org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java - sop/jgit - Git at Google

 /*
  * Copyright (C) 2012, 2017 GitHub Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
  * under the terms of the Eclipse Distribution License v1.0 which
  * accompanies this distribution, is reproduced below, and is
  * available at http://www.eclipse.org/org/documents/edl-v10.php
  *
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or
  * without modification, are permitted provided that the following
  * conditions are met:
  *
  * - Redistributions of source code must retain the above copyright
  *   notice, this list of conditions and the following disclaimer.
  *
  * - Redistributions in binary form must reproduce the above
  *   copyright notice, this list of conditions and the following
  *   disclaimer in the documentation and/or other materials provided
  *   with the distribution.
  *
  * - Neither the name of the Eclipse Foundation, Inc. nor the
  *   names of its contributors may be used to endorse or promote
  *   products derived from this software without specific prior
  *   written permission.
  *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
  * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
  * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
  * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
  * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
  * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
  * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
  * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
  * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
  * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
  * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
  * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
  * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 package org.eclipse.jgit.api;

 import java.io.IOException;
 import java.text.MessageFormat;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;

 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRefNameException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.NoHeadException;
 import org.eclipse.jgit.api.errors.StashApplyFailureException;
 import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheBuilder;
 import org.eclipse.jgit.dircache.DirCacheCheckout;
 import org.eclipse.jgit.dircache.DirCacheCheckout.CheckoutMetadata;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.dircache.DirCacheIterator;
 import org.eclipse.jgit.errors.CheckoutConflictException;
 import org.eclipse.jgit.events.WorkingTreeModifiedEvent;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.CoreConfig.EolStreamType;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.RepositoryState;
 import org.eclipse.jgit.merge.MergeStrategy;
 import org.eclipse.jgit.merge.ResolveMerger;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevTree;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.treewalk.AbstractTreeIterator;
 import org.eclipse.jgit.treewalk.FileTreeIterator;
 import org.eclipse.jgit.treewalk.TreeWalk;

 /**
  * Command class to apply a stashed commit.
  *
  * This class behaves like <em>git stash apply --index</em>, i.e. it tries to
  * recover the stashed index state in addition to the working tree state.
  *
  * @see <a href="http://www.kernel.org/pub/software/scm/git/docs/git-stash.html"
  *      >Git documentation about Stash</a>
  *
  * @since 2.0
  */
 public class StashApplyCommand extends GitCommand<ObjectId> {

 	private static final String DEFAULT_REF = Constants.STASH + "@{0}"; //$NON-NLS-1$

 	private String stashRef;

 	private boolean applyIndex = true;

 	private boolean applyUntracked = true;

 	private boolean ignoreRepositoryState;

 	private MergeStrategy strategy = MergeStrategy.RECURSIVE;

 	/**
 	 * Create command to apply the changes of a stashed commit
 	 *
 	 * @param repo
 	 */
 	public StashApplyCommand(final Repository repo) {
 		super(repo);
 	}

 	/**
 	 * Set the stash reference to apply
 	 * <p>
 	 * This will default to apply the latest stashed commit (stash@{0}) if
 	 * unspecified
 	 *
 	 * @param stashRef
 	 * @return {@code this}
 	 */
 	public StashApplyCommand setStashRef(final String stashRef) {
 		this.stashRef = stashRef;
 		return this;
 	}

 	/**
 	 * @param willIgnoreRepositoryState
 	 * @return {@code this}
 	 * @since 3.2
 	 */
 	public StashApplyCommand ignoreRepositoryState(boolean willIgnoreRepositoryState) {
 		this.ignoreRepositoryState = willIgnoreRepositoryState;
 		return this;
 	}

 	private ObjectId getStashId() throws GitAPIException {
 		final String revision = stashRef != null ? stashRef : DEFAULT_REF;
 		final ObjectId stashId;
 		try {
 			stashId = repo.resolve(revision);
 		} catch (IOException e) {
 			throw new InvalidRefNameException(MessageFormat.format(
 					JGitText.get().stashResolveFailed, revision), e);
 		}
 		if (stashId == null)
 			throw new InvalidRefNameException(MessageFormat.format(
 					JGitText.get().stashResolveFailed, revision));
 		return stashId;
 	}

