/*
    * Copyright (C) 2007, Dave Watson <dwatson@mimvista.com>
    * Copyright (C) 2008-2010, Google Inc.
    * Copyright (C) 2006-2010, Robin Rosenberg <robin.rosenberg@dewire.com>
    * Copyright (C) 2006-2012, Shawn O. Pearce <spearce@spearce.org>
    * Copyright (C) 2012, Daniel Megert <daniel_megert@ch.ibm.com>
    * and other copyright owners as documented in the project's IP log.
    *
    * This program and the accompanying materials are made available
   * under the terms of the Eclipse Distribution License v1.0 which
   * accompanies this distribution, is reproduced below, and is
   * available at http://www.eclipse.org/org/documents/edl-v10.php
   *
   * All rights reserved.
   *
   * Redistribution and use in source and binary forms, with or
   * without modification, are permitted provided that the following
   * conditions are met:
   *
   * - Redistributions of source code must retain the above copyright
   *   notice, this list of conditions and the following disclaimer.
   *
   * - Redistributions in binary form must reproduce the above
   *   copyright notice, this list of conditions and the following
   *   disclaimer in the documentation and/or other materials provided
   *   with the distribution.
   *
   * - Neither the name of the Eclipse Foundation, Inc. nor the
   *   names of its contributors may be used to endorse or promote
   *   products derived from this software without specific prior
   *   written permission.
   *
   * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
   * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
   * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
   * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
   * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
   * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
   * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
   * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
   * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
   * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
   * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
   * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
   * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
   */
  
  package org.eclipse.jgit.lib;
  
  import java.io.BufferedOutputStream;
  import java.io.File;
  import java.io.FileNotFoundException;
  import java.io.FileOutputStream;
  import java.io.IOException;
  import java.net.URISyntaxException;
  import java.text.MessageFormat;
  import java.util.Collection;
  import java.util.Collections;
  import java.util.HashMap;
  import java.util.HashSet;
  import java.util.LinkedList;
  import java.util.List;
  import java.util.Map;
  import java.util.Set;
  import java.util.concurrent.atomic.AtomicInteger;
  
  import org.eclipse.jgit.dircache.DirCache;
  import org.eclipse.jgit.errors.AmbiguousObjectException;
  import org.eclipse.jgit.errors.CorruptObjectException;
  import org.eclipse.jgit.errors.IncorrectObjectTypeException;
  import org.eclipse.jgit.errors.MissingObjectException;
  import org.eclipse.jgit.errors.NoWorkTreeException;
  import org.eclipse.jgit.errors.RevisionSyntaxException;
  import org.eclipse.jgit.events.IndexChangedEvent;
  import org.eclipse.jgit.events.IndexChangedListener;
  import org.eclipse.jgit.events.ListenerList;
  import org.eclipse.jgit.events.RepositoryEvent;
  import org.eclipse.jgit.internal.JGitText;
  import org.eclipse.jgit.revwalk.RevBlob;
  import org.eclipse.jgit.revwalk.RevCommit;
  import org.eclipse.jgit.revwalk.RevObject;
  import org.eclipse.jgit.revwalk.RevTree;
  import org.eclipse.jgit.revwalk.RevWalk;
  import org.eclipse.jgit.transport.RefSpec;
  import org.eclipse.jgit.transport.RemoteConfig;
  import org.eclipse.jgit.treewalk.TreeWalk;
  import org.eclipse.jgit.util.FS;
  import org.eclipse.jgit.util.FileUtils;
  import org.eclipse.jgit.util.IO;
  import org.eclipse.jgit.util.RawParseUtils;
  import org.eclipse.jgit.util.SystemReader;
  import org.eclipse.jgit.util.io.SafeBufferedOutputStream;
  
  /**
   * Represents a Git repository.
   * <p>
   * A repository holds all objects and refs used for managing source code (could
   * be any type of file, but source code is what SCM's are typically used for).
   * <p>
  * This class is thread-safe.
  */
 public abstract class Repository implements AutoCloseable {
 	private static final ListenerList globalListeners = new ListenerList();
 
 	/** @return the global listener list observing all events in this JVM. */
 	public static ListenerList getGlobalListenerList() {
 		return globalListeners;
 	}
 
 	private final AtomicInteger useCnt = new AtomicInteger(1);
 
 	/** Metadata directory holding the repository's critical files. */
 	private final File gitDir;
 
 	/** File abstraction used to resolve paths. */
 	private final FS fs;
 
 	private final ListenerList myListeners = new ListenerList();
 
 	/** If not bare, the top level directory of the working files. */
 	private final File workTree;
 
 	/** If not bare, the index file caching the working file states. */
 	private final File indexFile;
 
 	/**
 	 * Initialize a new repository instance.
 	 *
 	 * @param options
 	 *            options to configure the repository.
 	 */
 	protected Repository(final BaseRepositoryBuilder options) {
 		gitDir = options.getGitDir();
 		fs = options.getFS();
 		workTree = options.getWorkTree();
 		indexFile = options.getIndexFile();
 	}
 
 	/** @return listeners observing only events on this repository. */
 	public ListenerList getListenerList() {
 		return myListeners;
 	}
 
 	/**
 	 * Fire an event to all registered listeners.
 	 * <p>
 	 * The source repository of the event is automatically set to this
 	 * repository, before the event is delivered to any listeners.
 	 *
 	 * @param event
 	 *            the event to deliver.
 	 */
 	public void fireEvent(RepositoryEvent<?> event) {
 		event.setRepository(this);
 		myListeners.dispatch(event);
 		globalListeners.dispatch(event);
 	}
 
 	/**
 	 * Create a new Git repository.
 	 * <p>
 	 * Repository with working tree is created using this method. This method is
 	 * the same as {@code create(false)}.
 	 *
 	 * @throws IOException
 	 * @see #create(boolean)
 	 */
 	public void create() throws IOException {
 		create(false);
 	}
 
 	/**
 	 * Create a new Git repository initializing the necessary files and
 	 * directories.
 	 *
 	 * @param bare
 	 *            if true, a bare repository (a repository without a working
 	 *            directory) is created.
 	 * @throws IOException
 	 *             in case of IO problem
 	 */
 	public abstract void create(boolean bare) throws IOException;
 
 	/** @return local metadata directory; null if repository isn't local. */
 	public File getDirectory() {
 		return gitDir;
 	}
 
 	/**
 	 * @return the object database which stores this repository's data.
 	 */
 	public abstract ObjectDatabase getObjectDatabase();
 
 	/** @return a new inserter to create objects in {@link #getObjectDatabase()} */
 	public ObjectInserter newObjectInserter() {
 		return getObjectDatabase().newInserter();
 	}
 
 	/** @return a new reader to read objects from {@link #getObjectDatabase()} */
 	public ObjectReader newObjectReader() {
 		return getObjectDatabase().newReader();
 	}
 
 	/** @return the reference database which stores the reference namespace. */
 	public abstract RefDatabase getRefDatabase();
 
 	/**
 	 * @return the configuration of this repository
 	 */
 	public abstract StoredConfig getConfig();
 
 	/**
 	 * @return the used file system abstraction
 	 */
 	public FS getFS() {
 		return fs;
 	}
 
