/*
    * Copyright (C) 2014, Google Inc. 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.gitrepo;
  
  import static java.nio.charset.StandardCharsets.UTF_8;
  import static org.junit.Assert.assertEquals;
  import static org.junit.Assert.assertFalse;
  import static org.junit.Assert.assertNull;
  import static org.junit.Assert.assertTrue;
  import static org.junit.Assert.fail;
  
  import java.io.BufferedReader;
  import java.io.ByteArrayInputStream;
  import java.io.File;
  import java.io.IOException;
  import java.net.URI;
  import java.nio.file.Files;
  import java.nio.file.Path;
  import java.text.MessageFormat;
  import java.util.HashMap;
  import java.util.Map;
  
  import org.eclipse.jgit.api.Git;
  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.gitrepo.RepoCommand.RemoteFile;
  import org.eclipse.jgit.internal.JGitText;
  import org.eclipse.jgit.junit.JGitTestUtil;
  import org.eclipse.jgit.junit.RepositoryTestCase;
  import org.eclipse.jgit.lib.BlobBasedConfig;
  import org.eclipse.jgit.lib.Config;
  import org.eclipse.jgit.lib.Constants;
  import org.eclipse.jgit.lib.ObjectId;
  import org.eclipse.jgit.lib.ObjectReader;
  import org.eclipse.jgit.lib.Ref;
  import org.eclipse.jgit.lib.Repository;
  import org.eclipse.jgit.revwalk.RevCommit;
  import org.eclipse.jgit.storage.file.FileBasedConfig;
  import org.eclipse.jgit.treewalk.TreeWalk;
  import org.eclipse.jgit.util.FS;
  import org.eclipse.jgit.util.IO;
  import org.eclipse.jgit.util.RawParseUtils;
  import org.junit.Test;
  
  public class RepoCommandTest extends RepositoryTestCase {
  
  	private static final String BRANCH = "branch";
  	private static final String TAG = "release";
  
  	private Repository defaultDb;
  	private Repository notDefaultDb;
  	private Repository groupADb;
  	private Repository groupBDb;
  
  	private String rootUri;
  	private String defaultUri;
  	private String notDefaultUri;
  	private String groupAUri;
  	private String groupBUri;
  
  	private ObjectId oldCommitId;
  
  	@Override
  	public void setUp() throws Exception {
  		super.setUp();
  
  		defaultDb = createWorkRepository();
  		try (Git git = new Git(defaultDb)) {
  			JGitTestUtil.writeTrashFile(defaultDb, "hello.txt", "branch world");
  			git.add().addFilepattern("hello.txt").call();
  			oldCommitId = git.commit().setMessage("Initial commit").call().getId();
  			git.checkout().setName(BRANCH).setCreateBranch(true).call();
  			git.checkout().setName("master").call();
  			git.tag().setName(TAG).call();
  			JGitTestUtil.writeTrashFile(defaultDb, "hello.txt", "master world");
  			git.add().addFilepattern("hello.txt").call();
  			git.commit().setMessage("Second commit").call();
  			addRepoToClose(defaultDb);
  		}
  
  		notDefaultDb = createWorkRepository();
  		try (Git git = new Git(notDefaultDb)) {
  			JGitTestUtil.writeTrashFile(notDefaultDb, "world.txt", "hello");
  			git.add().addFilepattern("world.txt").call();
  			git.commit().setMessage("Initial commit").call();
  			addRepoToClose(notDefaultDb);
  		}
  
  		groupADb = createWorkRepository();
  		try (Git git = new Git(groupADb)) {
  			JGitTestUtil.writeTrashFile(groupADb, "a.txt", "world");
 			git.add().addFilepattern("a.txt").call();
 			git.commit().setMessage("Initial commit").call();
 			addRepoToClose(groupADb);
 		}
 
 		groupBDb = createWorkRepository();
 		try (Git git = new Git(groupBDb)) {
 			JGitTestUtil.writeTrashFile(groupBDb, "b.txt", "world");
 			git.add().addFilepattern("b.txt").call();
 			git.commit().setMessage("Initial commit").call();
 			addRepoToClose(groupBDb);
 		}
 
 		resolveRelativeUris();
 	}
 
 	static class IndexedRepos implements RepoCommand.RemoteReader {
 		Map<String, Repository> uriRepoMap;
 
 		IndexedRepos() {
 			uriRepoMap = new HashMap<>();
 		}
 
 		void put(String u, Repository r) {
 			uriRepoMap.put(u, r);
 		}
 
 		@Override
 		public ObjectId sha1(String uri, String refname) throws GitAPIException {
 			if (!uriRepoMap.containsKey(uri)) {
 				return null;
 			}
 
 			Repository r = uriRepoMap.get(uri);
 			try {
 				Ref ref = r.findRef(refname);
 				if (ref == null) return null;
 
 				ref = r.getRefDatabase().peel(ref);
 				ObjectId id = ref.getObjectId();
 				return id;
 			} catch (IOException e) {
 				throw new InvalidRemoteException("", e);
 			}
 		}
 
 		@Override
 		public RemoteFile readFileWithMode(String uri, String ref, String path)
 				throws GitAPIException, IOException {
 			Repository repo = uriRepoMap.get(uri);
 			ObjectId refCommitId = sha1(uri, ref);
 			if (refCommitId == null) {
 				throw new InvalidRefNameException(MessageFormat
 						.format(JGitText.get().refNotResolved, ref));
 			}
 			RevCommit commit = repo.parseCommit(refCommitId);
 			TreeWalk tw = TreeWalk.forPath(repo, path, commit.getTree());
 
 			// TODO(ifrade): Cope better with big files (e.g. using InputStream
 			// instead of byte[])
 			return new RemoteFile(tw.getObjectReader().open(tw.getObjectId(0))
 					.getCachedBytes(Integer.MAX_VALUE), tw.getFileMode(0));
 		}
 	}
 
 	private Repository cloneRepository(Repository repo, boolean bare)
 			throws Exception {
 		Repository r = Git.cloneRepository()
 				.setURI(repo.getDirectory().toURI().toString())
 				.setDirectory(createUniqueTestGitDir(true)).setBare(bare).call()
 				.getRepository();
 		if (bare) {
 			assertTrue(r.isBare());
 		} else {
 			assertFalse(r.isBare());
 		}
 		return r;
 	}
 
 	private static void assertContents(Path path, String expected)
 			throws IOException {
 		try (BufferedReader reader = Files.newBufferedReader(path, UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("Unexpected content in " + path.getFileName(),
 					expected, content);
 		}
 	}
 
