/*
 * Copyright (C) 2010, 2013 Mathias Kinzler <mathias.kinzler@sap.com>
 * Copyright (C) 2016, Laurent Delaigue <laurent.delaigue@obeo.fr>
 * and other copyright owners as documented in the project's IP log.
 *
 * This program and the accompanying materials are made available
 * under the terms of the Eclipse Distribution License v1.0 which
 * accompanies this distribution, is reproduced below, and is
 * available at http://www.eclipse.org/org/documents/edl-v10.php
 *
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or
 * without modification, are permitted provided that the following
 * conditions are met:
 *
 * - Redistributions of source code must retain the above copyright
 *   notice, this list of conditions and the following disclaimer.
 *
 * - Redistributions in binary form must reproduce the above
 *   copyright notice, this list of conditions and the following
 *   disclaimer in the documentation and/or other materials provided
 *   with the distribution.
 *
 * - Neither the name of the Eclipse Foundation, Inc. nor the
 *   names of its contributors may be used to endorse or promote
 *   products derived from this software without specific prior
 *   written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
 * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
 * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
 * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
 * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
 * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
 * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */
package org.eclipse.jgit.api;

import static java.nio.charset.StandardCharsets.UTF_8;

import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.text.MessageFormat;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import org.eclipse.jgit.api.RebaseResult.Status;
import org.eclipse.jgit.api.ResetCommand.ResetType;
import org.eclipse.jgit.api.errors.CheckoutConflictException;
import org.eclipse.jgit.api.errors.ConcurrentRefUpdateException;
import org.eclipse.jgit.api.errors.GitAPIException;
import org.eclipse.jgit.api.errors.InvalidRebaseStepException;
import org.eclipse.jgit.api.errors.InvalidRefNameException;
import org.eclipse.jgit.api.errors.JGitInternalException;
import org.eclipse.jgit.api.errors.NoHeadException;
import org.eclipse.jgit.api.errors.NoMessageException;
import org.eclipse.jgit.api.errors.RefAlreadyExistsException;
import org.eclipse.jgit.api.errors.RefNotFoundException;
import org.eclipse.jgit.api.errors.StashApplyFailureException;
import org.eclipse.jgit.api.errors.UnmergedPathsException;
import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
import org.eclipse.jgit.diff.DiffFormatter;
import org.eclipse.jgit.dircache.DirCache;
import org.eclipse.jgit.dircache.DirCacheCheckout;
import org.eclipse.jgit.dircache.DirCacheIterator;
import org.eclipse.jgit.errors.RevisionSyntaxException;
import org.eclipse.jgit.internal.JGitText;
import org.eclipse.jgit.lib.AbbreviatedObjectId;
import org.eclipse.jgit.lib.AnyObjectId;
import org.eclipse.jgit.lib.ConfigConstants;
import org.eclipse.jgit.lib.Constants;
import org.eclipse.jgit.lib.NullProgressMonitor;
import org.eclipse.jgit.lib.ObjectId;
import org.eclipse.jgit.lib.ObjectReader;
import org.eclipse.jgit.lib.PersonIdent;
import org.eclipse.jgit.lib.ProgressMonitor;
import org.eclipse.jgit.lib.RebaseTodoLine;
import org.eclipse.jgit.lib.RebaseTodoLine.Action;
import org.eclipse.jgit.lib.Ref;
import org.eclipse.jgit.lib.RefUpdate;
import org.eclipse.jgit.lib.RefUpdate.Result;
import org.eclipse.jgit.lib.Repository;
import org.eclipse.jgit.merge.MergeStrategy;
import org.eclipse.jgit.revwalk.RevCommit;
import org.eclipse.jgit.revwalk.RevWalk;
import org.eclipse.jgit.revwalk.filter.RevFilter;
import org.eclipse.jgit.submodule.SubmoduleWalk.IgnoreSubmoduleMode;
import org.eclipse.jgit.treewalk.TreeWalk;
import org.eclipse.jgit.treewalk.filter.TreeFilter;
import org.eclipse.jgit.util.FileUtils;
import org.eclipse.jgit.util.IO;
import org.eclipse.jgit.util.RawParseUtils;

A class used to execute a Rebase command. It has setters for all supported options and arguments of this command and a call() method to finally execute the command. Each instance of this class should only be used for one invocation of the command (means: one call to call()) 

See Also:
Git documentation about Rebase/**
 * A class used to execute a {@code Rebase} command. It has setters for all
 * supported options and arguments of this command and a {@link #call()} method
 * to finally execute the command. Each instance of this class should only be
 * used for one invocation of the command (means: one call to {@link #call()})
 * <p>
 *
 * @see <a
 *      href="http://www.kernel.org/pub/software/scm/git/docs/git-rebase.html"
 *      >Git documentation about Rebase</a>
 */
public class RebaseCommand extends GitCommand<RebaseResult> {
	
The name of the "rebase-merge" folder for interactive rebases.
/**
	 * The name of the "rebase-merge" folder for interactive rebases.
	 */
	public static final String REBASE_MERGE = "rebase-merge"; //$NON-NLS-1$

	
The name of the "rebase-apply" folder for non-interactive rebases.
/**
	 * The name of the "rebase-apply" folder for non-interactive rebases.
	 */
	private static final String REBASE_APPLY = "rebase-apply"; //$NON-NLS-1$

	
The name of the "stopped-sha" file
/**
	 * The name of the "stopped-sha" file
	 */
	public static final String STOPPED_SHA = "stopped-sha"; //$NON-NLS-1$

	private static final String AUTHOR_SCRIPT = "author-script"; //$NON-NLS-1$

	private static final String DONE = "done"; //$NON-NLS-1$

	private static final String GIT_AUTHOR_DATE = "GIT_AUTHOR_DATE"; //$NON-NLS-1$

	private static final String GIT_AUTHOR_EMAIL = "GIT_AUTHOR_EMAIL"; //$NON-NLS-1$

	private static final String GIT_AUTHOR_NAME = "GIT_AUTHOR_NAME"; //$NON-NLS-1$

	private static final String GIT_REBASE_TODO = "git-rebase-todo"; //$NON-NLS-1$

	private static final String HEAD_NAME = "head-name"; //$NON-NLS-1$

	private static final String INTERACTIVE = "interactive"; //$NON-NLS-1$

	private static final String QUIET = "quiet"; //$NON-NLS-1$

	private static final String MESSAGE = "message"; //$NON-NLS-1$

	private static final String ONTO = "onto"; //$NON-NLS-1$

	private static final String ONTO_NAME = "onto_name"; //$NON-NLS-1$

	private static final String PATCH = "patch"; //$NON-NLS-1$

	private static final String REBASE_HEAD = "orig-head"; //$NON-NLS-1$

	
Pre git 1.7.6 file name for REBASE_HEAD. /** Pre git 1.7.6 file name for {@link #REBASE_HEAD}. */
	private static final String REBASE_HEAD_LEGACY = "head"; //$NON-NLS-1$

	private static final String AMEND = "amend"; //$NON-NLS-1$

	private static final String MESSAGE_FIXUP = "message-fixup"; //$NON-NLS-1$

	private static final String MESSAGE_SQUASH = "message-squash"; //$NON-NLS-1$

	private static final String AUTOSTASH = "autostash"; //$NON-NLS-1$

	private static final String AUTOSTASH_MSG = "On {0}: autostash"; //$NON-NLS-1$

	
The folder containing the hashes of (potentially) rewritten commits when
--preserve-merges is used.

Native git rebase --merge uses a file of that name to record
commits to copy notes at the end of the whole rebase.