 	/**
 	 * @param objectId
 	 * @return true if the specified object is stored in this repo or any of the
 	 *         known shared repositories.
 	 */
 	public boolean hasObject(AnyObjectId objectId) {
 		try {
 			return getObjectDatabase().has(objectId);
 		} catch (IOException e) {
 			// Legacy API, assume error means "no"
 			return false;
 		}
 	}
 
 	/**
 	 * Open an object from this repository.
 	 * <p>
 	 * This is a one-shot call interface which may be faster than allocating a
 	 * {@link #newObjectReader()} to perform the lookup.
 	 *
 	 * @param objectId
 	 *            identity of the object to open.
 	 * @return a {@link ObjectLoader} for accessing the object.
 	 * @throws MissingObjectException
 	 *             the object does not exist.
 	 * @throws IOException
 	 *             the object store cannot be accessed.
 	 */
 	public ObjectLoader open(final AnyObjectId objectId)
 			throws MissingObjectException, IOException {
 		return getObjectDatabase().open(objectId);
 	}
 
 	/**
 	 * Open an object from this repository.
 	 * <p>
 	 * This is a one-shot call interface which may be faster than allocating a
 	 * {@link #newObjectReader()} to perform the lookup.
 	 *
 	 * @param objectId
 	 *            identity of the object to open.
 	 * @param typeHint
 	 *            hint about the type of object being requested, e.g.
 	 *            {@link Constants#OBJ_BLOB}; {@link ObjectReader#OBJ_ANY} if
 	 *            the object type is not known, or does not matter to the
 	 *            caller.
 	 * @return a {@link ObjectLoader} for accessing the object.
 	 * @throws MissingObjectException
 	 *             the object does not exist.
 	 * @throws IncorrectObjectTypeException
 	 *             typeHint was not OBJ_ANY, and the object's actual type does
 	 *             not match typeHint.
 	 * @throws IOException
 	 *             the object store cannot be accessed.
 	 */
 	public ObjectLoader open(AnyObjectId objectId, int typeHint)
 			throws MissingObjectException, IncorrectObjectTypeException,
 			IOException {
 		return getObjectDatabase().open(objectId, typeHint);
 	}
 
 	/**
 	 * Create a command to update, create or delete a ref in this repository.
 	 *
 	 * @param ref
 	 *            name of the ref the caller wants to modify.
 	 * @return an update command. The caller must finish populating this command
 	 *         and then invoke one of the update methods to actually make a
 	 *         change.
 	 * @throws IOException
 	 *             a symbolic ref was passed in and could not be resolved back
 	 *             to the base ref, as the symbolic ref could not be read.
 	 */
 	public RefUpdate updateRef(final String ref) throws IOException {
 		return updateRef(ref, false);
 	}
 
 	/**
 	 * Create a command to update, create or delete a ref in this repository.
 	 *
 	 * @param ref
 	 *            name of the ref the caller wants to modify.
 	 * @param detach
 	 *            true to create a detached head
 	 * @return an update command. The caller must finish populating this command
 	 *         and then invoke one of the update methods to actually make a
 	 *         change.
 	 * @throws IOException
 	 *             a symbolic ref was passed in and could not be resolved back
 	 *             to the base ref, as the symbolic ref could not be read.
 	 */
 	public RefUpdate updateRef(final String ref, final boolean detach) throws IOException {
 		return getRefDatabase().newUpdate(ref, detach);
 	}
 
 	/**
 	 * Create a command to rename a ref in this repository
 	 *
 	 * @param fromRef
 	 *            name of ref to rename from
 	 * @param toRef
 	 *            name of ref to rename to
 	 * @return an update command that knows how to rename a branch to another.
 	 * @throws IOException
 	 *             the rename could not be performed.
 	 *
 	 */
 	public RefRename renameRef(final String fromRef, final String toRef) throws IOException {
 		return getRefDatabase().newRename(fromRef, toRef);
 	}
 
 	/**
 	 * Parse a git revision string and return an object id.
 	 *
 	 * Combinations of these operators are supported:
 	 * <ul>
 	 * <li><b>HEAD</b>, <b>MERGE_HEAD</b>, <b>FETCH_HEAD</b></li>
 	 * <li><b>SHA-1</b>: a complete or abbreviated SHA-1</li>
 	 * <li><b>refs/...</b>: a complete reference name</li>
 	 * <li><b>short-name</b>: a short reference name under {@code refs/heads},
 	 * {@code refs/tags}, or {@code refs/remotes} namespace</li>
 	 * <li><b>tag-NN-gABBREV</b>: output from describe, parsed by treating
 	 * {@code ABBREV} as an abbreviated SHA-1.</li>
 	 * <li><i>id</i><b>^</b>: first parent of commit <i>id</i>, this is the same
 	 * as {@code id^1}</li>
 	 * <li><i>id</i><b>^0</b>: ensure <i>id</i> is a commit</li>
 	 * <li><i>id</i><b>^n</b>: n-th parent of commit <i>id</i></li>
 	 * <li><i>id</i><b>~n</b>: n-th historical ancestor of <i>id</i>, by first
 	 * parent. {@code id~3} is equivalent to {@code id^1^1^1} or {@code id^^^}.</li>
 	 * <li><i>id</i><b>:path</b>: Lookup path under tree named by <i>id</i></li>
 	 * <li><i>id</i><b>^{commit}</b>: ensure <i>id</i> is a commit</li>
 	 * <li><i>id</i><b>^{tree}</b>: ensure <i>id</i> is a tree</li>
 	 * <li><i>id</i><b>^{tag}</b>: ensure <i>id</i> is a tag</li>
 	 * <li><i>id</i><b>^{blob}</b>: ensure <i>id</i> is a blob</li>
 	 * </ul>
 	 *
 	 * <p>
 	 * The following operators are specified by Git conventions, but are not
 	 * supported by this method:
 	 * <ul>
 	 * <li><b>ref@{n}</b>: n-th version of ref as given by its reflog</li>
 	 * <li><b>ref@{time}</b>: value of ref at the designated time</li>
 	 * </ul>
 	 *
 	 * @param revstr
 	 *            A git object references expression
 	 * @return an ObjectId or null if revstr can't be resolved to any ObjectId
 	 * @throws AmbiguousObjectException
 	 *             {@code revstr} contains an abbreviated ObjectId and this
 	 *             repository contains more than one object which match to the
 	 *             input abbreviation.
 	 * @throws IncorrectObjectTypeException
 	 *             the id parsed does not meet the type required to finish
 	 *             applying the operators in the expression.
 	 * @throws RevisionSyntaxException
 	 *             the expression is not supported by this implementation, or
 	 *             does not meet the standard syntax.
 	 * @throws IOException
 	 *             on serious errors
 	 */
 	public ObjectId resolve(final String revstr)
 			throws AmbiguousObjectException, IncorrectObjectTypeException,
 			RevisionSyntaxException, IOException {
 		try (RevWalk rw = new RevWalk(this)) {
 			Object resolved = resolve(rw, revstr);
 			if (resolved instanceof String) {
 				final Ref ref = getRef((String)resolved);
 				return ref != null ? ref.getLeaf().getObjectId() : null;
 			} else {
 				return (ObjectId) resolved;
 			}
 		}
 	}
 
