Keep
 	 *4    D        F       D                 N       N       N           Conflict
 	 *5    D        F       F       Y         N       N       Y           Keep
 	 *5b   D        F       F       Y         N       N       N           Conflict
 	 *6    D        F       F       N         N       N       Y           Keep
 	 *6b   D        F       F       N         N       N       N           Conflict
 	 *7    F        D       F       Y         Y       N       N           Update
 	 *8    F        D       F       N         Y       N       N           Conflict
 	 *9    F        D       F       Y         N       N       N           Update
 	 *10   F        D       D                 N       N       Y           Keep
 	 *11   F        D       D                 N       N       N           Conflict
 	 *12   F        F       D       Y         N       Y       N           Update
 	 *13   F        F       D       N         N       Y       N           Conflict
 	 *14   F        F       D                 N       N       N           Conflict
 	 *15   0        F       D                 N       N       N           Conflict
 	 *16   0        D       F       Y         N       N       N           Update
 	 *17   0        D       F                 N       N       N           Conflict
 	 *18   F        0       D                                             Update
 	 *19   D        0       F                                             Update
 	 */
 	@Test
 	public void testDirectoryFileSimple() throws IOException {
 		ObjectId treeDF = buildTree(mkmap("DF", "DF"));
 		ObjectId treeDFDF = buildTree(mkmap("DF/DF", "DF/DF"));
 		buildIndex(mkmap("DF", "DF"));
 
 		prescanTwoTrees(treeDF, treeDFDF);
 
 		assertTrue(getRemoved().contains("DF"));
 		assertTrue(getUpdated().containsKey("DF/DF"));
 
 		recursiveDelete(new File(trash, "DF"));
 		buildIndex(mkmap("DF/DF", "DF/DF"));
 
 		prescanTwoTrees(treeDFDF, treeDF);
 		assertTrue(getRemoved().contains("DF/DF"));
 		assertTrue(getUpdated().containsKey("DF"));
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_1() throws Exception {
 		// 1
 		doit(mk("DF/DF"), mk("DF"), mk("DF/DF"));
 		assertNoConflicts();
 		assertUpdated("DF");
 		assertRemoved("DF/DF");
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_2() throws Exception {
 		// 2
 		setupCase(mk("DF/DF"), mk("DF"), mk("DF/DF"));
 		writeTrashFile("DF/DF", "different");
 		go();
 		assertConflict("DF/DF");
 
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_3() throws Exception {
 		// 3
 		doit(mk("DF/DF"), mk("DF/DF"), mk("DF"));
 		assertNoConflicts();
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_4() throws Exception {
 		// 4 (basically same as 3, just with H and M different)
 		doit(mk("DF/DF"), mkmap("DF/DF", "foo"), mk("DF"));
 		assertConflict("DF/DF");
 
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_5() throws Exception {
 		// 5
 		doit(mk("DF/DF"), mk("DF"), mk("DF"));
 		assertRemoved("DF/DF");
 		assertEquals(0, dco.getConflicts().size());
 		assertEquals(0, dco.getUpdated().size());
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_5b() throws Exception {
 		// 5
 		doit(mk("DF/DF"), mkmap("DF", "different"), mk("DF"));
 		assertRemoved("DF/DF");
 		assertConflict("DF");
 		assertEquals(0, dco.getUpdated().size());
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_6() throws Exception {
 		// 6
 		setupCase(mk("DF/DF"), mk("DF"), mk("DF"));
 		writeTrashFile("DF", "different");
 		go();
 		assertRemoved("DF/DF");
 		assertEquals(0, dco.getConflicts().size());
 		assertEquals(0, dco.getUpdated().size());
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_6b() throws Exception {
 		// 6
 		setupCase(mk("DF/DF"), mk("DF"), mkmap("DF", "different"));
 		writeTrashFile("DF", "again different");
 		go();
 		assertRemoved("DF/DF");
 		assertConflict("DF");
 		assertEquals(0, dco.getUpdated().size());
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_7() throws Exception {
 		// 7
 		doit(mk("DF"), mk("DF"), mk("DF/DF"));
 		assertUpdated("DF");
 		assertRemoved("DF/DF");
 
 		cleanUpDF();
 		setupCase(mk("DF/DF"), mk("DF/DF"), mk("DF/DF/DF/DF/DF"));
 		go();
 		assertRemoved("DF/DF/DF/DF/DF");
 		assertUpdated("DF/DF");
 
 		cleanUpDF();
 		setupCase(mk("DF/DF"), mk("DF/DF"), mk("DF/DF/DF/DF/DF"));
 		writeTrashFile("DF/DF/DF/DF/DF", "diff");
 		go();
 		assertConflict("DF/DF/DF/DF/DF");
 