/**
	 * The folder containing the hashes of (potentially) rewritten commits when
	 * --preserve-merges is used.
	 * <p>
	 * Native git rebase --merge uses a <em>file</em> of that name to record
	 * commits to copy notes at the end of the whole rebase.
	 * </p>
	 */
	private static final String REWRITTEN = "rewritten"; //$NON-NLS-1$

	
File containing the current commit(s) to cherry pick when --preserve-merges
is used.
/**
	 * File containing the current commit(s) to cherry pick when --preserve-merges
	 * is used.
	 */
	private static final String CURRENT_COMMIT = "current-commit"; //$NON-NLS-1$

	private static final String REFLOG_PREFIX = "rebase:"; //$NON-NLS-1$

	
The available operations
/**
	 * The available operations
	 */
	public enum Operation {
		
Initiates rebase
/**
		 * Initiates rebase
		 */
		BEGIN,
		
Continues after a conflict resolution
/**
		 * Continues after a conflict resolution
		 */
		CONTINUE,
		
Skips the "current" commit
/**
		 * Skips the "current" commit
		 */
		SKIP,
		
Aborts and resets the current rebase
/**
		 * Aborts and resets the current rebase
		 */
		ABORT,
		
Starts processing steps
Since:
3.2/**
		 * Starts processing steps
		 * @since 3.2
		 */
		PROCESS_STEPS;
	}

	private Operation operation = Operation.BEGIN;

	private RevCommit upstreamCommit;

	private String upstreamCommitName;

	private ProgressMonitor monitor = NullProgressMonitor.INSTANCE;

	private final RevWalk walk;

	private final RebaseState rebaseState;

	private InteractiveHandler interactiveHandler;

	private boolean stopAfterInitialization = false;

	private RevCommit newHead;

	private boolean lastStepWasForward;

	private MergeStrategy strategy = MergeStrategy.RECURSIVE;

	private boolean preserveMerges = false;

	

Constructor for RebaseCommand.

Params:
repo –  the Repository/**
	 * <p>
	 * Constructor for RebaseCommand.
	 * </p>
	 *
	 * @param repo
	 *            the {@link org.eclipse.jgit.lib.Repository}
	 */
	protected RebaseCommand(Repository repo) {
		super(repo);
		walk = new RevWalk(repo);
		rebaseState = new RebaseState(repo.getDirectory());
	}

	
{@inheritDoc}
 Executes the Rebase command with all the options and parameters collected by the setter methods of this class. Each instance of this class should only be used for one invocation of the command. Don't call this method twice on an instance. /**
	 * {@inheritDoc}
	 * <p>
	 * Executes the {@code Rebase} command with all the options and parameters
	 * collected by the setter methods of this class. Each instance of this
	 * class should only be used for one invocation of the command. Don't call
	 * this method twice on an instance.
	 */
	@Override
	public RebaseResult call() throws GitAPIException, NoHeadException,
			RefNotFoundException, WrongRepositoryStateException {
		newHead = null;
		lastStepWasForward = false;
		checkCallable();
		checkParameters();
		try {
			switch (operation) {
			case ABORT:
				try {
					return abort(RebaseResult.ABORTED_RESULT);
				} catch (IOException ioe) {
					throw new JGitInternalException(ioe.getMessage(), ioe);
				}
			case PROCESS_STEPS:
			case SKIP:
			case CONTINUE:
				String upstreamCommitId = rebaseState.readFile(ONTO);
				try {
					upstreamCommitName = rebaseState.readFile(ONTO_NAME);
				} catch (FileNotFoundException e) {
					// Fall back to commit ID if file doesn't exist (e.g. rebase
					// was started by C Git)
					upstreamCommitName = upstreamCommitId;
				}
				this.upstreamCommit = walk.parseCommit(repo
						.resolve(upstreamCommitId));
				preserveMerges = rebaseState.getRewrittenDir().isDirectory();
				break;
			case BEGIN:
				autoStash();
				if (stopAfterInitialization
						|| !walk.isMergedInto(
								walk.parseCommit(repo.resolve(Constants.HEAD)),
								upstreamCommit)) {
					org.eclipse.jgit.api.Status status = Git.wrap(repo)
							.status().setIgnoreSubmodules(IgnoreSubmoduleMode.ALL).call();
					if (status.hasUncommittedChanges()) {
						List<String> list = new ArrayList<>();
						list.addAll(status.getUncommittedChanges());
						return RebaseResult.uncommittedChanges(list);
					}
				}
				RebaseResult res = initFilesAndRewind();
				if (stopAfterInitialization)
					return RebaseResult.INTERACTIVE_PREPARED_RESULT;
				if (res != null) {
					autoStashApply();
					if (rebaseState.getDir().exists())
						FileUtils.delete(rebaseState.getDir(),
								FileUtils.RECURSIVE);
					return res;
				}
			}

			if (monitor.isCancelled())
				return abort(RebaseResult.ABORTED_RESULT);

			if (operation == Operation.CONTINUE) {
				newHead = continueRebase();
				List<RebaseTodoLine> doneLines = repo.readRebaseTodo(
						rebaseState.getPath(DONE), true);
				RebaseTodoLine step = doneLines.get(doneLines.size() - 1);
				if (newHead != null
						&& step.getAction() != Action.PICK) {
					RebaseTodoLine newStep = new RebaseTodoLine(
							step.getAction(),
							AbbreviatedObjectId.fromObjectId(newHead),
							step.getShortMessage());
					RebaseResult result = processStep(newStep, false);
					if (result != null)
						return result;
				}
				File amendFile = rebaseState.getFile(AMEND);
				boolean amendExists = amendFile.exists();
				if (amendExists) {
					FileUtils.delete(amendFile);
				}
				if (newHead == null && !amendExists) {
					// continueRebase() returns null only if no commit was
					// neccessary. This means that no changes where left over
					// after resolving all conflicts. In this case, cgit stops
					// and displays a nice message to the user, telling him to
					// either do changes or skip the commit instead of continue.
					return RebaseResult.NOTHING_TO_COMMIT_RESULT;
				}
			}

			if (operation == Operation.SKIP)
				newHead = checkoutCurrentHead();

			List<RebaseTodoLine> steps = repo.readRebaseTodo(
					rebaseState.getPath(GIT_REBASE_TODO), false);
			if (steps.isEmpty()) {
				return finishRebase(walk.parseCommit(repo.resolve(Constants.HEAD)), false);
			}
			if (isInteractive()) {
				interactiveHandler.prepareSteps(steps);
				repo.writeRebaseTodoFile(rebaseState.getPath(GIT_REBASE_TODO),
						steps, false);
			}
			checkSteps(steps);
			for (int i = 0; i < steps.size(); i++) {
				RebaseTodoLine step = steps.get(i);
				popSteps(1);
				RebaseResult result = processStep(step, true);
				if (result != null) {
					return result;
				}
			}
			return finishRebase(newHead, lastStepWasForward);
		} catch (CheckoutConflictException cce) {
			return RebaseResult.conflicts(cce.getConflictingPaths());
		} catch (IOException ioe) {
			throw new JGitInternalException(ioe.getMessage(), ioe);
		}
	}

	private void autoStash() throws GitAPIException, IOException {
		if (repo.getConfig().getBoolean(ConfigConstants.CONFIG_REBASE_SECTION,
				ConfigConstants.CONFIG_KEY_AUTOSTASH, false)) {
			String message = MessageFormat.format(
							AUTOSTASH_MSG,
							Repository
									.shortenRefName(getHeadName(getHead())));
			RevCommit stashCommit = Git.wrap(repo).stashCreate().setRef(null)
					.setWorkingDirectoryMessage(
							message)
					.call();
			if (stashCommit != null) {
				FileUtils.mkdir(rebaseState.getDir());
				rebaseState.createFile(AUTOSTASH, stashCommit.getName());
			}
		}
	}

	private boolean autoStashApply() throws IOException, GitAPIException {
		boolean conflicts = false;
		if (rebaseState.getFile(AUTOSTASH).exists()) {
			String stash = rebaseState.readFile(AUTOSTASH);
			try (Git git = Git.wrap(repo)) {
				git.stashApply().setStashRef(stash)
						.ignoreRepositoryState(true).setStrategy(strategy)
						.call();
			} catch (StashApplyFailureException e) {
				conflicts = true;
				try (RevWalk rw = new RevWalk(repo)) {
					ObjectId stashId = repo.resolve(stash);
					RevCommit commit = rw.parseCommit(stashId);
					updateStashRef(commit, commit.getAuthorIdent(),
							commit.getShortMessage());
				}
			}
		}
		return conflicts;
	}

	private void updateStashRef(ObjectId commitId, PersonIdent refLogIdent,
			String refLogMessage) throws IOException {
		Ref currentRef = repo.exactRef(Constants.R_STASH);
		RefUpdate refUpdate = repo.updateRef(Constants.R_STASH);
		refUpdate.setNewObjectId(commitId);
		refUpdate.setRefLogIdent(refLogIdent);
		refUpdate.setRefLogMessage(refLogMessage, false);
		refUpdate.setForceRefLog(true);
		if (currentRef != null)
			refUpdate.setExpectedOldObjectId(currentRef.getObjectId());
		else
			refUpdate.setExpectedOldObjectId(ObjectId.zeroId());
		refUpdate.forceUpdate();
	}

	private RebaseResult processStep(RebaseTodoLine step, boolean shouldPick)
			throws IOException, GitAPIException {
		if (Action.COMMENT.equals(step.getAction()))
			return null;
		if (preserveMerges
				&& shouldPick
				&& (Action.EDIT.equals(step.getAction()) || Action.PICK
						.equals(step.getAction()))) {
			writeRewrittenHashes();
		}
		ObjectReader or = repo.newObjectReader();