 	/**
 	 * Simplify an expression, but unlike {@link #resolve(String)} it will not
 	 * resolve a branch passed or resulting from the expression, such as @{-}.
 	 * Thus this method can be used to process an expression to a method that
 	 * expects a branch or revision id.
 	 *
 	 * @param revstr
 	 * @return object id or ref name from resolved expression
 	 * @throws AmbiguousObjectException
 	 * @throws IOException
 	 */
 	public String simplify(final String revstr)
 			throws AmbiguousObjectException, IOException {
 		try (RevWalk rw = new RevWalk(this)) {
 			Object resolved = resolve(rw, revstr);
 			if (resolved != null)
 				if (resolved instanceof String)
 					return (String) resolved;
 				else
 					return ((AnyObjectId) resolved).getName();
 			return null;
 		}
 	}
 
 	private Object resolve(final RevWalk rw, final String revstr)
 			throws IOException {
 		char[] revChars = revstr.toCharArray();
 		RevObject rev = null;
 		String name = null;
 		int done = 0;
 		for (int i = 0; i < revChars.length; ++i) {
 			switch (revChars[i]) {
 			case '^':
 				if (rev == null) {
 					if (name == null)
 						if (done == 0)
 							name = new String(revChars, done, i);
 						else {
 							done = i + 1;
 							break;
 						}
 					rev = parseSimple(rw, name);
 					name = null;
 					if (rev == null)
 						return null;
 				}
 				if (i + 1 < revChars.length) {
 					switch (revChars[i + 1]) {
 					case '0':
 					case '1':
 					case '2':
 					case '3':
 					case '4':
 					case '5':
 					case '6':
 					case '7':
 					case '8':
 					case '9':
 						int j;
 						rev = rw.parseCommit(rev);
 						for (j = i + 1; j < revChars.length; ++j) {
 							if (!Character.isDigit(revChars[j]))
 								break;
 						}
 						String parentnum = new String(revChars, i + 1, j - i
 								- 1);
 						int pnum;
 						try {
 							pnum = Integer.parseInt(parentnum);
 						} catch (NumberFormatException e) {
 							throw new RevisionSyntaxException(
 									JGitText.get().invalidCommitParentNumber,
 									revstr);
 						}
 						if (pnum != 0) {
 							RevCommit commit = (RevCommit) rev;
 							if (pnum > commit.getParentCount())
 								rev = null;
 							else
 								rev = commit.getParent(pnum - 1);
 						}
 						i = j - 1;
 						done = j;
 						break;
 					case '{':
 						int k;
 						String item = null;
 						for (k = i + 2; k < revChars.length; ++k) {
 							if (revChars[k] == '}') {
 								item = new String(revChars, i + 2, k - i - 2);
 								break;
 							}
 						}
 						i = k;
 						if (item != null)
 							if (item.equals("tree")) { //$NON-NLS-1$
 								rev = rw.parseTree(rev);
 							} else if (item.equals("commit")) { //$NON-NLS-1$
 								rev = rw.parseCommit(rev);
 							} else if (item.equals("blob")) { //$NON-NLS-1$
 								rev = rw.peel(rev);
 								if (!(rev instanceof RevBlob))
 									throw new IncorrectObjectTypeException(rev,
 											Constants.TYPE_BLOB);
 							} else if (item.equals("")) { //$NON-NLS-1$
 								rev = rw.peel(rev);
 							} else
 								throw new RevisionSyntaxException(revstr);
 						else
 							throw new RevisionSyntaxException(revstr);
 						done = k;
 						break;
 					default:
 						rev = rw.peel(rev);
 						if (rev instanceof RevCommit) {
 							RevCommit commit = ((RevCommit) rev);
 							if (commit.getParentCount() == 0)
 								rev = null;
 							else
 								rev = commit.getParent(0);
 						} else
 							throw new IncorrectObjectTypeException(rev,
 									Constants.TYPE_COMMIT);
 					}
 				} else {
 					rev = rw.peel(rev);
 					if (rev instanceof RevCommit) {
 						RevCommit commit = ((RevCommit) rev);
 						if (commit.getParentCount() == 0)
 							rev = null;
 						else
 							rev = commit.getParent(0);
 					} else
 						throw new IncorrectObjectTypeException(rev,
 								Constants.TYPE_COMMIT);
 				}
 				done = i + 1;
 				break;
 			case '~':
 				if (rev == null) {
 					if (name == null)
 						if (done == 0)
 							name = new String(revChars, done, i);
 						else {
 							done = i + 1;
 							break;
 						}
 					rev = parseSimple(rw, name);
 					name = null;
 					if (rev == null)
 						return null;
 				}
 				rev = rw.peel(rev);
 				if (!(rev instanceof RevCommit))
 					throw new IncorrectObjectTypeException(rev,
 							Constants.TYPE_COMMIT);
 				int l;
 				for (l = i + 1; l < revChars.length; ++l) {
 					if (!Character.isDigit(revChars[l]))
 						break;
 				}
 				int dist;
 				if (l - i > 1) {
 					String distnum = new String(revChars, i + 1, l - i - 1);
 					try {
 						dist = Integer.parseInt(distnum);
 					} catch (NumberFormatException e) {
 						throw new RevisionSyntaxException(
 								JGitText.get().invalidAncestryLength, revstr);
 					}
 				} else
 					dist = 1;
 				while (dist > 0) {
 					RevCommit commit = (RevCommit) rev;
 					if (commit.getParentCount() == 0) {
 						rev = null;
 						break;
 					}
 					commit = commit.getParent(0);
 					rw.parseHeaders(commit);
 					rev = commit;
 					--dist;
 				}
 				i = l - 1;
 				done = l;
 				break;
 			case '@':
 				if (rev != null)
 					throw new RevisionSyntaxException(revstr);
 				if (i + 1 < revChars.length && revChars[i + 1] != '{')
 					continue;
 				int m;
 				String time = null;
 				for (m = i + 2; m < revChars.length; ++m) {
 					if (revChars[m] == '}') {
 						time = new String(revChars, i + 2, m - i - 2);
 						break;
 					}
 				}
 				if (time != null) {
 					if (time.equals("upstream")) { //$NON-NLS-1$
 						if (name == null)
 							name = new String(revChars, done, i);
 						if (name.equals("")) //$NON-NLS-1$
 							// Currently checked out branch, HEAD if
 							// detached
 							name = Constants.HEAD;
 						if (!Repository.isValidRefName("x/" + name)) //$NON-NLS-1$
 							throw new RevisionSyntaxException(revstr);
 						Ref ref = getRef(name);
 						name = null;
 						if (ref == null)
 							return null;
 						if (ref.isSymbolic())
 							ref = ref.getLeaf();
 						name = ref.getName();
 
