/*
    * Copyright (C) 2007, Dave Watson <dwatson@mimvista.com>
    * Copyright (C) 2008, Robin Rosenberg <robin.rosenberg@dewire.com>
    * Copyright (C) 2008, Roger C. Soares <rogersoares@intelinet.com.br>
    * Copyright (C) 2006, Shawn O. Pearce <spearce@spearce.org>
    * Copyright (C) 2010, Chrisian Halstrick <christian.halstrick@sap.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.dircache;
  
  import static org.eclipse.jgit.treewalk.TreeWalk.OperationType.CHECKOUT_OP;
  
  import java.io.File;
  import java.io.FileOutputStream;
  import java.io.IOException;
  import java.io.OutputStream;
  import java.nio.file.StandardCopyOption;
  import java.text.MessageFormat;
  import java.time.Instant;
  import java.util.ArrayList;
  import java.util.HashMap;
  import java.util.HashSet;
  import java.util.Iterator;
  import java.util.List;
  import java.util.Map;
  import java.util.Set;
  
  import org.eclipse.jgit.api.errors.CanceledException;
  import org.eclipse.jgit.api.errors.FilterFailedException;
  import org.eclipse.jgit.attributes.FilterCommand;
  import org.eclipse.jgit.attributes.FilterCommandRegistry;
  import org.eclipse.jgit.errors.CheckoutConflictException;
  import org.eclipse.jgit.errors.CorruptObjectException;
  import org.eclipse.jgit.errors.IncorrectObjectTypeException;
  import org.eclipse.jgit.errors.IndexWriteException;
  import org.eclipse.jgit.errors.MissingObjectException;
  import org.eclipse.jgit.events.WorkingTreeModifiedEvent;
  import org.eclipse.jgit.internal.JGitText;
  import org.eclipse.jgit.lib.ConfigConstants;
  import org.eclipse.jgit.lib.Constants;
  import org.eclipse.jgit.lib.CoreConfig.AutoCRLF;
  import org.eclipse.jgit.lib.CoreConfig.EolStreamType;
  import org.eclipse.jgit.lib.CoreConfig.SymLinks;
  import org.eclipse.jgit.lib.FileMode;
  import org.eclipse.jgit.lib.NullProgressMonitor;
  import org.eclipse.jgit.lib.ObjectChecker;
  import org.eclipse.jgit.lib.ObjectId;
  import org.eclipse.jgit.lib.ObjectLoader;
  import org.eclipse.jgit.lib.ObjectReader;
  import org.eclipse.jgit.lib.ProgressMonitor;
  import org.eclipse.jgit.lib.Repository;
  import org.eclipse.jgit.treewalk.AbstractTreeIterator;
  import org.eclipse.jgit.treewalk.CanonicalTreeParser;
  import org.eclipse.jgit.treewalk.EmptyTreeIterator;
  import org.eclipse.jgit.treewalk.FileTreeIterator;
  import org.eclipse.jgit.treewalk.NameConflictTreeWalk;
  import org.eclipse.jgit.treewalk.TreeWalk;
  import org.eclipse.jgit.treewalk.WorkingTreeIterator;
  import org.eclipse.jgit.treewalk.WorkingTreeOptions;
  import org.eclipse.jgit.treewalk.filter.PathFilter;
  import org.eclipse.jgit.util.FS;
  import org.eclipse.jgit.util.FS.ExecutionResult;
  import org.eclipse.jgit.util.FileUtils;
  import org.eclipse.jgit.util.IntList;
  import org.eclipse.jgit.util.RawParseUtils;
 import org.eclipse.jgit.util.SystemReader;
 import org.eclipse.jgit.util.io.EolStreamTypeUtil;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /**
  * This class handles checking out one or two trees merging with the index.
  */
 public class DirCacheCheckout {
 	private static Logger LOG = LoggerFactory.getLogger(DirCacheCheckout.class);
 
 	private static final int MAX_EXCEPTION_TEXT_SIZE = 10 * 1024;
 
 	/**
 	 * Metadata used in checkout process
 	 *
 	 * @since 4.3
 	 */
 	public static class CheckoutMetadata {
 		/** git attributes */
 		public final EolStreamType eolStreamType;
 
 		/** filter command to apply */
 		public final String smudgeFilterCommand;
 
 		/**
 		 * @param eolStreamType
 		 * @param smudgeFilterCommand
 		 */
 		public CheckoutMetadata(EolStreamType eolStreamType,
 				String smudgeFilterCommand) {
 			this.eolStreamType = eolStreamType;
 			this.smudgeFilterCommand = smudgeFilterCommand;
 		}
 
 		static CheckoutMetadata EMPTY = new CheckoutMetadata(
 				EolStreamType.DIRECT, null);
 	}
 
 	private Repository repo;
 
 	private HashMap<String, CheckoutMetadata> updated = new HashMap<>();
 
 	private ArrayList<String> conflicts = new ArrayList<>();
 
 	private ArrayList<String> removed = new ArrayList<>();
 
 	private ArrayList<String> kept = new ArrayList<>();
 
 	private ObjectId mergeCommitTree;
 
 	private DirCache dc;
 
 	private DirCacheBuilder builder;
 
 	private NameConflictTreeWalk walk;
 
 	private ObjectId headCommitTree;
 
 	private WorkingTreeIterator workingTree;
 
 	private boolean failOnConflict = true;
 
 	private boolean force = false;
 
 	private ArrayList<String> toBeDeleted = new ArrayList<>();
 
 	private boolean initialCheckout;
 
 	private boolean performingCheckout;
 
 	private ProgressMonitor monitor = NullProgressMonitor.INSTANCE;
 
 	/**
 	 * Get list of updated paths and smudgeFilterCommands
 	 *
 	 * @return a list of updated paths and smudgeFilterCommands
 	 */
 	public Map<String, CheckoutMetadata> getUpdated() {
 		return updated;
 	}
 
 	/**
 	 * Get a list of conflicts created by this checkout
 	 *
 	 * @return a list of conflicts created by this checkout
 	 */
 	public List<String> getConflicts() {
 		return conflicts;
 	}
 
