/*
    * Copyright (C) 2014, Google Inc.
    * 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.gitrepo;
  
  import static java.nio.charset.StandardCharsets.UTF_8;
  import static org.eclipse.jgit.lib.Constants.DEFAULT_REMOTE_NAME;
  import static org.eclipse.jgit.lib.Constants.R_REMOTES;
  
  import java.io.File;
  import java.io.FileInputStream;
  import java.io.IOException;
  import java.io.InputStream;
  import java.net.URI;
  import java.text.MessageFormat;
  import java.util.ArrayList;
  import java.util.List;
  import java.util.Map;
  import java.util.Objects;
  import java.util.StringJoiner;
  import java.util.TreeMap;
  
  import org.eclipse.jgit.annotations.NonNull;
  import org.eclipse.jgit.annotations.Nullable;
  import org.eclipse.jgit.api.Git;
  import org.eclipse.jgit.api.GitCommand;
  import org.eclipse.jgit.api.SubmoduleAddCommand;
  import org.eclipse.jgit.api.errors.ConcurrentRefUpdateException;
  import org.eclipse.jgit.api.errors.GitAPIException;
  import org.eclipse.jgit.api.errors.InvalidRefNameException;
  import org.eclipse.jgit.api.errors.JGitInternalException;
  import org.eclipse.jgit.dircache.DirCache;
  import org.eclipse.jgit.dircache.DirCacheBuilder;
  import org.eclipse.jgit.dircache.DirCacheEntry;
  import org.eclipse.jgit.gitrepo.ManifestParser.IncludedFileReader;
  import org.eclipse.jgit.gitrepo.RepoProject.CopyFile;
  import org.eclipse.jgit.gitrepo.RepoProject.LinkFile;
  import org.eclipse.jgit.gitrepo.internal.RepoText;
  import org.eclipse.jgit.internal.JGitText;
  import org.eclipse.jgit.lib.CommitBuilder;
  import org.eclipse.jgit.lib.Config;
  import org.eclipse.jgit.lib.Constants;
  import org.eclipse.jgit.lib.FileMode;
  import org.eclipse.jgit.lib.ObjectId;
  import org.eclipse.jgit.lib.ObjectInserter;
  import org.eclipse.jgit.lib.PersonIdent;
  import org.eclipse.jgit.lib.ProgressMonitor;
  import org.eclipse.jgit.lib.Ref;
  import org.eclipse.jgit.lib.RefDatabase;
  import org.eclipse.jgit.lib.RefUpdate;
  import org.eclipse.jgit.lib.RefUpdate.Result;
  import org.eclipse.jgit.lib.Repository;
  import org.eclipse.jgit.revwalk.RevCommit;
  import org.eclipse.jgit.revwalk.RevWalk;
  import org.eclipse.jgit.treewalk.TreeWalk;
  import org.eclipse.jgit.util.FileUtils;
  
  /**
   * A class used to execute a repo command.
   *
  * This will parse a repo XML manifest, convert it into .gitmodules file and the
  * repository config file.
  *
  * If called against a bare repository, it will replace all the existing content
  * of the repository with the contents populated from the manifest.
  *
  * repo manifest allows projects overlapping, e.g. one project's manifestPath is
  * "foo" and another project's manifestPath is "foo/bar". This won't
  * work in git submodule, so we'll skip all the sub projects
  * ("foo/bar" in the example) while converting.
  *
  * @see <a href="https://code.google.com/p/git-repo/">git-repo project page</a>
  * @since 3.4
  */
 public class RepoCommand extends GitCommand<RevCommit> {
 	private String manifestPath;
 	private String baseUri;
 	private URI targetUri;
 	private String groupsParam;
 	private String branch;
 	private String targetBranch = Constants.HEAD;
 	private boolean recordRemoteBranch = true;
 	private boolean recordSubmoduleLabels = true;
 	private boolean recordShallowSubmodules = true;
 	private PersonIdent author;
 	private RemoteReader callback;
 	private InputStream inputStream;
 	private IncludedFileReader includedReader;
 	private boolean ignoreRemoteFailures = false;
 
 	private ProgressMonitor monitor;
 