 						RemoteConfig remoteConfig;
 						try {
 							remoteConfig = new RemoteConfig(getConfig(),
 									"origin"); //$NON-NLS-1$
 						} catch (URISyntaxException e) {
 							throw new RevisionSyntaxException(revstr);
 						}
 						String remoteBranchName = getConfig()
 								.getString(
 										ConfigConstants.CONFIG_BRANCH_SECTION,
 								Repository.shortenRefName(ref.getName()),
 										ConfigConstants.CONFIG_KEY_MERGE);
 						List<RefSpec> fetchRefSpecs = remoteConfig
 								.getFetchRefSpecs();
 						for (RefSpec refSpec : fetchRefSpecs) {
 							if (refSpec.matchSource(remoteBranchName)) {
 								RefSpec expandFromSource = refSpec
 										.expandFromSource(remoteBranchName);
 								name = expandFromSource.getDestination();
 								break;
 							}
 						}
 						if (name == null)
 							throw new RevisionSyntaxException(revstr);
 					} else if (time.matches("^-\\d+$")) { //$NON-NLS-1$
 						if (name != null)
 							throw new RevisionSyntaxException(revstr);
 						else {
 							String previousCheckout = resolveReflogCheckout(-Integer
 									.parseInt(time));
 							if (ObjectId.isId(previousCheckout))
 								rev = parseSimple(rw, previousCheckout);
 							else
 								name = previousCheckout;
 						}
 					} else {
 						if (name == null)
 							name = new String(revChars, done, i);
 						if (name.equals("")) //$NON-NLS-1$
 							name = Constants.HEAD;
 						if (!Repository.isValidRefName("x/" + name)) //$NON-NLS-1$
 							throw new RevisionSyntaxException(revstr);
 						Ref ref = getRef(name);
 						name = null;
 						if (ref == null)
 							return null;
 						// @{n} means current branch, not HEAD@{1} unless
 						// detached
 						if (ref.isSymbolic())
 							ref = ref.getLeaf();
 						rev = resolveReflog(rw, ref, time);
 					}
 					i = m;
 				} else
 					throw new RevisionSyntaxException(revstr);
 				break;
 			case ':': {
 				RevTree tree;
 				if (rev == null) {
 					if (name == null)
 						name = new String(revChars, done, i);
 					if (name.equals("")) //$NON-NLS-1$
 						name = Constants.HEAD;
 					rev = parseSimple(rw, name);
 					name = null;
 				}
 				if (rev == null)
 					return null;
 				tree = rw.parseTree(rev);
 				if (i == revChars.length - 1)
 					return tree.copy();
 
 				TreeWalk tw = TreeWalk.forPath(rw.getObjectReader(),
 						new String(revChars, i + 1, revChars.length - i - 1),
 						tree);
 				return tw != null ? tw.getObjectId(0) : null;
 			}
 			default:
 				if (rev != null)
 					throw new RevisionSyntaxException(revstr);
 			}
 		}
 		if (rev != null)
 			return rev.copy();
 		if (name != null)
 			return name;
 		if (done == revstr.length())
 			return null;
 		name = revstr.substring(done);
 		if (!Repository.isValidRefName("x/" + name)) //$NON-NLS-1$
 			throw new RevisionSyntaxException(revstr);
 		if (getRef(name) != null)
 			return name;
 		return resolveSimple(name);
 	}
 
 	private static boolean isHex(char c) {
 		return ('0' <= c && c <= '9') //
 				|| ('a' <= c && c <= 'f') //
 				|| ('A' <= c && c <= 'F');
 	}
 
 	private static boolean isAllHex(String str, int ptr) {
 		while (ptr < str.length()) {
 			if (!isHex(str.charAt(ptr++)))
 				return false;
 		}
 		return true;
 	}
 
 	private RevObject parseSimple(RevWalk rw, String revstr) throws IOException {
 		ObjectId id = resolveSimple(revstr);
 		return id != null ? rw.parseAny(id) : null;
 	}
 
 	private ObjectId resolveSimple(final String revstr) throws IOException {
 		if (ObjectId.isId(revstr))
 			return ObjectId.fromString(revstr);
 
 		if (Repository.isValidRefName("x/" + revstr)) { //$NON-NLS-1$
 			Ref r = getRefDatabase().getRef(revstr);
 			if (r != null)
 				return r.getObjectId();
 		}
 
 		if (AbbreviatedObjectId.isId(revstr))
 			return resolveAbbreviation(revstr);
 
 		int dashg = revstr.indexOf("-g"); //$NON-NLS-1$
 		if ((dashg + 5) < revstr.length() && 0 <= dashg
 				&& isHex(revstr.charAt(dashg + 2))
 				&& isHex(revstr.charAt(dashg + 3))
 				&& isAllHex(revstr, dashg + 4)) {
 			// Possibly output from git describe?
 			String s = revstr.substring(dashg + 2);
 			if (AbbreviatedObjectId.isId(s))
 				return resolveAbbreviation(s);
 		}
 
 		return null;
 	}
 
 	private String resolveReflogCheckout(int checkoutNo)
 			throws IOException {
 		ReflogReader reader = getReflogReader(Constants.HEAD);
 		if (reader == null) {
 			return null;
 		}
 		List<ReflogEntry> reflogEntries = reader.getReverseEntries();
 		for (ReflogEntry entry : reflogEntries) {
 			CheckoutEntry checkout = entry.parseCheckout();
 			if (checkout != null)
 				if (checkoutNo-- == 1)
 					return checkout.getFromBranch();
 		}
 		return null;
 	}
 
 	private RevCommit resolveReflog(RevWalk rw, Ref ref, String time)
 			throws IOException {
 		int number;
 		try {
 			number = Integer.parseInt(time);
 		} catch (NumberFormatException nfe) {
 			throw new RevisionSyntaxException(MessageFormat.format(
 					JGitText.get().invalidReflogRevision, time));
 		}
 		assert number >= 0;
 		ReflogReader reader = getReflogReader(ref.getName());
 		if (reader == null) {
 			throw new RevisionSyntaxException(
 					MessageFormat.format(JGitText.get().reflogEntryNotFound,
 							Integer.valueOf(number), ref.getName()));
 		}
 		ReflogEntry entry = reader.getReverseEntry(number);
 		if (entry == null)
 			throw new RevisionSyntaxException(MessageFormat.format(
 					JGitText.get().reflogEntryNotFound,
 					Integer.valueOf(number), ref.getName()));
 
 		return rw.parseCommit(entry.getNewId());
 	}
 
 	private ObjectId resolveAbbreviation(final String revstr) throws IOException,
 			AmbiguousObjectException {
 		AbbreviatedObjectId id = AbbreviatedObjectId.fromString(revstr);
 		try (ObjectReader reader = newObjectReader()) {
 			Collection<ObjectId> matches = reader.resolve(id);
 			if (matches.size() == 0)
 				return null;
 			else if (matches.size() == 1)
 				return matches.iterator().next();
 			else
 				throw new AmbiguousObjectException(id, matches);
 		}
 	}
 
 	/** Increment the use counter by one, requiring a matched {@link #close()}. */
 	public void incrementOpen() {
 		useCnt.incrementAndGet();
 	}
 
 	/** Decrement the use count, and maybe close resources. */
 	public void close() {
 		if (useCnt.decrementAndGet() == 0) {
 			doClose();
 		}
 	}
 
 	/**
 	 * Invoked when the use count drops to zero during {@link #close()}.
 	 * <p>
 	 * The default implementation closes the object and ref databases.
 	 */
 	protected void doClose() {
 		getObjectDatabase().close();
 		getRefDatabase().close();
 	}
 
 	@SuppressWarnings("nls")
 	public String toString() {
 		String desc;
 		if (getDirectory() != null)
 			desc = getDirectory().getPath();
 		else
 			desc = getClass().getSimpleName() + "-" //$NON-NLS-1$
 					+ System.identityHashCode(this);
 		return "Repository[" + desc + "]"; //$NON-NLS-1$
 	}
 