		Collection<ObjectId> ids = or.resolve(step.getCommit());
		if (ids.size() != 1)
			throw new JGitInternalException(
					JGitText.get().cannotResolveUniquelyAbbrevObjectId);
		RevCommit commitToPick = walk.parseCommit(ids.iterator().next());
		if (shouldPick) {
			if (monitor.isCancelled())
				return RebaseResult.result(Status.STOPPED, commitToPick);
			RebaseResult result = cherryPickCommit(commitToPick);
			if (result != null)
				return result;
		}
		boolean isSquash = false;
		switch (step.getAction()) {
		case PICK:
			return null; // continue rebase process on pick command
		case REWORD:
			String oldMessage = commitToPick.getFullMessage();
			String newMessage = interactiveHandler
					.modifyCommitMessage(oldMessage);
			try (Git git = new Git(repo)) {
				newHead = git.commit().setMessage(newMessage).setAmend(true)
						.setNoVerify(true).call();
			}
			return null;
		case EDIT:
			rebaseState.createFile(AMEND, commitToPick.name());
			return stop(commitToPick, Status.EDIT);
		case COMMENT:
			break;
		case SQUASH:
			isSquash = true;
			//$FALL-THROUGH$
		case FIXUP:
			resetSoftToParent();
			List<RebaseTodoLine> steps = repo.readRebaseTodo(
					rebaseState.getPath(GIT_REBASE_TODO), false);
			RebaseTodoLine nextStep = steps.isEmpty() ? null : steps.get(0);
			File messageFixupFile = rebaseState.getFile(MESSAGE_FIXUP);
			File messageSquashFile = rebaseState.getFile(MESSAGE_SQUASH);
			if (isSquash && messageFixupFile.exists())
				messageFixupFile.delete();
			newHead = doSquashFixup(isSquash, commitToPick, nextStep,
					messageFixupFile, messageSquashFile);
		}
		return null;
	}

	private RebaseResult cherryPickCommit(RevCommit commitToPick)
			throws IOException, GitAPIException, NoMessageException,
			UnmergedPathsException, ConcurrentRefUpdateException,
			WrongRepositoryStateException, NoHeadException {
		try {
			monitor.beginTask(MessageFormat.format(
					JGitText.get().applyingCommit,
					commitToPick.getShortMessage()), ProgressMonitor.UNKNOWN);
			if (preserveMerges)
				return cherryPickCommitPreservingMerges(commitToPick);
			else
				return cherryPickCommitFlattening(commitToPick);
		} finally {
			monitor.endTask();
		}
	}

	private RebaseResult cherryPickCommitFlattening(RevCommit commitToPick)
			throws IOException, GitAPIException, NoMessageException,
			UnmergedPathsException, ConcurrentRefUpdateException,
			WrongRepositoryStateException, NoHeadException {
		// If the first parent of commitToPick is the current HEAD,
		// we do a fast-forward instead of cherry-pick to avoid
		// unnecessary object rewriting
		newHead = tryFastForward(commitToPick);
		lastStepWasForward = newHead != null;
		if (!lastStepWasForward) {
			// TODO if the content of this commit is already merged
			// here we should skip this step in order to avoid
			// confusing pseudo-changed
			String ourCommitName = getOurCommitName();
			try (Git git = new Git(repo)) {
				CherryPickResult cherryPickResult = git.cherryPick()
					.include(commitToPick).setOurCommitName(ourCommitName)
					.setReflogPrefix(REFLOG_PREFIX).setStrategy(strategy)
					.call();
				switch (cherryPickResult.getStatus()) {
				case FAILED:
					if (operation == Operation.BEGIN)
						return abort(RebaseResult
								.failed(cherryPickResult.getFailingPaths()));
					else
						return stop(commitToPick, Status.STOPPED);
				case CONFLICTING:
					return stop(commitToPick, Status.STOPPED);
				case OK:
					newHead = cherryPickResult.getNewHead();
				}
			}
		}
		return null;
	}

	private RebaseResult cherryPickCommitPreservingMerges(RevCommit commitToPick)
			throws IOException, GitAPIException, NoMessageException,
			UnmergedPathsException, ConcurrentRefUpdateException,
			WrongRepositoryStateException, NoHeadException {

		writeCurrentCommit(commitToPick);

		List<RevCommit> newParents = getNewParents(commitToPick);
		boolean otherParentsUnchanged = true;
		for (int i = 1; i < commitToPick.getParentCount(); i++)
			otherParentsUnchanged &= newParents.get(i).equals(
					commitToPick.getParent(i));
		// If the first parent of commitToPick is the current HEAD,
		// we do a fast-forward instead of cherry-pick to avoid
		// unnecessary object rewriting
		newHead = otherParentsUnchanged ? tryFastForward(commitToPick) : null;
		lastStepWasForward = newHead != null;
		if (!lastStepWasForward) {
			ObjectId headId = getHead().getObjectId();
			// getHead() checks for null
			assert headId != null;
			if (!AnyObjectId.isEqual(headId, newParents.get(0)))
				checkoutCommit(headId.getName(), newParents.get(0));

			// Use the cherry-pick strategy if all non-first parents did not
			// change. This is different from C Git, which always uses the merge
			// strategy (see below).
			try (Git git = new Git(repo)) {
				if (otherParentsUnchanged) {
					boolean isMerge = commitToPick.getParentCount() > 1;
					String ourCommitName = getOurCommitName();
					CherryPickCommand pickCommand = git.cherryPick()
							.include(commitToPick)
							.setOurCommitName(ourCommitName)
							.setReflogPrefix(REFLOG_PREFIX)
							.setStrategy(strategy);
					if (isMerge) {
						pickCommand.setMainlineParentNumber(1);
						// We write a MERGE_HEAD and later commit explicitly
						pickCommand.setNoCommit(true);
						writeMergeInfo(commitToPick, newParents);
					}
					CherryPickResult cherryPickResult = pickCommand.call();
					switch (cherryPickResult.getStatus()) {
					case FAILED:
						if (operation == Operation.BEGIN)
							return abort(RebaseResult.failed(
									cherryPickResult.getFailingPaths()));
						else
							return stop(commitToPick, Status.STOPPED);
					case CONFLICTING:
						return stop(commitToPick, Status.STOPPED);
					case OK:
						if (isMerge) {
							// Commit the merge (setup above using
							// writeMergeInfo())
							CommitCommand commit = git.commit();
							commit.setAuthor(commitToPick.getAuthorIdent());
							commit.setReflogComment(REFLOG_PREFIX + " " //$NON-NLS-1$
									+ commitToPick.getShortMessage());
							newHead = commit.call();
						} else
							newHead = cherryPickResult.getNewHead();
						break;
					}
				} else {
					// Use the merge strategy to redo merges, which had some of
					// their non-first parents rewritten
					MergeCommand merge = git.merge()
							.setFastForward(MergeCommand.FastForwardMode.NO_FF)
							.setProgressMonitor(monitor)
							.setCommit(false);
					for (int i = 1; i < commitToPick.getParentCount(); i++)
						merge.include(newParents.get(i));
					MergeResult mergeResult = merge.call();
					if (mergeResult.getMergeStatus().isSuccessful()) {
						CommitCommand commit = git.commit();
						commit.setAuthor(commitToPick.getAuthorIdent());
						commit.setMessage(commitToPick.getFullMessage());
						commit.setReflogComment(REFLOG_PREFIX + " " //$NON-NLS-1$
								+ commitToPick.getShortMessage());
						newHead = commit.call();
					} else {
						if (operation == Operation.BEGIN && mergeResult
								.getMergeStatus() == MergeResult.MergeStatus.FAILED)
							return abort(RebaseResult
									.failed(mergeResult.getFailingPaths()));
						return stop(commitToPick, Status.STOPPED);
					}
				}
			}
		}
		return null;
	}

	// Prepare MERGE_HEAD and message for the next commit
	private void writeMergeInfo(RevCommit commitToPick,
			List<RevCommit> newParents) throws IOException {
		repo.writeMergeHeads(newParents.subList(1, newParents.size()));
		repo.writeMergeCommitMsg(commitToPick.getFullMessage());
	}