 	/**
 	 * A callback to get ref sha1 of a repository from its uri.
 	 *
 	 * We provided a default implementation {@link DefaultRemoteReader} to
 	 * use ls-remote command to read the sha1 from the repository and clone the
 	 * repository to read the file. Callers may have their own quicker
 	 * implementation.
 	 *
 	 * @since 3.4
 	 */
 	public interface RemoteReader {
 		/**
 		 * Read a remote ref sha1.
 		 *
 		 * @param uri
 		 *            The URI of the remote repository
 		 * @param ref
 		 *            Name of the ref to lookup. May be a short-hand form, e.g.
 		 *            "master" which is automatically expanded to
 		 *            "refs/heads/master" if "refs/heads/master" already exists.
 		 * @return the sha1 of the remote repository, or null if the ref does
 		 *         not exist.
 		 * @throws GitAPIException
 		 */
 		@Nullable
 		public ObjectId sha1(String uri, String ref) throws GitAPIException;
 
 		/**
 		 * Read a file from a remote repository.
 		 *
 		 * @param uri
 		 *            The URI of the remote repository
 		 * @param ref
 		 *            The ref (branch/tag/etc.) to read
 		 * @param path
 		 *            The relative path (inside the repo) to the file to read
 		 * @return the file content.
 		 * @throws GitAPIException
 		 * @throws IOException
 		 * @since 3.5
 		 *
 		 * @deprecated Use {@link #readFileWithMode(String, String, String)}
 		 *             instead
 		 */
 		@Deprecated
 		public default byte[] readFile(String uri, String ref, String path)
 				throws GitAPIException, IOException {
 			return readFileWithMode(uri, ref, path).getContents();
 		}
 
 		/**
 		 * Read contents and mode (i.e. permissions) of the file from a remote
 		 * repository.
 		 *
 		 * @param uri
 		 *            The URI of the remote repository
 		 * @param ref
 		 *            Name of the ref to lookup. May be a short-hand form, e.g.
 		 *            "master" which is automatically expanded to
 		 *            "refs/heads/master" if "refs/heads/master" already exists.
 		 * @param path
 		 *            The relative path (inside the repo) to the file to read
 		 * @return The contents and file mode of the file in the given
 		 *         repository and branch. Never null.
 		 * @throws GitAPIException
 		 *             If the ref have an invalid or ambiguous name, or it does
 		 *             not exist in the repository,
 		 * @throws IOException
 		 *             If the object does not exist or is too large
 		 * @since 5.2
 		 */
 		@NonNull
 		public RemoteFile readFileWithMode(String uri, String ref, String path)
 				throws GitAPIException, IOException;
 	}
 
 	/**
 	 * Read-only view of contents and file mode (i.e. permissions) for a file in
 	 * a remote repository.
 	 *
 	 * @since 5.2
 	 */
 	public static final class RemoteFile {
 		@NonNull
 		private final byte[] contents;
 
 		@NonNull
 		private final FileMode fileMode;
 
 		/**
 		 * @param contents
 		 *            Raw contents of the file.
 		 * @param fileMode
 		 *            Git file mode for this file (e.g. executable or regular)
 		 */
 		public RemoteFile(@NonNull byte[] contents,
 				@NonNull FileMode fileMode) {
 			this.contents = Objects.requireNonNull(contents);
 			this.fileMode = Objects.requireNonNull(fileMode);
 		}
 
 		/**
 		 * Contents of the file.
 		 * <p>
 		 * Callers who receive this reference must not modify its contents (as
 		 * it can point to internal cached data).
 		 *
 		 * @return Raw contents of the file. Do not modify it.
 		 */
 		@NonNull
 		public byte[] getContents() {
 			return contents;
 		}
 