 	@Test
 	public void runTwiceIsNOP() throws Exception {
 		try (Repository child = cloneRepository(groupADb, true);
 				Repository dest = cloneRepository(db, true)) {
 			StringBuilder xmlContent = new StringBuilder();
 			xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 					.append("<manifest>")
 					.append("<remote name=\"remote1\" fetch=\"..\" />")
 					.append("<default revision=\"master\" remote=\"remote1\" />")
 					.append("<project path=\"base\" name=\"platform/base\" />")
 					.append("</manifest>");
 			RepoCommand cmd = new RepoCommand(dest);
 
 			IndexedRepos repos = new IndexedRepos();
 			repos.put("platform/base", child);
 
 			RevCommit commit = cmd
 					.setInputStream(new ByteArrayInputStream(
 							xmlContent.toString().getBytes(UTF_8)))
 					.setRemoteReader(repos).setURI("platform/")
 					.setTargetURI("platform/superproject")
 					.setRecordRemoteBranch(true).setRecordSubmoduleLabels(true)
 					.call();
 
 			String firstIdStr = commit.getId().name() + ":" + ".gitmodules";
 			commit = new RepoCommand(dest)
 					.setInputStream(new ByteArrayInputStream(
 							xmlContent.toString().getBytes(UTF_8)))
 					.setRemoteReader(repos).setURI("platform/")
 					.setTargetURI("platform/superproject")
 					.setRecordRemoteBranch(true).setRecordSubmoduleLabels(true)
 					.call();
 			String idStr = commit.getId().name() + ":" + ".gitmodules";
 			assertEquals(firstIdStr, idStr);
 		}
 	}
 
 	@Test
 	public void androidSetup() throws Exception {
 		try (Repository child = cloneRepository(groupADb, true);
 				Repository dest = cloneRepository(db, true)) {
 			StringBuilder xmlContent = new StringBuilder();
 			xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 					.append("<manifest>")
 					.append("<remote name=\"remote1\" fetch=\"..\" />")
 					.append("<default revision=\"master\" remote=\"remote1\" />")
 					.append("<project path=\"base\" name=\"platform/base\" />")
 					.append("</manifest>");
 			RepoCommand cmd = new RepoCommand(dest);
 
 			IndexedRepos repos = new IndexedRepos();
 			repos.put("platform/base", child);
 
 			RevCommit commit = cmd
 					.setInputStream(new ByteArrayInputStream(
 							xmlContent.toString().getBytes(UTF_8)))
 					.setRemoteReader(repos).setURI("platform/")
 					.setTargetURI("platform/superproject")
 					.setRecordRemoteBranch(true).setRecordSubmoduleLabels(true)
 					.call();
 
 			String idStr = commit.getId().name() + ":" + ".gitmodules";
 			ObjectId modId = dest.resolve(idStr);
 
 			try (ObjectReader reader = dest.newObjectReader()) {
 				byte[] bytes = reader.open(modId)
 						.getCachedBytes(Integer.MAX_VALUE);
 				Config base = new Config();
 				BlobBasedConfig cfg = new BlobBasedConfig(base, bytes);
 				String subUrl = cfg.getString("submodule", "platform/base",
 						"url");
 				assertEquals(subUrl, "../base");
 			}
 		}
 	}
 
 	@Test
 	public void recordUnreachableRemotes() throws Exception {
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 			.append("<manifest>")
 			.append("<remote name=\"remote1\" fetch=\"https://host.com/\" />")
 			.append("<default revision=\"master\" remote=\"remote1\" />")
 			.append("<project path=\"base\" name=\"platform/base\" />")
 			.append("</manifest>");
 
 		try (Repository dest = cloneRepository(db, true)) {
 			RevCommit commit = new RepoCommand(dest)
 					.setInputStream(new ByteArrayInputStream(
 							xmlContent.toString().getBytes(UTF_8)))
 					.setRemoteReader(new IndexedRepos()).setURI("platform/")
 					.setTargetURI("platform/superproject")
 					.setRecordRemoteBranch(true).setIgnoreRemoteFailures(true)
 					.setRecordSubmoduleLabels(true).call();
 
 			String idStr = commit.getId().name() + ":" + ".gitmodules";
 			ObjectId modId = dest.resolve(idStr);
 
 			try (ObjectReader reader = dest.newObjectReader()) {
 				byte[] bytes = reader.open(modId)
 						.getCachedBytes(Integer.MAX_VALUE);
 				Config base = new Config();
 				BlobBasedConfig cfg = new BlobBasedConfig(base, bytes);
 				String subUrl = cfg.getString("submodule", "platform/base",
 						"url");
 				assertEquals(subUrl, "https://host.com/platform/base");
 			}
 		}
 	}
 
 	@Test
 	public void gerritSetup() throws Exception {
 		try (Repository child = cloneRepository(groupADb, true);
 				Repository dest = cloneRepository(db, true)) {
 			StringBuilder xmlContent = new StringBuilder();
 			xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 					.append("<manifest>")
 					.append("<remote name=\"remote1\" fetch=\".\" />")
 					.append("<default revision=\"master\" remote=\"remote1\" />")
 					.append("<project path=\"plugins/cookbook\" name=\"plugins/cookbook\" />")
 					.append("</manifest>");
 			RepoCommand cmd = new RepoCommand(dest);
 
 			IndexedRepos repos = new IndexedRepos();
 			repos.put("plugins/cookbook", child);
 
 			RevCommit commit = cmd
 					.setInputStream(new ByteArrayInputStream(
 							xmlContent.toString().getBytes(UTF_8)))
 					.setRemoteReader(repos).setURI("").setTargetURI("gerrit")
 					.setRecordRemoteBranch(true).setRecordSubmoduleLabels(true)
 					.call();
 
 			String idStr = commit.getId().name() + ":" + ".gitmodules";
 			ObjectId modId = dest.resolve(idStr);
 
 			try (ObjectReader reader = dest.newObjectReader()) {
 				byte[] bytes = reader.open(modId)
 						.getCachedBytes(Integer.MAX_VALUE);
 				Config base = new Config();
 				BlobBasedConfig cfg = new BlobBasedConfig(base, bytes);
 				String subUrl = cfg.getString("submodule", "plugins/cookbook",
 						"url");
 				assertEquals(subUrl, "../plugins/cookbook");
 			}
 		}
 	}
 
 	@Test
 	public void absoluteRemoteURL() throws Exception {
 		try (Repository child = cloneRepository(groupADb, true);
 				Repository dest = cloneRepository(db, true)) {
 			String abs = "https://chromium.googlesource.com";
 			String repoUrl = "https://chromium.googlesource.com/chromium/src";
 			boolean fetchSlash = false;
 			boolean baseSlash = false;
 			do {
 				do {
 					String fetchUrl = fetchSlash ? abs + "/" : abs;
 					String baseUrl = baseSlash ? abs + "/" : abs;
 