 		// assertUpdated("DF/DF");
 		// Why do we expect an update on DF/DF. H==M,
 		// H&M are files and index contains a dir, index
 		// is dirty: that case is not in the table but
 		// we cannot update DF/DF to a file, this would
 		// require that we delete DF/DF/DF/DF/DF in workdir
 		// throwing away unsaved contents.
 		// This test would fail in DirCacheCheckoutTests.
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_8() throws Exception {
 		// 8
 		setupCase(mk("DF"), mk("DF"), mk("DF/DF"));
 		recursiveDelete(new File(db.getWorkTree(), "DF"));
 		writeTrashFile("DF", "xy");
 		go();
 		assertConflict("DF/DF");
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_9() throws Exception {
 		// 9
 		doit(mkmap("DF", "QP"), mkmap("DF", "QP"), mkmap("DF/DF", "DF/DF"));
 		assertRemoved("DF/DF");
 		assertUpdated("DF");
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_10() throws Exception {
 		// 10
 		cleanUpDF();
 		doit(mk("DF"), mk("DF/DF"), mk("DF/DF"));
 		assertNoConflicts();
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_11() throws Exception {
 		// 11
 		doit(mk("DF"), mk("DF/DF"), mkmap("DF/DF", "asdf"));
 		assertConflict("DF/DF");
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_12() throws Exception {
 		// 12
 		cleanUpDF();
 		doit(mk("DF"), mk("DF/DF"), mk("DF"));
 		assertRemoved("DF");
 		assertUpdated("DF/DF");
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_13() throws Exception {
 		// 13
 		cleanUpDF();
 		setupCase(mk("DF"), mk("DF/DF"), mk("DF"));
 		writeTrashFile("DF", "asdfsdf");
 		go();
 		assertConflict("DF");
 		assertUpdated("DF/DF");
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_14() throws Exception {
 		// 14
 		cleanUpDF();
 		doit(mk("DF"), mk("DF/DF"), mkmap("DF", "Foo"));
 		assertConflict("DF");
 		assertUpdated("DF/DF");
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_15() throws Exception {
 		// 15
 		doit(mkmap(), mk("DF/DF"), mk("DF"));
 
 		// This test would fail in DirCacheCheckoutTests. I think this test is wrong,
 		// it should check for conflicts according to rule 15
 		// assertRemoved("DF");
 
 		assertUpdated("DF/DF");
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_15b() throws Exception {
 		// 15, take 2, just to check multi-leveled
 		doit(mkmap(), mk("DF/DF/DF/DF"), mk("DF"));
 
 		// I think this test is wrong, it should
 		// check for conflicts according to rule 15
 		// This test would fail in DirCacheCheckouts
 		// assertRemoved("DF");
 
 		assertUpdated("DF/DF/DF/DF");
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_16() throws Exception {
 		// 16
 		cleanUpDF();
 		doit(mkmap(), mk("DF"), mk("DF/DF/DF"));
 		assertRemoved("DF/DF/DF");
 		assertUpdated("DF");
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_17() throws Exception {
 		// 17
 		cleanUpDF();
 		setupCase(mkmap(), mk("DF"), mk("DF/DF/DF"));
 		writeTrashFile("DF/DF/DF", "asdf");
 		go();
 		assertConflict("DF/DF/DF");
 
 		// Why do we expect an update on DF. If we really update
 		// DF and update also the working tree we would have to
 		// overwrite a dirty file in the work-tree DF/DF/DF
 		// This test would fail in DirCacheCheckout
 		// assertUpdated("DF");
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_18() throws Exception {
 		// 18
 		cleanUpDF();
 		doit(mk("DF/DF"), mk("DF/DF/DF/DF"), null);
 		assertRemoved("DF/DF");
 		assertUpdated("DF/DF/DF/DF");
 	}
 
 	@Test
 	public void testDirectoryFileConflicts_19() throws Exception {
 		// 19
 		cleanUpDF();
 		doit(mk("DF/DF/DF/DF"), mk("DF/DF/DF"), null);
 		assertRemoved("DF/DF/DF/DF");
 		assertUpdated("DF/DF/DF");
 	}
 
 	protected void cleanUpDF() throws Exception {
 		tearDown();
 		setUp();
 		recursiveDelete(new File(trash, "DF"));
 	}
 
 	protected void assertConflict(String s) {
 		assertTrue(getConflicts().contains(s));
 	}
 
 	protected void assertUpdated(String s) {
 		assertTrue(getUpdated().containsKey(s));
 	}
 
 	protected void assertRemoved(String s) {
 		assertTrue(getRemoved().contains(s));
 	}
 
 	protected void assertNoConflicts() {
 		assertTrue(getConflicts().isEmpty());
 	}
 
 	protected void doit(HashMap<String, String> h, HashMap<String, String> m, HashMap<String, String> i)
 			throws IOException {
 				setupCase(h, m, i);
 				go();
 			}
 
 	@Test
 	public void testUntrackedConflicts() throws IOException {
 		setupCase(null, mk("foo"), null);
 		writeTrashFile("foo", "foo");
 		go();
 
 		// test that we don't overwrite untracked files when there is a HEAD
 		recursiveDelete(new File(trash, "foo"));
 		setupCase(mk("other"), mkmap("other", "other", "foo", "foo"),
 				mk("other"));
 		writeTrashFile("foo", "bar");
 		try {
 			checkout();
 			fail("didn't get the expected exception");
 		} catch (CheckoutConflictException e) {
 			assertConflict("foo");
 			assertEquals("foo", e.getConflictingFiles()[0]);
 			assertWorkDir(mkmap("foo", "bar", "other", "other"));
 			assertIndex(mk("other"));
 		}
 
 		// test that we don't overwrite untracked files when there is no HEAD
 		recursiveDelete(new File(trash, "other"));
 		recursiveDelete(new File(trash, "foo"));
 		setupCase(null, mk("foo"), null);
 		writeTrashFile("foo", "bar");
 		try {
 			checkout();
 			fail("didn't get the expected exception");
 		} catch (CheckoutConflictException e) {
 			assertConflict("foo");
 			assertWorkDir(mkmap("foo", "bar"));
 			assertIndex(mkmap("other", "other"));
 		}
 