 		/**
 		 * @return Git file mode for this file (e.g. executable or regular)
 		 */
 		@NonNull
 		public FileMode getFileMode() {
 			return fileMode;
 		}
 
 	}
 
 	/** A default implementation of {@link RemoteReader} callback. */
 	public static class DefaultRemoteReader implements RemoteReader {
 
 		@Override
 		public ObjectId sha1(String uri, String ref) throws GitAPIException {
 			Map<String, Ref> map = Git
 					.lsRemoteRepository()
 					.setRemote(uri)
 					.callAsMap();
 			Ref r = RefDatabase.findRef(map, ref);
 			return r != null ? r.getObjectId() : null;
 		}
 
 		@Override
 		public RemoteFile readFileWithMode(String uri, String ref, String path)
 				throws GitAPIException, IOException {
 			File dir = FileUtils.createTempDir("jgit_", ".git", null); //$NON-NLS-1$ //$NON-NLS-2$
 			try (Git git = Git.cloneRepository().setBare(true).setDirectory(dir)
 					.setURI(uri).call()) {
 				Repository repo = git.getRepository();
 				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));
 			} finally {
 				FileUtils.delete(dir, FileUtils.RECURSIVE);
 			}
 		}
 	}
 
 	@SuppressWarnings("serial")
 	private static class ManifestErrorException extends GitAPIException {
 		ManifestErrorException(Throwable cause) {
 			super(RepoText.get().invalidManifest, cause);
 		}
 	}
 
 	@SuppressWarnings("serial")
 	private static class RemoteUnavailableException extends GitAPIException {
 		RemoteUnavailableException(String uri) {
 			super(MessageFormat.format(RepoText.get().errorRemoteUnavailable, uri));
 		}
 	}
 
 	/**
 	 * Constructor for RepoCommand
 	 *
 	 * @param repo
 	 *            the {@link org.eclipse.jgit.lib.Repository}
 	 */
 	public RepoCommand(Repository repo) {
 		super(repo);
 	}
 
 	/**
 	 * Set path to the manifest XML file.
 	 * <p>
 	 * Calling {@link #setInputStream} will ignore the path set here.
 	 *
 	 * @param path
 	 *            (with <code>/</code> as separator)
 	 * @return this command
 	 */
 	public RepoCommand setPath(String path) {
 		this.manifestPath = path;
 		return this;
 	}
 
 	/**
 	 * Set the input stream to the manifest XML.
 	 * <p>
 	 * Setting inputStream will ignore the path set. It will be closed in
 	 * {@link #call}.
 	 *
 	 * @param inputStream a {@link java.io.InputStream} object.
 	 * @return this command
 	 * @since 3.5
 	 */
 	public RepoCommand setInputStream(InputStream inputStream) {
 		this.inputStream = inputStream;
 		return this;
 	}
 
 	/**
 	 * Set base URI of the paths inside the XML. This is typically the name of
 	 * the directory holding the manifest repository, eg. for
 	 * https://android.googlesource.com/platform/manifest, this should be
 	 * /platform (if you would run this on android.googlesource.com) or
 	 * https://android.googlesource.com/platform elsewhere.
 	 *
 	 * @param uri
 	 *            the base URI
 	 * @return this command
 	 */
 	public RepoCommand setURI(String uri) {
 		this.baseUri = uri;
 		return this;
 	}
 
 	/**
 	 * Set the URI of the superproject (this repository), so the .gitmodules
 	 * file can specify the submodule URLs relative to the superproject.
 	 *
 	 * @param uri
 	 *            the URI of the repository holding the superproject.
 	 * @return this command
 	 * @since 4.8
 	 */
 	public RepoCommand setTargetURI(String uri) {
 		// The repo name is interpreted as a directory, for example
 		// Gerrit (http://gerrit.googlesource.com/gerrit) has a
 		// .gitmodules referencing ../plugins/hooks, which is
 		// on http://gerrit.googlesource.com/plugins/hooks,
 		this.targetUri = URI.create(uri + "/"); //$NON-NLS-1$
 		return this;
 	}
 