 	/**
 	 * Apply the changes in a stashed commit to the working directory and index
 	 *
 	 * @return id of stashed commit that was applied TODO: Does anyone depend on
 	 *         this, or could we make it more like Merge/CherryPick/Revert?
 	 * @throws GitAPIException
 	 * @throws WrongRepositoryStateException
 	 * @throws NoHeadException
 	 * @throws StashApplyFailureException
 	 */
 	@Override
 	public ObjectId call() throws GitAPIException,
 			WrongRepositoryStateException, NoHeadException,
 			StashApplyFailureException {
 		checkCallable();

 		if (!ignoreRepositoryState
 				&& repo.getRepositoryState() != RepositoryState.SAFE)
 			throw new WrongRepositoryStateException(MessageFormat.format(
 					JGitText.get().stashApplyOnUnsafeRepository,
 					repo.getRepositoryState()));

 		try (ObjectReader reader = repo.newObjectReader();
 				RevWalk revWalk = new RevWalk(reader)) {

 			ObjectId headCommit = repo.resolve(Constants.HEAD);
 			if (headCommit == null)
 				throw new NoHeadException(JGitText.get().stashApplyWithoutHead);

 			final ObjectId stashId = getStashId();
 			RevCommit stashCommit = revWalk.parseCommit(stashId);
 			if (stashCommit.getParentCount() < 2
 					|| stashCommit.getParentCount() > 3)
 				throw new JGitInternalException(MessageFormat.format(
 						JGitText.get().stashCommitIncorrectNumberOfParents,
 						stashId.name(),
 						Integer.valueOf(stashCommit.getParentCount())));

 			ObjectId headTree = repo.resolve(Constants.HEAD + "^{tree}"); //$NON-NLS-1$
 			ObjectId stashIndexCommit = revWalk.parseCommit(stashCommit
 					.getParent(1));
 			ObjectId stashHeadCommit = stashCommit.getParent(0);
 			ObjectId untrackedCommit = null;
 			if (applyUntracked && stashCommit.getParentCount() == 3)
 				untrackedCommit = revWalk.parseCommit(stashCommit.getParent(2));

 			ResolveMerger merger = (ResolveMerger) strategy.newMerger(repo);
 			merger.setCommitNames(new String[] { "stashed HEAD", "HEAD", //$NON-NLS-1$ //$NON-NLS-2$
 					"stash" }); //$NON-NLS-1$
 			merger.setBase(stashHeadCommit);
 			merger.setWorkingTreeIterator(new FileTreeIterator(repo));
 			boolean mergeSucceeded = merger.merge(headCommit, stashCommit);
 			List<String> modifiedByMerge = merger.getModifiedFiles();
 			if (!modifiedByMerge.isEmpty()) {
 				repo.fireEvent(
 						new WorkingTreeModifiedEvent(modifiedByMerge, null));
 			}
 			if (mergeSucceeded) {
 				DirCache dc = repo.lockDirCache();
 				DirCacheCheckout dco = new DirCacheCheckout(repo, headTree,
 						dc, merger.getResultTreeId());
 				dco.setFailOnConflict(true);
 				dco.checkout(); // Ignoring failed deletes....
 				if (applyIndex) {
 					ResolveMerger ixMerger = (ResolveMerger) strategy
 							.newMerger(repo, true);
 					ixMerger.setCommitNames(new String[] { "stashed HEAD", //$NON-NLS-1$
 							"HEAD", "stashed index" }); //$NON-NLS-1$//$NON-NLS-2$
 					ixMerger.setBase(stashHeadCommit);
 					boolean ok = ixMerger.merge(headCommit, stashIndexCommit);
 					if (ok) {
 						resetIndex(revWalk
 								.parseTree(ixMerger.getResultTreeId()));
 					} else {
 						throw new StashApplyFailureException(
 								JGitText.get().stashApplyConflict);
 					}
 				}