 		// TODO: Why should we expect conflicts here?
 		// H and M are empty and according to rule #5 of
 		// the carry-over rules a dirty index is no reason
 		// for a conflict. (I also feel it should be a
 		// conflict because we are going to overwrite
 		// unsaved content in the working tree
 		// This test would fail in DirCacheCheckoutTest
 		// assertConflict("foo");
 
 		recursiveDelete(new File(trash, "foo"));
 		recursiveDelete(new File(trash, "other"));
 		setupCase(null, mk("foo"), null);
 		writeTrashFile("foo/bar/baz", "");
 		writeTrashFile("foo/blahblah", "");
 		go();
 
 		assertConflict("foo");
 		assertConflict("foo/bar/baz");
 		assertConflict("foo/blahblah");
 
 		recursiveDelete(new File(trash, "foo"));
 
 		setupCase(mkmap("foo/bar", "", "foo/baz", ""),
 				mk("foo"), mkmap("foo/bar", "", "foo/baz", ""));
 		assertTrue(new File(trash, "foo/bar").exists());
 		go();
 
 		assertNoConflicts();
 	}
 
 	@Test
 	public void testCloseNameConflictsX0() throws IOException {
 		setupCase(mkmap("a/a", "a/a-c"), mkmap("a/a","a/a", "b.b/b.b","b.b/b.bs"), mkmap("a/a", "a/a-c") );
 		checkout();
 		assertIndex(mkmap("a/a", "a/a", "b.b/b.b", "b.b/b.bs"));
 		assertWorkDir(mkmap("a/a", "a/a", "b.b/b.b", "b.b/b.bs"));
 		go();
 		assertIndex(mkmap("a/a", "a/a", "b.b/b.b", "b.b/b.bs"));
 		assertWorkDir(mkmap("a/a", "a/a", "b.b/b.b", "b.b/b.bs"));
 		assertNoConflicts();
 	}
 
 	@Test
 	public void testCloseNameConflicts1() throws IOException {
 		setupCase(mkmap("a/a", "a/a-c"), mkmap("a/a","a/a", "a.a/a.a","a.a/a.a"), mkmap("a/a", "a/a-c") );
 		checkout();
 		assertIndex(mkmap("a/a", "a/a", "a.a/a.a", "a.a/a.a"));
 		assertWorkDir(mkmap("a/a", "a/a", "a.a/a.a", "a.a/a.a"));
 		go();
 		assertIndex(mkmap("a/a", "a/a", "a.a/a.a", "a.a/a.a"));
 		assertWorkDir(mkmap("a/a", "a/a", "a.a/a.a", "a.a/a.a"));
 		assertNoConflicts();
 	}
 
 	@Test
 	public void testCheckoutHierarchy() throws IOException {
 		setupCase(
 				mkmap("a", "a", "b/c", "b/c", "d", "d", "e/f", "e/f", "e/g",
 						"e/g"),
 				mkmap("a", "a2", "b/c", "b/c", "d", "d", "e/f", "e/f", "e/g",
 						"e/g2"),
 				mkmap("a", "a", "b/c", "b/c", "d", "d", "e/f", "e/f", "e/g",
 						"e/g3"));
 		try {
 			checkout();
 		} catch (CheckoutConflictException e) {
 			assertWorkDir(mkmap("a", "a", "b/c", "b/c", "d", "d", "e/f",
 					"e/f", "e/g", "e/g3"));
 			assertConflict("e/g");
 			assertEquals("e/g", e.getConflictingFiles()[0]);
 		}
 	}
 
 	@Test
 	public void testCheckoutOutChanges() throws IOException {
 		setupCase(mk("foo"), mk("foo/bar"), mk("foo"));
 		checkout();
 		assertIndex(mk("foo/bar"));
 		assertWorkDir(mk("foo/bar"));
 
 		assertFalse(new File(trash, "foo").isFile());
 		assertTrue(new File(trash, "foo/bar").isFile());
 		recursiveDelete(new File(trash, "foo"));
 
 		assertWorkDir(mkmap());
 
 		setupCase(mk("foo/bar"), mk("foo"), mk("foo/bar"));
 		checkout();
 
 		assertIndex(mk("foo"));
 		assertWorkDir(mk("foo"));
 
 		assertFalse(new File(trash, "foo/bar").isFile());
 		assertTrue(new File(trash, "foo").isFile());
 
 		setupCase(mk("foo"), mkmap("foo", "qux"), mkmap("foo", "bar"));
 
 		assertIndex(mkmap("foo", "bar"));
 		assertWorkDir(mkmap("foo", "bar"));
 
 		try {
 			checkout();
 			fail("did not throw exception");
 		} catch (CheckoutConflictException e) {
 			assertIndex(mkmap("foo", "bar"));
 			assertWorkDir(mkmap("foo", "bar"));
 		}
 	}
 
 	@Test
 	public void testCheckoutChangeLinkToEmptyDir() throws Exception {
 		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
 		String fname = "was_file";
 		Git git = Git.wrap(db);
 
 		// Add a file
 		writeTrashFile(fname, "a");
 		git.add().addFilepattern(fname).call();
 
 		// Add a link to file
 		String linkName = "link";
 		File link = writeLink(linkName, fname).toFile();
 		git.add().addFilepattern(linkName).call();
 		git.commit().setMessage("Added file and link").call();
 
 		assertWorkDir(mkmap(linkName, "a", fname, "a"));
 
 		// replace link with empty directory
 		FileUtils.delete(link);
 		FileUtils.mkdir(link);
 		assertTrue("Link must be a directory now", link.isDirectory());
 
 		// modify file
 		writeTrashFile(fname, "b");
 		assertWorkDir(mkmap(fname, "b", linkName, "/"));
 
 		// revert both paths to HEAD state
 		git.checkout().setStartPoint(Constants.HEAD)
 				.addPath(fname).addPath(linkName).call();
 
 		assertWorkDir(mkmap(fname, "a", linkName, "a"));
 