 					StringBuilder xmlContent = new StringBuilder();
 					xmlContent.append(
 							"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 							.append("<manifest>")
 							.append("<remote name=\"origin\" fetch=\""
 									+ fetchUrl + "\" />")
 							.append("<default revision=\"master\" remote=\"origin\" />")
 							.append("<project path=\"src\" name=\"chromium/src\" />")
 							.append("</manifest>");
 					RepoCommand cmd = new RepoCommand(dest);
 
 					IndexedRepos repos = new IndexedRepos();
 					repos.put(repoUrl, child);
 
 					RevCommit commit = cmd
 							.setInputStream(new ByteArrayInputStream(
 									xmlContent.toString().getBytes(UTF_8)))
 							.setRemoteReader(repos).setURI(baseUrl)
 							.setTargetURI("gerrit").setRecordRemoteBranch(true)
 							.setRecordSubmoduleLabels(true).call();
 
 					String idStr = commit.getId().name() + ":" + ".gitmodules";
 					ObjectId modId = dest.resolve(idStr);
 
 					try (ObjectReader reader = dest.newObjectReader()) {
 						byte[] bytes = reader.open(modId)
 								.getCachedBytes(Integer.MAX_VALUE);
 						Config base = new Config();
 						BlobBasedConfig cfg = new BlobBasedConfig(base, bytes);
 						String subUrl = cfg.getString("submodule",
 								"chromium/src", "url");
 						assertEquals(
 								"https://chromium.googlesource.com/chromium/src",
 								subUrl);
 					}
 					fetchSlash = !fetchSlash;
 				} while (fetchSlash);
 				baseSlash = !baseSlash;
 			} while (baseSlash);
 		}
 	}
 
 	@Test
 	public void absoluteRemoteURLAbsoluteTargetURL() throws Exception {
 		try (Repository child = cloneRepository(groupADb, true);
 				Repository dest = cloneRepository(db, true)) {
 			String abs = "https://chromium.googlesource.com";
 			String repoUrl = "https://chromium.googlesource.com/chromium/src";
 			boolean fetchSlash = false;
 			boolean baseSlash = false;
 			do {
 				do {
 					String fetchUrl = fetchSlash ? abs + "/" : abs;
 					String baseUrl = baseSlash ? abs + "/" : abs;
 
 					StringBuilder xmlContent = new StringBuilder();
 					xmlContent.append(
 							"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 							.append("<manifest>")
 							.append("<remote name=\"origin\" fetch=\""
 									+ fetchUrl + "\" />")
 							.append("<default revision=\"master\" remote=\"origin\" />")
 							.append("<project path=\"src\" name=\"chromium/src\" />")
 							.append("</manifest>");
 					RepoCommand cmd = new RepoCommand(dest);
 
 					IndexedRepos repos = new IndexedRepos();
 					repos.put(repoUrl, child);
 
 					RevCommit commit = cmd
 							.setInputStream(new ByteArrayInputStream(
 									xmlContent.toString().getBytes(UTF_8)))
 							.setRemoteReader(repos).setURI(baseUrl)
 							.setTargetURI(abs + "/superproject")
 							.setRecordRemoteBranch(true)
 							.setRecordSubmoduleLabels(true).call();
 
 					String idStr = commit.getId().name() + ":" + ".gitmodules";
 					ObjectId modId = dest.resolve(idStr);
 
 					try (ObjectReader reader = dest.newObjectReader()) {
 						byte[] bytes = reader.open(modId)
 								.getCachedBytes(Integer.MAX_VALUE);
 						Config base = new Config();
 						BlobBasedConfig cfg = new BlobBasedConfig(base, bytes);
 						String subUrl = cfg.getString("submodule",
 								"chromium/src", "url");
 						assertEquals("../chromium/src", subUrl);
 					}
 					fetchSlash = !fetchSlash;
 				} while (fetchSlash);
 				baseSlash = !baseSlash;
 			} while (baseSlash);
 		}
 	}
 
 	@Test
 	public void testAddRepoManifest() throws Exception {
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 			.append("<manifest>")
 			.append("<remote name=\"remote1\" fetch=\".\" />")
 			.append("<default revision=\"master\" remote=\"remote1\" />")
 			.append("<project path=\"foo\" name=\"")
 			.append(defaultUri)
 			.append("\" />")
 			.append("</manifest>");
 		writeTrashFile("manifest.xml", xmlContent.toString());
 		RepoCommand command = new RepoCommand(db);
 		command.setPath(db.getWorkTree().getAbsolutePath() + "/manifest.xml")
 			.setURI(rootUri)
 			.call();
 		File hello = new File(db.getWorkTree(), "foo/hello.txt");
 		assertTrue("submodule should be checked out", hello.exists());
 		assertContents(hello.toPath(), "master world");
 	}
 
 	@Test
 	public void testRepoManifestGroups() throws Exception {
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 			.append("<manifest>")
 			.append("<remote name=\"remote1\" fetch=\".\" />")
 			.append("<default revision=\"master\" remote=\"remote1\" />")
 			.append("<project path=\"foo\" name=\"")
 			.append(defaultUri)
 			.append("\" groups=\"a,test\" />")
 			.append("<project path=\"bar\" name=\"")
 			.append(notDefaultUri)
 			.append("\" groups=\"notdefault\" />")
 			.append("<project path=\"a\" name=\"")
 			.append(groupAUri)
 			.append("\" groups=\"a\" />")
 			.append("<project path=\"b\" name=\"")
 			.append(groupBUri)
 			.append("\" groups=\"b\" />")
 			.append("</manifest>");
 
 		// default should have foo, a & b
 		Repository localDb = createWorkRepository();
 		JGitTestUtil.writeTrashFile(
 				localDb, "manifest.xml", xmlContent.toString());
 		RepoCommand command = new RepoCommand(localDb);
 		command
 			.setPath(localDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 			.setURI(rootUri)
 			.call();
 		File file = new File(localDb.getWorkTree(), "foo/hello.txt");
 		assertTrue("default should have foo", file.exists());
 		file = new File(localDb.getWorkTree(), "bar/world.txt");
 		assertFalse("default shouldn't have bar", file.exists());
 		file = new File(localDb.getWorkTree(), "a/a.txt");
 		assertTrue("default should have a", file.exists());
 		file = new File(localDb.getWorkTree(), "b/b.txt");
 		assertTrue("default should have b", file.exists());
 
