/*
    * Copyright (C) 2010, Chris Aniszczyk <caniszczyk@gmail.com>
    * Copyright (C) 2011, Matthias Sohn <matthias.sohn@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.api;
  
  import static org.eclipse.jgit.lib.Constants.MASTER;
  import static org.eclipse.jgit.lib.Constants.R_HEADS;
  import static org.hamcrest.CoreMatchers.is;
  import static org.hamcrest.MatcherAssert.assertThat;
  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.assertSame;
  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.net.MalformedURLException;
  import java.net.URISyntaxException;
  
  import org.eclipse.jgit.api.CheckoutResult.Status;
  import org.eclipse.jgit.api.CreateBranchCommand.SetupUpstreamMode;
  import org.eclipse.jgit.api.errors.GitAPIException;
  import org.eclipse.jgit.api.errors.InvalidRefNameException;
  import org.eclipse.jgit.api.errors.InvalidRemoteException;
  import org.eclipse.jgit.api.errors.JGitInternalException;
  import org.eclipse.jgit.api.errors.RefAlreadyExistsException;
  import org.eclipse.jgit.api.errors.RefNotFoundException;
  import org.eclipse.jgit.api.errors.TransportException;
  import org.eclipse.jgit.dircache.DirCache;
  import org.eclipse.jgit.dircache.DirCacheEntry;
  import org.eclipse.jgit.junit.JGitTestUtil;
  import org.eclipse.jgit.junit.RepositoryTestCase;
  import org.eclipse.jgit.lfs.BuiltinLFS;
  import org.eclipse.jgit.lib.ConfigConstants;
  import org.eclipse.jgit.lib.Constants;
  import org.eclipse.jgit.lib.Ref;
  import org.eclipse.jgit.lib.RefUpdate;
  import org.eclipse.jgit.lib.Repository;
  import org.eclipse.jgit.lib.Sets;
  import org.eclipse.jgit.lib.StoredConfig;
  import org.eclipse.jgit.revwalk.RevCommit;
  import org.eclipse.jgit.storage.file.FileBasedConfig;
  import org.eclipse.jgit.transport.RemoteConfig;
  import org.eclipse.jgit.transport.URIish;
  import org.eclipse.jgit.util.FileUtils;
  import org.eclipse.jgit.util.SystemReader;
  import org.junit.Before;
  import org.junit.Test;
  
  public class CheckoutCommandTest extends RepositoryTestCase {
  	private Git git;
  
  	RevCommit initialCommit;
  
  	RevCommit secondCommit;
 
 	@Override
 	@Before
 	public void setUp() throws Exception {
 		BuiltinLFS.register();
 		super.setUp();
 		git = new Git(db);
 		// commit something
 		writeTrashFile("Test.txt", "Hello world");
 		git.add().addFilepattern("Test.txt").call();
 		initialCommit = git.commit().setMessage("Initial commit").call();
 
 		// create a master branch and switch to it
 		git.branchCreate().setName("test").call();
 		RefUpdate rup = db.updateRef(Constants.HEAD);
 		rup.link("refs/heads/test");
 
 		// commit something on the test branch
 		writeTrashFile("Test.txt", "Some change");
 		git.add().addFilepattern("Test.txt").call();
 		secondCommit = git.commit().setMessage("Second commit").call();
 	}
 
 	@Test
 	public void testSimpleCheckout() throws Exception {
 		git.checkout().setName("test").call();
 	}
 
 	@Test
 	public void testCheckout() throws Exception {
 		git.checkout().setName("test").call();
 		assertEquals("[Test.txt, mode:100644, content:Some change]",
 				indexState(CONTENT));
 		Ref result = git.checkout().setName("master").call();
 		assertEquals("[Test.txt, mode:100644, content:Hello world]",
 				indexState(CONTENT));
 		assertEquals("refs/heads/master", result.getName());
 		assertEquals("refs/heads/master", git.getRepository().getFullBranch());
 	}
 
 	@Test
 	public void testCreateBranchOnCheckout() throws Exception {
 		git.checkout().setCreateBranch(true).setName("test2").call();
 		assertNotNull(db.exactRef("refs/heads/test2"));
 	}
 