 		Status st = git.status().call();
 		assertTrue(st.isClean());
 	}
 
 	@Test
 	public void testCheckoutChangeLinkToEmptyDirs() throws Exception {
 		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
 		String fname = "was_file";
 		Git git = Git.wrap(db);
 
 		// Add a file
 		writeTrashFile(fname, "a");
 		git.add().addFilepattern(fname).call();
 
 		// Add a link to file
 		String linkName = "link";
 		File link = writeLink(linkName, fname).toFile();
 		git.add().addFilepattern(linkName).call();
 		git.commit().setMessage("Added file and link").call();
 
 		assertWorkDir(mkmap(linkName, "a", fname, "a"));
 
 		// replace link with directory containing only directories, no files
 		FileUtils.delete(link);
 		FileUtils.mkdirs(new File(link, "dummyDir"));
 		assertTrue("Link must be a directory now", link.isDirectory());
 
 		assertFalse("Must not delete non empty directory", link.delete());
 
 		// modify file
 		writeTrashFile(fname, "b");
 		assertWorkDir(mkmap(fname, "b", linkName + "/dummyDir", "/"));
 
 		// revert both paths to HEAD state
 		git.checkout().setStartPoint(Constants.HEAD)
 				.addPath(fname).addPath(linkName).call();
 
 		assertWorkDir(mkmap(fname, "a", linkName, "a"));
 
 		Status st = git.status().call();
 		assertTrue(st.isClean());
 	}
 
 	@Test
 	public void testCheckoutChangeLinkToNonEmptyDirs() throws Exception {
 		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
 		String fname = "file";
 		Git git = Git.wrap(db);
 
 		// Add a file
 		writeTrashFile(fname, "a");
 		git.add().addFilepattern(fname).call();
 
 		// Add a link to file
 		String linkName = "link";
 		File link = writeLink(linkName, fname).toFile();
 		git.add().addFilepattern(linkName).call();
 		git.commit().setMessage("Added file and link").call();
 
 		assertWorkDir(mkmap(linkName, "a", fname, "a"));
 
 		// replace link with directory containing only directories, no files
 		FileUtils.delete(link);
 
 		// create but do not add a file in the new directory to the index
 		writeTrashFile(linkName + "/dir1", "file1", "c");
 
 		// create but do not add a file in the new directory to the index
 		writeTrashFile(linkName + "/dir2", "file2", "d");
 
 		assertTrue("File must be a directory now", link.isDirectory());
 		assertFalse("Must not delete non empty directory", link.delete());
 
 		// 2 extra files are created
 		assertWorkDir(mkmap(fname, "a", linkName + "/dir1/file1", "c",
 				linkName + "/dir2/file2", "d"));
 
 		// revert path to HEAD state
 		git.checkout().setStartPoint(Constants.HEAD).addPath(linkName).call();
 
 		// expect only the one added to the index
 		assertWorkDir(mkmap(linkName, "a", fname, "a"));
 
 		Status st = git.status().call();
 		assertTrue(st.isClean());
 	}
 
 	@Test
 	public void testCheckoutChangeLinkToNonEmptyDirsAndNewIndexEntry()
 			throws Exception {
 		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
 		String fname = "file";
 		Git git = Git.wrap(db);
 
 		// Add a file
 		writeTrashFile(fname, "a");
 		git.add().addFilepattern(fname).call();
 
 		// Add a link to file
 		String linkName = "link";
 		File link = writeLink(linkName, fname).toFile();
 		git.add().addFilepattern(linkName).call();
 		git.commit().setMessage("Added file and link").call();
 
 		assertWorkDir(mkmap(linkName, "a", fname, "a"));
 
 		// replace link with directory containing only directories, no files
 		FileUtils.delete(link);
 
 		// create and add a file in the new directory to the index
 		writeTrashFile(linkName + "/dir1", "file1", "c");
 		git.add().addFilepattern(linkName + "/dir1/file1").call();
 
 		// create but do not add a file in the new directory to the index
 		writeTrashFile(linkName + "/dir2", "file2", "d");
 
 		assertTrue("File must be a directory now", link.isDirectory());
 		assertFalse("Must not delete non empty directory", link.delete());
 
 		// 2 extra files are created
 		assertWorkDir(mkmap(fname, "a", linkName + "/dir1/file1", "c",
 				linkName + "/dir2/file2", "d"));
 
 		// revert path to HEAD state
 		git.checkout().setStartPoint(Constants.HEAD).addPath(linkName).call();
 
 		// original file and link
 		assertWorkDir(mkmap(linkName, "a", fname, "a"));
 
 		Status st = git.status().call();
 		assertTrue(st.isClean());
 	}
 
 	@Test
 	public void testCheckoutChangeFileToEmptyDir() throws Exception {
 		String fname = "was_file";
 		Git git = Git.wrap(db);
 
 		// Add a file
 		File file = writeTrashFile(fname, "a");
 		git.add().addFilepattern(fname).call();
 		git.commit().setMessage("Added file").call();
 
 		// replace file with empty directory
 		FileUtils.delete(file);
 		FileUtils.mkdir(file);
 		assertTrue("File must be a directory now", file.isDirectory());
 
 		assertWorkDir(mkmap(fname, "/"));
 
 		// revert path to HEAD state
 		git.checkout().setStartPoint(Constants.HEAD).addPath(fname).call();
 
 		assertWorkDir(mkmap(fname, "a"));
 
 		Status st = git.status().call();
 		assertTrue(st.isClean());
 	}
 
 	@Test
 	public void testCheckoutChangeFileToEmptyDirs() throws Exception {
 		String fname = "was_file";
 		Git git = Git.wrap(db);
 