 	/**
 	 * Set groups to sync
 	 *
 	 * @param groups groups separated by comma, examples: default|all|G1,-G2,-G3
 	 * @return this command
 	 */
 	public RepoCommand setGroups(String groups) {
 		this.groupsParam = groups;
 		return this;
 	}
 
 	/**
 	 * Set default branch.
 	 * <p>
 	 * This is generally the name of the branch the manifest file was in. If
 	 * there's no default revision (branch) specified in manifest and no
 	 * revision specified in project, this branch will be used.
 	 *
 	 * @param branch
 	 *            a branch name
 	 * @return this command
 	 */
 	public RepoCommand setBranch(String branch) {
 		this.branch = branch;
 		return this;
 	}
 
 	/**
 	 * Set target branch.
 	 * <p>
 	 * This is the target branch of the super project to be updated. If not set,
 	 * default is HEAD.
 	 * <p>
 	 * For non-bare repositories, HEAD will always be used and this will be
 	 * ignored.
 	 *
 	 * @param branch
 	 *            branch name
 	 * @return this command
 	 * @since 4.1
 	 */
 	public RepoCommand setTargetBranch(String branch) {
 		this.targetBranch = Constants.R_HEADS + branch;
 		return this;
 	}
 
 	/**
 	 * Set whether the branch name should be recorded in .gitmodules.
 	 * <p>
 	 * Submodule entries in .gitmodules can include a "branch" field
 	 * to indicate what remote branch each submodule tracks.
 	 * <p>
 	 * That field is used by "git submodule update --remote" to update
 	 * to the tip of the tracked branch when asked and by Gerrit to
 	 * update the superproject when a change on that branch is merged.
 	 * <p>
 	 * Subprojects that request a specific commit or tag will not have
 	 * a branch name recorded.
 	 * <p>
 	 * Not implemented for non-bare repositories.
 	 *
 	 * @param enable Whether to record the branch name
 	 * @return this command
 	 * @since 4.2
 	 */
 	public RepoCommand setRecordRemoteBranch(boolean enable) {
 		this.recordRemoteBranch = enable;
 		return this;
 	}
 
 	/**
 	 * Set whether the labels field should be recorded as a label in
 	 * .gitattributes.
 	 * <p>
 	 * Not implemented for non-bare repositories.
 	 *
 	 * @param enable Whether to record the labels in the .gitattributes
 	 * @return this command
 	 * @since 4.4
 	 */
 	public RepoCommand setRecordSubmoduleLabels(boolean enable) {
 		this.recordSubmoduleLabels = enable;
 		return this;
 	}
 
 	/**
 	 * Set whether the clone-depth field should be recorded as a shallow
 	 * recommendation in .gitmodules.
 	 * <p>
 	 * Not implemented for non-bare repositories.
 	 *
 	 * @param enable Whether to record the shallow recommendation.
 	 * @return this command
 	 * @since 4.4
 	 */
 	public RepoCommand setRecommendShallow(boolean enable) {
 		this.recordShallowSubmodules = enable;
 		return this;
 	}
 
 	/**
 	 * The progress monitor associated with the clone operation. By default,
 	 * this is set to <code>NullProgressMonitor</code>
 	 *
 	 * @see org.eclipse.jgit.lib.NullProgressMonitor
 	 * @param monitor
 	 *            a {@link org.eclipse.jgit.lib.ProgressMonitor}
 	 * @return this command
 	 */
 	public RepoCommand setProgressMonitor(ProgressMonitor monitor) {
 		this.monitor = monitor;
 		return this;
 	}
 
 	/**
 	 * Set whether to skip projects whose commits don't exist remotely.
 	 * <p>
 	 * When set to true, we'll just skip the manifest entry and continue
 	 * on to the next one.
 	 * <p>
 	 * When set to false (default), we'll throw an error when remote
 	 * failures occur.
 	 * <p>
 	 * Not implemented for non-bare repositories.
 	 *
 	 * @param ignore Whether to ignore the remote failures.
 	 * @return this command
 	 * @since 4.3
 	 */
 	public RepoCommand setIgnoreRemoteFailures(boolean ignore) {
 		this.ignoreRemoteFailures = ignore;
 		return this;
 	}
 