 	@Test
 	public void testCheckoutToNonExistingBranch() throws GitAPIException {
 		try {
 			git.checkout().setName("badbranch").call();
 			fail("Should have failed");
 		} catch (RefNotFoundException e) {
 			// except to hit here
 		}
 	}
 
 	@Test
 	public void testCheckoutWithConflict() {
 		CheckoutCommand co = git.checkout();
 		try {
 			writeTrashFile("Test.txt", "Another change");
 			assertEquals(Status.NOT_TRIED, co.getResult().getStatus());
 			co.setName("master").call();
 			fail("Should have failed");
 		} catch (Exception e) {
 			assertEquals(Status.CONFLICTS, co.getResult().getStatus());
 			assertTrue(co.getResult().getConflictList().contains("Test.txt"));
 		}
 	}
 
 	@Test
 	public void testCheckoutWithNonDeletedFiles() throws Exception {
 		File testFile = writeTrashFile("temp", "");
 		try (FileInputStream fis = new FileInputStream(testFile)) {
 			FileUtils.delete(testFile);
 			return;
 		} catch (IOException e) {
 			// the test makes only sense if deletion of
 			// a file with open stream fails
 		}
 		FileUtils.delete(testFile);
 		CheckoutCommand co = git.checkout();
 		// delete Test.txt in branch test
 		testFile = new File(db.getWorkTree(), "Test.txt");
 		assertTrue(testFile.exists());
 		FileUtils.delete(testFile);
 		assertFalse(testFile.exists());
 		git.add().addFilepattern("Test.txt");
 		git.commit().setMessage("Delete Test.txt").setAll(true).call();
 		git.checkout().setName("master").call();
 		assertTrue(testFile.exists());
 		// lock the file so it can't be deleted (in Windows, that is)
 		try (FileInputStream fis = new FileInputStream(testFile)) {
 			assertEquals(Status.NOT_TRIED, co.getResult().getStatus());
 			co.setName("test").call();
 			assertTrue(testFile.exists());
 			assertEquals(Status.NONDELETED, co.getResult().getStatus());
 			assertTrue(co.getResult().getUndeletedList().contains("Test.txt"));
 		}
 	}
 
 	@Test
 	public void testCheckoutCommit() throws Exception {
 		Ref result = git.checkout().setName(initialCommit.name()).call();
 		assertEquals("[Test.txt, mode:100644, content:Hello world]",
 				indexState(CONTENT));
 		assertNull(result);
 		assertEquals(initialCommit.name(), git.getRepository().getFullBranch());
 	}
 
 	@Test
 	public void testCheckoutLightweightTag() throws Exception {
 		git.tag().setAnnotated(false).setName("test-tag")
 				.setObjectId(initialCommit).call();
 		Ref result = git.checkout().setName("test-tag").call();
 
 		assertNull(result);
 		assertEquals(initialCommit.getId(), db.resolve(Constants.HEAD));
 		assertHeadDetached();
 	}
 
 	@Test
 	public void testCheckoutAnnotatedTag() throws Exception {
 		git.tag().setAnnotated(true).setName("test-tag")
 				.setObjectId(initialCommit).call();
 		Ref result = git.checkout().setName("test-tag").call();
 
 		assertNull(result);
 		assertEquals(initialCommit.getId(), db.resolve(Constants.HEAD));
 		assertHeadDetached();
 	}
 
 	@Test
 	public void testCheckoutRemoteTrackingWithUpstream() throws Exception {
 		Repository db2 = createRepositoryWithRemote();
 
 		Git.wrap(db2).checkout().setCreateBranch(true).setName("test")
 				.setStartPoint("origin/test")
 				.setUpstreamMode(SetupUpstreamMode.TRACK).call();
 
 		assertEquals("refs/heads/test",
 				db2.exactRef(Constants.HEAD).getTarget().getName());
 		StoredConfig config = db2.getConfig();
 		assertEquals("origin", config.getString(
 				ConfigConstants.CONFIG_BRANCH_SECTION, "test",
 				ConfigConstants.CONFIG_KEY_REMOTE));
 		assertEquals("refs/heads/test", config.getString(
 				ConfigConstants.CONFIG_BRANCH_SECTION, "test",
 				ConfigConstants.CONFIG_KEY_MERGE));
 	}
 