 		// Add a file
 		File file = writeTrashFile(fname, "a");
 		git.add().addFilepattern(fname).call();
 		git.commit().setMessage("Added file").call();
 
 		// replace file with directory containing only directories, no files
 		FileUtils.delete(file);
 		FileUtils.mkdirs(new File(file, "dummyDir"));
 		assertTrue("File must be a directory now", file.isDirectory());
 		assertFalse("Must not delete non empty directory", file.delete());
 
 		assertWorkDir(mkmap(fname + "/dummyDir", "/"));
 
 		// revert path to HEAD state
 		git.checkout().setStartPoint(Constants.HEAD).addPath(fname).call();
 
 		assertWorkDir(mkmap(fname, "a"));
 
 		Status st = git.status().call();
 		assertTrue(st.isClean());
 	}
 
 	@Test
 	public void testCheckoutChangeFileToNonEmptyDirs() throws Exception {
 		String fname = "was_file";
 		Git git = Git.wrap(db);
 
 		// Add a file
 		File file = writeTrashFile(fname, "a");
 		git.add().addFilepattern(fname).call();
 		git.commit().setMessage("Added file").call();
 
 		assertWorkDir(mkmap(fname, "a"));
 
 		// replace file with directory containing only directories, no files
 		FileUtils.delete(file);
 
 		// create but do not add a file in the new directory to the index
 		writeTrashFile(fname + "/dir1", "file1", "c");
 
 		// create but do not add a file in the new directory to the index
 		writeTrashFile(fname + "/dir2", "file2", "d");
 
 		assertTrue("File must be a directory now", file.isDirectory());
 		assertFalse("Must not delete non empty directory", file.delete());
 
 		// 2 extra files are created
 		assertWorkDir(
 				mkmap(fname + "/dir1/file1", "c", fname + "/dir2/file2", "d"));
 
 		// revert path to HEAD state
 		git.checkout().setStartPoint(Constants.HEAD).addPath(fname).call();
 
 		// expect only the one added to the index
 		assertWorkDir(mkmap(fname, "a"));
 
 		Status st = git.status().call();
 		assertTrue(st.isClean());
 	}
 
 	@Test
 	public void testCheckoutChangeFileToNonEmptyDirsAndNewIndexEntry()
 			throws Exception {
 		String fname = "was_file";
 		Git git = Git.wrap(db);
 
 		// Add a file
 		File file = writeTrashFile(fname, "a");
 		git.add().addFilepattern(fname).call();
 		git.commit().setMessage("Added file").call();
 
 		assertWorkDir(mkmap(fname, "a"));
 
 		// replace file with directory containing only directories, no files
 		FileUtils.delete(file);
 
 		// create and add a file in the new directory to the index
 		writeTrashFile(fname + "/dir", "file1", "c");
 		git.add().addFilepattern(fname + "/dir/file1").call();
 
 		// create but do not add a file in the new directory to the index
 		writeTrashFile(fname + "/dir", "file2", "d");
 
 		assertTrue("File must be a directory now", file.isDirectory());
 		assertFalse("Must not delete non empty directory", file.delete());
 
 		// 2 extra files are created
 		assertWorkDir(
 				mkmap(fname + "/dir/file1", "c", fname + "/dir/file2", "d"));
 
 		// revert path to HEAD state
 		git.checkout().setStartPoint(Constants.HEAD).addPath(fname).call();
 		assertWorkDir(mkmap(fname, "a"));
 
 		Status st = git.status().call();
 		assertTrue(st.isClean());
 	}
 
 	@Test
 	public void testCheckoutOutChangesAutoCRLFfalse() throws IOException {
 		setupCase(mk("foo"), mkmap("foo/bar", "foo\nbar"), mk("foo"));
 		checkout();
 		assertIndex(mkmap("foo/bar", "foo\nbar"));
 		assertWorkDir(mkmap("foo/bar", "foo\nbar"));
 	}
 
 	@Test
 	public void testCheckoutOutChangesAutoCRLFInput() throws IOException {
 		setupCase(mk("foo"), mkmap("foo/bar", "foo\nbar"), mk("foo"));
 		db.getConfig().setString("core", null, "autocrlf", "input");
 		checkout();
 		assertIndex(mkmap("foo/bar", "foo\nbar"));
 		assertWorkDir(mkmap("foo/bar", "foo\nbar"));
 	}
 
 	@Test
 	public void testCheckoutOutChangesAutoCRLFtrue() throws IOException {
 		setupCase(mk("foo"), mkmap("foo/bar", "foo\nbar"), mk("foo"));
 		db.getConfig().setString("core", null, "autocrlf", "true");
 		checkout();
 		assertIndex(mkmap("foo/bar", "foo\nbar"));
 		assertWorkDir(mkmap("foo/bar", "foo\r\nbar"));
 	}
 
 	@Test
 	public void testCheckoutOutChangesAutoCRLFtrueBinary() throws IOException {
 		setupCase(mk("foo"), mkmap("foo/bar", "foo\nb\u0000ar"), mk("foo"));
 		db.getConfig().setString("core", null, "autocrlf", "true");
 		checkout();
 		assertIndex(mkmap("foo/bar", "foo\nb\u0000ar"));
 		assertWorkDir(mkmap("foo/bar", "foo\nb\u0000ar"));
 	}
 
 	@Test
 	public void testCheckoutUncachedChanges() throws IOException {
 		setupCase(mk("foo"), mk("foo"), mk("foo"));
 		writeTrashFile("foo", "otherData");
 		checkout();
 		assertIndex(mk("foo"));
 		assertWorkDir(mkmap("foo", "otherData"));
 		assertTrue(new File(trash, "foo").isFile());
 	}
 
