Allow explicit configuration of git directory in CloneCommand

This feature is needed to support the new submodule layout where the
.git folder of the submodules is under .git/modules/<submodule>.

Change-Id: If5f13426cfd09b7677e23478e9700c8c25a6dae5

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java

 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
 import org.eclipse.jgit.api.ListBranchCommand.ListMode;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
+import org.eclipse.jgit.errors.NoWorkTreeException;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.lib.ConfigConstants;
 				fetchRefSpec(git2.getRepository()));
 	}
 
+	@Test
+	public void testCloneRepositoryExplicitGitDir() throws IOException,
+			JGitInternalException, GitAPIException {
+		File directory = createTempDirectory("testCloneRepository");
+		CloneCommand command = Git.cloneRepository();
+		command.setDirectory(directory);
+		command.setGitDir(new File(directory, ".git"));
+		command.setURI(fileUri());
+		Git git2 = command.call();
+		assertEquals(directory, git2.getRepository().getWorkTree());
+		assertEquals(new File(directory, ".git"), git2.getRepository()
+				.getDirectory());
+	}
+
+	@Test
+	public void testCloneRepositoryExplicitGitDirNonStd() throws IOException,
+			JGitInternalException, GitAPIException {
+		File directory = createTempDirectory("testCloneRepository");
+		File gDir = createTempDirectory("testCloneRepository.git");
+		CloneCommand command = Git.cloneRepository();
+		command.setDirectory(directory);
+		command.setGitDir(gDir);
+		command.setURI(fileUri());
+		Git git2 = command.call();
+		assertEquals(directory, git2.getRepository().getWorkTree());
+		assertEquals(gDir, git2.getRepository()
+				.getDirectory());
+		assertTrue(new File(directory, ".git").isFile());
+		assertFalse(new File(gDir, ".git").exists());
+	}
+
+	@Test
+	public void testCloneRepositoryExplicitGitDirBare() throws IOException,
+			JGitInternalException, GitAPIException {
+		File gDir = createTempDirectory("testCloneRepository.git");
+		CloneCommand command = Git.cloneRepository();
+		command.setBare(true);
+		command.setGitDir(gDir);
+		command.setURI(fileUri());
+		Git git2 = command.call();
+		try {
+			assertNull(null, git2.getRepository().getWorkTree());
+			fail("Expected NoWorkTreeException");
+		} catch (NoWorkTreeException e) {
+			assertEquals(gDir, git2.getRepository().getDirectory());
+		}
+	}
+
 	@Test
 	public void testBareCloneRepository() throws IOException,
 			JGitInternalException, GitAPIException, URISyntaxException {

org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java

 
 	private File directory;
 
+	private File gitDir;
+
 	private boolean bare;
 
 	private String remote = Constants.DEFAULT_REMOTE_NAME;
 	private Repository init(URIish u) throws GitAPIException {
 		InitCommand command = Git.init();
 		command.setBare(bare);
-		if (directory == null)
+		if (directory == null && gitDir == null)
 			directory = new File(u.getHumanishName(), Constants.DOT_GIT);
-		if (directory.exists() && directory.listFiles().length != 0)
+		if (directory != null && directory.exists()
+				&& directory.listFiles().length != 0)
 			throw new JGitInternalException(MessageFormat.format(
 					JGitText.get().cloneNonEmptyDirectory, directory.getName()));
-		command.setDirectory(directory);
+		if (gitDir != null && gitDir.exists() && gitDir.listFiles().length != 0)
+			throw new JGitInternalException(MessageFormat.format(
+					JGitText.get().cloneNonEmptyDirectory, gitDir.getName()));
+		if (directory != null)
+			command.setDirectory(directory);
+		if (gitDir != null)
+			command.setGitDir(gitDir);
 		return command.call().getRepository();
 	}
 
 	 * @param directory
 	 *            the directory to clone to
 	 * @return this instance
+	 * @throws IllegalStateException
+	 *             if the combination of directory, gitDir and bare is illegal.
+	 *             E.g. if for a non-bare repository directory and gitDir point
+	 *             to the same directory of if for a bare repository both
+	 *             directory and gitDir are specified
 	 */
 	public CloneCommand setDirectory(File directory) {
+		validateDirs(directory, gitDir, bare);
 		this.directory = directory;
 		return this;
 	}
 
+	/**
+	 * @param gitDir
+	 *            the repository meta directory
+	 * @return this instance
+	 * @throws IllegalStateException
+	 *             if the combination of directory, gitDir and bare is illegal.
+	 *             E.g. if for a non-bare repository directory and gitDir point
+	 *             to the same directory of if for a bare repository both
+	 *             directory and gitDir are specified
+	 * @since 3.6
+	 */
+	public CloneCommand setGitDir(File gitDir) {
+		validateDirs(directory, gitDir, bare);
+		this.gitDir = gitDir;
+		return this;
+	}
+
 	/**
 	 * @param bare
 	 *            whether the cloned repository is bare or not
 	 * @return this instance
+	 * @throws IllegalStateException
+	 *             if the combination of directory, gitDir and bare is illegal.
+	 *             E.g. if for a non-bare repository directory and gitDir point
+	 *             to the same directory of if for a bare repository both
+	 *             directory and gitDir are specified
 	 */
-	public CloneCommand setBare(boolean bare) {
+	public CloneCommand setBare(boolean bare) throws IllegalStateException {
+		validateDirs(directory, gitDir, bare);
 		this.bare = bare;
 		return this;
 	}
 		this.noCheckout = noCheckout;
 		return this;
 	}
+
+	private static void validateDirs(File directory, File gitDir, boolean bare)
+			throws IllegalStateException {
+		if (directory != null) {
+			if (bare) {
+				if (gitDir != null && !gitDir.equals(directory))
+					throw new IllegalStateException(MessageFormat.format(
+							JGitText.get().initFailedBareRepoDifferentDirs,
+							gitDir, directory));
+			} else {
+				if (gitDir != null && gitDir.equals(directory))
+					throw new IllegalStateException(MessageFormat.format(
+							JGitText.get().initFailedNonBareRepoSameDirs,
+							gitDir, directory));
+			}
+		}
+	}
 }