 	/**
 	 * Get list of paths of files which couldn't be deleted during last call to
 	 * {@link #checkout()}
 	 *
 	 * @return a list of paths (relative to the start of the working tree) of
 	 *         files which couldn't be deleted during last call to
 	 *         {@link #checkout()} . {@link #checkout()} detected that these
 	 *         files should be deleted but the deletion in the filesystem failed
 	 *         (e.g. because a file was locked). To have a consistent state of
 	 *         the working tree these files have to be deleted by the callers of
 	 *         {@link org.eclipse.jgit.dircache.DirCacheCheckout}.
 	 */
 	public List<String> getToBeDeleted() {
 		return toBeDeleted;
 	}
 
 	/**
 	 * Get list of all files removed by this checkout
 	 *
 	 * @return a list of all files removed by this checkout
 	 */
 	public List<String> getRemoved() {
 		return removed;
 	}
 
 	/**
 	 * Constructs a DirCacheCeckout for merging and checking out two trees (HEAD
 	 * and mergeCommitTree) and the index.
 	 *
 	 * @param repo
 	 *            the repository in which we do the checkout
 	 * @param headCommitTree
 	 *            the id of the tree of the head commit
 	 * @param dc
 	 *            the (already locked) Dircache for this repo
 	 * @param mergeCommitTree
 	 *            the id of the tree we want to fast-forward to
 	 * @param workingTree
 	 *            an iterator over the repositories Working Tree
 	 * @throws java.io.IOException
 	 */
 	public DirCacheCheckout(Repository repo, ObjectId headCommitTree, DirCache dc,
 			ObjectId mergeCommitTree, WorkingTreeIterator workingTree)
 			throws IOException {
 		this.repo = repo;
 		this.dc = dc;
 		this.headCommitTree = headCommitTree;
 		this.mergeCommitTree = mergeCommitTree;
 		this.workingTree = workingTree;
 		this.initialCheckout = !repo.isBare() && !repo.getIndexFile().exists();
 	}
 
 	/**
 	 * Constructs a DirCacheCeckout for merging and checking out two trees (HEAD
 	 * and mergeCommitTree) and the index. As iterator over the working tree
 	 * this constructor creates a standard
 	 * {@link org.eclipse.jgit.treewalk.FileTreeIterator}
 	 *
 	 * @param repo
 	 *            the repository in which we do the checkout
 	 * @param headCommitTree
 	 *            the id of the tree of the head commit
 	 * @param dc
 	 *            the (already locked) Dircache for this repo
 	 * @param mergeCommitTree
 	 *            the id of the tree we want to fast-forward to
 	 * @throws java.io.IOException
 	 */
 	public DirCacheCheckout(Repository repo, ObjectId headCommitTree,
 			DirCache dc, ObjectId mergeCommitTree) throws IOException {
 		this(repo, headCommitTree, dc, mergeCommitTree, new FileTreeIterator(repo));
 	}
 
 	/**
 	 * Constructs a DirCacheCeckout for checking out one tree, merging with the
 	 * index.
 	 *
 	 * @param repo
 	 *            the repository in which we do the checkout
 	 * @param dc
 	 *            the (already locked) Dircache for this repo
 	 * @param mergeCommitTree
 	 *            the id of the tree we want to fast-forward to
 	 * @param workingTree
 	 *            an iterator over the repositories Working Tree
 	 * @throws java.io.IOException
 	 */
 	public DirCacheCheckout(Repository repo, DirCache dc,
 			ObjectId mergeCommitTree, WorkingTreeIterator workingTree)
 			throws IOException {
 		this(repo, null, dc, mergeCommitTree, workingTree);
 	}
 
 	/**
 	 * Constructs a DirCacheCeckout for checking out one tree, merging with the
 	 * index. As iterator over the working tree this constructor creates a
 	 * standard {@link org.eclipse.jgit.treewalk.FileTreeIterator}
 	 *
 	 * @param repo
 	 *            the repository in which we do the checkout
 	 * @param dc
 	 *            the (already locked) Dircache for this repo
 	 * @param mergeCommitTree
 	 *            the id of the tree of the
 	 * @throws java.io.IOException
 	 */
 	public DirCacheCheckout(Repository repo, DirCache dc,
 			ObjectId mergeCommitTree) throws IOException {
 		this(repo, null, dc, mergeCommitTree, new FileTreeIterator(repo));
 	}
 
 	/**
 	 * Set a progress monitor which can be passed to built-in filter commands,
 	 * providing progress information for long running tasks.
 	 *
 	 * @param monitor
 	 *            the {@link ProgressMonitor}
 	 * @since 4.11
 	 */
 	public void setProgressMonitor(ProgressMonitor monitor) {
 		this.monitor = monitor != null ? monitor : NullProgressMonitor.INSTANCE;
 	}
 
 	/**
 	 * Scan head, index and merge tree. Used during normal checkout or merge
 	 * operations.
 	 *
 	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 * @throws java.io.IOException
 	 */
 	public void preScanTwoTrees() throws CorruptObjectException, IOException {
 		removed.clear();
 		updated.clear();
 		conflicts.clear();
 		walk = new NameConflictTreeWalk(repo);
 		builder = dc.builder();
 
 		addTree(walk, headCommitTree);
 		addTree(walk, mergeCommitTree);
 		int dciPos = walk.addTree(new DirCacheBuildIterator(builder));
 		walk.addTree(workingTree);
 		workingTree.setDirCacheIterator(walk, dciPos);
 
 		while (walk.next()) {
 			processEntry(walk.getTree(0, CanonicalTreeParser.class),
 					walk.getTree(1, CanonicalTreeParser.class),
 					walk.getTree(2, DirCacheBuildIterator.class),
 					walk.getTree(3, WorkingTreeIterator.class));
 			if (walk.isSubtree())
 				walk.enterSubtree();
 		}
 	}
 
 	private void addTree(TreeWalk tw, ObjectId id) throws MissingObjectException, IncorrectObjectTypeException, IOException {
 		if (id == null)
 			tw.addTree(new EmptyTreeIterator());
 		else
 			tw.addTree(id);
 	}
 