 	@Test
 	public void testDontOverwriteDirtyFile() throws IOException {
 		setupCase(mk("foo"), mk("other"), mk("foo"));
 		writeTrashFile("foo", "different");
 		try {
 			checkout();
 			fail("Didn't got the expected conflict");
 		} catch (CheckoutConflictException e) {
 			assertIndex(mk("foo"));
 			assertWorkDir(mkmap("foo", "different"));
 			assertEquals(Arrays.asList("foo"), getConflicts());
 			assertTrue(new File(trash, "foo").isFile());
 		}
 	}
 
 	@Test
 	public void testDontOverwriteEmptyFolder() throws IOException {
 		setupCase(mk("foo"), mk("foo"), mk("foo"));
 		FileUtils.mkdir(new File(db.getWorkTree(), "d"));
 		checkout();
 		assertWorkDir(mkmap("foo", "foo", "d", "/"));
 	}
 
 	@Test
 	public void testOverwriteUntrackedIgnoredFile() throws IOException,
 			GitAPIException {
 		String fname="file.txt";
 		Git git = Git.wrap(db);
 
 		// Add a file
 		writeTrashFile(fname, "a");
 		git.add().addFilepattern(fname).call();
 		git.commit().setMessage("create file").call();
 
 		// Create branch
 		git.branchCreate().setName("side").call();
 
 		// Modify file
 		writeTrashFile(fname, "b");
 		git.add().addFilepattern(fname).call();
 		git.commit().setMessage("modify file").call();
 
 		// Switch branches
 		git.checkout().setName("side").call();
 		git.rm().addFilepattern(fname).call();
 		writeTrashFile(".gitignore", fname);
 		git.add().addFilepattern(".gitignore").call();
 		git.commit().setMessage("delete and ignore file").call();
 
 		writeTrashFile(fname, "Something different");
 		git.checkout().setName("master").call();
 		assertWorkDir(mkmap(fname, "b"));
 		assertTrue(git.status().call().isClean());
 	}
 
 	@Test
 	public void testOverwriteUntrackedFileModeChange()
 			throws IOException, GitAPIException {
 		String fname = "file.txt";
 		Git git = Git.wrap(db);
 
 		// Add a file
 		File file = writeTrashFile(fname, "a");
 		git.add().addFilepattern(fname).call();
 		git.commit().setMessage("create file").call();
 		assertWorkDir(mkmap(fname, "a"));
 
 		// Create branch
 		git.branchCreate().setName("side").call();
 
 		// Switch branches
 		git.checkout().setName("side").call();
 
 		// replace file with directory containing files
 		FileUtils.delete(file);
 
 		// create and add a file in the new directory to the index
 		writeTrashFile(fname + "/dir1", "file1", "c");
 		git.add().addFilepattern(fname + "/dir1/file1").call();
 
 		// create but do not add a file in the new directory to the index
 		writeTrashFile(fname + "/dir2", "file2", "d");
 
 		assertTrue("File must be a directory now", file.isDirectory());
 		assertFalse("Must not delete non empty directory", file.delete());
 
 		// 2 extra files are created
 		assertWorkDir(
 				mkmap(fname + "/dir1/file1", "c", fname + "/dir2/file2", "d"));
 
 		try {
 			git.checkout().setName("master").call();
 			fail("did not throw exception");
 		} catch (Exception e) {
 			// 2 extra files are still there
 			assertWorkDir(mkmap(fname + "/dir1/file1", "c",
 					fname + "/dir2/file2", "d"));
 		}
 	}
 
 	@Test
 	public void testOverwriteUntrackedLinkModeChange()
 			throws Exception {
 		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
 		String fname = "file.txt";
 		Git git = Git.wrap(db);
 
 		// Add a file
 		writeTrashFile(fname, "a");
 		git.add().addFilepattern(fname).call();
 
 		// Add a link to file
 		String linkName = "link";
 		File link = writeLink(linkName, fname).toFile();
 		git.add().addFilepattern(linkName).call();
 		git.commit().setMessage("Added file and link").call();
 
 		assertWorkDir(mkmap(linkName, "a", fname, "a"));
 
 		// Create branch
 		git.branchCreate().setName("side").call();
 
 		// Switch branches
 		git.checkout().setName("side").call();
 
 		// replace link with directory containing files
 		FileUtils.delete(link);
 
 		// create and add a file in the new directory to the index
 		writeTrashFile(linkName + "/dir1", "file1", "c");
 		git.add().addFilepattern(linkName + "/dir1/file1").call();
 
 		// create but do not add a file in the new directory to the index
 		writeTrashFile(linkName + "/dir2", "file2", "d");
 
 		assertTrue("Link must be a directory now", link.isDirectory());
 		assertFalse("Must not delete non empty directory", link.delete());
 
 		// 2 extra files are created
 		assertWorkDir(mkmap(fname, "a", linkName + "/dir1/file1", "c",
 				linkName + "/dir2/file2", "d"));
 
 		try {
 			git.checkout().setName("master").call();
 			fail("did not throw exception");
 		} catch (Exception e) {
 			// 2 extra files are still there
 			assertWorkDir(mkmap(fname, "a", linkName + "/dir1/file1", "c",
 					linkName + "/dir2/file2", "d"));
 		}
 	}
 
 	@Test
 	public void testFileModeChangeWithNoContentChangeUpdate() throws Exception {
 		if (!FS.DETECTED.supportsExecute())
 			return;
 