 				if (untrackedCommit != null) {
 					ResolveMerger untrackedMerger = (ResolveMerger) strategy
 							.newMerger(repo, true);
 					untrackedMerger.setCommitNames(new String[] {
 							"null", "HEAD", "untracked files" }); //$NON-NLS-1$//$NON-NLS-2$//$NON-NLS-3$
 					// There is no common base for HEAD & untracked files
 					// because the commit for untracked files has no parent. If
 					// we use stashHeadCommit as common base (as in the other
 					// merges) we potentially report conflicts for files
 					// which are not even member of untracked files commit
 					untrackedMerger.setBase(null);
 					boolean ok = untrackedMerger.merge(headCommit,
 							untrackedCommit);
 					if (ok) {
 						try {
 							RevTree untrackedTree = revWalk
 									.parseTree(untrackedCommit);
 							resetUntracked(untrackedTree);
 						} catch (CheckoutConflictException e) {
 							throw new StashApplyFailureException(
 									JGitText.get().stashApplyConflict, e);
 						}
 					} else {
 						throw new StashApplyFailureException(
 								JGitText.get().stashApplyConflict);
 					}
 				}
 			} else {
 				throw new StashApplyFailureException(
 						JGitText.get().stashApplyConflict);
 			}
 			return stashId;

 		} catch (JGitInternalException e) {
 			throw e;
 		} catch (IOException e) {
 			throw new JGitInternalException(JGitText.get().stashApplyFailed, e);
 		}
 	}

 	/**
 	 * @param applyIndex
 	 *            true (default) if the command should restore the index state
 	 */
 	public void setApplyIndex(boolean applyIndex) {
 		this.applyIndex = applyIndex;
 	}

 	/**
 	 * @param strategy
 	 *            The merge strategy to use in order to merge during this
 	 *            command execution.
 	 * @return {@code this}
 	 * @since 3.4
 	 */
 	public StashApplyCommand setStrategy(MergeStrategy strategy) {
 		this.strategy = strategy;
 		return this;
 	}

 	/**
 	 * @param applyUntracked
 	 *            true (default) if the command should restore untracked files
 	 * @since 3.4
 	 */
 	public void setApplyUntracked(boolean applyUntracked) {
 		this.applyUntracked = applyUntracked;
 	}

 	private void resetIndex(RevTree tree) throws IOException {
 		DirCache dc = repo.lockDirCache();
 		try (TreeWalk walk = new TreeWalk(repo)) {
 			DirCacheBuilder builder = dc.builder();

 			walk.addTree(tree);
 			walk.addTree(new DirCacheIterator(dc));
 			walk.setRecursive(true);

 			while (walk.next()) {
 				AbstractTreeIterator cIter = walk.getTree(0,
 						AbstractTreeIterator.class);
 				if (cIter == null) {
 					// Not in commit, don't add to new index
 					continue;
 				}

 				final DirCacheEntry entry = new DirCacheEntry(walk.getRawPath());
 				entry.setFileMode(cIter.getEntryFileMode());
 				entry.setObjectIdFromRaw(cIter.idBuffer(), cIter.idOffset());

 				DirCacheIterator dcIter = walk.getTree(1,
 						DirCacheIterator.class);
 				if (dcIter != null && dcIter.idEqual(cIter)) {
 					DirCacheEntry indexEntry = dcIter.getDirCacheEntry();
 					entry.setLastModified(indexEntry.getLastModified());
 					entry.setLength(indexEntry.getLength());
 				}

 				builder.add(entry);
 			}

 			builder.commit();
 		} finally {
 			dc.unlock();
 		}
 	}

 	private void resetUntracked(RevTree tree) throws CheckoutConflictException,
 			IOException {
 		Set<String> actuallyModifiedPaths = new HashSet<>();
 		// TODO maybe NameConflictTreeWalk ?
 		try (TreeWalk walk = new TreeWalk(repo)) {
 			walk.addTree(tree);
 			walk.addTree(new FileTreeIterator(repo));
 			walk.setRecursive(true);