 		// all,-a should have bar & b
 		localDb = createWorkRepository();
 		JGitTestUtil.writeTrashFile(
 				localDb, "manifest.xml", xmlContent.toString());
 		command = new RepoCommand(localDb);
 		command
 			.setPath(localDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 			.setURI(rootUri)
 			.setGroups("all,-a")
 			.call();
 		file = new File(localDb.getWorkTree(), "foo/hello.txt");
 		assertFalse("\"all,-a\" shouldn't have foo", file.exists());
 		file = new File(localDb.getWorkTree(), "bar/world.txt");
 		assertTrue("\"all,-a\" should have bar", file.exists());
 		file = new File(localDb.getWorkTree(), "a/a.txt");
 		assertFalse("\"all,-a\" shuoldn't have a", file.exists());
 		file = new File(localDb.getWorkTree(), "b/b.txt");
 		assertTrue("\"all,-a\" should have b", file.exists());
 	}
 
 	@Test
 	public void testRepoManifestCopyFile() throws Exception {
 		Repository localDb = createWorkRepository();
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 			.append("<manifest>")
 			.append("<remote name=\"remote1\" fetch=\".\" />")
 			.append("<default revision=\"master\" remote=\"remote1\" />")
 			.append("<project path=\"foo\" name=\"")
 			.append(defaultUri)
 			.append("\">")
 			.append("<copyfile src=\"hello.txt\" dest=\"Hello\" />")
 			.append("</project>")
 			.append("</manifest>");
 		JGitTestUtil.writeTrashFile(
 				localDb, "manifest.xml", xmlContent.toString());
 		RepoCommand command = new RepoCommand(localDb);
 		command
 			.setPath(localDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 			.setURI(rootUri)
 			.call();
 		// The original file should exist
 		File hello = new File(localDb.getWorkTree(), "foo/hello.txt");
 		assertTrue("The original file should exist", hello.exists());
 		assertFalse("The original file should not be executable",
 				hello.canExecute());
 		assertContents(hello.toPath(), "master world");
 		// The dest file should also exist
 		hello = new File(localDb.getWorkTree(), "Hello");
 		assertTrue("The destination file should exist", hello.exists());
 		assertFalse("The destination file should not be executable",
 				hello.canExecute());
 		assertContents(hello.toPath(), "master world");
 	}
 
 	@Test
 	public void testRepoManifestCopyFile_executable() throws Exception {
 		try (Git git = new Git(defaultDb)) {
 			git.checkout().setName("master").call();
 			File f = JGitTestUtil.writeTrashFile(defaultDb, "hello.sh",
 					"content of the executable file");
 			f.setExecutable(true);
 			git.add().addFilepattern("hello.sh").call();
 			git.commit().setMessage("Add binary file").call();
 		}
 
 		Repository localDb = createWorkRepository();
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"master\" remote=\"remote1\" />")
 				.append("<project path=\"foo\" name=\"").append(defaultUri)
 				.append("\">")
 				.append("<copyfile src=\"hello.sh\" dest=\"copy-hello.sh\" />")
 				.append("</project>").append("</manifest>");
 		JGitTestUtil.writeTrashFile(localDb, "manifest.xml",
 				xmlContent.toString());
 		RepoCommand command = new RepoCommand(localDb);
 		command.setPath(
 				localDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 				.setURI(rootUri).call();
 
 		// The original file should exist and be an executable
 		File hello = new File(localDb.getWorkTree(), "foo/hello.sh");
 		assertTrue("The original file should exist", hello.exists());
 		assertTrue("The original file must be executable", hello.canExecute());
 		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
 				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("The original file should have expected content",
 					"content of the executable file", content);
 		}
 
 		// The destination file should also exist and be an executable
 		hello = new File(localDb.getWorkTree(), "copy-hello.sh");
 		assertTrue("The destination file should exist", hello.exists());
 		assertTrue("The destination file must be executable",
 				hello.canExecute());
 		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
 				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("The destination file should have expected content",
 					"content of the executable file", content);
 		}
 	}
 
 	@Test
 	public void testBareRepo() throws Exception {
 		Repository remoteDb = createBareRepository();
 		Repository tempDb = createWorkRepository();
 
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"master\" remote=\"remote1\" />")
 				.append("<project path=\"foo\" name=\"").append(defaultUri)
 				.append("\" />").append("</manifest>");
 		JGitTestUtil.writeTrashFile(tempDb, "manifest.xml",
 				xmlContent.toString());
 		RepoCommand command = new RepoCommand(remoteDb);
 		command.setPath(
 				tempDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 				.setURI(rootUri).call();
 		// Clone it
 		File directory = createTempDirectory("testBareRepo");
 		try (Repository localDb = Git.cloneRepository().setDirectory(directory)
 				.setURI(remoteDb.getDirectory().toURI().toString()).call()
 				.getRepository()) {
 			// The .gitmodules file should exist
 			File gitmodules = new File(localDb.getWorkTree(), ".gitmodules");
 			assertTrue("The .gitmodules file should exist",
 					gitmodules.exists());
 			// The first line of .gitmodules file should be expected
 			try (BufferedReader reader = Files
 					.newBufferedReader(gitmodules.toPath(), UTF_8)) {
 				String content = reader.readLine();
 				assertEquals(
 						"The first line of .gitmodules file should be as expected",
 						"[submodule \"" + defaultUri + "\"]", content);
 			}
 			// The gitlink should be the same as remote head sha1
 			String gitlink = localDb.resolve(Constants.HEAD + ":foo").name();
 			String remote = defaultDb.resolve(Constants.HEAD).name();
 			assertEquals("The gitlink should be the same as remote head",
 					remote, gitlink);
 		}
 	}
 
 	@Test
 	public void testRevision() throws Exception {
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 			.append("<manifest>")
 			.append("<remote name=\"remote1\" fetch=\".\" />")
 			.append("<default revision=\"master\" remote=\"remote1\" />")
 			.append("<project path=\"foo\" name=\"")
 			.append(defaultUri)
 			.append("\" revision=\"")
 			.append(oldCommitId.name())
 			.append("\" />")
 			.append("</manifest>");
 		writeTrashFile("manifest.xml", xmlContent.toString());
 		RepoCommand command = new RepoCommand(db);
 		command.setPath(db.getWorkTree().getAbsolutePath() + "/manifest.xml")
 			.setURI(rootUri)
 			.call();
 		File hello = new File(db.getWorkTree(), "foo/hello.txt");
 		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
 				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("submodule content should be as expected",
 					"branch world", content);
 		}
 	}
 
 	@Test
 	public void testRevisionBranch() throws Exception {
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 			.append("<manifest>")
 			.append("<remote name=\"remote1\" fetch=\".\" />")
 			.append("<default revision=\"")
 			.append(BRANCH)
 			.append("\" remote=\"remote1\" />")
 			.append("<project path=\"foo\" name=\"")
 			.append(defaultUri)
 			.append("\" />")
 			.append("</manifest>");
 		writeTrashFile("manifest.xml", xmlContent.toString());
 		RepoCommand command = new RepoCommand(db);
 		command.setPath(db.getWorkTree().getAbsolutePath() + "/manifest.xml")
 			.setURI(rootUri)
 			.call();
 		File hello = new File(db.getWorkTree(), "foo/hello.txt");
 		assertContents(hello.toPath(), "branch world");
 	}
 