 	/**
 	 * Set the author/committer for the bare repository commit.
 	 * <p>
 	 * For non-bare repositories, the current user will be used and this will be
 	 * ignored.
 	 *
 	 * @param author
 	 *            the author's {@link org.eclipse.jgit.lib.PersonIdent}
 	 * @return this command
 	 */
 	public RepoCommand setAuthor(PersonIdent author) {
 		this.author = author;
 		return this;
 	}
 
 	/**
 	 * Set the GetHeadFromUri callback.
 	 *
 	 * This is only used in bare repositories.
 	 *
 	 * @param callback
 	 *            a {@link org.eclipse.jgit.gitrepo.RepoCommand.RemoteReader}
 	 *            object.
 	 * @return this command
 	 */
 	public RepoCommand setRemoteReader(RemoteReader callback) {
 		this.callback = callback;
 		return this;
 	}
 
 	/**
 	 * Set the IncludedFileReader callback.
 	 *
 	 * @param reader
 	 *            a
 	 *            {@link org.eclipse.jgit.gitrepo.ManifestParser.IncludedFileReader}
 	 *            object.
 	 * @return this command
 	 * @since 4.0
 	 */
 	public RepoCommand setIncludedFileReader(IncludedFileReader reader) {
 		this.includedReader = reader;
 		return this;
 	}
 
 	/** {@inheritDoc} */
 	@Override
 	public RevCommit call() throws GitAPIException {
 		checkCallable();
 		if (baseUri == null) {
 			baseUri = ""; //$NON-NLS-1$
 		}
 		if (inputStream == null) {
 			if (manifestPath == null || manifestPath.length() == 0)
 				throw new IllegalArgumentException(
 						JGitText.get().pathNotConfigured);
 			try {
 				inputStream = new FileInputStream(manifestPath);
 			} catch (IOException e) {
 				throw new IllegalArgumentException(
 						JGitText.get().pathNotConfigured);
 			}
 		}
 
 		List<RepoProject> filteredProjects;
 		try {
 			ManifestParser parser = new ManifestParser(includedReader,
 					manifestPath, branch, baseUri, groupsParam, repo);
 			parser.read(inputStream);
 			filteredProjects = parser.getFilteredProjects();
 		} catch (IOException e) {
 			throw new ManifestErrorException(e);
 		} finally {
 			try {
 				inputStream.close();
 			} catch (IOException e) {
 				// Just ignore it, it's not important.
 			}
 		}
 
 		if (repo.isBare()) {
 			if (author == null)
 				author = new PersonIdent(repo);
 			if (callback == null)
 				callback = new DefaultRemoteReader();
 			List<RepoProject> renamedProjects = renameProjects(filteredProjects);
 
 			DirCache index = DirCache.newInCore();
 			DirCacheBuilder builder = index.builder();
 			ObjectInserter inserter = repo.newObjectInserter();
 			try (RevWalkRevWalk.html#RevWalk">RevWalk rw = new RevWalk(repo)) {
 				Config cfg = new Config();
 				StringBuilder attributes = new StringBuilder();
 				for (RepoProject proj : renamedProjects) {
 					String name = proj.getName();
 					String path = proj.getPath();
 					String url = proj.getUrl();
 					ObjectId objectId;
 					if (ObjectId.isId(proj.getRevision())) {
 						objectId = ObjectId.fromString(proj.getRevision());
 					} else {
 						objectId = callback.sha1(url, proj.getRevision());
 						if (objectId == null && !ignoreRemoteFailures) {
 							throw new RemoteUnavailableException(url);
 						}
 						if (recordRemoteBranch) {
 							// can be branch or tag
 							cfg.setString("submodule", name, "branch", //$NON-NLS-1$ //$NON-NLS-2$
 									proj.getRevision());
 						}
 