 	@Test
 	public void testCheckoutRemoteTrackingWithoutLocalBranch() throws Exception {
 		Repository db2 = createRepositoryWithRemote();
 
 		// checkout remote tracking branch in second repository
 		// (no local branches exist yet in second repository)
 		Git.wrap(db2).checkout().setName("remotes/origin/test").call();
 		assertEquals("[Test.txt, mode:100644, content:Some change]",
 				indexState(db2, CONTENT));
 	}
 
 
 
 	@Test
 	public void testCheckoutOfFileWithInexistentParentDir() throws Exception {
 		File a = writeTrashFile("dir/a.txt", "A");
 		writeTrashFile("dir/b.txt", "A");
 		git.add().addFilepattern("dir/a.txt").addFilepattern("dir/b.txt")
 				.call();
 		git.commit().setMessage("Added dir").call();
 
 		File dir = new File(db.getWorkTree(), "dir");
 		FileUtils.delete(dir, FileUtils.RECURSIVE);
 
 		git.checkout().addPath("dir/a.txt").call();
 		assertTrue(a.exists());
 	}
 
 	@Test
 	public void testCheckoutOfDirectoryShouldBeRecursive() throws Exception {
 		File a = writeTrashFile("dir/a.txt", "A");
 		File b = writeTrashFile("dir/sub/b.txt", "B");
 		git.add().addFilepattern("dir").call();
 		git.commit().setMessage("Added dir").call();
 
 		write(a, "modified");
 		write(b, "modified");
 		git.checkout().addPath("dir").call();
 
 		assertThat(read(a), is("A"));
 		assertThat(read(b), is("B"));
 	}
 
 	@Test
 	public void testCheckoutAllPaths() throws Exception {
 		File a = writeTrashFile("dir/a.txt", "A");
 		File b = writeTrashFile("dir/sub/b.txt", "B");
 		git.add().addFilepattern("dir").call();
 		git.commit().setMessage("Added dir").call();
 
 		write(a, "modified");
 		write(b, "modified");
 		git.checkout().setAllPaths(true).call();
 
 		assertThat(read(a), is("A"));
 		assertThat(read(b), is("B"));
 	}
 
 	@Test
 	public void testCheckoutWithStartPoint() throws Exception {
 		File a = writeTrashFile("a.txt", "A");
 		git.add().addFilepattern("a.txt").call();
 		RevCommit first = git.commit().setMessage("Added a").call();
 
 		write(a, "other");
 		git.commit().setAll(true).setMessage("Other").call();
 
 		git.checkout().setCreateBranch(true).setName("a")
 				.setStartPoint(first.getId().getName()).call();
 
 		assertThat(read(a), is("A"));
 	}
 
 	@Test
 	public void testCheckoutWithStartPointOnlyCertainFiles() throws Exception {
 		File a = writeTrashFile("a.txt", "A");
 		File b = writeTrashFile("b.txt", "B");
 		git.add().addFilepattern("a.txt").addFilepattern("b.txt").call();
 		RevCommit first = git.commit().setMessage("First").call();
 
 		write(a, "other");
 		write(b, "other");
 		git.commit().setAll(true).setMessage("Other").call();
 
 		git.checkout().setCreateBranch(true).setName("a")
 				.setStartPoint(first.getId().getName()).addPath("a.txt").call();
 
 		assertThat(read(a), is("A"));
 		assertThat(read(b), is("other"));
 	}
 
 	@Test
 	public void testDetachedHeadOnCheckout() throws JGitInternalException,
 			IOException, GitAPIException {
 		CheckoutCommand co = git.checkout();
 		co.setName("master").call();
 
 		String commitId = db.exactRef(R_HEADS + MASTER).getObjectId().name();
 		co = git.checkout();
 		co.setName(commitId).call();
 
 		assertHeadDetached();
 	}
 
 	@Test
 	public void testUpdateSmudgedEntries() throws Exception {
 		git.branchCreate().setName("test2").call();
 		RefUpdate rup = db.updateRef(Constants.HEAD);
 		rup.link("refs/heads/test2");
 