 		Git git = Git.wrap(db);
 
 		// Add non-executable file
 		File file = writeTrashFile("file.txt", "a");
 		git.add().addFilepattern("file.txt").call();
 		git.commit().setMessage("commit1").call();
 		assertFalse(db.getFS().canExecute(file));
 
 		// Create branch
 		git.branchCreate().setName("b1").call();
 
 		// Make file executable
 		db.getFS().setExecute(file, true);
 		git.add().addFilepattern("file.txt").call();
 		git.commit().setMessage("commit2").call();
 
 		// Verify executable and working directory is clean
 		Status status = git.status().call();
 		assertTrue(status.getModified().isEmpty());
 		assertTrue(status.getChanged().isEmpty());
 		assertTrue(db.getFS().canExecute(file));
 
 		// Switch branches
 		git.checkout().setName("b1").call();
 
 		// Verify not executable and working directory is clean
 		status = git.status().call();
 		assertTrue(status.getModified().isEmpty());
 		assertTrue(status.getChanged().isEmpty());
 		assertFalse(db.getFS().canExecute(file));
 	}
 
 	@Test
 	public void testFileModeChangeAndContentChangeConflict() throws Exception {
 		if (!FS.DETECTED.supportsExecute())
 			return;
 
 		Git git = Git.wrap(db);
 
 		// Add non-executable file
 		File file = writeTrashFile("file.txt", "a");
 		git.add().addFilepattern("file.txt").call();
 		git.commit().setMessage("commit1").call();
 		assertFalse(db.getFS().canExecute(file));
 
 		// Create branch
 		git.branchCreate().setName("b1").call();
 
 		// Make file executable
 		db.getFS().setExecute(file, true);
 		git.add().addFilepattern("file.txt").call();
 		git.commit().setMessage("commit2").call();
 
 		// Verify executable and working directory is clean
 		Status status = git.status().call();
 		assertTrue(status.getModified().isEmpty());
 		assertTrue(status.getChanged().isEmpty());
 		assertTrue(db.getFS().canExecute(file));
 
 		writeTrashFile("file.txt", "b");
 
 		// Switch branches
 		CheckoutCommand checkout = git.checkout().setName("b1");
 		try {
 			checkout.call();
 			fail("Checkout exception not thrown");
 		} catch (org.eclipse.jgit.api.errors.CheckoutConflictException e) {
 			CheckoutResult result = checkout.getResult();
 			assertNotNull(result);
 			assertNotNull(result.getConflictList());
 			assertEquals(1, result.getConflictList().size());
 			assertTrue(result.getConflictList().contains("file.txt"));
 		}
 	}
 
 	@Test
 	public void testDirtyFileModeEqualHeadMerge()
 			throws Exception {
 		if (!FS.DETECTED.supportsExecute())
 			return;
 
 		Git git = Git.wrap(db);
 
 		// Add non-executable file
 		File file = writeTrashFile("file.txt", "a");
 		git.add().addFilepattern("file.txt").call();
 		git.commit().setMessage("commit1").call();
 		assertFalse(db.getFS().canExecute(file));
 
 		// Create branch
 		git.branchCreate().setName("b1").call();
 
 		// Create second commit and don't touch file
 		writeTrashFile("file2.txt", "");
 		git.add().addFilepattern("file2.txt").call();
 		git.commit().setMessage("commit2").call();
 
 		// stage a mode change
 		writeTrashFile("file.txt", "a");
 		db.getFS().setExecute(file, true);
 		git.add().addFilepattern("file.txt").call();
 
 		// dirty the file
 		writeTrashFile("file.txt", "b");
 
 		assertEquals(
 				"[file.txt, mode:100755, content:a][file2.txt, mode:100644, content:]",
 				indexState(CONTENT));
 		assertWorkDir(mkmap("file.txt", "b", "file2.txt", ""));
 
 		// Switch branches and check that the dirty file survived in worktree
 		// and index
 		git.checkout().setName("b1").call();
 		assertEquals("[file.txt, mode:100755, content:a]", indexState(CONTENT));
 		assertWorkDir(mkmap("file.txt", "b"));
 	}
 
 	@Test
 	public void testDirtyFileModeEqualIndexMerge()
 			throws Exception {
 		if (!FS.DETECTED.supportsExecute())
 			return;
 
 		Git git = Git.wrap(db);
 
 		// Add non-executable file
 		File file = writeTrashFile("file.txt", "a");
 		git.add().addFilepattern("file.txt").call();
 		git.commit().setMessage("commit1").call();
 		assertFalse(db.getFS().canExecute(file));
 
 		// Create branch
 		git.branchCreate().setName("b1").call();
 
 		// Create second commit with executable file
 		file = writeTrashFile("file.txt", "b");
 		db.getFS().setExecute(file, true);
 		git.add().addFilepattern("file.txt").call();
 		git.commit().setMessage("commit2").call();
 
 		// stage the same content as in the branch we want to switch to
 		writeTrashFile("file.txt", "a");
 		db.getFS().setExecute(file, false);
 		git.add().addFilepattern("file.txt").call();
 
 		// dirty the file
 		writeTrashFile("file.txt", "c");
 		db.getFS().setExecute(file, true);
 
 		assertEquals("[file.txt, mode:100644, content:a]", indexState(CONTENT));
 		assertWorkDir(mkmap("file.txt", "c"));
 
 		// Switch branches and check that the dirty file survived in worktree
 		// and index
 		git.checkout().setName("b1").call();
 		assertEquals("[file.txt, mode:100644, content:a]", indexState(CONTENT));
 		assertWorkDir(mkmap("file.txt", "c"));
 	}
 