 						if (recordShallowSubmodules && proj.getRecommendShallow() != null) {
 							// The shallow recommendation is losing information.
 							// As the repo manifests stores the recommended
 							// depth in the 'clone-depth' field, while
 							// git core only uses a binary 'shallow = true/false'
 							// hint, we'll map any depth to 'shallow = true'
 							cfg.setBoolean("submodule", name, "shallow", //$NON-NLS-1$ //$NON-NLS-2$
 									true);
 						}
 					}
 					if (recordSubmoduleLabels) {
 						StringBuilder rec = new StringBuilder();
 						rec.append("/"); //$NON-NLS-1$
 						rec.append(path);
 						for (String group : proj.getGroups()) {
 							rec.append(" "); //$NON-NLS-1$
 							rec.append(group);
 						}
 						rec.append("\n"); //$NON-NLS-1$
 						attributes.append(rec.toString());
 					}
 
 					URI submodUrl = URI.create(url);
 					if (targetUri != null) {
 						submodUrl = relativize(targetUri, submodUrl);
 					}
 					cfg.setString("submodule", name, "path", path); //$NON-NLS-1$ //$NON-NLS-2$
 					cfg.setString("submodule", name, "url", //$NON-NLS-1$ //$NON-NLS-2$
 							submodUrl.toString());
 
 					// create gitlink
 					if (objectId != null) {
 						DirCacheEntry dcEntry = new DirCacheEntry(path);
 						dcEntry.setObjectId(objectId);
 						dcEntry.setFileMode(FileMode.GITLINK);
 						builder.add(dcEntry);
 
 						for (CopyFile copyfile : proj.getCopyFiles()) {
 							RemoteFile rf = callback.readFileWithMode(
 								url, proj.getRevision(), copyfile.src);
 							objectId = inserter.insert(Constants.OBJ_BLOB,
 									rf.getContents());
 							dcEntry = new DirCacheEntry(copyfile.dest);
 							dcEntry.setObjectId(objectId);
 							dcEntry.setFileMode(rf.getFileMode());
 							builder.add(dcEntry);
 						}
 						for (LinkFile linkfile : proj.getLinkFiles()) {
 							String link;
 							if (linkfile.dest.contains("/")) { //$NON-NLS-1$
 								link = FileUtils.relativizeGitPath(
 									linkfile.dest.substring(0,
 										linkfile.dest.lastIndexOf('/')),
 									proj.getPath() + "/" + linkfile.src); //$NON-NLS-1$
 							} else {
 								link = proj.getPath() + "/" + linkfile.src; //$NON-NLS-1$
 							}
 
 							objectId = inserter.insert(Constants.OBJ_BLOB,
 									link.getBytes(UTF_8));
 							dcEntry = new DirCacheEntry(linkfile.dest);
 							dcEntry.setObjectId(objectId);
 							dcEntry.setFileMode(FileMode.SYMLINK);
 							builder.add(dcEntry);
 						}
 					}
 				}
 				String content = cfg.toText();
 
 				// create a new DirCacheEntry for .gitmodules file.
 				final DirCacheEntrytry.html#DirCacheEntry">DirCacheEntry dcEntry = new DirCacheEntry(Constants.DOT_GIT_MODULES);
 				ObjectId objectId = inserter.insert(Constants.OBJ_BLOB,
 						content.getBytes(UTF_8));
 				dcEntry.setObjectId(objectId);
 				dcEntry.setFileMode(FileMode.REGULAR_FILE);
 				builder.add(dcEntry);
 
 				if (recordSubmoduleLabels) {
 					// create a new DirCacheEntry for .gitattributes file.
 					final DirCacheEntryhtml#DirCacheEntry">DirCacheEntry dcEntryAttr = new DirCacheEntry(Constants.DOT_GIT_ATTRIBUTES);
 					ObjectId attrId = inserter.insert(Constants.OBJ_BLOB,
 							attributes.toString().getBytes(UTF_8));
 					dcEntryAttr.setObjectId(attrId);
 					dcEntryAttr.setFileMode(FileMode.REGULAR_FILE);
 					builder.add(dcEntryAttr);
 				}
 
 				builder.finish();
 				ObjectId treeId = index.writeTree(inserter);
 