 			final ObjectReader reader = walk.getObjectReader();

 			while (walk.next()) {
 				final AbstractTreeIterator cIter = walk.getTree(0,
 						AbstractTreeIterator.class);
 				if (cIter == null)
 					// Not in commit, don't create untracked
 					continue;

 				final EolStreamType eolStreamType = walk.getEolStreamType();
 				final DirCacheEntry entry = new DirCacheEntry(walk.getRawPath());
 				entry.setFileMode(cIter.getEntryFileMode());
 				entry.setObjectIdFromRaw(cIter.idBuffer(), cIter.idOffset());

 				FileTreeIterator fIter = walk
 						.getTree(1, FileTreeIterator.class);
 				if (fIter != null) {
 					if (fIter.isModified(entry, true, reader)) {
 						// file exists and is dirty
 						throw new CheckoutConflictException(
 								entry.getPathString());
 					}
 				}

 				checkoutPath(entry, reader,
 						new CheckoutMetadata(eolStreamType, null));
 				actuallyModifiedPaths.add(entry.getPathString());
 			}
 		} finally {
 			if (!actuallyModifiedPaths.isEmpty()) {
 				repo.fireEvent(new WorkingTreeModifiedEvent(
 						actuallyModifiedPaths, null));
 			}
 		}
 	}

 	private void checkoutPath(DirCacheEntry entry, ObjectReader reader,
 			CheckoutMetadata checkoutMetadata) {
 		try {
 			DirCacheCheckout.checkoutEntry(repo, entry, reader, true,
 					checkoutMetadata);
 		} catch (IOException e) {
 			throw new JGitInternalException(MessageFormat.format(
 					JGitText.get().checkoutConflictWithFile,
 					entry.getPathString()), e);
 		}
 	}
 }
	/*
	* Copyright (C) 2012, 2017 GitHub Inc.
	* and other copyright owners as documented in the project's IP log.
	*
	* This program and the accompanying materials are made available
	* under the terms of the Eclipse Distribution License v1.0 which
	* accompanies this distribution, is reproduced below, and is
	* available at http://www.eclipse.org/org/documents/edl-v10.php
	*
	* All rights reserved.
	*
	* Redistribution and use in source and binary forms, with or
	* without modification, are permitted provided that the following
	* conditions are met:
	*
	* - Redistributions of source code must retain the above copyright
	* notice, this list of conditions and the following disclaimer.
	*
	* - Redistributions in binary form must reproduce the above
	* copyright notice, this list of conditions and the following
	* disclaimer in the documentation and/or other materials provided
	* with the distribution.
	*
	* - Neither the name of the Eclipse Foundation, Inc. nor the
	* names of its contributors may be used to endorse or promote
	* products derived from this software without specific prior
	* written permission.
	*
	* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
	* CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
	* INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
	* OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
	* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
	* CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
	* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
	* NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
	* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
	* CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
	* STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
	* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
	* ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
	*/
	package org.eclipse.jgit.api;

	import java.io.IOException;
	import java.text.MessageFormat;
	import java.util.HashSet;
	import java.util.List;
	import java.util.Set;