 		File file = new File(db.getWorkTree(), "Test.txt");
 		long size = file.length();
 		long mTime = file.lastModified() - 5000L;
 		assertTrue(file.setLastModified(mTime));
 
 		DirCache cache = DirCache.lock(db.getIndexFile(), db.getFS());
 		DirCacheEntry entry = cache.getEntry("Test.txt");
 		assertNotNull(entry);
 		entry.setLength(0);
 		entry.setLastModified(0);
 		cache.write();
 		assertTrue(cache.commit());
 
 		cache = DirCache.read(db.getIndexFile(), db.getFS());
 		entry = cache.getEntry("Test.txt");
 		assertNotNull(entry);
 		assertEquals(0, entry.getLength());
 		assertEquals(0, entry.getLastModified());
 
 		db.getIndexFile().setLastModified(
 				db.getIndexFile().lastModified() - 5000);
 
 		assertNotNull(git.checkout().setName("test").call());
 
 		cache = DirCache.read(db.getIndexFile(), db.getFS());
 		entry = cache.getEntry("Test.txt");
 		assertNotNull(entry);
 		assertEquals(size, entry.getLength());
 		assertEquals(mTime, entry.getLastModified());
 	}
 
 	@Test
 	public void testCheckoutOrphanBranch() throws Exception {
 		CheckoutCommand co = newOrphanBranchCommand();
 		assertCheckoutRef(co.call());
 
 		File HEAD = new File(trash, ".git/HEAD");
 		String headRef = read(HEAD);
 		assertEquals("ref: refs/heads/orphanbranch\n", headRef);
 		assertEquals(2, trash.list().length);
 
 		File heads = new File(trash, ".git/refs/heads");
 		assertEquals(2, heads.listFiles().length);
 
 		this.assertNoHead();
 		this.assertRepositoryCondition(1);
 		assertEquals(CheckoutResult.NOT_TRIED_RESULT, co.getResult());
 	}
 
 	private Repository createRepositoryWithRemote() throws IOException,
 			URISyntaxException, MalformedURLException, GitAPIException,
 			InvalidRemoteException, TransportException {
 		// create second repository
 		Repository db2 = createWorkRepository();
 		try (Git git2 = new Git(db2)) {
 			// setup the second repository to fetch from the first repository
 			final StoredConfig config = db2.getConfig();
 			RemoteConfig remoteConfig = new RemoteConfig(config, "origin");
 			URIish uri = new URIish(db.getDirectory().toURI().toURL());
 			remoteConfig.addURI(uri);
 			remoteConfig.update(config);
 			config.save();
 
 			// fetch from first repository
 			git2.fetch().setRemote("origin")
 					.setRefSpecs("+refs/heads/*:refs/remotes/origin/*").call();
 			return db2;
 		}
 	}
 
 	private CheckoutCommand newOrphanBranchCommand() {
 		return git.checkout().setOrphan(true)
 				.setName("orphanbranch");
 	}
 
 	private static void assertCheckoutRef(Ref ref) {
 		assertNotNull(ref);
 		assertEquals("refs/heads/orphanbranch", ref.getTarget().getName());
 	}
 
 	private void assertNoHead() throws IOException {
 		assertNull(db.resolve("HEAD"));
 	}
 
 	private void assertHeadDetached() throws IOException {
 		Ref head = db.exactRef(Constants.HEAD);
 		assertFalse(head.isSymbolic());
 		assertSame(head, head.getTarget());
 	}
 
 	private void assertRepositoryCondition(int files) throws GitAPIException {
 		org.eclipse.jgit.api.Status status = this.git.status().call();
 		assertFalse(status.isClean());
 		assertEquals(files, status.getAdded().size());
 	}
 
 	@Test
 	public void testCreateOrphanBranchWithStartCommit() throws Exception {
 		CheckoutCommand co = newOrphanBranchCommand();
 		Ref ref = co.setStartPoint(initialCommit).call();
 		assertCheckoutRef(ref);
 		assertEquals(2, trash.list().length);
 		this.assertNoHead();
 		this.assertRepositoryCondition(1);
 	}
 