 				// Create a Commit object, populate it and write it
 				ObjectId headId = repo.resolve(targetBranch + "^{commit}"); //$NON-NLS-1$
 				if (headId != null && rw.parseCommit(headId).getTree().getId().equals(treeId)) {
 					// No change. Do nothing.
 					return rw.parseCommit(headId);
 				}
 
 				CommitBuilder commit = new CommitBuilder();
 				commit.setTreeId(treeId);
 				if (headId != null)
 					commit.setParentIds(headId);
 				commit.setAuthor(author);
 				commit.setCommitter(author);
 				commit.setMessage(RepoText.get().repoCommitMessage);
 
 				ObjectId commitId = inserter.insert(commit);
 				inserter.flush();
 
 				RefUpdate ru = repo.updateRef(targetBranch);
 				ru.setNewObjectId(commitId);
 				ru.setExpectedOldObjectId(headId != null ? headId : ObjectId.zeroId());
 				Result rc = ru.update(rw);
 
 				switch (rc) {
 					case NEW:
 					case FORCED:
 					case FAST_FORWARD:
 						// Successful. Do nothing.
 						break;
 					case REJECTED:
 					case LOCK_FAILURE:
 						throw new ConcurrentRefUpdateException(
 								MessageFormat.format(
 										JGitText.get().cannotLock, targetBranch),
 								ru.getRef(),
 								rc);
 					default:
 						throw new JGitInternalException(MessageFormat.format(
 								JGitText.get().updatingRefFailed,
 								targetBranch, commitId.name(), rc));
 				}
 
 				return rw.parseCommit(commitId);
 			} catch (GitAPIException | IOException e) {
 				throw new ManifestErrorException(e);
 			}
 		} else {
 			try (Gitit.html#Git">Git git = new Git(repo)) {
 				for (RepoProject proj : filteredProjects) {
 					addSubmodule(proj.getName(), proj.getUrl(), proj.getPath(),
 							proj.getRevision(), proj.getCopyFiles(),
 							proj.getLinkFiles(), git);
 				}
 				return git.commit().setMessage(RepoText.get().repoCommitMessage)
 						.call();
 			} catch (GitAPIException | IOException e) {
 				throw new ManifestErrorException(e);
 			}
 		}
 	}
 
 	private void addSubmodule(String name, String url, String path,
 			String revision, List<CopyFile> copyfiles, List<LinkFile> linkfiles,
 			Git git) throws GitAPIException, IOException {
 		assert (!repo.isBare());
 		assert (git != null);
 		if (!linkfiles.isEmpty()) {
 			throw new UnsupportedOperationException(
 					JGitText.get().nonBareLinkFilesNotSupported);
 		}
 
 		SubmoduleAddCommand add = git.submoduleAdd().setName(name).setPath(path)
 				.setURI(url);
 		if (monitor != null)
 			add.setProgressMonitor(monitor);
 
 		Repository subRepo = add.call();
 		if (revision != null) {
 			try (Gitit.html#Git">Git sub = new Git(subRepo)) {
 				sub.checkout().setName(findRef(revision, subRepo)).call();
 			}
 			subRepo.close();
 			git.add().addFilepattern(path).call();
 		}
 		for (CopyFile copyfile : copyfiles) {
 			copyfile.copy();
 			git.add().addFilepattern(copyfile.dest).call();
 		}
 	}
 