 	@Test
 	public void testRevisionTag() throws Exception {
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 			.append("<manifest>")
 			.append("<remote name=\"remote1\" fetch=\".\" />")
 			.append("<default revision=\"master\" remote=\"remote1\" />")
 			.append("<project path=\"foo\" name=\"")
 			.append(defaultUri)
 			.append("\" revision=\"")
 			.append(TAG)
 			.append("\" />")
 			.append("</manifest>");
 		writeTrashFile("manifest.xml", xmlContent.toString());
 		RepoCommand command = new RepoCommand(db);
 		command.setPath(db.getWorkTree().getAbsolutePath() + "/manifest.xml")
 			.setURI(rootUri)
 			.call();
 		File hello = new File(db.getWorkTree(), "foo/hello.txt");
 		assertContents(hello.toPath(), "branch world");
 	}
 
 	@Test
 	public void testRevisionBare() throws Exception {
 		Repository remoteDb = createBareRepository();
 		Repository tempDb = createWorkRepository();
 
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"").append(BRANCH)
 				.append("\" remote=\"remote1\" />")
 				.append("<project path=\"foo\" name=\"").append(defaultUri)
 				.append("\" />").append("</manifest>");
 		JGitTestUtil.writeTrashFile(tempDb, "manifest.xml",
 				xmlContent.toString());
 		RepoCommand command = new RepoCommand(remoteDb);
 		command.setPath(
 				tempDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 				.setURI(rootUri).call();
 		// Clone it
 		File directory = createTempDirectory("testRevisionBare");
 		try (Repository localDb = Git.cloneRepository().setDirectory(directory)
 				.setURI(remoteDb.getDirectory().toURI().toString()).call()
 				.getRepository()) {
 			// The gitlink should be the same as oldCommitId
 			String gitlink = localDb.resolve(Constants.HEAD + ":foo").name();
 			assertEquals("The gitlink is same as remote head",
 					oldCommitId.name(), gitlink);
 
 			File dotmodules = new File(localDb.getWorkTree(),
 					Constants.DOT_GIT_MODULES);
 			assertTrue(dotmodules.exists());
 			// The .gitmodules file should have "branch" lines
 			String gitModulesContents = RawParseUtils
 					.decode(IO.readFully(dotmodules));
 			assertTrue(gitModulesContents.contains("branch = branch"));
 		}
 	}
 
 	@Test
 	public void testRevisionBare_ignoreTags() throws Exception {
 		Repository remoteDb = createBareRepository();
 		Repository tempDb = createWorkRepository();
 
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"").append("refs/tags/" + TAG)
 				.append("\" remote=\"remote1\" />")
 				.append("<project path=\"foo\" name=\"")
 				.append(defaultUri)
 				.append("\" />").append("</manifest>");
 		JGitTestUtil.writeTrashFile(tempDb, "manifest.xml",
 				xmlContent.toString());
 		RepoCommand command = new RepoCommand(remoteDb);
 		command.setPath(
 				tempDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 				.setURI(rootUri).call();
 		// Clone it
 		File directory = createTempDirectory("testReplaceManifestBare");
 		File dotmodules;
 		try (Repository localDb = Git.cloneRepository().setDirectory(directory)
 				.setURI(remoteDb.getDirectory().toURI().toString()).call()
 				.getRepository()) {
 			dotmodules = new File(localDb.getWorkTree(),
 					Constants.DOT_GIT_MODULES);
 			assertTrue(dotmodules.exists());
 		}
 
 		// The .gitmodules file should not have "branch" lines
 		String gitModulesContents = RawParseUtils
 				.decode(IO.readFully(dotmodules));
 		assertFalse(gitModulesContents.contains("branch"));
 		assertTrue(gitModulesContents.contains("ref = refs/tags/" + TAG));
 	}
 
 	@Test
 	public void testCopyFileBare() throws Exception {
 		Repository remoteDb = createBareRepository();
 		Repository tempDb = createWorkRepository();
 
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"master\" remote=\"remote1\" />")
 				.append("<project path=\"foo\" name=\"").append(defaultUri)
 				.append("\" revision=\"").append(BRANCH).append("\" >")
 				.append("<copyfile src=\"hello.txt\" dest=\"Hello\" />")
 				.append("<copyfile src=\"hello.txt\" dest=\"foo/Hello\" />")
 				.append("</project>").append("</manifest>");
 		JGitTestUtil.writeTrashFile(tempDb, "manifest.xml",
 				xmlContent.toString());
 		RepoCommand command = new RepoCommand(remoteDb);
 		command.setPath(
 				tempDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 				.setURI(rootUri).call();
 		// Clone it
 		File directory = createTempDirectory("testCopyFileBare");
 		try (Repository localDb = Git.cloneRepository().setDirectory(directory)
 				.setURI(remoteDb.getDirectory().toURI().toString()).call()
 				.getRepository()) {
 			// The Hello file should exist
 			File hello = new File(localDb.getWorkTree(), "Hello");
 			assertTrue("The Hello file should exist", hello.exists());
 			// The foo/Hello file should be skipped.
 			File foohello = new File(localDb.getWorkTree(), "foo/Hello");
 			assertFalse("The foo/Hello file should be skipped",
 					foohello.exists());
 			// The content of Hello file should be expected
 			assertContents(hello.toPath(), "branch world");
 		}
 	}
 
 	@Test
 	public void testCopyFileBare_executable() throws Exception {
 		try (Git git = new Git(defaultDb)) {
 			git.checkout().setName(BRANCH).call();
 			File f = JGitTestUtil.writeTrashFile(defaultDb, "hello.sh",
 					"content of the executable file");
 			f.setExecutable(true);
 			git.add().addFilepattern("hello.sh").call();
 			git.commit().setMessage("Add binary file").call();
 		}
 
 		Repository remoteDb = createBareRepository();
 		Repository tempDb = createWorkRepository();
 