 	@Test
 	public void testCreateOrphanBranchWithStartPoint() throws Exception {
 		CheckoutCommand co = newOrphanBranchCommand();
 		Ref ref = co.setStartPoint("HEAD^").call();
 		assertCheckoutRef(ref);
 
 		assertEquals(2, trash.list().length);
 		this.assertNoHead();
 		this.assertRepositoryCondition(1);
 	}
 
 	@Test
 	public void testInvalidRefName() throws Exception {
 		try {
 			git.checkout().setOrphan(true).setName("../invalidname").call();
 			fail("Should have failed");
 		} catch (InvalidRefNameException e) {
 			// except to hit here
 		}
 	}
 
 	@Test
 	public void testNullRefName() throws Exception {
 		try {
 			git.checkout().setOrphan(true).setName(null).call();
 			fail("Should have failed");
 		} catch (InvalidRefNameException e) {
 			// except to hit here
 		}
 	}
 
 	@Test
 	public void testAlreadyExists() throws Exception {
 		this.git.checkout().setCreateBranch(true).setName("orphanbranch")
 				.call();
 		this.git.checkout().setName("master").call();
 
 		try {
 			newOrphanBranchCommand().call();
 			fail("Should have failed");
 		} catch (RefAlreadyExistsException e) {
 			// except to hit here
 		}
 	}
 
 	// TODO: write a faster test which depends less on characteristics of
 	// underlying filesystem/OS.
 	@Test
 	public void testCheckoutAutoCrlfTrue() throws Exception {
 		int nrOfAutoCrlfTestFiles = 200;
 
 		FileBasedConfig c = db.getConfig();
 		c.setString("core", null, "autocrlf", "true");
 		c.save();
 
 		AddCommand add = git.add();
 		for (int i = 100; i < 100 + nrOfAutoCrlfTestFiles; i++) {
 			writeTrashFile("Test_" + i + ".txt", "Hello " + i
 					+ " world\nX\nYU\nJK\n");
 			add.addFilepattern("Test_" + i + ".txt");
 		}
 		fsTick(null);
 		add.call();
 		RevCommit c1 = git.commit().setMessage("add some lines").call();
 
 		add = git.add();
 		for (int i = 100; i < 100 + nrOfAutoCrlfTestFiles; i++) {
 			writeTrashFile("Test_" + i + ".txt", "Hello " + i
 					+ " world\nX\nY\n");
 			add.addFilepattern("Test_" + i + ".txt");
 		}
 		fsTick(null);
 		add.call();
 		git.commit().setMessage("add more").call();
 
 		git.checkout().setName(c1.getName()).call();
 
 		boolean foundUnsmudged = false;
 		DirCache dc = db.readDirCache();
 		for (int i = 100; i < 100 + nrOfAutoCrlfTestFiles; i++) {
 			DirCacheEntry entry = dc.getEntry(
 					"Test_" + i + ".txt");
 			if (!entry.isSmudged()) {
 				foundUnsmudged = true;
 				assertEquals("unexpected file length in git index", 28,
 						entry.getLength());
 			}
 		}
 		org.junit.Assume.assumeTrue(foundUnsmudged);
 	}
 
 	@Test
 	public void testSmudgeFilter_modifyExisting() throws IOException, GitAPIException {
 		File script = writeTempFile("sed s/o/e/g");
 		StoredConfig config = git.getRepository().getConfig();
 		config.setString("filter", "lfs", "smudge",
 				"sh " + slashify(script.getPath()));
 		config.save();
 
 		writeTrashFile(".gitattributes", "*.txt filter=lfs");
 		git.add().addFilepattern(".gitattributes").call();
 		git.commit().setMessage("add filter").call();
 
 		writeTrashFile("src/a.tmp", "x");
 		// Caution: we need a trailing '\n' since sed on mac always appends
 		// linefeeds if missing
 		writeTrashFile("src/a.txt", "x\n");
 		git.add().addFilepattern("src/a.tmp").addFilepattern("src/a.txt")
 				.call();
 		RevCommit content1 = git.commit().setMessage("add content").call();
 