 	/**
 	 * Rename the projects if there's a conflict when converted to submodules.
 	 *
 	 * @param projects
 	 *            parsed projects
 	 * @return projects that are renamed if necessary
 	 */
 	private List<RepoProject> renameProjects(List<RepoProject> projects) {
 		Map<String, List<RepoProject>> m = new TreeMap<>();
 		for (RepoProject proj : projects) {
 			List<RepoProject> l = m.get(proj.getName());
 			if (l == null) {
 				l = new ArrayList<>();
 				m.put(proj.getName(), l);
 			}
 			l.add(proj);
 		}
 
 		List<RepoProject> ret = new ArrayList<>();
 		for (List<RepoProject> ps : m.values()) {
 			boolean nameConflict = ps.size() != 1;
 			for (RepoProject proj : ps) {
 				String name = proj.getName();
 				if (nameConflict) {
 					name += SLASH + proj.getPath();
 				}
 				RepoProject p = new RepoProject(name,
 						proj.getPath(), proj.getRevision(), null,
 						proj.getGroups(), proj.getRecommendShallow());
 				p.setUrl(proj.getUrl());
 				p.addCopyFiles(proj.getCopyFiles());
 				p.addLinkFiles(proj.getLinkFiles());
 				ret.add(p);
 			}
 		}
 		return ret;
 	}
 
 	/*
 	 * Assume we are document "a/b/index.html", what should we put in a href to get to "a/" ?
 	 * Returns the child if either base or child is not a bare path. This provides a missing feature in
 	 * java.net.URI (see http://bugs.java.com/view_bug.do?bug_id=6226081).
 	 */
 	private static final String SLASH = "/"; //$NON-NLS-1$
 	static URI relativize(URI current, URI target) {
 		if (!Objects.equals(current.getHost(), target.getHost())) {
 			return target;
 		}
 
 		String cur = current.normalize().getPath();
 		String dest = target.normalize().getPath();
 
 		// TODO(hanwen): maybe (absolute, relative) should throw an exception.
 		if (cur.startsWith(SLASH) != dest.startsWith(SLASH)) {
 			return target;
 		}
 
 		while (cur.startsWith(SLASH)) {
 			cur = cur.substring(1);
 		}
 		while (dest.startsWith(SLASH)) {
 			dest = dest.substring(1);
 		}
 
 		if (cur.indexOf('/') == -1 || dest.indexOf('/') == -1) {
 			// Avoid having to special-casing in the next two ifs.
 			String prefix = "prefix/"; //$NON-NLS-1$
 			cur = prefix + cur;
 			dest = prefix + dest;
 		}
 
 		if (!cur.endsWith(SLASH)) {
 			// The current file doesn't matter.
 			int lastSlash = cur.lastIndexOf('/');
 			cur = cur.substring(0, lastSlash);
 		}
 		String destFile = ""; //$NON-NLS-1$
 		if (!dest.endsWith(SLASH)) {
 			// We always have to provide the destination file.
 			int lastSlash = dest.lastIndexOf('/');
 			destFile = dest.substring(lastSlash + 1, dest.length());
 			dest = dest.substring(0, dest.lastIndexOf('/'));
 		}
 
 		String[] cs = cur.split(SLASH);
 		String[] ds = dest.split(SLASH);
 
 		int common = 0;
 		while (common < cs.length && common < ds.length && cs[common].equals(ds[common])) {
 			common++;
 		}
 
 		StringJoiner j = new StringJoiner(SLASH);
 		for (int i = common; i < cs.length; i++) {
 			j.add(".."); //$NON-NLS-1$
 		}
 		for (int i = common; i < ds.length; i++) {
 			j.add(ds[i]);
 		}
 
 		j.add(destFile);
 		return URI.create(j.toString());
 	}
 
 	private static String findRef(String ref, Repository repo)
 			throws IOException {
 		if (!ObjectId.isId(ref)) {
 			Ref r = repo.exactRef(R_REMOTES + DEFAULT_REMOTE_NAME + "/" + ref); //$NON-NLS-1$
 			if (r != null)
 				return r.getName();
 		}
 		return ref;
 	}
 }