	// Get the rewritten equivalents for the parents of the given commit
	private List<RevCommit> getNewParents(RevCommit commitToPick)
			throws IOException {
		List<RevCommit> newParents = new ArrayList<>();
		for (int p = 0; p < commitToPick.getParentCount(); p++) {
			String parentHash = commitToPick.getParent(p).getName();
			if (!new File(rebaseState.getRewrittenDir(), parentHash).exists())
				newParents.add(commitToPick.getParent(p));
			else {
				String newParent = RebaseState.readFile(
						rebaseState.getRewrittenDir(), parentHash);
				if (newParent.length() == 0)
					newParents.add(walk.parseCommit(repo
							.resolve(Constants.HEAD)));
				else
					newParents.add(walk.parseCommit(ObjectId
							.fromString(newParent)));
			}
		}
		return newParents;
	}

	private void writeCurrentCommit(RevCommit commit) throws IOException {
		RebaseState.appendToFile(rebaseState.getFile(CURRENT_COMMIT),
				commit.name());
	}

	private void writeRewrittenHashes() throws RevisionSyntaxException,
			IOException, RefNotFoundException {
		File currentCommitFile = rebaseState.getFile(CURRENT_COMMIT);
		if (!currentCommitFile.exists())
			return;

		ObjectId headId = getHead().getObjectId();
		// getHead() checks for null
		assert headId != null;
		String head = headId.getName();
		String currentCommits = rebaseState.readFile(CURRENT_COMMIT);
		for (String current : currentCommits.split("\n")) //$NON-NLS-1$
			RebaseState
					.createFile(rebaseState.getRewrittenDir(), current, head);
		FileUtils.delete(currentCommitFile);
	}

	private RebaseResult finishRebase(RevCommit finalHead,
			boolean lastStepIsForward) throws IOException, GitAPIException {
		String headName = rebaseState.readFile(HEAD_NAME);
		updateHead(headName, finalHead, upstreamCommit);
		boolean stashConflicts = autoStashApply();
		getRepository().autoGC(monitor);
		FileUtils.delete(rebaseState.getDir(), FileUtils.RECURSIVE);
		if (stashConflicts)
			return RebaseResult.STASH_APPLY_CONFLICTS_RESULT;
		if (lastStepIsForward || finalHead == null)
			return RebaseResult.FAST_FORWARD_RESULT;
		return RebaseResult.OK_RESULT;
	}

	private void checkSteps(List<RebaseTodoLine> steps)
			throws InvalidRebaseStepException, IOException {
		if (steps.isEmpty())
			return;
		if (RebaseTodoLine.Action.SQUASH.equals(steps.get(0).getAction())
				|| RebaseTodoLine.Action.FIXUP.equals(steps.get(0).getAction())) {
			if (!rebaseState.getFile(DONE).exists()
					|| rebaseState.readFile(DONE).trim().length() == 0) {
				throw new InvalidRebaseStepException(MessageFormat.format(
						JGitText.get().cannotSquashFixupWithoutPreviousCommit,
						steps.get(0).getAction().name()));
			}
		}

	}

	private RevCommit doSquashFixup(boolean isSquash, RevCommit commitToPick,
			RebaseTodoLine nextStep, File messageFixup, File messageSquash)
			throws IOException, GitAPIException {

		if (!messageSquash.exists()) {
			// init squash/fixup sequence
			ObjectId headId = repo.resolve(Constants.HEAD);
			RevCommit previousCommit = walk.parseCommit(headId);

			initializeSquashFixupFile(MESSAGE_SQUASH,
					previousCommit.getFullMessage());
			if (!isSquash)
				initializeSquashFixupFile(MESSAGE_FIXUP,
					previousCommit.getFullMessage());
		}
		String currSquashMessage = rebaseState
				.readFile(MESSAGE_SQUASH);

		int count = parseSquashFixupSequenceCount(currSquashMessage) + 1;

		String content = composeSquashMessage(isSquash,
				commitToPick, currSquashMessage, count);
		rebaseState.createFile(MESSAGE_SQUASH, content);
		if (messageFixup.exists())
			rebaseState.createFile(MESSAGE_FIXUP, content);

		return squashIntoPrevious(
				!messageFixup.exists(),
				nextStep);
	}

	private void resetSoftToParent() throws IOException,
			GitAPIException, CheckoutConflictException {
		Ref ref = repo.exactRef(Constants.ORIG_HEAD);
		ObjectId orig_head = ref == null ? null : ref.getObjectId();
		try (Git git = Git.wrap(repo)) {
			// we have already committed the cherry-picked commit.
			// what we need is to have changes introduced by this
			// commit to be on the index
			// resetting is a workaround
			git.reset().setMode(ResetType.SOFT)
					.setRef("HEAD~1").call(); //$NON-NLS-1$
		} finally {
			// set ORIG_HEAD back to where we started because soft
			// reset moved it
			repo.writeOrigHead(orig_head);
		}
	}

	private RevCommit squashIntoPrevious(boolean sequenceContainsSquash,
			RebaseTodoLine nextStep)
			throws IOException, GitAPIException {
		RevCommit retNewHead;
		String commitMessage = rebaseState
				.readFile(MESSAGE_SQUASH);

		try (Git git = new Git(repo)) {
			if (nextStep == null || ((nextStep.getAction() != Action.FIXUP)
					&& (nextStep.getAction() != Action.SQUASH))) {
				// this is the last step in this sequence
				if (sequenceContainsSquash) {
					commitMessage = interactiveHandler
							.modifyCommitMessage(commitMessage);
				}
				retNewHead = git.commit()
						.setMessage(stripCommentLines(commitMessage))
						.setAmend(true).setNoVerify(true).call();
				rebaseState.getFile(MESSAGE_SQUASH).delete();
				rebaseState.getFile(MESSAGE_FIXUP).delete();

			} else {
				// Next step is either Squash or Fixup
				retNewHead = git.commit().setMessage(commitMessage)
						.setAmend(true).setNoVerify(true).call();
			}
		}
		return retNewHead;
	}

	private static String stripCommentLines(String commitMessage) {
		StringBuilder result = new StringBuilder();
		for (String line : commitMessage.split("\n")) { //$NON-NLS-1$
			if (!line.trim().startsWith("#")) //$NON-NLS-1$
				result.append(line).append("\n"); //$NON-NLS-1$
		}
		if (!commitMessage.endsWith("\n")) { //$NON-NLS-1$
			int bufferSize = result.length();
			if (bufferSize > 0 && result.charAt(bufferSize - 1) == '\n') {
				result.deleteCharAt(bufferSize - 1);
			}
		}
		return result.toString();
	}

	@SuppressWarnings("nls")
	private static String composeSquashMessage(boolean isSquash,
			RevCommit commitToPick, String currSquashMessage, int count) {
		StringBuilder sb = new StringBuilder();
		String ordinal = getOrdinal(count);
		sb.setLength(0);
		sb.append("# This is a combination of ").append(count)
				.append(" commits.\n");
		// Add the previous message without header (i.e first line)
		sb.append(currSquashMessage.substring(currSquashMessage.indexOf("\n") + 1));
		sb.append("\n");
		if (isSquash) {
			sb.append("# This is the ").append(count).append(ordinal)
					.append(" commit message:\n");
			sb.append(commitToPick.getFullMessage());
		} else {
			sb.append("# The ").append(count).append(ordinal)
					.append(" commit message will be skipped:\n# ");
			sb.append(commitToPick.getFullMessage().replaceAll("([\n\r])",
					"$1# "));
		}
		return sb.toString();
	}

	private static String getOrdinal(int count) {
		switch (count % 10) {
		case 1:
			return "st"; //$NON-NLS-1$
		case 2:
			return "nd"; //$NON-NLS-1$
		case 3:
			return "rd"; //$NON-NLS-1$
		default:
			return "th"; //$NON-NLS-1$
		}
	}