 		writeTrashFile("src/a.tmp", "foo");
 		writeTrashFile("src/a.txt", "foo\n");
 		git.add().addFilepattern("src/a.tmp").addFilepattern("src/a.txt")
 				.call();
 		RevCommit content2 = git.commit().setMessage("changed content").call();
 
 		git.checkout().setName(content1.getName()).call();
 		git.checkout().setName(content2.getName()).call();
 
 		assertEquals(
 				"[.gitattributes, mode:100644, content:*.txt filter=lfs][Test.txt, mode:100644, content:Some change][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:foo\n]",
 				indexState(CONTENT));
 		assertEquals(Sets.of("src/a.txt"), git.status().call().getModified());
 		assertEquals("foo", read("src/a.tmp"));
 		assertEquals("fee\n", read("src/a.txt"));
 	}
 
 	@Test
 	public void testSmudgeFilter_createNew()
 			throws IOException, GitAPIException {
 		File script = writeTempFile("sed s/o/e/g");
 		StoredConfig config = git.getRepository().getConfig();
 		config.setString("filter", "lfs", "smudge",
 				"sh " + slashify(script.getPath()));
 		config.save();
 
 		writeTrashFile("foo", "foo");
 		git.add().addFilepattern("foo").call();
 		RevCommit initial = git.commit().setMessage("initial").call();
 
 		writeTrashFile(".gitattributes", "*.txt filter=lfs");
 		git.add().addFilepattern(".gitattributes").call();
 		git.commit().setMessage("add filter").call();
 
 		writeTrashFile("src/a.tmp", "foo");
 		// Caution: we need a trailing '\n' since sed on mac always appends
 		// linefeeds if missing
 		writeTrashFile("src/a.txt", "foo\n");
 		git.add().addFilepattern("src/a.tmp").addFilepattern("src/a.txt")
 				.call();
 		RevCommit content = git.commit().setMessage("added content").call();
 
 		git.checkout().setName(initial.getName()).call();
 		git.checkout().setName(content.getName()).call();
 
 		assertEquals(
 				"[.gitattributes, mode:100644, content:*.txt filter=lfs][Test.txt, mode:100644, content:Some change][foo, mode:100644, content:foo][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:foo\n]",
 				indexState(CONTENT));
 		assertEquals("foo", read("src/a.tmp"));
 		assertEquals("fee\n", read("src/a.txt"));
 	}
 
 	@Test
 	public void testSmudgeFilter_deleteFileAndRestoreFromCommit()
 			throws IOException, GitAPIException {
 		File script = writeTempFile("sed s/o/e/g");
 		StoredConfig config = git.getRepository().getConfig();
 		config.setString("filter", "lfs", "smudge",
 				"sh " + slashify(script.getPath()));
 		config.save();
 
 		writeTrashFile("foo", "foo");
 		git.add().addFilepattern("foo").call();
 		git.commit().setMessage("initial").call();
 
 		writeTrashFile(".gitattributes", "*.txt filter=lfs");
 		git.add().addFilepattern(".gitattributes").call();
 		git.commit().setMessage("add filter").call();
 
 		writeTrashFile("src/a.tmp", "foo");
 		// Caution: we need a trailing '\n' since sed on mac always appends
 		// linefeeds if missing
 		writeTrashFile("src/a.txt", "foo\n");
 		git.add().addFilepattern("src/a.tmp").addFilepattern("src/a.txt")
 				.call();
 		RevCommit content = git.commit().setMessage("added content").call();
 
 		deleteTrashFile("src/a.txt");
 		git.checkout().setStartPoint(content.getName()).addPath("src/a.txt")
 				.call();
 
 		assertEquals(
 				"[.gitattributes, mode:100644, content:*.txt filter=lfs][Test.txt, mode:100644, content:Some change][foo, mode:100644, content:foo][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:foo\n]",
 				indexState(CONTENT));
 		assertEquals("foo", read("src/a.tmp"));
 		assertEquals("fee\n", read("src/a.txt"));
 	}
 