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"master\" remote=\"remote1\" />")
 				.append("<project path=\"foo\" name=\"").append(defaultUri)
 				.append("\" revision=\"").append(BRANCH)
 				.append("\" >")
 				.append("<copyfile src=\"hello.txt\" dest=\"Hello\" />")
 				.append("<copyfile src=\"hello.txt\" dest=\"foo/Hello\" />")
 				.append("<copyfile src=\"hello.sh\" dest=\"copy-hello.sh\" />")
 				.append("</project>").append("</manifest>");
 		JGitTestUtil.writeTrashFile(tempDb, "manifest.xml",
 				xmlContent.toString());
 		RepoCommand command = new RepoCommand(remoteDb);
 		command.setPath(
 				tempDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 				.setURI(rootUri).call();
 		// Clone it
 		File directory = createTempDirectory("testCopyFileBare");
 		try (Repository localDb = Git.cloneRepository().setDirectory(directory)
 				.setURI(remoteDb.getDirectory().toURI().toString()).call()
 				.getRepository()) {
 			// The Hello file should exist
 			File hello = new File(localDb.getWorkTree(), "Hello");
 			assertTrue("The Hello file should exist", hello.exists());
 			// The foo/Hello file should be skipped.
 			File foohello = new File(localDb.getWorkTree(), "foo/Hello");
 			assertFalse("The foo/Hello file should be skipped",
 					foohello.exists());
 			// The content of Hello file should be expected
 			try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
 					UTF_8)) {
 				String content = reader.readLine();
 				assertEquals("The Hello file should have expected content",
 						"branch world", content);
 			}
 
 			// The executable file must be there and preserve the executable bit
 			File helloSh = new File(localDb.getWorkTree(), "copy-hello.sh");
 			assertTrue("Destination file should exist", helloSh.exists());
 			assertContents(helloSh.toPath(), "content of the executable file");
 			assertTrue("Destination file should be executable",
 					helloSh.canExecute());
 
 		}
 	}
 
 	@Test
 	public void testReplaceManifestBare() throws Exception {
 		Repository remoteDb = createBareRepository();
 		Repository tempDb = createWorkRepository();
 
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"master\" remote=\"remote1\" />")
 				.append("<project path=\"foo\" name=\"").append(defaultUri)
 				.append("\" revision=\"").append(BRANCH).append("\" >")
 				.append("<copyfile src=\"hello.txt\" dest=\"Hello\" />")
 				.append("</project>").append("</manifest>");
 		JGitTestUtil.writeTrashFile(tempDb, "old.xml", xmlContent.toString());
 		RepoCommand command = new RepoCommand(remoteDb);
 		command.setPath(tempDb.getWorkTree().getAbsolutePath() + "/old.xml")
 				.setURI(rootUri).call();
 		xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"master\" remote=\"remote1\" />")
 				.append("<project path=\"bar\" name=\"").append(notDefaultUri)
 				.append("\" >")
 				.append("<copyfile src=\"world.txt\" dest=\"World.txt\" />")
 				.append("</project>").append("</manifest>");
 		JGitTestUtil.writeTrashFile(tempDb, "new.xml", xmlContent.toString());
 		command = new RepoCommand(remoteDb);
 		command.setPath(tempDb.getWorkTree().getAbsolutePath() + "/new.xml")
 				.setURI(rootUri).call();
 		// Clone it
 		File directory = createTempDirectory("testReplaceManifestBare");
 		File dotmodules;
 		try (Repository localDb = Git.cloneRepository().setDirectory(directory)
 				.setURI(remoteDb.getDirectory().toURI().toString()).call()
 				.getRepository()) {
 			// The Hello file should not exist
 			File hello = new File(localDb.getWorkTree(), "Hello");
 			assertFalse("The Hello file shouldn't exist", hello.exists());
 			// The Hello.txt file should exist
 			File hellotxt = new File(localDb.getWorkTree(), "World.txt");
 			assertTrue("The World.txt file should exist", hellotxt.exists());
 			dotmodules = new File(localDb.getWorkTree(),
 					Constants.DOT_GIT_MODULES);
 		}
 		// The .gitmodules file should have 'submodule "bar"' and shouldn't
 		// have
 		// 'submodule "foo"' lines.
 		try (BufferedReader reader = Files
 				.newBufferedReader(dotmodules.toPath(), UTF_8)) {
 			boolean foo = false;
 			boolean bar = false;
 			while (true) {
 				String line = reader.readLine();
 				if (line == null)
 					break;
 				if (line.contains("submodule \"" + defaultUri + "\""))
 					foo = true;
 				if (line.contains("submodule \"" + notDefaultUri + "\""))
 					bar = true;
 			}
 			assertTrue("The bar submodule should exist", bar);
 			assertFalse("The foo submodule shouldn't exist", foo);
 		}
 	}
 
 	@Test
 	public void testRemoveOverlappingBare() throws Exception {
 		Repository remoteDb = createBareRepository();
 		Repository tempDb = createWorkRepository();
 
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"master\" remote=\"remote1\" />")
 				.append("<project path=\"foo/bar\" name=\"").append(groupBUri)
 				.append("\" />").append("<project path=\"a\" name=\"")
 				.append(groupAUri).append("\" />")
 				.append("<project path=\"foo\" name=\"").append(defaultUri)
 				.append("\" />").append("</manifest>");
 		JGitTestUtil.writeTrashFile(tempDb, "manifest.xml",
 				xmlContent.toString());
 		RepoCommand command = new RepoCommand(remoteDb);
 		command.setPath(
 				tempDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 				.setURI(rootUri).call();
 		// Clone it
 		File directory = createTempDirectory("testRemoveOverlappingBare");
 		File dotmodules;
 		try (Repository localDb = Git.cloneRepository().setDirectory(directory)
 				.setURI(remoteDb.getDirectory().toURI().toString()).call()
 				.getRepository()) {
 			dotmodules = new File(localDb.getWorkTree(),
 				Constants.DOT_GIT_MODULES);
 		}
 
 		// Check .gitmodules file
 		try (BufferedReader reader = Files
 				.newBufferedReader(dotmodules.toPath(), UTF_8)) {
 			boolean foo = false;
 			boolean foobar = false;
 			boolean a = false;
 			while (true) {
 				String line = reader.readLine();
 				if (line == null)
 					break;
 				if (line.contains("submodule \"" + defaultUri + "\""))
 					foo = true;
 				if (line.contains("submodule \"" + groupBUri + "\""))
 					foobar = true;
 				if (line.contains("submodule \"" + groupAUri + "\""))
 					a = true;
 			}
 			assertTrue("The " + defaultUri + " submodule should exist", foo);
 			assertFalse("The " + groupBUri + " submodule shouldn't exist",
 					foobar);
 			assertTrue("The " + groupAUri + " submodule should exist", a);
 		}
 	}
 
 	@Test
 	public void testIncludeTag() throws Exception {
 		Repository localDb = createWorkRepository();
 		Repository tempDb = createWorkRepository();
 
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 			.append("<manifest>")
 			.append("<include name=\"_include.xml\" />")
 			.append("<default revision=\"master\" remote=\"remote1\" />")
 			.append("</manifest>");
 		JGitTestUtil.writeTrashFile(
 				tempDb, "manifest.xml", xmlContent.toString());
 
 		xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 			.append("<manifest>")
 			.append("<remote name=\"remote1\" fetch=\".\" />")
 			.append("<default revision=\"master\" remote=\"remote1\" />")
 			.append("<project path=\"foo\" name=\"")
 			.append(defaultUri)
 			.append("\" />")
 			.append("</manifest>");
 		JGitTestUtil.writeTrashFile(
 				tempDb, "_include.xml", xmlContent.toString());
 