 	/**
 	 * Scan index and merge tree (no HEAD). Used e.g. for initial checkout when
 	 * there is no head yet.
 	 *
 	 * @throws org.eclipse.jgit.errors.MissingObjectException
 	 * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
 	 * @throws org.eclipse.jgit.errors.CorruptObjectException
 	 * @throws java.io.IOException
 	 */
 	public void prescanOneTree()
 			throws MissingObjectException, IncorrectObjectTypeException,
 			CorruptObjectException, IOException {
 		removed.clear();
 		updated.clear();
 		conflicts.clear();
 
 		builder = dc.builder();
 
 		walk = new NameConflictTreeWalk(repo);
 		addTree(walk, mergeCommitTree);
 		int dciPos = walk.addTree(new DirCacheBuildIterator(builder));
 		walk.addTree(workingTree);
 		workingTree.setDirCacheIterator(walk, dciPos);
 
 		while (walk.next()) {
 			processEntry(walk.getTree(0, CanonicalTreeParser.class),
 					walk.getTree(1, DirCacheBuildIterator.class),
 					walk.getTree(2, WorkingTreeIterator.class));
 			if (walk.isSubtree())
 				walk.enterSubtree();
 		}
 		conflicts.removeAll(removed);
 	}
 
 	/**
 	 * Processing an entry in the context of {@link #prescanOneTree()} when only
 	 * one tree is given
 	 *
 	 * @param m the tree to merge
 	 * @param i the index
 	 * @param f the working tree
 	 * @throws IOException
 	 */
 	void processEntry(CanonicalTreeParser m, DirCacheBuildIterator i,
 			WorkingTreeIterator f) throws IOException {
 		if (m != null) {
 			checkValidPath(m);
 			// There is an entry in the merge commit. Means: we want to update
 			// what's currently in the index and working-tree to that one
 			if (i == null) {
 				// The index entry is missing
 				if (f != null && !FileMode.TREE.equals(f.getEntryFileMode())
 						&& !f.isEntryIgnored()) {
 					if (failOnConflict) {
 						// don't overwrite an untracked and not ignored file
 						conflicts.add(walk.getPathString());
 					} else {
 						// failOnConflict is false. Putting something to conflicts
 						// would mean we delete it. Instead we want the mergeCommit
 						// content to be checked out.
 						update(m.getEntryPathString(), m.getEntryObjectId(),
 								m.getEntryFileMode());
 					}
 				} else
 					update(m.getEntryPathString(), m.getEntryObjectId(),
 						m.getEntryFileMode());
 			} else if (f == null || !m.idEqual(i)) {
 				// The working tree file is missing or the merge content differs
 				// from index content
 				update(m.getEntryPathString(), m.getEntryObjectId(),
 						m.getEntryFileMode());
 			} else if (i.getDirCacheEntry() != null) {
 				// The index contains a file (and not a folder)
 				if (f.isModified(i.getDirCacheEntry(), true,
 						this.walk.getObjectReader())
 						|| i.getDirCacheEntry().getStage() != 0)
 					// The working tree file is dirty or the index contains a
 					// conflict
 					update(m.getEntryPathString(), m.getEntryObjectId(),
 							m.getEntryFileMode());
 				else {
 					// update the timestamp of the index with the one from the
 					// file if not set, as we are sure to be in sync here.
 					DirCacheEntry entry = i.getDirCacheEntry();
 					Instant mtime = entry.getLastModifiedInstant();
 					if (mtime == null || mtime.equals(Instant.EPOCH)) {
 						entry.setLastModified(f.getEntryLastModifiedInstant());
 					}
 					keep(i.getEntryPathString(), entry, f);
 				}
 			} else
 				// The index contains a folder
 				keep(i.getEntryPathString(), i.getDirCacheEntry(), f);
 		} else {
 			// There is no entry in the merge commit. Means: we want to delete
 			// what's currently in the index and working tree
 			if (f != null) {
 				// There is a file/folder for that path in the working tree
 				if (walk.isDirectoryFileConflict()) {
 					// We put it in conflicts. Even if failOnConflict is false
 					// this would cause the path to be deleted. Thats exactly what
 					// we want in this situation
 					conflicts.add(walk.getPathString());
 				} else {
 					// No file/folder conflict exists. All entries are files or
 					// all entries are folders
 					if (i != null) {
 						// ... and the working tree contained a file or folder
 						// -> add it to the removed set and remove it from
 						// conflicts set
 						remove(i.getEntryPathString());
 						conflicts.remove(i.getEntryPathString());
 					} else {
 						// untracked file, neither contained in tree to merge
 						// nor in index
 					}
 				}
 			} else {
 				// There is no file/folder for that path in the working tree,
 				// nor in the merge head.
 				// The only entry we have is the index entry. Like the case
 				// where there is a file with the same name, remove it,
 			}
 		}
 	}
 
 	/**
 	 * Execute this checkout. A
 	 * {@link org.eclipse.jgit.events.WorkingTreeModifiedEvent} is fired if the
 	 * working tree was modified; even if the checkout fails.
 	 *
 	 * @return <code>false</code> if this method could not delete all the files
 	 *         which should be deleted (e.g. because one of the files was
 	 *         locked). In this case {@link #getToBeDeleted()} lists the files
 	 *         which should be tried to be deleted outside of this method.
 	 *         Although <code>false</code> is returned the checkout was
 	 *         successful and the working tree was updated for all other files.
 	 *         <code>true</code> is returned when no such problem occurred
 	 * @throws java.io.IOException
 	 */
 	public boolean checkout() throws IOException {
 		try {
 			return doCheckout();
 		} catch (CanceledException ce) {
 			// should actually be propagated, but this would change a LOT of
 			// APIs
 			throw new IOException(ce);
 		} finally {
 			try {
 				dc.unlock();
 			} finally {
 				if (performingCheckout) {
 					Set<String> touched = new HashSet<>(conflicts);
 					touched.addAll(getUpdated().keySet());
 					touched.addAll(kept);
 					WorkingTreeModifiedEvent event = new WorkingTreeModifiedEvent(
 							touched, getRemoved());
 					if (!event.isEmpty()) {
 						repo.fireEvent(event);
 					}
 				}
 			}
 		}
 	}
 