	
Parse the count from squashed commit messages
Params:
currSquashMessage – 
           the squashed commit message to be parsed
Returns:
the count of squashed messages in the given string/**
	 * Parse the count from squashed commit messages
	 *
	 * @param currSquashMessage
	 *            the squashed commit message to be parsed
	 * @return the count of squashed messages in the given string
	 */
	static int parseSquashFixupSequenceCount(String currSquashMessage) {
		String regex = "This is a combination of (.*) commits"; //$NON-NLS-1$
		String firstLine = currSquashMessage.substring(0,
				currSquashMessage.indexOf("\n")); //$NON-NLS-1$
		Pattern pattern = Pattern.compile(regex);
		Matcher matcher = pattern.matcher(firstLine);
		if (!matcher.find())
			throw new IllegalArgumentException();
		return Integer.parseInt(matcher.group(1));
	}

	private void initializeSquashFixupFile(String messageFile,
			String fullMessage) throws IOException {
		rebaseState
				.createFile(
						messageFile,
						"# This is a combination of 1 commits.\n# The first commit's message is:\n" + fullMessage); //$NON-NLS-1$);
	}

	private String getOurCommitName() {
		// If onto is different from upstream, this should say "onto", but
		// RebaseCommand doesn't support a different "onto" at the moment.
		String ourCommitName = "Upstream, based on " //$NON-NLS-1$
				+ Repository.shortenRefName(upstreamCommitName);
		return ourCommitName;
	}

	private void updateHead(String headName, RevCommit aNewHead, RevCommit onto)
			throws IOException {
		// point the previous head (if any) to the new commit

		if (headName.startsWith(Constants.R_REFS)) {
			RefUpdate rup = repo.updateRef(headName);
			rup.setNewObjectId(aNewHead);
			rup.setRefLogMessage("rebase finished: " + headName + " onto " //$NON-NLS-1$ //$NON-NLS-2$
					+ onto.getName(), false);
			Result res = rup.forceUpdate();
			switch (res) {
			case FAST_FORWARD:
			case FORCED:
			case NO_CHANGE:
				break;
			default:
				throw new JGitInternalException(
						JGitText.get().updatingHeadFailed);
			}
			rup = repo.updateRef(Constants.HEAD);
			rup.setRefLogMessage("rebase finished: returning to " + headName, //$NON-NLS-1$
					false);
			res = rup.link(headName);
			switch (res) {
			case FAST_FORWARD:
			case FORCED:
			case NO_CHANGE:
				break;
			default:
				throw new JGitInternalException(
						JGitText.get().updatingHeadFailed);
			}
		}
	}

	private RevCommit checkoutCurrentHead() throws IOException, NoHeadException {
		ObjectId headTree = repo.resolve(Constants.HEAD + "^{tree}"); //$NON-NLS-1$
		if (headTree == null)
			throw new NoHeadException(
					JGitText.get().cannotRebaseWithoutCurrentHead);
		DirCache dc = repo.lockDirCache();
		try {
			DirCacheCheckout dco = new DirCacheCheckout(repo, dc, headTree);
			dco.setFailOnConflict(false);
			dco.setProgressMonitor(monitor);
			boolean needsDeleteFiles = dco.checkout();
			if (needsDeleteFiles) {
				List<String> fileList = dco.getToBeDeleted();
				for (String filePath : fileList) {
					File fileToDelete = new File(repo.getWorkTree(), filePath);
					if (repo.getFS().exists(fileToDelete))
						FileUtils.delete(fileToDelete, FileUtils.RECURSIVE
								| FileUtils.RETRY);
				}
			}
		} finally {
			dc.unlock();
		}
		try (RevWalk rw = new RevWalk(repo)) {
			RevCommit commit = rw.parseCommit(repo.resolve(Constants.HEAD));
			return commit;
		}
	}

	
Throws:
GitAPIException – 
IOException – 
Returns:
the commit if we had to do a commit, otherwise null/**
	 * @return the commit if we had to do a commit, otherwise null
	 * @throws GitAPIException
	 * @throws IOException
	 */
	private RevCommit continueRebase() throws GitAPIException, IOException {
		// if there are still conflicts, we throw a specific Exception
		DirCache dc = repo.readDirCache();
		boolean hasUnmergedPaths = dc.hasUnmergedPaths();
		if (hasUnmergedPaths)
			throw new UnmergedPathsException();

		// determine whether we need to commit
		boolean needsCommit;
		try (TreeWalk treeWalk = new TreeWalk(repo)) {
			treeWalk.reset();
			treeWalk.setRecursive(true);
			treeWalk.addTree(new DirCacheIterator(dc));
			ObjectId id = repo.resolve(Constants.HEAD + "^{tree}"); //$NON-NLS-1$
			if (id == null)
				throw new NoHeadException(
						JGitText.get().cannotRebaseWithoutCurrentHead);

			treeWalk.addTree(id);

			treeWalk.setFilter(TreeFilter.ANY_DIFF);

			needsCommit = treeWalk.next();
		}
		if (needsCommit) {
			try (Git git = new Git(repo)) {
				CommitCommand commit = git.commit();
				commit.setMessage(rebaseState.readFile(MESSAGE));
				commit.setAuthor(parseAuthor());
				return commit.call();
			}
		}
		return null;
	}

	private PersonIdent parseAuthor() throws IOException {
		File authorScriptFile = rebaseState.getFile(AUTHOR_SCRIPT);
		byte[] raw;
		try {
			raw = IO.readFully(authorScriptFile);
		} catch (FileNotFoundException notFound) {
			if (authorScriptFile.exists()) {
				throw notFound;
			}
			return null;
		}
		return parseAuthor(raw);
	}

	private RebaseResult stop(RevCommit commitToPick, RebaseResult.Status status)
			throws IOException {
		PersonIdent author = commitToPick.getAuthorIdent();
		String authorScript = toAuthorScript(author);
		rebaseState.createFile(AUTHOR_SCRIPT, authorScript);
		rebaseState.createFile(MESSAGE, commitToPick.getFullMessage());
		ByteArrayOutputStream bos = new ByteArrayOutputStream();
		try (DiffFormatter df = new DiffFormatter(bos)) {
			df.setRepository(repo);
			df.format(commitToPick.getParent(0), commitToPick);
		}
		rebaseState.createFile(PATCH, new String(bos.toByteArray(), UTF_8));
		rebaseState.createFile(STOPPED_SHA,
				repo.newObjectReader()
				.abbreviate(
				commitToPick).name());
		// Remove cherry pick state file created by CherryPickCommand, it's not
		// needed for rebase
		repo.writeCherryPickHead(null);
		return RebaseResult.result(status, commitToPick);
	}

	String toAuthorScript(PersonIdent author) {
		StringBuilder sb = new StringBuilder(100);
		sb.append(GIT_AUTHOR_NAME);
		sb.append("='"); //$NON-NLS-1$
		sb.append(author.getName());
		sb.append("'\n"); //$NON-NLS-1$
		sb.append(GIT_AUTHOR_EMAIL);
		sb.append("='"); //$NON-NLS-1$
		sb.append(author.getEmailAddress());
		sb.append("'\n"); //$NON-NLS-1$
		// the command line uses the "external String"
		// representation for date and timezone
		sb.append(GIT_AUTHOR_DATE);
		sb.append("='"); //$NON-NLS-1$
		sb.append("@"); // @ for time in seconds since 1970 //$NON-NLS-1$
		String externalString = author.toExternalString();
		sb
				.append(externalString.substring(externalString
						.lastIndexOf('>') + 2));
		sb.append("'\n"); //$NON-NLS-1$
		return sb.toString();
	}

	
Removes the number of lines given in the parameter from the
git-rebase-todo file but preserves comments and other lines
that can not be parsed as steps
Params:
numSteps – 
Throws:
IOException – /**
	 * Removes the number of lines given in the parameter from the
	 * <code>git-rebase-todo</code> file but preserves comments and other lines
	 * that can not be parsed as steps
	 *
	 * @param numSteps
	 * @throws IOException
	 */
	private void popSteps(int numSteps) throws IOException {
		if (numSteps == 0)
			return;
		List<RebaseTodoLine> todoLines = new LinkedList<>();
		List<RebaseTodoLine> poppedLines = new LinkedList<>();

		for (RebaseTodoLine line : repo.readRebaseTodo(
				rebaseState.getPath(GIT_REBASE_TODO), true)) {
			if (poppedLines.size() >= numSteps
					|| RebaseTodoLine.Action.COMMENT.equals(line.getAction()))
				todoLines.add(line);
			else
				poppedLines.add(line);
		}

		repo.writeRebaseTodoFile(rebaseState.getPath(GIT_REBASE_TODO),
				todoLines, false);
		if (!poppedLines.isEmpty()) {
			repo.writeRebaseTodoFile(rebaseState.getPath(DONE), poppedLines,
					true);
		}
	}

	private RebaseResult initFilesAndRewind() throws IOException,
			GitAPIException {
		// we need to store everything into files so that we can implement
		// --skip, --continue, and --abort