 		RepoCommand command = new RepoCommand(localDb);
 		command
 			.setPath(tempDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 			.setURI(rootUri)
 			.call();
 		File hello = new File(localDb.getWorkTree(), "foo/hello.txt");
 		assertTrue("submodule should be checked out", hello.exists());
 		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
 				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("submodule content should be as expected",
 					"master world", content);
 		}
 	}
 	@Test
 	public void testRemoteAlias() throws Exception {
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 			.append("<manifest>")
 			.append("<remote name=\"remote1\" fetch=\".\" alias=\"remote2\" />")
 			.append("<default revision=\"master\" remote=\"remote2\" />")
 			.append("<project path=\"foo\" name=\"")
 			.append(defaultUri)
 			.append("\" />")
 			.append("</manifest>");
 
 		Repository localDb = createWorkRepository();
 		JGitTestUtil.writeTrashFile(
 				localDb, "manifest.xml", xmlContent.toString());
 		RepoCommand command = new RepoCommand(localDb);
 		command
 			.setPath(localDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 			.setURI(rootUri)
 			.call();
 		File file = new File(localDb.getWorkTree(), "foo/hello.txt");
 		assertTrue("We should have foo", file.exists());
 	}
 
 	@Test
 	public void testTargetBranch() throws Exception {
 		Repository remoteDb1 = createBareRepository();
 		Repository remoteDb2 = createBareRepository();
 		Repository tempDb = createWorkRepository();
 
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"master\" remote=\"remote1\" />")
 				.append("<project path=\"foo\" name=\"").append(defaultUri)
 				.append("\" />").append("</manifest>");
 		JGitTestUtil.writeTrashFile(tempDb, "manifest.xml",
 				xmlContent.toString());
 		RepoCommand command = new RepoCommand(remoteDb1);
 		command.setPath(
 				tempDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 				.setURI(rootUri).setTargetBranch("test").call();
 		ObjectId branchId = remoteDb1
 				.resolve(Constants.R_HEADS + "test^{tree}");
 		command = new RepoCommand(remoteDb2);
 		command.setPath(
 				tempDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 				.setURI(rootUri).call();
 		ObjectId defaultId = remoteDb2.resolve(Constants.HEAD + "^{tree}");
 		assertEquals(
 				"The tree id of branch db and default db should be the same",
 				branchId, defaultId);
 	}
 
 	@Test
 	public void testRecordRemoteBranch() throws Exception {
 		Repository remoteDb = createBareRepository();
 		Repository tempDb = createWorkRepository();
 
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"master\" remote=\"remote1\" />")
 				.append("<project path=\"with-branch\" ")
 				.append("revision=\"master\" ").append("name=\"")
 				.append(notDefaultUri).append("\" />")
 				.append("<project path=\"with-long-branch\" ")
 				.append("revision=\"refs/heads/master\" ").append("name=\"")
 				.append(defaultUri).append("\" />").append("</manifest>");
 		JGitTestUtil.writeTrashFile(tempDb, "manifest.xml",
 				xmlContent.toString());
 
 		RepoCommand command = new RepoCommand(remoteDb);
 		command.setPath(
 				tempDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 				.setURI(rootUri).setRecordRemoteBranch(true).call();
 		// Clone it
 		File directory = createTempDirectory("testBareRepo");
 		try (Repository localDb = Git.cloneRepository().setDirectory(directory)
 				.setURI(remoteDb.getDirectory().toURI().toString()).call()
 				.getRepository();) {
 			// The .gitmodules file should exist
 			File gitmodules = new File(localDb.getWorkTree(), ".gitmodules");
 			assertTrue("The .gitmodules file should exist",
 					gitmodules.exists());
 			FileBasedConfig c = new FileBasedConfig(gitmodules, FS.DETECTED);
 			c.load();
 			assertEquals(
 					"Recording remote branches should work for short branch descriptions",
 					"master",
 					c.getString("submodule", notDefaultUri, "branch"));
 			assertEquals(
 					"Recording remote branches should work for full ref specs",
 					"refs/heads/master",
 					c.getString("submodule", defaultUri, "branch"));
 		}
 	}
 
 
 	@Test
 	public void testRecordSubmoduleLabels() throws Exception {
 		Repository remoteDb = createBareRepository();
 		Repository tempDb = createWorkRepository();
 
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"master\" remote=\"remote1\" />")
 				.append("<project path=\"test\" ")
 				.append("revision=\"master\" ").append("name=\"")
 				.append(notDefaultUri).append("\" ")
 				.append("groups=\"a1,a2\" />").append("</manifest>");
 		JGitTestUtil.writeTrashFile(tempDb, "manifest.xml",
 				xmlContent.toString());
 
 		RepoCommand command = new RepoCommand(remoteDb);
 		command.setPath(
 				tempDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 				.setURI(rootUri).setRecordSubmoduleLabels(true).call();
 		// Clone it
 		File directory = createTempDirectory("testBareRepo");
 		try (Repository localDb = Git.cloneRepository().setDirectory(directory)
 				.setURI(remoteDb.getDirectory().toURI().toString()).call()
 				.getRepository();) {
 			// The .gitattributes file should exist
 			File gitattributes = new File(localDb.getWorkTree(),
 					".gitattributes");
 			assertTrue("The .gitattributes file should exist",
 					gitattributes.exists());
 			try (BufferedReader reader = Files
 					.newBufferedReader(gitattributes.toPath(),
 					UTF_8)) {
 				String content = reader.readLine();
 				assertEquals(".gitattributes content should be as expected",
 						"/test a1 a2", content);
 			}
 		}
 	}
 
 	@Test
 	public void testRecordShallowRecommendation() throws Exception {
 		Repository remoteDb = createBareRepository();
 		Repository tempDb = createWorkRepository();
 
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"master\" remote=\"remote1\" />")
 				.append("<project path=\"shallow-please\" ").append("name=\"")
 				.append(defaultUri).append("\" ").append("clone-depth=\"1\" />")
 				.append("<project path=\"non-shallow\" ").append("name=\"")
 				.append(notDefaultUri).append("\" />").append("</manifest>");
 		JGitTestUtil.writeTrashFile(tempDb, "manifest.xml",
 				xmlContent.toString());
 