 	private boolean doCheckout() throws CorruptObjectException, IOException,
 			MissingObjectException, IncorrectObjectTypeException,
 			CheckoutConflictException, IndexWriteException, CanceledException {
 		toBeDeleted.clear();
 		try (ObjectReader objectReader = repo.getObjectDatabase().newReader()) {
 			if (headCommitTree != null)
 				preScanTwoTrees();
 			else
 				prescanOneTree();
 
 			if (!conflicts.isEmpty()) {
 				if (failOnConflict) {
 					throw new CheckoutConflictException(conflicts.toArray(new String[0]));
 				}
 				cleanUpConflicts();
 			}
 
 			// update our index
 			builder.finish();
 
 			// init progress reporting
 			int numTotal = removed.size() + updated.size() + conflicts.size();
 			monitor.beginTask(JGitText.get().checkingOutFiles, numTotal);
 
 			performingCheckout = true;
 			File file = null;
 			String last = null;
 			// when deleting files process them in the opposite order as they have
 			// been reported. This ensures the files are deleted before we delete
 			// their parent folders
 			IntList nonDeleted = new IntList();
 			for (int i = removed.size() - 1; i >= 0; i--) {
 				String r = removed.get(i);
 				file = new File(repo.getWorkTree(), r);
 				if (!file.delete() && repo.getFS().exists(file)) {
 					// The list of stuff to delete comes from the index
 					// which will only contain a directory if it is
 					// a submodule, in which case we shall not attempt
 					// to delete it. A submodule is not empty, so it
 					// is safe to check this after a failed delete.
 					if (!repo.getFS().isDirectory(file)) {
 						nonDeleted.add(i);
 						toBeDeleted.add(r);
 					}
 				} else {
 					if (last != null && !isSamePrefix(r, last))
 						removeEmptyParents(new File(repo.getWorkTree(), last));
 					last = r;
 				}
 				monitor.update(1);
 				if (monitor.isCancelled()) {
 					throw new CanceledException(MessageFormat.format(
 							JGitText.get().operationCanceled,
 							JGitText.get().checkingOutFiles));
 				}
 			}
 			if (file != null) {
 				removeEmptyParents(file);
 			}
 			removed = filterOut(removed, nonDeleted);
 			nonDeleted = null;
 			Iterator<Map.Entry<String, CheckoutMetadata>> toUpdate = updated
 					.entrySet().iterator();
 			Map.Entry<String, CheckoutMetadata> e = null;
 			try {
 				while (toUpdate.hasNext()) {
 					e = toUpdate.next();
 					String path = e.getKey();
 					CheckoutMetadata meta = e.getValue();
 					DirCacheEntry entry = dc.getEntry(path);
 					if (FileMode.GITLINK.equals(entry.getRawMode())) {
 						checkoutGitlink(path, entry);
 					} else {
 						checkoutEntry(repo, entry, objectReader, false, meta);
 					}
 					e = null;
 
 					monitor.update(1);
 					if (monitor.isCancelled()) {
 						throw new CanceledException(MessageFormat.format(
 								JGitText.get().operationCanceled,
 								JGitText.get().checkingOutFiles));
 					}
 				}
 			} catch (Exception ex) {
 				// We didn't actually modify the current entry nor any that
 				// might follow.
 				if (e != null) {
 					toUpdate.remove();
 				}
 				while (toUpdate.hasNext()) {
 					e = toUpdate.next();
 					toUpdate.remove();
 				}
 				throw ex;
 			}
 			for (String conflict : conflicts) {
 				// the conflicts are likely to have multiple entries in the
 				// dircache, we only want to check out the one for the "theirs"
 				// tree
 				int entryIdx = dc.findEntry(conflict);
 				if (entryIdx >= 0) {
 					while (entryIdx < dc.getEntryCount()) {
 						DirCacheEntry entry = dc.getEntry(entryIdx);
 						if (!entry.getPathString().equals(conflict)) {
 							break;
 						}
 						if (entry.getStage() == DirCacheEntry.STAGE_3) {
 							checkoutEntry(repo, entry, objectReader, false,
 									null);
 							break;
 						}
 						++entryIdx;
 					}
 				}
 
 				monitor.update(1);
 				if (monitor.isCancelled()) {
 					throw new CanceledException(MessageFormat.format(
 							JGitText.get().operationCanceled,
 							JGitText.get().checkingOutFiles));
 				}
 			}
 			monitor.endTask();
 
 			// commit the index builder - a new index is persisted
 			if (!builder.commit())
 				throw new IndexWriteException();
 		}
 		return toBeDeleted.isEmpty();
 	}
 
 	private void checkoutGitlink(String path, DirCacheEntry entry)
 			throws IOException {
 		File gitlinkDir = new File(repo.getWorkTree(), path);
 		FileUtils.mkdirs(gitlinkDir, true);
 		FS fs = repo.getFS();
 		entry.setLastModified(fs.lastModifiedInstant(gitlinkDir));
 	}
 
 	private static ArrayList<String> filterOut(ArrayList<String> strings,
 			IntList indicesToRemove) {
 		int n = indicesToRemove.size();
 		if (n == strings.size()) {
 			return new ArrayList<>(0);
 		}
 		switch (n) {
 		case 0:
 			return strings;
 		case 1:
 			strings.remove(indicesToRemove.get(0));
 			return strings;
 		default:
 			int length = strings.size();
 			ArrayList<String> result = new ArrayList<>(length - n);
 			// Process indicesToRemove from the back; we know that it
 			// contains indices in descending order.
 			int j = n - 1;
 			int idx = indicesToRemove.get(j);
 			for (int i = 0; i < length; i++) {
 				if (i == idx) {
 					idx = (--j >= 0) ? indicesToRemove.get(j) : -1;
 				} else {
 					result.add(strings.get(i));
 				}
 			}
 			return result;
 		}
 	}
 
 	private static boolean isSamePrefix(String a, String b) {
 		int as = a.lastIndexOf('/');
 		int bs = b.lastIndexOf('/');
 		return a.substring(0, as + 1).equals(b.substring(0, bs + 1));
 	}
 
 	 private void removeEmptyParents(File f) {
 		File parentFile = f.getParentFile();
 
 		while (parentFile != null && !parentFile.equals(repo.getWorkTree())) {
 			if (!parentFile.delete())
 				break;
 			parentFile = parentFile.getParentFile();
 		}
 	}
 