 	/**
 	 * Get the name of the reference that {@code HEAD} points to.
 	 * <p>
 	 * This is essentially the same as doing:
 	 *
 	 * <pre>
 	 * return getRef(Constants.HEAD).getTarget().getName()
 	 * </pre>
 	 *
 	 * Except when HEAD is detached, in which case this method returns the
 	 * current ObjectId in hexadecimal string format.
 	 *
 	 * @return name of current branch (for example {@code refs/heads/master}) or
 	 *         an ObjectId in hex format if the current branch is detached.
 	 * @throws IOException
 	 */
 	public String getFullBranch() throws IOException {
 		Ref head = getRef(Constants.HEAD);
 		if (head == null)
 			return null;
 		if (head.isSymbolic())
 			return head.getTarget().getName();
 		if (head.getObjectId() != null)
 			return head.getObjectId().name();
 		return null;
 	}
 
 	/**
 	 * Get the short name of the current branch that {@code HEAD} points to.
 	 * <p>
 	 * This is essentially the same as {@link #getFullBranch()}, except the
 	 * leading prefix {@code refs/heads/} is removed from the reference before
 	 * it is returned to the caller.
 	 *
 	 * @return name of current branch (for example {@code master}), or an
 	 *         ObjectId in hex format if the current branch is detached.
 	 * @throws IOException
 	 */
 	public String getBranch() throws IOException {
 		String name = getFullBranch();
 		if (name != null)
 			return shortenRefName(name);
 		return name;
 	}
 
 	/**
 	 * Objects known to exist but not expressed by {@link #getAllRefs()}.
 	 * <p>
 	 * When a repository borrows objects from another repository, it can
 	 * advertise that it safely has that other repository's references, without
 	 * exposing any other details about the other repository.  This may help
 	 * a client trying to push changes avoid pushing more than it needs to.
 	 *
 	 * @return unmodifiable collection of other known objects.
 	 */
 	public Set<ObjectId> getAdditionalHaves() {
 		return Collections.emptySet();
 	}
 
 	/**
 	 * Get a ref by name.
 	 *
 	 * @param name
 	 *            the name of the ref to lookup. May be a short-hand form, e.g.
 	 *            "master" which is is automatically expanded to
 	 *            "refs/heads/master" if "refs/heads/master" already exists.
 	 * @return the Ref with the given name, or null if it does not exist
 	 * @throws IOException
 	 */
 	public Ref getRef(final String name) throws IOException {
 		return getRefDatabase().getRef(name);
 	}
 
 	/**
 	 * @return mutable map of all known refs (heads, tags, remotes).
 	 */
 	public Map<String, Ref> getAllRefs() {
 		try {
 			return getRefDatabase().getRefs(RefDatabase.ALL);
 		} catch (IOException e) {
 			return new HashMap<String, Ref>();
 		}
 	}
 
 	/**
 	 * @return mutable map of all tags; key is short tag name ("v1.0") and value
 	 *         of the entry contains the ref with the full tag name
 	 *         ("refs/tags/v1.0").
 	 */
 	public Map<String, Ref> getTags() {
 		try {
 			return getRefDatabase().getRefs(Constants.R_TAGS);
 		} catch (IOException e) {
 			return new HashMap<String, Ref>();
 		}
 	}
 
 	/**
 	 * Peel a possibly unpeeled reference to an annotated tag.
 	 * <p>
 	 * If the ref cannot be peeled (as it does not refer to an annotated tag)
 	 * the peeled id stays null, but {@link Ref#isPeeled()} will be true.
 	 *
 	 * @param ref
 	 *            The ref to peel
 	 * @return <code>ref</code> if <code>ref.isPeeled()</code> is true; else a
 	 *         new Ref object representing the same data as Ref, but isPeeled()
 	 *         will be true and getPeeledObjectId will contain the peeled object
 	 *         (or null).
 	 */
 	public Ref peel(final Ref ref) {
 		try {
 			return getRefDatabase().peel(ref);
 		} catch (IOException e) {
 			// Historical accident; if the reference cannot be peeled due
 			// to some sort of repository access problem we claim that the
 			// same as if the reference was not an annotated tag.
 			return ref;
 		}
 	}
 
 	/**
 	 * @return a map with all objects referenced by a peeled ref.
 	 */
 	public Map<AnyObjectId, Set<Ref>> getAllRefsByPeeledObjectId() {
 		Map<String, Ref> allRefs = getAllRefs();
 		Map<AnyObjectId, Set<Ref>> ret = new HashMap<AnyObjectId, Set<Ref>>(allRefs.size());
 		for (Ref ref : allRefs.values()) {
 			ref = peel(ref);
 			AnyObjectId target = ref.getPeeledObjectId();
 			if (target == null)
 				target = ref.getObjectId();
 			// We assume most Sets here are singletons
 			Set<Ref> oset = ret.put(target, Collections.singleton(ref));
 			if (oset != null) {
 				// that was not the case (rare)
 				if (oset.size() == 1) {
 					// Was a read-only singleton, we must copy to a new Set
 					oset = new HashSet<Ref>(oset);
 				}
 				ret.put(target, oset);
 				oset.add(ref);
 			}
 		}
 		return ret;
 	}
 
 	/**
 	 * @return the index file location
 	 * @throws NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
 	public File getIndexFile() throws NoWorkTreeException {
 		if (isBare())
 			throw new NoWorkTreeException();
 		return indexFile;
 	}
 
 	/**
 	 * Create a new in-core index representation and read an index from disk.
 	 * <p>
 	 * The new index will be read before it is returned to the caller. Read
 	 * failures are reported as exceptions and therefore prevent the method from
 	 * returning a partially populated index.
 	 *
 	 * @return a cache representing the contents of the specified index file (if
 	 *         it exists) or an empty cache if the file does not exist.
 	 * @throws NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 * @throws IOException
 	 *             the index file is present but could not be read.
 	 * @throws CorruptObjectException
 	 *             the index file is using a format or extension that this
 	 *             library does not support.
 	 */
 	public DirCache readDirCache() throws NoWorkTreeException,
 			CorruptObjectException, IOException {
 		return DirCache.read(this);
 	}
 
 	/**
 	 * Create a new in-core index representation, lock it, and read from disk.
 	 * <p>
 	 * The new index will be locked and then read before it is returned to the
 	 * caller. Read failures are reported as exceptions and therefore prevent
 	 * the method from returning a partially populated index.
 	 *
 	 * @return a cache representing the contents of the specified index file (if
 	 *         it exists) or an empty cache if the file does not exist.
 	 * @throws NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 * @throws IOException
 	 *             the index file is present but could not be read, or the lock
 	 *             could not be obtained.
 	 * @throws CorruptObjectException
 	 *             the index file is using a format or extension that this
 	 *             library does not support.
 	 */
 	public DirCache lockDirCache() throws NoWorkTreeException,
 			CorruptObjectException, IOException {
 		// we want DirCache to inform us so that we can inform registered
 		// listeners about index changes
 		IndexChangedListener l = new IndexChangedListener() {
 
 			public void onIndexChanged(IndexChangedEvent event) {
 				notifyIndexChanged();
 			}
 		};
 		return DirCache.lock(this, l);
 	}
 
 	static byte[] gitInternalSlash(byte[] bytes) {
 		if (File.separatorChar == '/')
 			return bytes;
 		for (int i=0; i<bytes.length; ++i)
 			if (bytes[i] == File.separatorChar)
 				bytes[i] = '/';
 		return bytes;
 	}
 