 	@Test
 	public void testSmudgeFilter_deleteFileAndRestoreFromIndex()
 			throws IOException, GitAPIException {
 		File script = writeTempFile("sed s/o/e/g");
 		StoredConfig config = git.getRepository().getConfig();
 		config.setString("filter", "lfs", "smudge",
 				"sh " + slashify(script.getPath()));
 		config.save();
 
 		writeTrashFile("foo", "foo");
 		git.add().addFilepattern("foo").call();
 		git.commit().setMessage("initial").call();
 
 		writeTrashFile(".gitattributes", "*.txt filter=lfs");
 		git.add().addFilepattern(".gitattributes").call();
 		git.commit().setMessage("add filter").call();
 
 		writeTrashFile("src/a.tmp", "foo");
 		// Caution: we need a trailing '\n' since sed on mac always appends
 		// linefeeds if missing
 		writeTrashFile("src/a.txt", "foo\n");
 		git.add().addFilepattern("src/a.tmp").addFilepattern("src/a.txt")
 				.call();
 		git.commit().setMessage("added content").call();
 
 		deleteTrashFile("src/a.txt");
 		git.checkout().addPath("src/a.txt").call();
 
 		assertEquals(
 				"[.gitattributes, mode:100644, content:*.txt filter=lfs][Test.txt, mode:100644, content:Some change][foo, mode:100644, content:foo][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:foo\n]",
 				indexState(CONTENT));
 		assertEquals("foo", read("src/a.tmp"));
 		assertEquals("fee\n", read("src/a.txt"));
 	}
 
 	@Test
 	public void testSmudgeFilter_deleteFileAndCreateBranchAndRestoreFromCommit()
 			throws IOException, GitAPIException {
 		File script = writeTempFile("sed s/o/e/g");
 		StoredConfig config = git.getRepository().getConfig();
 		config.setString("filter", "lfs", "smudge",
 				"sh " + slashify(script.getPath()));
 		config.save();
 
 		writeTrashFile("foo", "foo");
 		git.add().addFilepattern("foo").call();
 		git.commit().setMessage("initial").call();
 
 		writeTrashFile(".gitattributes", "*.txt filter=lfs");
 		git.add().addFilepattern(".gitattributes").call();
 		git.commit().setMessage("add filter").call();
 
 		writeTrashFile("src/a.tmp", "foo");
 		// Caution: we need a trailing '\n' since sed on mac always appends
 		// linefeeds if missing
 		writeTrashFile("src/a.txt", "foo\n");
 		git.add().addFilepattern("src/a.tmp").addFilepattern("src/a.txt")
 				.call();
 		RevCommit content = git.commit().setMessage("added content").call();
 
 		deleteTrashFile("src/a.txt");
 		git.checkout().setName("newBranch").setCreateBranch(true)
 				.setStartPoint(content).addPath("src/a.txt").call();
 
 		assertEquals(
 				"[.gitattributes, mode:100644, content:*.txt filter=lfs][Test.txt, mode:100644, content:Some change][foo, mode:100644, content:foo][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:foo\n]",
 				indexState(CONTENT));
 		assertEquals("foo", read("src/a.tmp"));
 		assertEquals("fee\n", read("src/a.txt"));
 	}
 
 	@Test
 	public void testSmudgeAndClean() throws Exception {
 		File clean_filter = writeTempFile("sed s/V1/@version/g");
 		File smudge_filter = writeTempFile("sed s/@version/V1/g");
 
 		try (Git git2 = new Git(db)) {
 			StoredConfig config = git.getRepository().getConfig();
 			config.setString("filter", "lfs", "smudge",
 					"sh " + slashify(smudge_filter.getPath()));
 			config.setString("filter", "lfs", "clean",
 					"sh " + slashify(clean_filter.getPath()));
 			config.setBoolean("filter", "lfs", "useJGitBuiltin", true);
 			config.save();
 			writeTrashFile(".gitattributes", "filterTest.txt filter=lfs");
 			git2.add().addFilepattern(".gitattributes").call();
 			git2.commit().setMessage("add attributes").call();
 
 			fsTick(writeTrashFile("filterTest.txt", "hello world, V1\n"));
 			git2.add().addFilepattern("filterTest.txt").call();
 			RevCommit one = git2.commit().setMessage("add filterText.txt").call();
 			assertEquals(
 					"[.gitattributes, mode:100644, content:filterTest.txt filter=lfs][Test.txt, mode:100644, content:Some change][filterTest.txt, mode:100644, content:version https://git-lfs.github.com/spec/v1\noid sha256:7bd5d32e5c494354aa4c2473a1306d0ce7b52cc3bffeb342c03cd517ef8cf8da\nsize 16\n]",
 					indexState(CONTENT));
 