 	/**
 	 * Compares whether two pairs of ObjectId and FileMode are equal.
 	 *
 	 * @param id1
 	 * @param mode1
 	 * @param id2
 	 * @param mode2
 	 * @return <code>true</code> if FileModes and ObjectIds are equal.
 	 *         <code>false</code> otherwise
 	 */
 	private boolean equalIdAndMode(ObjectIdrg/eclipse/jgit/lib/ObjectId.html#ObjectId">ObjectId id1, FileMode mode1, ObjectId id2,
 			FileMode mode2) {
 		if (!mode1.equals(mode2))
 			return false;
 		return id1 != null ? id1.equals(id2) : id2 == null;
 	}
 
 	/**
 	 * Here the main work is done. This method is called for each existing path
 	 * in head, index and merge. This method decides what to do with the
 	 * corresponding index entry: keep it, update it, remove it or mark a
 	 * conflict.
 	 *
 	 * @param h
 	 *            the entry for the head
 	 * @param m
 	 *            the entry for the merge
 	 * @param i
 	 *            the entry for the index
 	 * @param f
 	 *            the file in the working tree
 	 * @throws IOException
 	 */
 
 	void processEntry(CanonicalTreeParser../../org/eclipse/jgit/treewalk/CanonicalTreeParser.html#CanonicalTreeParser">CanonicalTreeParser h, CanonicalTreeParser m,
 			DirCacheBuildIterator i, WorkingTreeIterator f) throws IOException {
 		DirCacheEntry dce = i != null ? i.getDirCacheEntry() : null;
 
 		String name = walk.getPathString();
 
 		if (m != null)
 			checkValidPath(m);
 
 		if (i == null && m == null && h == null) {
 			// File/Directory conflict case #20
 			if (walk.isDirectoryFileConflict())
 				// TODO: check whether it is always correct to report a conflict here
 				conflict(name, null, null, null);
 
 			// file only exists in working tree -> ignore it
 			return;
 		}
 
 		ObjectId iId = (i == null ? null : i.getEntryObjectId());
 		ObjectId mId = (m == null ? null : m.getEntryObjectId());
 		ObjectId hId = (h == null ? null : h.getEntryObjectId());
 		FileMode iMode = (i == null ? null : i.getEntryFileMode());
 		FileMode mMode = (m == null ? null : m.getEntryFileMode());
 		FileMode hMode = (h == null ? null : h.getEntryFileMode());
 
 		/**
 		 * <pre>
 		 *  File/Directory conflicts:
 		 *  the following table from ReadTreeTest tells what to do in case of directory/file
 		 *  conflicts. I give comments here
 		 *
 		 *      H        I       M     Clean     H==M     H==I    I==M         Result
 		 *      ------------------------------------------------------------------
 		 * 1    D        D       F       Y         N       Y       N           Update
 		 * 2    D        D       F       N         N       Y       N           Conflict
 		 * 3    D        F       D                 Y       N       N           Keep
 		 * 4    D        F       D                 N       N       N           Conflict
 		 * 5    D        F       F       Y         N       N       Y           Keep
 		 * 5b   D        F       F       Y         N       N       N           Conflict
 		 * 6    D        F       F       N         N       N       Y           Keep
 		 * 6b   D        F       F       N         N       N       N           Conflict
 		 * 7    F        D       F       Y         Y       N       N           Update
 		 * 8    F        D       F       N         Y       N       N           Conflict
 		 * 9    F        D       F                 N       N       N           Conflict
 		 * 10   F        D       D                 N       N       Y           Keep
 		 * 11   F        D       D                 N       N       N           Conflict
 		 * 12   F        F       D       Y         N       Y       N           Update
 		 * 13   F        F       D       N         N       Y       N           Conflict
 		 * 14   F        F       D                 N       N       N           Conflict
 		 * 15   0        F       D                 N       N       N           Conflict
 		 * 16   0        D       F       Y         N       N       N           Update
 		 * 17   0        D       F                 N       N       N           Conflict
 		 * 18   F        0       D                                             Update
 		 * 19   D        0       F                                             Update
 		 * 20   0        0       F       N (worktree=dir)                      Conflict
 		 * </pre>
 		 */
 
 		// The information whether head,index,merge iterators are currently
 		// pointing to file/folder/non-existing is encoded into this variable.
 		//
 		// To decode write down ffMask in hexadecimal form. The last digit
 		// represents the state for the merge iterator, the second last the
 		// state for the index iterator and the third last represents the state
 		// for the head iterator. The hexadecimal constant "F" stands for
 		// "file", a "D" stands for "directory" (tree), and a "0" stands for
 		// non-existing. Symbolic links and git links are treated as File here.
 		//
 		// Examples:
 		// ffMask == 0xFFD -> Head=File, Index=File, Merge=Tree
 		// ffMask == 0xDD0 -> Head=Tree, Index=Tree, Merge=Non-Existing
 
 		int ffMask = 0;
 		if (h != null)
 			ffMask = FileMode.TREE.equals(hMode) ? 0xD00 : 0xF00;
 		if (i != null)
 			ffMask |= FileMode.TREE.equals(iMode) ? 0x0D0 : 0x0F0;
 		if (m != null)
 			ffMask |= FileMode.TREE.equals(mMode) ? 0x00D : 0x00F;
 