		Ref head = getHead();

		ObjectId headId = head.getObjectId();
		if (headId == null) {
			throw new RefNotFoundException(MessageFormat.format(
					JGitText.get().refNotResolved, Constants.HEAD));
		}
		String headName = getHeadName(head);
		RevCommit headCommit = walk.lookupCommit(headId);
		RevCommit upstream = walk.lookupCommit(upstreamCommit.getId());

		if (!isInteractive() && walk.isMergedInto(upstream, headCommit))
			return RebaseResult.UP_TO_DATE_RESULT;
		else if (!isInteractive() && walk.isMergedInto(headCommit, upstream)) {
			// head is already merged into upstream, fast-foward
			monitor.beginTask(MessageFormat.format(
					JGitText.get().resettingHead,
					upstreamCommit.getShortMessage()), ProgressMonitor.UNKNOWN);
			checkoutCommit(headName, upstreamCommit);
			monitor.endTask();

			updateHead(headName, upstreamCommit, upstream);
			return RebaseResult.FAST_FORWARD_RESULT;
		}

		monitor.beginTask(JGitText.get().obtainingCommitsForCherryPick,
				ProgressMonitor.UNKNOWN);

		// create the folder for the meta information
		FileUtils.mkdir(rebaseState.getDir(), true);

		repo.writeOrigHead(headId);
		rebaseState.createFile(REBASE_HEAD, headId.name());
		rebaseState.createFile(REBASE_HEAD_LEGACY, headId.name());
		rebaseState.createFile(HEAD_NAME, headName);
		rebaseState.createFile(ONTO, upstreamCommit.name());
		rebaseState.createFile(ONTO_NAME, upstreamCommitName);
		if (isInteractive() || preserveMerges) {
			// --preserve-merges is an interactive mode for native git. Without
			// this, native git rebase --continue after a conflict would fall
			// into merge mode.
			rebaseState.createFile(INTERACTIVE, ""); //$NON-NLS-1$
		}
		rebaseState.createFile(QUIET, ""); //$NON-NLS-1$

		ArrayList<RebaseTodoLine> toDoSteps = new ArrayList<>();
		toDoSteps.add(new RebaseTodoLine("# Created by EGit: rebasing " + headId.name() //$NON-NLS-1$
						+ " onto " + upstreamCommit.name())); //$NON-NLS-1$
		// determine the commits to be applied
		List<RevCommit> cherryPickList = calculatePickList(headCommit);
		ObjectReader reader = walk.getObjectReader();
		for (RevCommit commit : cherryPickList)
			toDoSteps.add(new RebaseTodoLine(Action.PICK, reader
					.abbreviate(commit), commit.getShortMessage()));
		repo.writeRebaseTodoFile(rebaseState.getPath(GIT_REBASE_TODO),
				toDoSteps, false);

		monitor.endTask();

		// we rewind to the upstream commit
		monitor.beginTask(MessageFormat.format(JGitText.get().rewinding,
				upstreamCommit.getShortMessage()), ProgressMonitor.UNKNOWN);
		boolean checkoutOk = false;
		try {
			checkoutOk = checkoutCommit(headName, upstreamCommit);
		} finally {
			if (!checkoutOk)
				FileUtils.delete(rebaseState.getDir(), FileUtils.RECURSIVE);
		}
		monitor.endTask();

		return null;
	}

	private List<RevCommit> calculatePickList(RevCommit headCommit)
			throws GitAPIException, NoHeadException, IOException {
		Iterable<RevCommit> commitsToUse;
		try (Git git = new Git(repo)) {
			LogCommand cmd = git.log().addRange(upstreamCommit, headCommit);
			commitsToUse = cmd.call();
		}
		List<RevCommit> cherryPickList = new ArrayList<>();
		for (RevCommit commit : commitsToUse) {
			if (preserveMerges || commit.getParentCount() == 1)
				cherryPickList.add(commit);
		}
		Collections.reverse(cherryPickList);

		if (preserveMerges) {
			// When preserving merges we only rewrite commits which have at
			// least one parent that is itself rewritten (or a merge base)
			File rewrittenDir = rebaseState.getRewrittenDir();
			FileUtils.mkdir(rewrittenDir, false);
			walk.reset();
			walk.setRevFilter(RevFilter.MERGE_BASE);
			walk.markStart(upstreamCommit);
			walk.markStart(headCommit);
			RevCommit base;
			while ((base = walk.next()) != null)
				RebaseState.createFile(rewrittenDir, base.getName(),
						upstreamCommit.getName());

			Iterator<RevCommit> iterator = cherryPickList.iterator();
			pickLoop: while(iterator.hasNext()){
				RevCommit commit = iterator.next();
				for (int i = 0; i < commit.getParentCount(); i++) {
					boolean parentRewritten = new File(rewrittenDir, commit
							.getParent(i).getName()).exists();
					if (parentRewritten) {
						new File(rewrittenDir, commit.getName()).createNewFile();
						continue pickLoop;
					}
				}
				// commit is only merged in, needs not be rewritten
				iterator.remove();
			}
		}
		return cherryPickList;
	}

	private static String getHeadName(Ref head) {
		String headName;
		if (head.isSymbolic()) {
			headName = head.getTarget().getName();
		} else {
			ObjectId headId = head.getObjectId();
			// the callers are checking this already
			assert headId != null;
			headName = headId.getName();
		}
		return headName;
	}

	private Ref getHead() throws IOException, RefNotFoundException {
		Ref head = repo.exactRef(Constants.HEAD);
		if (head == null || head.getObjectId() == null)
			throw new RefNotFoundException(MessageFormat.format(
					JGitText.get().refNotResolved, Constants.HEAD));
		return head;
	}

	private boolean isInteractive() {
		return interactiveHandler != null;
	}

	
Check if we can fast-forward and returns the new head if it is possible
Params:
newCommit –  a RevCommit object to check if we can fast-forward to.
Throws:
IOException – 
GitAPIException – 
Returns:
the new head, or null/**
	 * Check if we can fast-forward and returns the new head if it is possible
	 *
	 * @param newCommit
	 *            a {@link org.eclipse.jgit.revwalk.RevCommit} object to check
	 *            if we can fast-forward to.
	 * @return the new head, or null
	 * @throws java.io.IOException
	 * @throws org.eclipse.jgit.api.errors.GitAPIException
	 */
	public RevCommit tryFastForward(RevCommit newCommit) throws IOException,
			GitAPIException {
		Ref head = getHead();

		ObjectId headId = head.getObjectId();
		if (headId == null)
			throw new RefNotFoundException(MessageFormat.format(
					JGitText.get().refNotResolved, Constants.HEAD));
		RevCommit headCommit = walk.lookupCommit(headId);
		if (walk.isMergedInto(newCommit, headCommit))
			return newCommit;

		String headName = getHeadName(head);
		return tryFastForward(headName, headCommit, newCommit);
	}

	private RevCommit tryFastForward(String headName, RevCommit oldCommit,
			RevCommit newCommit) throws IOException, GitAPIException {
		boolean tryRebase = false;
		for (RevCommit parentCommit : newCommit.getParents())
			if (parentCommit.equals(oldCommit))
				tryRebase = true;
		if (!tryRebase)
			return null;