 	/**
 	 * @return an important state
 	 */
 	public RepositoryState getRepositoryState() {
 		if (isBare() || getDirectory() == null)
 			return RepositoryState.BARE;
 
 		// Pre Git-1.6 logic
 		if (new File(getWorkTree(), ".dotest").exists()) //$NON-NLS-1$
 			return RepositoryState.REBASING;
 		if (new File(getDirectory(), ".dotest-merge").exists()) //$NON-NLS-1$
 			return RepositoryState.REBASING_INTERACTIVE;
 
 		// From 1.6 onwards
 		if (new File(getDirectory(),"rebase-apply/rebasing").exists()) //$NON-NLS-1$
 			return RepositoryState.REBASING_REBASING;
 		if (new File(getDirectory(),"rebase-apply/applying").exists()) //$NON-NLS-1$
 			return RepositoryState.APPLY;
 		if (new File(getDirectory(),"rebase-apply").exists()) //$NON-NLS-1$
 			return RepositoryState.REBASING;
 
 		if (new File(getDirectory(),"rebase-merge/interactive").exists()) //$NON-NLS-1$
 			return RepositoryState.REBASING_INTERACTIVE;
 		if (new File(getDirectory(),"rebase-merge").exists()) //$NON-NLS-1$
 			return RepositoryState.REBASING_MERGE;
 
 		// Both versions
 		if (new File(getDirectory(), Constants.MERGE_HEAD).exists()) {
 			// we are merging - now check whether we have unmerged paths
 			try {
 				if (!readDirCache().hasUnmergedPaths()) {
 					// no unmerged paths -> return the MERGING_RESOLVED state
 					return RepositoryState.MERGING_RESOLVED;
 				}
 			} catch (IOException e) {
 				// Can't decide whether unmerged paths exists. Return
 				// MERGING state to be on the safe side (in state MERGING
 				// you are not allow to do anything)
 			}
 			return RepositoryState.MERGING;
 		}
 
 		if (new File(getDirectory(), "BISECT_LOG").exists()) //$NON-NLS-1$
 			return RepositoryState.BISECTING;
 
 		if (new File(getDirectory(), Constants.CHERRY_PICK_HEAD).exists()) {
 			try {
 				if (!readDirCache().hasUnmergedPaths()) {
 					// no unmerged paths
 					return RepositoryState.CHERRY_PICKING_RESOLVED;
 				}
 			} catch (IOException e) {
 				// fall through to CHERRY_PICKING
 			}
 
 			return RepositoryState.CHERRY_PICKING;
 		}
 
 		if (new File(getDirectory(), Constants.REVERT_HEAD).exists()) {
 			try {
 				if (!readDirCache().hasUnmergedPaths()) {
 					// no unmerged paths
 					return RepositoryState.REVERTING_RESOLVED;
 				}
 			} catch (IOException e) {
 				// fall through to REVERTING
 			}
 
 			return RepositoryState.REVERTING;
 		}
 
 		return RepositoryState.SAFE;
 	}
 
 	/**
 	 * Check validity of a ref name. It must not contain character that has
 	 * a special meaning in a Git object reference expression. Some other
 	 * dangerous characters are also excluded.
 	 *
 	 * For portability reasons '\' is excluded
 	 *
 	 * @param refName
 	 *
 	 * @return true if refName is a valid ref name
 	 */
 	public static boolean isValidRefName(final String refName) {
 		final int len = refName.length();
 		if (len == 0)
 			return false;
 		if (refName.endsWith(".lock")) //$NON-NLS-1$
 			return false;
 
 		// Refs may be stored as loose files so invalid paths
 		// on the local system must also be invalid refs.
 		try {
 			SystemReader.getInstance().checkPath(refName);
 		} catch (CorruptObjectException e) {
 			return false;
 		}
 
 		int components = 1;
 		char p = '\0';
 		for (int i = 0; i < len; i++) {
 			final char c = refName.charAt(i);
 			if (c <= ' ')
 				return false;
 			switch (c) {
 			case '.':
 				switch (p) {
 				case '\0': case '/': case '.':
 					return false;
 				}
 				if (i == len -1)
 					return false;
 				break;
 			case '/':
 				if (i == 0 || i == len - 1)
 					return false;
 				if (p == '/')
 					return false;
 				components++;
 				break;
 			case '{':
 				if (p == '@')
 					return false;
 				break;
 			case '~': case '^': case ':':
 			case '?': case '[': case '*':
 			case '\\':
 			case '\u007F':
 				return false;
 			}
 			p = c;
 		}
 		return components > 1;
 	}
 
 	/**
 	 * Strip work dir and return normalized repository path.
 	 *
 	 * @param workDir Work dir
 	 * @param file File whose path shall be stripped of its workdir
 	 * @return normalized repository relative path or the empty
 	 *         string if the file is not relative to the work directory.
 	 */
 	public static String stripWorkDir(File workDir, File file) {
 		final String filePath = file.getPath();
 		final String workDirPath = workDir.getPath();
 
 		if (filePath.length() <= workDirPath.length() ||
 		    filePath.charAt(workDirPath.length()) != File.separatorChar ||
 		    !filePath.startsWith(workDirPath)) {
 			File absWd = workDir.isAbsolute() ? workDir : workDir.getAbsoluteFile();
 			File absFile = file.isAbsolute() ? file : file.getAbsoluteFile();
 			if (absWd == workDir && absFile == file)
 				return ""; //$NON-NLS-1$
 			return stripWorkDir(absWd, absFile);
 		}
 
 		String relName = filePath.substring(workDirPath.length() + 1);
 		if (File.separatorChar != '/')
 			relName = relName.replace(File.separatorChar, '/');
 		return relName;
 	}
 
 	/**
 	 * @return true if this is bare, which implies it has no working directory.
 	 */
 	public boolean isBare() {
 		return workTree == null;
 	}
 
 	/**
 	 * @return the root directory of the working tree, where files are checked
 	 *         out for viewing and editing.
 	 * @throws NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
 	public File getWorkTree() throws NoWorkTreeException {
 		if (isBare())
 			throw new NoWorkTreeException();
 		return workTree;
 	}
 
 	/**
 	 * Force a scan for changed refs.
 	 *
 	 * @throws IOException
 	 */
 	public abstract void scanForRepoChanges() throws IOException;
 
 	/**
 	 * Notify that the index changed
 	 */
 	public abstract void notifyIndexChanged();
 
 	/**
 	 * @param refName
 	 *
 	 * @return a more user friendly ref name
 	 */
 	public static String shortenRefName(String refName) {
 		if (refName.startsWith(Constants.R_HEADS))
 			return refName.substring(Constants.R_HEADS.length());
 		if (refName.startsWith(Constants.R_TAGS))
 			return refName.substring(Constants.R_TAGS.length());
 		if (refName.startsWith(Constants.R_REMOTES))
 			return refName.substring(Constants.R_REMOTES.length());
 		return refName;
 	}
 