 		// Check whether we have a possible file/folder conflict. Therefore we
 		// need a least one file and one folder.
 		if (((ffMask & 0x222) != 0x000)
 				&& (((ffMask & 0x00F) == 0x00D) || ((ffMask & 0x0F0) == 0x0D0) || ((ffMask & 0xF00) == 0xD00))) {
 
 			// There are 3*3*3=27 possible combinations of file/folder
 			// conflicts. Some of them are not-relevant because
 			// they represent no conflict, e.g. 0xFFF, 0xDDD, ... The following
 			// switch processes all relevant cases.
 			switch (ffMask) {
 			case 0xDDF: // 1 2
 				if (f != null && isModifiedSubtree_IndexWorkingtree(name)) {
 					conflict(name, dce, h, m); // 1
 				} else {
 					update(name, mId, mMode); // 2
 				}
 
 				break;
 			case 0xDFD: // 3 4
 				keep(name, dce, f);
 				break;
 			case 0xF0D: // 18
 				remove(name);
 				break;
 			case 0xDFF: // 5 5b 6 6b
 				if (equalIdAndMode(iId, iMode, mId, mMode))
 					keep(name, dce, f); // 5 6
 				else
 					conflict(name, dce, h, m); // 5b 6b
 				break;
 			case 0xFDD: // 10 11
 				// TODO: make use of tree extension as soon as available in jgit
 				// we would like to do something like
 				// if (!equalIdAndMode(iId, iMode, mId, mMode)
 				//   conflict(name, i.getDirCacheEntry(), h, m);
 				// But since we don't know the id of a tree in the index we do
 				// nothing here and wait that conflicts between index and merge
 				// are found later
 				break;
 			case 0xD0F: // 19
 				update(name, mId, mMode);
 				break;
 			case 0xDF0: // conflict without a rule
 			case 0x0FD: // 15
 				conflict(name, dce, h, m);
 				break;
 			case 0xFDF: // 7 8 9
 				if (equalIdAndMode(hId, hMode, mId, mMode)) {
 					if (isModifiedSubtree_IndexWorkingtree(name))
 						conflict(name, dce, h, m); // 8
 					else
 						update(name, mId, mMode); // 7
 				} else
 					conflict(name, dce, h, m); // 9
 				break;
 			case 0xFD0: // keep without a rule
 				keep(name, dce, f);
 				break;
 			case 0xFFD: // 12 13 14
 				if (equalIdAndMode(hId, hMode, iId, iMode))
 					if (f != null
 							&& f.isModified(dce, true,
 									this.walk.getObjectReader()))
 						conflict(name, dce, h, m); // 13
 					else
 						remove(name); // 12
 				else
 					conflict(name, dce, h, m); // 14
 				break;
 			case 0x0DF: // 16 17
 				if (!isModifiedSubtree_IndexWorkingtree(name))
 					update(name, mId, mMode);
 				else
 					conflict(name, dce, h, m);
 				break;
 			default:
 				keep(name, dce, f);
 			}
 			return;
 		}
 
 		if ((ffMask & 0x222) == 0) {
 			// HEAD, MERGE and index don't contain a file (e.g. all contain a
 			// folder)
 			if (f == null || FileMode.TREE.equals(f.getEntryFileMode())) {
 				// the workingtree entry doesn't exist or also contains a folder
 				// -> no problem
 				return;
 			}
 			// the workingtree entry exists and is not a folder
 			if (!idEqual(h, m)) {
 				// Because HEAD and MERGE differ we will try to update the
 				// workingtree with a folder -> return a conflict
 				conflict(name, null, null, null);
 			}
 			return;
 		}
 
 		if ((ffMask == 0x00F) && f != null && FileMode.TREE.equals(f.getEntryFileMode())) {
 			// File/Directory conflict case #20
 			conflict(name, null, h, m);
 			return;
 		}
 
 		if (i == null) {
 			// Nothing in Index
 			// At least one of Head, Index, Merge is not empty
 			// make sure not to overwrite untracked files
 			if (f != null && !f.isEntryIgnored()) {
 				// A submodule is not a file. We should ignore it
 				if (!FileMode.GITLINK.equals(mMode)) {
 					// a dirty worktree: the index is empty but we have a
 					// workingtree-file
 					if (mId == null
 							|| !equalIdAndMode(mId, mMode,
 									f.getEntryObjectId(), f.getEntryFileMode())) {
 						conflict(name, null, h, m);
 						return;
 					}
 				}
 			}
 
 			/**
 			 * <pre>
 			 * 	          I (index)     H        M     H==M  Result
 			 * 	        -------------------------------------------
 			 * 	        0 nothing    nothing  nothing        (does not happen)
 			 * 	        1 nothing    nothing  exists         use M
 			 * 	        2 nothing    exists   nothing        remove path from index
 			 * 	        3 nothing    exists   exists   yes   keep index if not in initial checkout
 			 *                                               , otherwise use M
 			 * 	          nothing    exists   exists   no    fail
 			 * </pre>
 			 */
 
 			if (h == null)
 				// Nothing in Head
 				// Nothing in Index
 				// At least one of Head, Index, Merge is not empty
 				// -> only Merge contains something for this path. Use it!
 				// Potentially update the file
 				update(name, mId, mMode); // 1
 			else if (m == null)
 				// Nothing in Merge
 				// Something in Head
 				// Nothing in Index
 				// -> only Head contains something for this path and it should
 				// be deleted. Potentially removes the file!
 				remove(name); // 2
 			else { // 3
 				// Something in Merge
 				// Something in Head
 				// Nothing in Index
 				// -> Head and Merge contain something (maybe not the same) and
 				// in the index there is nothing (e.g. 'git rm ...' was
 				// called before). Ignore the cached deletion and use what we
 				// find in Merge. Potentially updates the file.
 				if (equalIdAndMode(hId, hMode, mId, mMode)) {
 					if (initialCheckout)
 						update(name, mId, mMode);
 					else
 						keep(name, dce, f);
 				} else
 					conflict(name, dce, h, m);
 			}
 		} else {
 			// Something in Index
 			if (h == null) {
 				// Nothing in Head
 				// Something in Index
 				/**
 				 * <pre>
 				 * 	          clean I==H  I==M       H        M        Result
 				 * 	         -----------------------------------------------------
 				 * 	        4 yes   N/A   N/A     nothing  nothing  keep index
 				 * 	        5 no    N/A   N/A     nothing  nothing  keep index
 				 *
 				 * 	        6 yes   N/A   yes     nothing  exists   keep index
 				 * 	        7 no    N/A   yes     nothing  exists   keep index
 				 * 	        8 yes   N/A   no      nothing  exists   fail
 				 * 	        9 no    N/A   no      nothing  exists   fail
 				 * </pre>
 				 */
 