 		RepoCommand command = new RepoCommand(remoteDb);
 		command.setPath(
 				tempDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 				.setURI(rootUri).setRecommendShallow(true).call();
 		// Clone it
 		File directory = createTempDirectory("testBareRepo");
 		try (Repository localDb = Git.cloneRepository().setDirectory(directory)
 				.setURI(remoteDb.getDirectory().toURI().toString()).call()
 				.getRepository();) {
 			// The .gitmodules file should exist
 			File gitmodules = new File(localDb.getWorkTree(), ".gitmodules");
 			assertTrue("The .gitmodules file should exist",
 					gitmodules.exists());
 			FileBasedConfig c = new FileBasedConfig(gitmodules, FS.DETECTED);
 			c.load();
 			assertEquals("Recording shallow configuration should work", "true",
 					c.getString("submodule", defaultUri, "shallow"));
 			assertNull("Recording non shallow configuration should work",
 					c.getString("submodule", notDefaultUri, "shallow"));
 		}
 	}
 
 	@Test
 	public void testRemoteRevision() throws Exception {
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 			.append("<manifest>")
 			.append("<remote name=\"remote1\" fetch=\".\" />")
 			.append("<remote name=\"remote2\" fetch=\".\" revision=\"")
 			.append(BRANCH)
 			.append("\" />")
 			.append("<default remote=\"remote1\" revision=\"master\" />")
 			.append("<project path=\"foo\" remote=\"remote2\" name=\"")
 			.append(defaultUri)
 			.append("\" />")
 			.append("</manifest>");
 		writeTrashFile("manifest.xml", xmlContent.toString());
 		RepoCommand command = new RepoCommand(db);
 		command.setPath(db.getWorkTree().getAbsolutePath() + "/manifest.xml")
 			.setURI(rootUri)
 			.call();
 		File hello = new File(db.getWorkTree(), "foo/hello.txt");
 		assertContents(hello.toPath(), "branch world");
 	}
 
 	@Test
 	public void testDefaultRemoteRevision() throws Exception {
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 			.append("<manifest>")
 			.append("<remote name=\"remote1\" fetch=\".\" revision=\"")
 			.append(BRANCH)
 			.append("\" />")
 			.append("<default remote=\"remote1\" />")
 			.append("<project path=\"foo\" name=\"")
 			.append(defaultUri)
 			.append("\" />")
 			.append("</manifest>");
 		writeTrashFile("manifest.xml", xmlContent.toString());
 		RepoCommand command = new RepoCommand(db);
 		command.setPath(db.getWorkTree().getAbsolutePath() + "/manifest.xml")
 			.setURI(rootUri)
 			.call();
 		File hello = new File(db.getWorkTree(), "foo/hello.txt");
 		try (BufferedReader reader = Files.newBufferedReader(hello.toPath(),
 				UTF_8)) {
 			String content = reader.readLine();
 			assertEquals("submodule content should be as expected",
 					"branch world", content);
 		}
 	}
 
 	@Test
 	public void testTwoPathUseTheSameName() throws Exception {
 		Repository remoteDb = createBareRepository();
 		Repository tempDb = createWorkRepository();
 
 		StringBuilder xmlContent = new StringBuilder();
 		xmlContent.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
 				.append("<manifest>")
 				.append("<remote name=\"remote1\" fetch=\".\" />")
 				.append("<default revision=\"master\" remote=\"remote1\" />")
 				.append("<project path=\"path1\" ").append("name=\"")
 				.append(defaultUri).append("\" />")
 				.append("<project path=\"path2\" ").append("name=\"")
 				.append(defaultUri).append("\" />").append("</manifest>");
 		JGitTestUtil.writeTrashFile(tempDb, "manifest.xml",
 				xmlContent.toString());
 
 		RepoCommand command = new RepoCommand(remoteDb);
 		command.setPath(
 				tempDb.getWorkTree().getAbsolutePath() + "/manifest.xml")
 				.setURI(rootUri).setRecommendShallow(true).call();
 		File directory = createTempDirectory("testBareRepo");
 		try (Repository localDb = Git.cloneRepository().setDirectory(directory)
 				.setURI(remoteDb.getDirectory().toURI().toString()).call()
 				.getRepository();) {
 			File gitmodules = new File(localDb.getWorkTree(), ".gitmodules");
 			assertTrue("The .gitmodules file should exist",
 					gitmodules.exists());
 			FileBasedConfig c = new FileBasedConfig(gitmodules, FS.DETECTED);
 			c.load();
 			assertEquals("A module should exist for path1", "path1",
 					c.getString("submodule", defaultUri + "/path1", "path"));
 			assertEquals("A module should exist for path2", "path2",
 					c.getString("submodule", defaultUri + "/path2", "path"));
 		}
 	}
 
 	private void resolveRelativeUris() {
 		// Find the longest common prefix ends with "/" as rootUri.
 		defaultUri = defaultDb.getDirectory().toURI().toString();
 		notDefaultUri = notDefaultDb.getDirectory().toURI().toString();
 		groupAUri = groupADb.getDirectory().toURI().toString();
 		groupBUri = groupBDb.getDirectory().toURI().toString();
 		int start = 0;
 		while (start <= defaultUri.length()) {
 			int newStart = defaultUri.indexOf('/', start + 1);
 			String prefix = defaultUri.substring(0, newStart);
 			if (!notDefaultUri.startsWith(prefix) ||
 					!groupAUri.startsWith(prefix) ||
 					!groupBUri.startsWith(prefix)) {
 				start++;
 				rootUri = defaultUri.substring(0, start) + "manifest";
 				defaultUri = defaultUri.substring(start);
 				notDefaultUri = notDefaultUri.substring(start);
 				groupAUri = groupAUri.substring(start);
 				groupBUri = groupBUri.substring(start);
 				return;
 			}
 			start = newStart;
 		}
 	}
 
 	void testRelative(String a, String b, String want) {
 		String got = RepoCommand.relativize(URI.create(a), URI.create(b)).toString();
 
 		if (!got.equals(want)) {
 			fail(String.format("relative('%s', '%s') = '%s', want '%s'", a, b, got, want));
 		}
 	}
 
 	@Test
 	public void relative() {
 		testRelative("a/b/", "a/", "../");
 		// Normalization:
 		testRelative("a/p/..//b/", "a/", "../");
 		testRelative("a/b", "a/", "");
 		testRelative("a/", "a/b/", "b/");
 		testRelative("a/", "a/b", "b");
 		testRelative("/a/b/c", "/b/c", "../../b/c");
 		testRelative("/abc", "bcd", "bcd");
 		testRelative("abc", "def", "def");
 		testRelative("abc", "/bcd", "/bcd");
 		testRelative("http://a", "a/b", "a/b");
 		testRelative("http://base.com/a/", "http://child.com/a/b", "http://child.com/a/b");
 		testRelative("http://base.com/a/", "http://base.com/a/b", "b");
 	}
 }