 	/**
 	 * @param refName
 	 * @return the remote branch name part of <code>refName</code>, i.e. without
 	 *         the <code>refs/remotes/&lt;remote&gt;</code> prefix, if
 	 *         <code>refName</code> represents a remote tracking branch;
 	 *         otherwise null.
 	 * @since 3.4
 	 */
 	public String shortenRemoteBranchName(String refName) {
 		for (String remote : getRemoteNames()) {
 			String remotePrefix = Constants.R_REMOTES + remote + "/"; //$NON-NLS-1$
 			if (refName.startsWith(remotePrefix))
 				return refName.substring(remotePrefix.length());
 		}
 		return null;
 	}
 
 	/**
 	 * @param refName
 	 * @return the remote name part of <code>refName</code>, i.e. without the
 	 *         <code>refs/remotes/&lt;remote&gt;</code> prefix, if
 	 *         <code>refName</code> represents a remote tracking branch;
 	 *         otherwise null.
 	 * @since 3.4
 	 */
 	public String getRemoteName(String refName) {
 		for (String remote : getRemoteNames()) {
 			String remotePrefix = Constants.R_REMOTES + remote + "/"; //$NON-NLS-1$
 			if (refName.startsWith(remotePrefix))
 				return remote;
 		}
 		return null;
 	}
 
 	/**
 	 * @param refName
 	 * @return a {@link ReflogReader} for the supplied refname, or null if the
 	 *         named ref does not exist.
 	 * @throws IOException
 	 *             the ref could not be accessed.
 	 * @since 3.0
 	 */
 	public abstract ReflogReader getReflogReader(String refName)
 			throws IOException;
 
 	/**
 	 * Return the information stored in the file $GIT_DIR/MERGE_MSG. In this
 	 * file operations triggering a merge will store a template for the commit
 	 * message of the merge commit.
 	 *
 	 * @return a String containing the content of the MERGE_MSG file or
 	 *         {@code null} if this file doesn't exist
 	 * @throws IOException
 	 * @throws NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
 	public String readMergeCommitMsg() throws IOException, NoWorkTreeException {
 		return readCommitMsgFile(Constants.MERGE_MSG);
 	}
 
 	/**
 	 * Write new content to the file $GIT_DIR/MERGE_MSG. In this file operations
 	 * triggering a merge will store a template for the commit message of the
 	 * merge commit. If <code>null</code> is specified as message the file will
 	 * be deleted.
 	 *
 	 * @param msg
 	 *            the message which should be written or <code>null</code> to
 	 *            delete the file
 	 *
 	 * @throws IOException
 	 */
 	public void writeMergeCommitMsg(String msg) throws IOException {
 		File mergeMsgFile = new File(gitDir, Constants.MERGE_MSG);
 		writeCommitMsg(mergeMsgFile, msg);
 	}
 
 	/**
 	 * Return the information stored in the file $GIT_DIR/COMMIT_EDITMSG. In
 	 * this file hooks triggered by an operation may read or modify the current
 	 * commit message.
 	 *
 	 * @return a String containing the content of the COMMIT_EDITMSG file or
 	 *         {@code null} if this file doesn't exist
 	 * @throws IOException
 	 * @throws NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 * @since 4.0
 	 */
 	public String readCommitEditMsg() throws IOException, NoWorkTreeException {
 		return readCommitMsgFile(Constants.COMMIT_EDITMSG);
 	}
 
 	/**
 	 * Write new content to the file $GIT_DIR/COMMIT_EDITMSG. In this file hooks
 	 * triggered by an operation may read or modify the current commit message.
 	 * If {@code null} is specified as message the file will be deleted.
 	 *
 	 * @param msg
 	 *            the message which should be written or {@code null} to delete
 	 *            the file
 	 *
 	 * @throws IOException
 	 * @since 4.0
 	 */
 	public void writeCommitEditMsg(String msg) throws IOException {
 		File commiEditMsgFile = new File(gitDir, Constants.COMMIT_EDITMSG);
 		writeCommitMsg(commiEditMsgFile, msg);
 	}
 
 	/**
 	 * Return the information stored in the file $GIT_DIR/MERGE_HEAD. In this
 	 * file operations triggering a merge will store the IDs of all heads which
 	 * should be merged together with HEAD.
 	 *
 	 * @return a list of commits which IDs are listed in the MERGE_HEAD file or
 	 *         {@code null} if this file doesn't exist. Also if the file exists
 	 *         but is empty {@code null} will be returned
 	 * @throws IOException
 	 * @throws NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
 	public List<ObjectId> readMergeHeads() throws IOException, NoWorkTreeException {
 		if (isBare() || getDirectory() == null)
 			throw new NoWorkTreeException();
 
 		byte[] raw = readGitDirectoryFile(Constants.MERGE_HEAD);
 		if (raw == null)
 			return null;
 
 		LinkedList<ObjectId> heads = new LinkedList<ObjectId>();
 		for (int p = 0; p < raw.length;) {
 			heads.add(ObjectId.fromString(raw, p));
 			p = RawParseUtils
 					.nextLF(raw, p + Constants.OBJECT_ID_STRING_LENGTH);
 		}
 		return heads;
 	}
 
 	/**
 	 * Write new merge-heads into $GIT_DIR/MERGE_HEAD. In this file operations
 	 * triggering a merge will store the IDs of all heads which should be merged
 	 * together with HEAD. If <code>null</code> is specified as list of commits
 	 * the file will be deleted
 	 *
 	 * @param heads
 	 *            a list of commits which IDs should be written to
 	 *            $GIT_DIR/MERGE_HEAD or <code>null</code> to delete the file
 	 * @throws IOException
 	 */
 	public void writeMergeHeads(List<? extends ObjectId> heads) throws IOException {
 		writeHeadsFile(heads, Constants.MERGE_HEAD);
 	}
 
 	/**
 	 * Return the information stored in the file $GIT_DIR/CHERRY_PICK_HEAD.
 	 *
 	 * @return object id from CHERRY_PICK_HEAD file or {@code null} if this file
 	 *         doesn't exist. Also if the file exists but is empty {@code null}
 	 *         will be returned
 	 * @throws IOException
 	 * @throws NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
 	public ObjectId readCherryPickHead() throws IOException,
 			NoWorkTreeException {
 		if (isBare() || getDirectory() == null)
 			throw new NoWorkTreeException();
 
 		byte[] raw = readGitDirectoryFile(Constants.CHERRY_PICK_HEAD);
 		if (raw == null)
 			return null;
 
 		return ObjectId.fromString(raw, 0);
 	}
 
 	/**
 	 * Return the information stored in the file $GIT_DIR/REVERT_HEAD.
 	 *
 	 * @return object id from REVERT_HEAD file or {@code null} if this file
 	 *         doesn't exist. Also if the file exists but is empty {@code null}
 	 *         will be returned
 	 * @throws IOException
 	 * @throws NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
 	public ObjectId readRevertHead() throws IOException, NoWorkTreeException {
 		if (isBare() || getDirectory() == null)
 			throw new NoWorkTreeException();
 
 		byte[] raw = readGitDirectoryFile(Constants.REVERT_HEAD);
 		if (raw == null)
 			return null;
 		return ObjectId.fromString(raw, 0);
 	}
 