 				if (m == null
 						|| !isModified_IndexTree(name, iId, iMode, mId, mMode,
 								mergeCommitTree)) {
 					// Merge contains nothing or the same as Index
 					// Nothing in Head
 					// Something in Index
 					if (m==null && walk.isDirectoryFileConflict()) {
 						// Nothing in Merge and current path is part of
 						// File/Folder conflict
 						// Nothing in Head
 						// Something in Index
 						if (dce != null
 								&& (f == null || f.isModified(dce, true,
 										this.walk.getObjectReader())))
 							// No file or file is dirty
 							// Nothing in Merge and current path is part of
 							// File/Folder conflict
 							// Nothing in Head
 							// Something in Index
 							// -> File folder conflict and Merge wants this
 							// path to be removed. Since the file is dirty
 							// report a conflict
 							conflict(name, dce, h, m);
 						else
 							// A file is present and file is not dirty
 							// Nothing in Merge and current path is part of
 							// File/Folder conflict
 							// Nothing in Head
 							// Something in Index
 							// -> File folder conflict and Merge wants this path
 							// to be removed. Since the file is not dirty remove
 							// file and index entry
 							remove(name);
 					} else
 						// Something in Merge or current path is not part of
 						// File/Folder conflict
 						// Merge contains nothing or the same as Index
 						// Nothing in Head
 						// Something in Index
 						// -> Merge contains nothing new. Keep the index.
 						keep(name, dce, f);
 				} else
 					// Merge contains something and it is not the same as Index
 					// Nothing in Head
 					// Something in Index
 					// -> Index contains something new (different from Head)
 					// and Merge is different from Index. Report a conflict
 					conflict(name, dce, h, m);
 			} else if (m == null) {
 				// Nothing in Merge
 				// Something in Head
 				// Something in Index
 
 				/**
 				 * <pre>
 				 * 	           clean I==H  I==M       H        M        Result
 				 * 	         -----------------------------------------------------
 				 * 	        10 yes   yes   N/A     exists   nothing  remove path from index
 				 * 	        11 no    yes   N/A     exists   nothing  keep file
 				 * 	        12 yes   no    N/A     exists   nothing  fail
 				 * 	        13 no    no    N/A     exists   nothing  fail
 				 * </pre>
 				 */
 
 				if (iMode == FileMode.GITLINK) {
 					// A submodule in Index
 					// Nothing in Merge
 					// Something in Head
 					// Submodules that disappear from the checkout must
 					// be removed from the index, but not deleted from disk.
 					remove(name);
 				} else {
 					// Something different from a submodule in Index
 					// Nothing in Merge
 					// Something in Head
 					if (!isModified_IndexTree(name, iId, iMode, hId, hMode,
 							headCommitTree)) {
 						// Index contains the same as Head
 						// Something different from a submodule in Index
 						// Nothing in Merge
 						// Something in Head
 						if (f != null
 								&& f.isModified(dce, true,
 										this.walk.getObjectReader())) {
 							// file is dirty
 							// Index contains the same as Head
 							// Something different from a submodule in Index
 							// Nothing in Merge
 							// Something in Head
 
 							if (!FileMode.TREE.equals(f.getEntryFileMode())
 									&& FileMode.TREE.equals(iMode)) {
 								// The workingtree contains a file and the index semantically contains a folder.
 								// Git considers the workingtree file as untracked. Just keep the untracked file.
 								return;
 							}
 							// -> file is dirty and tracked but is should be
 							// removed. That's a conflict
 							conflict(name, dce, h, m);
 						} else {
 							// file doesn't exist or is clean
 							// Index contains the same as Head
 							// Something different from a submodule in Index
 							// Nothing in Merge
 							// Something in Head
 							// -> Remove from index and delete the file
 							remove(name);
 						}
 					} else {
 						// Index contains something different from Head
 						// Something different from a submodule in Index
 						// Nothing in Merge
 						// Something in Head
 						// -> Something new is in index (and maybe even on the
 						// filesystem). But Merge wants the path to be removed.
 						// Report a conflict
 						conflict(name, dce, h, m);
 					}
 				}
 			} else {
 				// Something in Merge
 				// Something in Head
 				// Something in Index
 				if (!equalIdAndMode(hId, hMode, mId, mMode)
 						&& isModified_IndexTree(name, iId, iMode, hId, hMode,
 								headCommitTree)
 						&& isModified_IndexTree(name, iId, iMode, mId, mMode,
 								mergeCommitTree))
 					// All three contents in Head, Merge, Index differ from each
 					// other
 					// -> All contents differ. Report a conflict.
 					conflict(name, dce, h, m);
 				else
 					// At least two of the contents of Head, Index, Merge
 					// are the same
 					// Something in Merge
 					// Something in Head
 					// Something in Index
 
 				if (!isModified_IndexTree(name, iId, iMode, hId, hMode,
 						headCommitTree)
 						&& isModified_IndexTree(name, iId, iMode, mId, mMode,
 								mergeCommitTree)) {
 						// Head contains the same as Index. Merge differs
 						// Something in Merge
 
 					// For submodules just update the index with the new SHA-1
 					if (dce != null
 							&& FileMode.GITLINK.equals(dce.getFileMode())) {
 						// Index and Head contain the same submodule. Merge
 						// differs
 						// Something in Merge
 						// -> Nothing new in index. Move to merge.
 						// Potentially updates the file
 