		CheckoutCommand co = new CheckoutCommand(repo);
		try {
			co.setProgressMonitor(monitor);
			co.setName(newCommit.name()).call();
			if (headName.startsWith(Constants.R_HEADS)) {
				RefUpdate rup = repo.updateRef(headName);
				rup.setExpectedOldObjectId(oldCommit);
				rup.setNewObjectId(newCommit);
				rup.setRefLogMessage("Fast-forward from " + oldCommit.name() //$NON-NLS-1$
						+ " to " + newCommit.name(), false); //$NON-NLS-1$
				Result res = rup.update(walk);
				switch (res) {
				case FAST_FORWARD:
				case NO_CHANGE:
				case FORCED:
					break;
				default:
					throw new IOException("Could not fast-forward"); //$NON-NLS-1$
				}
			}
			return newCommit;
		} catch (RefAlreadyExistsException | RefNotFoundException
				| InvalidRefNameException | CheckoutConflictException e) {
			throw new JGitInternalException(e.getMessage(), e);
		}
	}

	private void checkParameters() throws WrongRepositoryStateException {
		if (this.operation == Operation.PROCESS_STEPS) {
			if (rebaseState.getFile(DONE).exists())
				throw new WrongRepositoryStateException(MessageFormat.format(
						JGitText.get().wrongRepositoryState, repo
								.getRepositoryState().name()));
		}
		if (this.operation != Operation.BEGIN) {
			// these operations are only possible while in a rebasing state
			switch (repo.getRepositoryState()) {
			case REBASING_INTERACTIVE:
			case REBASING:
			case REBASING_REBASING:
			case REBASING_MERGE:
				break;
			default:
				throw new WrongRepositoryStateException(MessageFormat.format(
						JGitText.get().wrongRepositoryState, repo
								.getRepositoryState().name()));
			}
		} else
			switch (repo.getRepositoryState()) {
			case SAFE:
				if (this.upstreamCommit == null)
					throw new JGitInternalException(MessageFormat
							.format(JGitText.get().missingRequiredParameter,
									"upstream")); //$NON-NLS-1$
				return;
			default:
				throw new WrongRepositoryStateException(MessageFormat.format(
						JGitText.get().wrongRepositoryState, repo
								.getRepositoryState().name()));

			}
	}

	private RebaseResult abort(RebaseResult result) throws IOException,
			GitAPIException {
		ObjectId origHead = getOriginalHead();
		try {
			String commitId = origHead != null ? origHead.name() : null;
			monitor.beginTask(MessageFormat.format(
					JGitText.get().abortingRebase, commitId),
					ProgressMonitor.UNKNOWN);

			DirCacheCheckout dco;
			if (commitId == null)
				throw new JGitInternalException(
						JGitText.get().abortingRebaseFailedNoOrigHead);
			ObjectId id = repo.resolve(commitId);
			RevCommit commit = walk.parseCommit(id);
			if (result.getStatus().equals(Status.FAILED)) {
				RevCommit head = walk.parseCommit(repo.resolve(Constants.HEAD));
				dco = new DirCacheCheckout(repo, head.getTree(),
						repo.lockDirCache(), commit.getTree());
			} else {
				dco = new DirCacheCheckout(repo, repo.lockDirCache(),
						commit.getTree());
			}
			dco.setFailOnConflict(false);
			dco.checkout();
			walk.close();
		} finally {
			monitor.endTask();
		}
		try {
			String headName = rebaseState.readFile(HEAD_NAME);
				monitor.beginTask(MessageFormat.format(
						JGitText.get().resettingHead, headName),
						ProgressMonitor.UNKNOWN);

			Result res = null;
			RefUpdate refUpdate = repo.updateRef(Constants.HEAD, false);
			refUpdate.setRefLogMessage("rebase: aborting", false); //$NON-NLS-1$
			if (headName.startsWith(Constants.R_REFS)) {
				// update the HEAD
				res = refUpdate.link(headName);
			} else {
				refUpdate.setNewObjectId(origHead);
				res = refUpdate.forceUpdate();

			}
			switch (res) {
			case FAST_FORWARD:
			case FORCED:
			case NO_CHANGE:
				break;
			default:
				throw new JGitInternalException(
						JGitText.get().abortingRebaseFailed);
			}
			boolean stashConflicts = autoStashApply();
			// cleanup the files
			FileUtils.delete(rebaseState.getDir(), FileUtils.RECURSIVE);
			repo.writeCherryPickHead(null);
			repo.writeMergeHeads(null);
			if (stashConflicts)
				return RebaseResult.STASH_APPLY_CONFLICTS_RESULT;
			return result;

		} finally {
			monitor.endTask();
		}
	}

	private ObjectId getOriginalHead() throws IOException {
		try {
			return ObjectId.fromString(rebaseState.readFile(REBASE_HEAD));
		} catch (FileNotFoundException e) {
			try {
				return ObjectId
						.fromString(rebaseState.readFile(REBASE_HEAD_LEGACY));
			} catch (FileNotFoundException ex) {
				return repo.readOrigHead();
			}
		}
	}

	private boolean checkoutCommit(String headName, RevCommit commit)
			throws IOException,
			CheckoutConflictException {
		try {
			RevCommit head = walk.parseCommit(repo.resolve(Constants.HEAD));
			DirCacheCheckout dco = new DirCacheCheckout(repo, head.getTree(),
					repo.lockDirCache(), commit.getTree());
			dco.setFailOnConflict(true);
			dco.setProgressMonitor(monitor);
			try {
				dco.checkout();
			} catch (org.eclipse.jgit.errors.CheckoutConflictException cce) {
				throw new CheckoutConflictException(dco.getConflicts(), cce);
			}
			// update the HEAD
			RefUpdate refUpdate = repo.updateRef(Constants.HEAD, true);
			refUpdate.setExpectedOldObjectId(head);
			refUpdate.setNewObjectId(commit);
			refUpdate.setRefLogMessage(
					"checkout: moving from " //$NON-NLS-1$
							+ Repository.shortenRefName(headName)
							+ " to " + commit.getName(), false); //$NON-NLS-1$
			Result res = refUpdate.forceUpdate();
			switch (res) {
			case FAST_FORWARD:
			case NO_CHANGE:
			case FORCED:
				break;
			default:
				throw new IOException(
						JGitText.get().couldNotRewindToUpstreamCommit);
			}
		} finally {
			walk.close();
			monitor.endTask();
		}
		return true;
	}


	
Set upstream RevCommit 
Params:
upstream – 
           the upstream commit
Returns:
this/**
	 * Set upstream {@code RevCommit}
	 *
	 * @param upstream
	 *            the upstream commit
	 * @return {@code this}
	 */
	public RebaseCommand setUpstream(RevCommit upstream) {
		this.upstreamCommit = upstream;
		this.upstreamCommitName = upstream.name();
		return this;
	}

	
Set the upstream commit
Params:
upstream – 
           id of the upstream commit
Returns:
this/**
	 * Set the upstream commit
	 *
	 * @param upstream
	 *            id of the upstream commit
	 * @return {@code this}
	 */
	public RebaseCommand setUpstream(AnyObjectId upstream) {
		try {
			this.upstreamCommit = walk.parseCommit(upstream);
			this.upstreamCommitName = upstream.name();
		} catch (IOException e) {
			throw new JGitInternalException(MessageFormat.format(
					JGitText.get().couldNotReadObjectWhileParsingCommit,
					upstream.name()), e);
		}
		return this;
	}

	
Set the upstream branch
Params:
upstream – 
           the name of the upstream branch
Throws:
RefNotFoundException – 
Returns:
this/**
	 * Set the upstream branch
	 *
	 * @param upstream
	 *            the name of the upstream branch
	 * @return {@code this}
	 * @throws org.eclipse.jgit.api.errors.RefNotFoundException
	 */
	public RebaseCommand setUpstream(String upstream)
			throws RefNotFoundException {
		try {
			ObjectId upstreamId = repo.resolve(upstream);
			if (upstreamId == null)
				throw new RefNotFoundException(MessageFormat.format(JGitText
						.get().refNotResolved, upstream));
			upstreamCommit = walk.parseCommit(repo.resolve(upstream));
			upstreamCommitName = upstream;
			return this;
		} catch (IOException ioe) {
			throw new JGitInternalException(ioe.getMessage(), ioe);
		}
	}

	
Optionally override the name of the upstream. If this is used, it has to come after any setUpstream call. 
Params:
upstreamName – 
           the name which will be used to refer to upstream in conflicts
Returns:
this/**
	 * Optionally override the name of the upstream. If this is used, it has to
	 * come after any {@link #setUpstream} call.
	 *
	 * @param upstreamName
	 *            the name which will be used to refer to upstream in conflicts
	 * @return {@code this}
	 */
	public RebaseCommand setUpstreamName(String upstreamName) {
		if (upstreamCommit == null) {
			throw new IllegalStateException(
					"setUpstreamName must be called after setUpstream."); //$NON-NLS-1$
		}
		this.upstreamCommitName = upstreamName;
		return this;
	}

	
Set the operation to execute during rebase
Params:
operation – 
           the operation to perform
Returns:
this/**
	 * Set the operation to execute during rebase
	 *
	 * @param operation
	 *            the operation to perform
	 * @return {@code this}
	 */
	public RebaseCommand setOperation(Operation operation) {
		this.operation = operation;
		return this;
	}