 			fsTick(writeTrashFile("filterTest.txt", "bon giorno world, V1\n"));
 			git2.add().addFilepattern("filterTest.txt").call();
 			RevCommit two = git2.commit().setMessage("modified filterTest.txt").call();
 
 			assertTrue(git2.status().call().isClean());
 			assertEquals(
 					"[.gitattributes, mode:100644, content:filterTest.txt filter=lfs][Test.txt, mode:100644, content:Some change][filterTest.txt, mode:100644, content:version https://git-lfs.github.com/spec/v1\noid sha256:087148cccf53b0049c56475c1595113c9da4b638997c3489af8ac7108d51ef13\nsize 21\n]",
 					indexState(CONTENT));
 
 			git2.checkout().setName(one.getName()).call();
 			assertTrue(git2.status().call().isClean());
 			assertEquals(
 					"[.gitattributes, mode:100644, content:filterTest.txt filter=lfs][Test.txt, mode:100644, content:Some change][filterTest.txt, mode:100644, content:version https://git-lfs.github.com/spec/v1\noid sha256:7bd5d32e5c494354aa4c2473a1306d0ce7b52cc3bffeb342c03cd517ef8cf8da\nsize 16\n]",
 					indexState(CONTENT));
 			assertEquals("hello world, V1\n", read("filterTest.txt"));
 
 			git2.checkout().setName(two.getName()).call();
 			assertTrue(git2.status().call().isClean());
 			assertEquals(
 					"[.gitattributes, mode:100644, content:filterTest.txt filter=lfs][Test.txt, mode:100644, content:Some change][filterTest.txt, mode:100644, content:version https://git-lfs.github.com/spec/v1\noid sha256:087148cccf53b0049c56475c1595113c9da4b638997c3489af8ac7108d51ef13\nsize 21\n]",
 					indexState(CONTENT));
 			assertEquals("bon giorno world, V1\n", read("filterTest.txt"));
 		}
 	}
 
 	@Test
 	public void testNonDeletableFilesOnWindows()
 			throws GitAPIException, IOException {
 		// Only on windows a FileInputStream blocks us from deleting a file
 		org.junit.Assume.assumeTrue(SystemReader.getInstance().isWindows());
 		writeTrashFile("toBeModified.txt", "a");
 		writeTrashFile("toBeDeleted.txt", "a");
 		git.add().addFilepattern(".").call();
 		RevCommit addFiles = git.commit().setMessage("add more files").call();
 
 		git.rm().setCached(false).addFilepattern("Test.txt")
 				.addFilepattern("toBeDeleted.txt").call();
 		writeTrashFile("toBeModified.txt", "b");
 		writeTrashFile("toBeCreated.txt", "a");
 		git.add().addFilepattern(".").call();
 		RevCommit crudCommit = git.commit().setMessage("delete, modify, add")
 				.call();
 		git.checkout().setName(addFiles.getName()).call();
 		try ( FileInputStream fis=new FileInputStream(new File(db.getWorkTree(), "Test.txt")) ) {
 			CheckoutCommand coCommand = git.checkout();
 			coCommand.setName(crudCommit.getName()).call();
 			CheckoutResult result = coCommand.getResult();
 			assertEquals(Status.NONDELETED, result.getStatus());
 			assertEquals("[Test.txt, toBeDeleted.txt]",
 					result.getRemovedList().toString());
 			assertEquals("[toBeCreated.txt, toBeModified.txt]",
 					result.getModifiedList().toString());
 			assertEquals("[Test.txt]", result.getUndeletedList().toString());
 			assertTrue(result.getConflictList().isEmpty());
 		}
 	}
 
 	private File writeTempFile(String body) throws IOException {
 		File f = File.createTempFile("CheckoutCommandTest_", "");
 		JGitTestUtil.write(f, body);
 		return f;
 	}
 }