	import org.eclipse.jgit.api.errors.GitAPIException;
	import org.eclipse.jgit.api.errors.InvalidRefNameException;
	import org.eclipse.jgit.api.errors.JGitInternalException;
	import org.eclipse.jgit.api.errors.NoHeadException;
	import org.eclipse.jgit.api.errors.StashApplyFailureException;
	import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
	import org.eclipse.jgit.dircache.DirCache;
	import org.eclipse.jgit.dircache.DirCacheBuilder;
	import org.eclipse.jgit.dircache.DirCacheCheckout;
	import org.eclipse.jgit.dircache.DirCacheCheckout.CheckoutMetadata;
	import org.eclipse.jgit.dircache.DirCacheEntry;
	import org.eclipse.jgit.dircache.DirCacheIterator;
	import org.eclipse.jgit.errors.CheckoutConflictException;
	import org.eclipse.jgit.events.WorkingTreeModifiedEvent;
	import org.eclipse.jgit.internal.JGitText;
	import org.eclipse.jgit.lib.Constants;
	import org.eclipse.jgit.lib.CoreConfig.EolStreamType;
	import org.eclipse.jgit.lib.ObjectId;
	import org.eclipse.jgit.lib.ObjectReader;
	import org.eclipse.jgit.lib.Repository;
	import org.eclipse.jgit.lib.RepositoryState;
	import org.eclipse.jgit.merge.MergeStrategy;
	import org.eclipse.jgit.merge.ResolveMerger;
	import org.eclipse.jgit.revwalk.RevCommit;
	import org.eclipse.jgit.revwalk.RevTree;
	import org.eclipse.jgit.revwalk.RevWalk;
	import org.eclipse.jgit.treewalk.AbstractTreeIterator;
	import org.eclipse.jgit.treewalk.FileTreeIterator;
	import org.eclipse.jgit.treewalk.TreeWalk;

	/**
	* Command class to apply a stashed commit.
	*
	* This class behaves like <em>git stash apply --index</em>, i.e. it tries to
	* recover the stashed index state in addition to the working tree state.
	*
	* @see <a href="http://www.kernel.org/pub/software/scm/git/docs/git-stash.html"
	* >Git documentation about Stash</a>
	*
	* @since 2.0
	*/
	public class StashApplyCommand extends GitCommand<ObjectId> {

	private static final String DEFAULT_REF = Constants.STASH + "@{0}"; //$NON-NLS-1$

	private String stashRef;

	private boolean applyIndex = true;

	private boolean applyUntracked = true;

	private boolean ignoreRepositoryState;

	private MergeStrategy strategy = MergeStrategy.RECURSIVE;

	/**
	* Create command to apply the changes of a stashed commit
	*
	* @param repo
	*/
	public StashApplyCommand(final Repository repo) {
	super(repo);
	}

	/**
	* Set the stash reference to apply
	* <p>
	* This will default to apply the latest stashed commit (stash@{0}) if
	* unspecified
	*
	* @param stashRef
	* @return {@code this}
	*/
	public StashApplyCommand setStashRef(final String stashRef) {
	this.stashRef = stashRef;
	return this;
	}

	/**
	* @param willIgnoreRepositoryState
	* @return {@code this}
	* @since 3.2
	*/
	public StashApplyCommand ignoreRepositoryState(boolean willIgnoreRepositoryState) {
	this.ignoreRepositoryState = willIgnoreRepositoryState;
	return this;
	}

	private ObjectId getStashId() throws GitAPIException {
	final String revision = stashRef != null ? stashRef : DEFAULT_REF;
	final ObjectId stashId;
	try {
	stashId = repo.resolve(revision);
	} catch (IOException e) {
	throw new InvalidRefNameException(MessageFormat.format(
	JGitText.get().stashResolveFailed, revision), e);
	}
	if (stashId == null)
	throw new InvalidRefNameException(MessageFormat.format(
	JGitText.get().stashResolveFailed, revision));
	return stashId;
	}

	/**
	* Apply the changes in a stashed commit to the working directory and index
	*
	* @return id of stashed commit that was applied TODO: Does anyone depend on
	* this, or could we make it more like Merge/CherryPick/Revert?
	* @throws GitAPIException
	* @throws WrongRepositoryStateException
	* @throws NoHeadException
	* @throws StashApplyFailureException
	*/
	@Override
	public ObjectId call() throws GitAPIException,
	WrongRepositoryStateException, NoHeadException,
	StashApplyFailureException {
	checkCallable();

	if (!ignoreRepositoryState
	&& repo.getRepositoryState() != RepositoryState.SAFE)
	throw new WrongRepositoryStateException(MessageFormat.format(
	JGitText.get().stashApplyOnUnsafeRepository,
	repo.getRepositoryState()));

	try (ObjectReader reader = repo.newObjectReader();
	RevWalk revWalk = new RevWalk(reader)) {