	
Set progress monitor
Params:
monitor – 
           a progress monitor
Returns:
this instance/**
	 * Set progress monitor
	 *
	 * @param monitor
	 *            a progress monitor
	 * @return this instance
	 */
	public RebaseCommand setProgressMonitor(ProgressMonitor monitor) {
		if (monitor == null) {
			monitor = NullProgressMonitor.INSTANCE;
		}
		this.monitor = monitor;
		return this;
	}

	
Enable interactive rebase
 Does not stop after initialization of interactive rebase. This is equivalent to 
runInteractively(handler, false); 
Params:
handler –  the InteractiveHandler to use
Returns:
this/**
	 * Enable interactive rebase
	 * <p>
	 * Does not stop after initialization of interactive rebase. This is
	 * equivalent to
	 * {@link org.eclipse.jgit.api.RebaseCommand#runInteractively(InteractiveHandler, boolean)
	 * runInteractively(handler, false)};
	 * </p>
	 *
	 * @param handler
	 *            the
	 *            {@link org.eclipse.jgit.api.RebaseCommand.InteractiveHandler}
	 *            to use
	 * @return this
	 */
	public RebaseCommand runInteractively(InteractiveHandler handler) {
		return runInteractively(handler, false);
	}

	
Enable interactive rebase
 If stopAfterRebaseInteractiveInitialization is true the rebase stops after initialization of interactive rebase returning RebaseResult.INTERACTIVE_PREPARED_RESULT 
Params:
handler –  the InteractiveHandler to use
stopAfterRebaseInteractiveInitialization –  if true the rebase stops after initialization
Returns:
this instance
Since:
3.2/**
	 * Enable interactive rebase
	 * <p>
	 * If stopAfterRebaseInteractiveInitialization is {@code true} the rebase
	 * stops after initialization of interactive rebase returning
	 * {@link org.eclipse.jgit.api.RebaseResult#INTERACTIVE_PREPARED_RESULT}
	 * </p>
	 *
	 * @param handler
	 *            the
	 *            {@link org.eclipse.jgit.api.RebaseCommand.InteractiveHandler}
	 *            to use
	 * @param stopAfterRebaseInteractiveInitialization
	 *            if {@code true} the rebase stops after initialization
	 * @return this instance
	 * @since 3.2
	 */
	public RebaseCommand runInteractively(InteractiveHandler handler,
			final boolean stopAfterRebaseInteractiveInitialization) {
		this.stopAfterInitialization = stopAfterRebaseInteractiveInitialization;
		this.interactiveHandler = handler;
		return this;
	}

	
Set the MergeStrategy.
Params:
strategy – 
           The merge strategy to use during this rebase operation.
Returns:
this
Since:
3.4/**
	 * Set the <code>MergeStrategy</code>.
	 *
	 * @param strategy
	 *            The merge strategy to use during this rebase operation.
	 * @return {@code this}
	 * @since 3.4
	 */
	public RebaseCommand setStrategy(MergeStrategy strategy) {
		this.strategy = strategy;
		return this;
	}

	
Whether to preserve merges during rebase
Params:
preserve –  true to re-create merges during rebase. Defaults to false, a flattening rebase.
Returns:
this
Since:
3.5/**
	 * Whether to preserve merges during rebase
	 *
	 * @param preserve
	 *            {@code true} to re-create merges during rebase. Defaults to
	 *            {@code false}, a flattening rebase.
	 * @return {@code this}
	 * @since 3.5
	 */
	public RebaseCommand setPreserveMerges(boolean preserve) {
		this.preserveMerges = preserve;
		return this;
	}

	
Allows configure rebase interactive process and modify commit message
/**
	 * Allows configure rebase interactive process and modify commit message
	 */
	public interface InteractiveHandler {
		
Given list of steps should be modified according to user rebase configuration 
Params:
steps – 
           initial configuration of rebase interactive/**
		 * Given list of {@code steps} should be modified according to user
		 * rebase configuration
		 * @param steps
		 *            initial configuration of rebase interactive
		 */
		void prepareSteps(List<RebaseTodoLine> steps);

		
Used for editing commit message on REWORD
Params:
commit – 
Returns:
new commit message/**
		 * Used for editing commit message on REWORD
		 *
		 * @param commit
		 * @return new commit message
		 */
		String modifyCommitMessage(String commit);
	}


	PersonIdent parseAuthor(byte[] raw) {
		if (raw.length == 0)
			return null;

		Map<String, String> keyValueMap = new HashMap<>();
		for (int p = 0; p < raw.length;) {
			int end = RawParseUtils.nextLF(raw, p);
			if (end == p)
				break;
			int equalsIndex = RawParseUtils.next(raw, p, '=');
			if (equalsIndex == end)
				break;
			String key = RawParseUtils.decode(raw, p, equalsIndex - 1);
			String value = RawParseUtils.decode(raw, equalsIndex + 1, end - 2);
			p = end;
			keyValueMap.put(key, value);
		}

		String name = keyValueMap.get(GIT_AUTHOR_NAME);
		String email = keyValueMap.get(GIT_AUTHOR_EMAIL);
		String time = keyValueMap.get(GIT_AUTHOR_DATE);

		// the time is saved as <seconds since 1970> <timezone offset>
		int timeStart = 0;
		if (time.startsWith("@")) //$NON-NLS-1$
			timeStart = 1;
		else
			timeStart = 0;
		long when = Long
				.parseLong(time.substring(timeStart, time.indexOf(' '))) * 1000;
		String tzOffsetString = time.substring(time.indexOf(' ') + 1);
		int multiplier = -1;
		if (tzOffsetString.charAt(0) == '+')
			multiplier = 1;
		int hours = Integer.parseInt(tzOffsetString.substring(1, 3));
		int minutes = Integer.parseInt(tzOffsetString.substring(3, 5));
		// this is in format (+/-)HHMM (hours and minutes)
		// we need to convert into minutes
		int tz = (hours * 60 + minutes) * multiplier;
		if (name != null && email != null)
			return new PersonIdent(name, email, when, tz);
		return null;
	}

	private static class RebaseState {

		private final File repoDirectory;
		private File dir;

		public RebaseState(File repoDirectory) {
			this.repoDirectory = repoDirectory;
		}

		public File getDir() {
			if (dir == null) {
				File rebaseApply = new File(repoDirectory, REBASE_APPLY);
				if (rebaseApply.exists()) {
					dir = rebaseApply;
				} else {
					File rebaseMerge = new File(repoDirectory, REBASE_MERGE);
					dir = rebaseMerge;
				}
			}
			return dir;
		}

		
Returns:
Directory with rewritten commit hashes, usually exists if RebaseCommand.preserveMerges is true/**
		 * @return Directory with rewritten commit hashes, usually exists if
		 *         {@link RebaseCommand#preserveMerges} is true
		 **/
		public File getRewrittenDir() {
			return new File(getDir(), REWRITTEN);
		}

		public String readFile(String name) throws IOException {
			try {
				return readFile(getDir(), name);
			} catch (FileNotFoundException e) {
				if (ONTO_NAME.equals(name)) {
					// Older JGit mistakenly wrote a file "onto-name" instead of
					// "onto_name". Try that wrong name just in case somebody
					// upgraded while a rebase started by JGit was in progress.
					File oldFile = getFile(ONTO_NAME.replace('_', '-'));
					if (oldFile.exists()) {
						return readFile(oldFile);
					}
				}
				throw e;
			}
		}

		public void createFile(String name, String content) throws IOException {
			createFile(getDir(), name, content);
		}

		public File getFile(String name) {
			return new File(getDir(), name);
		}

		public String getPath(String name) {
			return (getDir().getName() + "/" + name); //$NON-NLS-1$
		}

		private static String readFile(File file) throws IOException {
			byte[] content = IO.readFully(file);
			// strip off the last LF
			int end = RawParseUtils.prevLF(content, content.length);
			return RawParseUtils.decode(content, 0, end + 1);
		}

		private static String readFile(File directory, String fileName)
				throws IOException {
			return readFile(new File(directory, fileName));
		}

		private static void createFile(File parentDir, String name,
				String content)
				throws IOException {
			File file = new File(parentDir, name);
			try (FileOutputStream fos = new FileOutputStream(file)) {
				fos.write(content.getBytes(UTF_8));
				fos.write('\n');
			}
		}

		private static void appendToFile(File file, String content)
				throws IOException {
			try (FileOutputStream fos = new FileOutputStream(file, true)) {
				fos.write(content.getBytes(UTF_8));
				fos.write('\n');
			}
		}
	}
}