 	/**
 	 * Write cherry pick commit into $GIT_DIR/CHERRY_PICK_HEAD. This is used in
 	 * case of conflicts to store the cherry which was tried to be picked.
 	 *
 	 * @param head
 	 *            an object id of the cherry commit or <code>null</code> to
 	 *            delete the file
 	 * @throws IOException
 	 */
 	public void writeCherryPickHead(ObjectId head) throws IOException {
 		List<ObjectId> heads = (head != null) ? Collections.singletonList(head)
 				: null;
 		writeHeadsFile(heads, Constants.CHERRY_PICK_HEAD);
 	}
 
 	/**
 	 * Write revert commit into $GIT_DIR/REVERT_HEAD. This is used in case of
 	 * conflicts to store the revert which was tried to be picked.
 	 *
 	 * @param head
 	 *            an object id of the revert commit or <code>null</code> to
 	 *            delete the file
 	 * @throws IOException
 	 */
 	public void writeRevertHead(ObjectId head) throws IOException {
 		List<ObjectId> heads = (head != null) ? Collections.singletonList(head)
 				: null;
 		writeHeadsFile(heads, Constants.REVERT_HEAD);
 	}
 
 	/**
 	 * Write original HEAD commit into $GIT_DIR/ORIG_HEAD.
 	 *
 	 * @param head
 	 *            an object id of the original HEAD commit or <code>null</code>
 	 *            to delete the file
 	 * @throws IOException
 	 */
 	public void writeOrigHead(ObjectId head) throws IOException {
 		List<ObjectId> heads = head != null ? Collections.singletonList(head)
 				: null;
 		writeHeadsFile(heads, Constants.ORIG_HEAD);
 	}
 
 	/**
 	 * Return the information stored in the file $GIT_DIR/ORIG_HEAD.
 	 *
 	 * @return object id from ORIG_HEAD file or {@code null} if this file
 	 *         doesn't exist. Also if the file exists but is empty {@code null}
 	 *         will be returned
 	 * @throws IOException
 	 * @throws NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
 	public ObjectId readOrigHead() throws IOException, NoWorkTreeException {
 		if (isBare() || getDirectory() == null)
 			throw new NoWorkTreeException();
 
 		byte[] raw = readGitDirectoryFile(Constants.ORIG_HEAD);
 		return raw != null ? ObjectId.fromString(raw, 0) : null;
 	}
 
 	/**
 	 * Return the information stored in the file $GIT_DIR/SQUASH_MSG. In this
 	 * file operations triggering a squashed merge will store a template for the
 	 * commit message of the squash commit.
 	 *
 	 * @return a String containing the content of the SQUASH_MSG file or
 	 *         {@code null} if this file doesn't exist
 	 * @throws IOException
 	 * @throws NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
 	 *             See {@link #isBare()}.
 	 */
 	public String readSquashCommitMsg() throws IOException {
 		return readCommitMsgFile(Constants.SQUASH_MSG);
 	}
 
 	/**
 	 * Write new content to the file $GIT_DIR/SQUASH_MSG. In this file
 	 * operations triggering a squashed merge will store a template for the
 	 * commit message of the squash commit. If <code>null</code> is specified as
 	 * message the file will be deleted.
 	 *
 	 * @param msg
 	 *            the message which should be written or <code>null</code> to
 	 *            delete the file
 	 *
 	 * @throws IOException
 	 */
 	public void writeSquashCommitMsg(String msg) throws IOException {
 		File squashMsgFile = new File(gitDir, Constants.SQUASH_MSG);
 		writeCommitMsg(squashMsgFile, msg);
 	}
 
 	private String readCommitMsgFile(String msgFilename) throws IOException {
 		if (isBare() || getDirectory() == null)
 			throw new NoWorkTreeException();
 
 		File mergeMsgFile = new File(getDirectory(), msgFilename);
 		try {
 			return RawParseUtils.decode(IO.readFully(mergeMsgFile));
 		} catch (FileNotFoundException e) {
 			// the file has disappeared in the meantime ignore it
 			return null;
 		}
 	}
 
 	private void writeCommitMsg(File msgFile, String msg) throws IOException {
 		if (msg != null) {
 			FileOutputStream fos = new FileOutputStream(msgFile);
 			try {
 				fos.write(msg.getBytes(Constants.CHARACTER_ENCODING));
 			} finally {
 				fos.close();
 			}
 		} else {
 			FileUtils.delete(msgFile, FileUtils.SKIP_MISSING);
 		}
 	}
 
 	/**
 	 * Read a file from the git directory.
 	 *
 	 * @param filename
 	 * @return the raw contents or null if the file doesn't exist or is empty
 	 * @throws IOException
 	 */
 	private byte[] readGitDirectoryFile(String filename) throws IOException {
 		File file = new File(getDirectory(), filename);
 		try {
 			byte[] raw = IO.readFully(file);
 			return raw.length > 0 ? raw : null;
 		} catch (FileNotFoundException notFound) {
 			return null;
 		}
 	}
 
 	/**
 	 * Write the given heads to a file in the git directory.
 	 *
 	 * @param heads
 	 *            a list of object ids to write or null if the file should be
 	 *            deleted.
 	 * @param filename
 	 * @throws FileNotFoundException
 	 * @throws IOException
 	 */
 	private void writeHeadsFile(List<? extends ObjectId> heads, String filename)
 			throws FileNotFoundException, IOException {
 		File headsFile = new File(getDirectory(), filename);
 		if (heads != null) {
 			BufferedOutputStream bos = new SafeBufferedOutputStream(
 					new FileOutputStream(headsFile));
 			try {
 				for (ObjectId id : heads) {
 					id.copyTo(bos);
 					bos.write('\n');
 				}
 			} finally {
 				bos.close();
 			}
 		} else {
 			FileUtils.delete(headsFile, FileUtils.SKIP_MISSING);
 		}
 	}
 
 	/**
 	 * Read a file formatted like the git-rebase-todo file. The "done" file is
 	 * also formatted like the git-rebase-todo file. These files can be found in
 	 * .git/rebase-merge/ or .git/rebase-append/ folders.
 	 *
 	 * @param path
 	 *            path to the file relative to the repository's git-dir. E.g.
 	 *            "rebase-merge/git-rebase-todo" or "rebase-append/done"
 	 * @param includeComments
 	 *            <code>true</code> if also comments should be reported
 	 * @return the list of steps
 	 * @throws IOException
 	 * @since 3.2
 	 */
 	public List<RebaseTodoLine> readRebaseTodo(String path,
 			boolean includeComments)
 			throws IOException {
 		return new RebaseTodoFile(this).readRebaseTodo(path, includeComments);
 	}
 
 	/**
 	 * Write a file formatted like a git-rebase-todo file.
 	 *
 	 * @param path
 	 *            path to the file relative to the repository's git-dir. E.g.
 	 *            "rebase-merge/git-rebase-todo" or "rebase-append/done"
 	 * @param steps
 	 *            the steps to be written
 	 * @param append
 	 *            whether to append to an existing file or to write a new file
 	 * @throws IOException
 	 * @since 3.2
 	 */
 	public void writeRebaseTodoFile(String path, List<RebaseTodoLine> steps,
 			boolean append)
 			throws IOException {
 		new RebaseTodoFile(this).writeRebaseTodoFile(path, steps, append);
 	}
 
 	/**
 	 * @return the names of all known remotes
 	 * @since 3.4
 	 */
 	public Set<String> getRemoteNames() {
 		return getConfig()
 				.getSubsections(ConfigConstants.CONFIG_REMOTE_SECTION);
 	}
 }