	ObjectId headCommit = repo.resolve(Constants.HEAD);
	if (headCommit == null)
	throw new NoHeadException(JGitText.get().stashApplyWithoutHead);

	final ObjectId stashId = getStashId();
	RevCommit stashCommit = revWalk.parseCommit(stashId);
	if (stashCommit.getParentCount() < 2
	\|\| stashCommit.getParentCount() > 3)
	throw new JGitInternalException(MessageFormat.format(
	JGitText.get().stashCommitIncorrectNumberOfParents,
	stashId.name(),
	Integer.valueOf(stashCommit.getParentCount())));

	ObjectId headTree = repo.resolve(Constants.HEAD + "^{tree}"); //$NON-NLS-1$
	ObjectId stashIndexCommit = revWalk.parseCommit(stashCommit
	.getParent(1));
	ObjectId stashHeadCommit = stashCommit.getParent(0);
	ObjectId untrackedCommit = null;
	if (applyUntracked && stashCommit.getParentCount() == 3)
	untrackedCommit = revWalk.parseCommit(stashCommit.getParent(2));

	ResolveMerger merger = (ResolveMerger) strategy.newMerger(repo);
	merger.setCommitNames(new String[] { "stashed HEAD", "HEAD", //$NON-NLS-1$ //$NON-NLS-2$
	"stash" }); //$NON-NLS-1$
	merger.setBase(stashHeadCommit);
	merger.setWorkingTreeIterator(new FileTreeIterator(repo));
	boolean mergeSucceeded = merger.merge(headCommit, stashCommit);
	List<String> modifiedByMerge = merger.getModifiedFiles();
	if (!modifiedByMerge.isEmpty()) {
	repo.fireEvent(
	new WorkingTreeModifiedEvent(modifiedByMerge, null));
	}
	if (mergeSucceeded) {
	DirCache dc = repo.lockDirCache();
	DirCacheCheckout dco = new DirCacheCheckout(repo, headTree,
	dc, merger.getResultTreeId());
	dco.setFailOnConflict(true);
	dco.checkout(); // Ignoring failed deletes....
	if (applyIndex) {
	ResolveMerger ixMerger = (ResolveMerger) strategy
	.newMerger(repo, true);
	ixMerger.setCommitNames(new String[] { "stashed HEAD", //$NON-NLS-1$
	"HEAD", "stashed index" }); //$NON-NLS-1$//$NON-NLS-2$
	ixMerger.setBase(stashHeadCommit);
	boolean ok = ixMerger.merge(headCommit, stashIndexCommit);
	if (ok) {
	resetIndex(revWalk
	.parseTree(ixMerger.getResultTreeId()));
	} else {
	throw new StashApplyFailureException(
	JGitText.get().stashApplyConflict);
	}
	}

	if (untrackedCommit != null) {
	ResolveMerger untrackedMerger = (ResolveMerger) strategy
	.newMerger(repo, true);
	untrackedMerger.setCommitNames(new String[] {
	"null", "HEAD", "untracked files" }); //$NON-NLS-1$//$NON-NLS-2$//$NON-NLS-3$
	// There is no common base for HEAD & untracked files
	// because the commit for untracked files has no parent. If
	// we use stashHeadCommit as common base (as in the other
	// merges) we potentially report conflicts for files
	// which are not even member of untracked files commit
	untrackedMerger.setBase(null);
	boolean ok = untrackedMerger.merge(headCommit,
	untrackedCommit);
	if (ok) {
	try {
	RevTree untrackedTree = revWalk
	.parseTree(untrackedCommit);
	resetUntracked(untrackedTree);
	} catch (CheckoutConflictException e) {
	throw new StashApplyFailureException(
	JGitText.get().stashApplyConflict, e);
	}
	} else {
	throw new StashApplyFailureException(
	JGitText.get().stashApplyConflict);
	}
	}
	} else {
	throw new StashApplyFailureException(
	JGitText.get().stashApplyConflict);
	}
	return stashId;

	} catch (JGitInternalException e) {
	throw e;
	} catch (IOException e) {
	throw new JGitInternalException(JGitText.get().stashApplyFailed, e);
	}
	}