 	@Test
 	public void testFileModeChangeAndContentChangeNoConflict() throws Exception {
 		if (!FS.DETECTED.supportsExecute())
 			return;
 
 		Git git = Git.wrap(db);
 
 		// Add first file
 		File file1 = writeTrashFile("file1.txt", "a");
 		git.add().addFilepattern("file1.txt").call();
 		git.commit().setMessage("commit1").call();
 		assertFalse(db.getFS().canExecute(file1));
 
 		// Add second file
 		File file2 = writeTrashFile("file2.txt", "b");
 		git.add().addFilepattern("file2.txt").call();
 		git.commit().setMessage("commit2").call();
 		assertFalse(db.getFS().canExecute(file2));
 
 		// Create branch from first commit
 		assertNotNull(git.checkout().setCreateBranch(true).setName("b1")
 				.setStartPoint(Constants.HEAD + "~1").call());
 
 		// Change content and file mode in working directory and index
 		file1 = writeTrashFile("file1.txt", "c");
 		db.getFS().setExecute(file1, true);
 		git.add().addFilepattern("file1.txt").call();
 
 		// Switch back to 'master'
 		assertNotNull(git.checkout().setName(Constants.MASTER).call());
 	}
 
 	@Test(expected = CheckoutConflictException.class)
 	public void testFolderFileConflict() throws Exception {
 		RevCommit headCommit = commitFile("f/a", "initial content", "master");
 		RevCommit checkoutCommit = commitFile("f/a", "side content", "side");
 		FileUtils.delete(new File(db.getWorkTree(), "f"), FileUtils.RECURSIVE);
 		writeTrashFile("f", "file instead of folder");
 		new DirCacheCheckout(db, headCommit.getTree(), db.lockDirCache(),
 				checkoutCommit.getTree()).checkout();
 	}
 
 	@Test
 	public void testMultipleContentConflicts() throws Exception {
 		commitFile("a", "initial content", "master");
 		RevCommit headCommit = commitFile("b", "initial content", "master");
 		commitFile("a", "side content", "side");
 		RevCommit checkoutCommit = commitFile("b", "side content", "side");
 		writeTrashFile("a", "changed content");
 		writeTrashFile("b", "changed content");
 
 		try {
 			new DirCacheCheckout(db, headCommit.getTree(), db.lockDirCache(),
 					checkoutCommit.getTree()).checkout();
 			fail();
 		} catch (CheckoutConflictException expected) {
 			assertEquals(2, expected.getConflictingFiles().length);
 			assertTrue(Arrays.asList(expected.getConflictingFiles())
 					.contains("a"));
 			assertTrue(Arrays.asList(expected.getConflictingFiles())
 					.contains("b"));
 			assertEquals("changed content", read("a"));
 			assertEquals("changed content", read("b"));
 		}
 	}
 
 	@Test
 	public void testFolderFileAndContentConflicts() throws Exception {
 		RevCommit headCommit = commitFile("f/a", "initial content", "master");
 		commitFile("b", "side content", "side");
 		RevCommit checkoutCommit = commitFile("f/a", "side content", "side");
 		FileUtils.delete(new File(db.getWorkTree(), "f"), FileUtils.RECURSIVE);
 		writeTrashFile("f", "file instead of a folder");
 		writeTrashFile("b", "changed content");
 
 		try {
 			new DirCacheCheckout(db, headCommit.getTree(), db.lockDirCache(),
 					checkoutCommit.getTree()).checkout();
 			fail();
 		} catch (CheckoutConflictException expected) {
 			assertEquals(2, expected.getConflictingFiles().length);
 			assertTrue(Arrays.asList(expected.getConflictingFiles())
 					.contains("b"));
 			assertTrue(Arrays.asList(expected.getConflictingFiles())
 					.contains("f"));
 			assertEquals("file instead of a folder", read("f"));
 			assertEquals("changed content", read("b"));
 		}
 	}
 
 	public void assertWorkDir(Map<String, String> i)
 			throws CorruptObjectException,
 			IOException {
 		try (TreeWalk walk = new TreeWalk(db)) {
 			walk.setRecursive(false);
 			walk.addTree(new FileTreeIterator(db));
 			String expectedValue;
 			String path;
 			int nrFiles = 0;
 			FileTreeIterator ft;
 			while (walk.next()) {
 				ft = walk.getTree(0, FileTreeIterator.class);
 				path = ft.getEntryPathString();
 				expectedValue = i.get(path);
 				File file = new File(db.getWorkTree(), path);
 				assertTrue(file.exists());
 				if (file.isFile()) {
 					assertNotNull("found unexpected file for path " + path
 							+ " in workdir", expectedValue);
 					FileInputStream is = new FileInputStream(file);
 					byte[] buffer = new byte[(int) file.length()];
 					int offset = 0;
 					int numRead = 0;
 					while (offset < buffer.length
 							&& (numRead = is.read(buffer, offset, buffer.length
 									- offset)) >= 0) {
 						offset += numRead;
 					}
 					is.close();
 					assertArrayEquals("unexpected content for path " + path
 							+ " in workDir. ", buffer, i.get(path).getBytes());
 					nrFiles++;
 				} else if (file.isDirectory()) {
 					String[] files = file.list();
 					if (files != null && files.length == 0) {
 						assertEquals("found unexpected empty folder for path "
 								+ path + " in workDir. ", "/", i.get(path));
 						nrFiles++;
 					}
 				}
 				if (walk.isSubtree()) {
 					walk.enterSubtree();
 				}
 			}
 			assertEquals("WorkDir has not the right size.", i.size(), nrFiles);
 		}
 	}
 }