	/**
	* @param applyIndex
	* true (default) if the command should restore the index state
	*/
	public void setApplyIndex(boolean applyIndex) {
	this.applyIndex = applyIndex;
	}

	/**
	* @param strategy
	* The merge strategy to use in order to merge during this
	* command execution.
	* @return {@code this}
	* @since 3.4
	*/
	public StashApplyCommand setStrategy(MergeStrategy strategy) {
	this.strategy = strategy;
	return this;
	}

	/**
	* @param applyUntracked
	* true (default) if the command should restore untracked files
	* @since 3.4
	*/
	public void setApplyUntracked(boolean applyUntracked) {
	this.applyUntracked = applyUntracked;
	}

	private void resetIndex(RevTree tree) throws IOException {
	DirCache dc = repo.lockDirCache();
	try (TreeWalk walk = new TreeWalk(repo)) {
	DirCacheBuilder builder = dc.builder();

	walk.addTree(tree);
	walk.addTree(new DirCacheIterator(dc));
	walk.setRecursive(true);

	while (walk.next()) {
	AbstractTreeIterator cIter = walk.getTree(0,
	AbstractTreeIterator.class);
	if (cIter == null) {
	// Not in commit, don't add to new index
	continue;
	}

	final DirCacheEntry entry = new DirCacheEntry(walk.getRawPath());
	entry.setFileMode(cIter.getEntryFileMode());
	entry.setObjectIdFromRaw(cIter.idBuffer(), cIter.idOffset());

	DirCacheIterator dcIter = walk.getTree(1,
	DirCacheIterator.class);
	if (dcIter != null && dcIter.idEqual(cIter)) {
	DirCacheEntry indexEntry = dcIter.getDirCacheEntry();
	entry.setLastModified(indexEntry.getLastModified());
	entry.setLength(indexEntry.getLength());
	}

	builder.add(entry);
	}

	builder.commit();
	} finally {
	dc.unlock();
	}
	}

	private void resetUntracked(RevTree tree) throws CheckoutConflictException,
	IOException {
	Set<String> actuallyModifiedPaths = new HashSet<>();
	// TODO maybe NameConflictTreeWalk ?
	try (TreeWalk walk = new TreeWalk(repo)) {
	walk.addTree(tree);
	walk.addTree(new FileTreeIterator(repo));
	walk.setRecursive(true);

	final ObjectReader reader = walk.getObjectReader();

	while (walk.next()) {
	final AbstractTreeIterator cIter = walk.getTree(0,
	AbstractTreeIterator.class);
	if (cIter == null)
	// Not in commit, don't create untracked
	continue;

	final EolStreamType eolStreamType = walk.getEolStreamType();
	final DirCacheEntry entry = new DirCacheEntry(walk.getRawPath());
	entry.setFileMode(cIter.getEntryFileMode());
	entry.setObjectIdFromRaw(cIter.idBuffer(), cIter.idOffset());

	FileTreeIterator fIter = walk
	.getTree(1, FileTreeIterator.class);
	if (fIter != null) {
	if (fIter.isModified(entry, true, reader)) {
	// file exists and is dirty
	throw new CheckoutConflictException(
	entry.getPathString());
	}
	}

	checkoutPath(entry, reader,
	new CheckoutMetadata(eolStreamType, null));
	actuallyModifiedPaths.add(entry.getPathString());
	}
	} finally {
	if (!actuallyModifiedPaths.isEmpty()) {
	repo.fireEvent(new WorkingTreeModifiedEvent(
	actuallyModifiedPaths, null));
	}
	}
	}

	private void checkoutPath(DirCacheEntry entry, ObjectReader reader,
	CheckoutMetadata checkoutMetadata) {
	try {
	DirCacheCheckout.checkoutEntry(repo, entry, reader, true,
	checkoutMetadata);
	} catch (IOException e) {
	throw new JGitInternalException(MessageFormat.format(
	JGitText.get().checkoutConflictWithFile,
	entry.getPathString()), e);
	}
	}
	}