 						// TODO check that we don't overwrite some unsaved
 						// file content
 						update(name, mId, mMode);
 					} else if (dce != null
 							&& (f != null && f.isModified(dce, true,
 									this.walk.getObjectReader()))) {
 						// File exists and is dirty
 						// Head and Index don't contain a submodule
 						// Head contains the same as Index. Merge differs
 						// Something in Merge
 						// -> Merge wants the index and file to be updated
 						// but the file is dirty. Report a conflict
 						conflict(name, dce, h, m);
 					} else {
 						// File doesn't exist or is clean
 						// Head and Index don't contain a submodule
 						// Head contains the same as Index. Merge differs
 						// Something in Merge
 						// -> Standard case when switching between branches:
 						// Nothing new in index but something different in
 						// Merge. Update index and file
 						update(name, mId, mMode);
 					}
 				} else {
 					// Head differs from index or merge is same as index
 					// At least two of the contents of Head, Index, Merge
 					// are the same
 					// Something in Merge
 					// Something in Head
 					// Something in Index
 
 					// Can be formulated as: Either all three states are
 					// equal or Merge is equal to Head or Index and differs
 					// to the other one.
 					// -> In all three cases we don't touch index and file.
 
 					keep(name, dce, f);
 				}
 			}
 		}
 	}
 
 	private static boolean idEqual(AbstractTreeIterator a,
 			AbstractTreeIterator b) {
 		if (a == b) {
 			return true;
 		}
 		if (a == null || b == null) {
 			return false;
 		}
 		return a.getEntryObjectId().equals(b.getEntryObjectId());
 	}
 
 	/**
 	 * A conflict is detected - add the three different stages to the index
 	 * @param path the path of the conflicting entry
 	 * @param e the previous index entry
 	 * @param h the first tree you want to merge (the HEAD)
 	 * @param m the second tree you want to merge
 	 */
 	private void conflict(String path, DirCacheEntry e, AbstractTreeIterator./../org/eclipse/jgit/treewalk/AbstractTreeIterator.html#AbstractTreeIterator">AbstractTreeIterator h, AbstractTreeIterator m) {
 		conflicts.add(path);
 
 		DirCacheEntry entry;
 		if (e != null) {
 			entry = new DirCacheEntry(e.getPathString(), DirCacheEntry.STAGE_1);
 			entry.copyMetaData(e, true);
 			builder.add(entry);
 		}
 
 		if (h != null && !FileMode.TREE.equals(h.getEntryFileMode())) {
 			entry = new DirCacheEntry(h.getEntryPathString(), DirCacheEntry.STAGE_2);
 			entry.setFileMode(h.getEntryFileMode());
 			entry.setObjectId(h.getEntryObjectId());
 			builder.add(entry);
 		}
 
 		if (m != null && !FileMode.TREE.equals(m.getEntryFileMode())) {
 			entry = new DirCacheEntry(m.getEntryPathString(), DirCacheEntry.STAGE_3);
 			entry.setFileMode(m.getEntryFileMode());
 			entry.setObjectId(m.getEntryObjectId());
 			builder.add(entry);
 		}
 	}
 
 	private void keep(String path, DirCacheEntry e, WorkingTreeIterator f)
 			throws IOException {
 		if (e != null && !FileMode.TREE.equals(e.getFileMode()))
 			builder.add(e);
 		if (force) {
 			if (f.isModified(e, true, walk.getObjectReader())) {
 				kept.add(path);
 				checkoutEntry(repo, e, walk.getObjectReader(), false,
 						new CheckoutMetadata(walk.getEolStreamType(CHECKOUT_OP),
 								walk.getFilterCommand(
 										Constants.ATTR_FILTER_TYPE_SMUDGE)));
 			}
 		}
 	}
 
 	private void remove(String path) {
 		removed.add(path);
 	}
 
 	private void update(String path, ObjectId mId, FileMode mode)
 			throws IOException {
 		if (!FileMode.TREE.equals(mode)) {
 			updated.put(path, new CheckoutMetadata(
 					walk.getEolStreamType(CHECKOUT_OP),
 					walk.getFilterCommand(Constants.ATTR_FILTER_TYPE_SMUDGE)));
 
 			DirCacheEntry entry = new DirCacheEntry(path, DirCacheEntry.STAGE_0);
 			entry.setObjectId(mId);
 			entry.setFileMode(mode);
 			builder.add(entry);
 		}
 	}
 
 	/**
 	 * If <code>true</code>, will scan first to see if it's possible to check
 	 * out, otherwise throw
 	 * {@link org.eclipse.jgit.errors.CheckoutConflictException}. If
 	 * <code>false</code>, it will silently deal with the problem.
 	 *
 	 * @param failOnConflict
 	 *            a boolean.
 	 */
 	public void setFailOnConflict(boolean failOnConflict) {
 		this.failOnConflict = failOnConflict;
 	}
 
 	/**
 	 * If <code>true</code>, dirty worktree files may be overridden. If
 	 * <code>false</code> dirty worktree files will not be overridden in order
 	 * not to delete unsaved content. This corresponds to native git's 'git
 	 * checkout -f' option. By default this option is set to false.
 	 *
 	 * @param force
 	 *            a boolean.
 	 * @since 5.3
 	 */
 	public void setForce(boolean force) {
 		this.force = force;
 	}
 
 	/**
 	 * This method implements how to handle conflicts when
 	 * {@link #failOnConflict} is false
 	 *
 	 * @throws CheckoutConflictException
 	 */
 	private void cleanUpConflicts() throws CheckoutConflictException {
 		// TODO: couldn't we delete unsaved worktree content here?
 		for (String c : conflicts) {
 			File conflict = new File(repo.getWorkTree(), c);
 			if (!conflict.delete())
 				throw new CheckoutConflictException(MessageFormat.format(
 						JGitText.get().cannotDeleteFile, c));
 			removeEmptyParents(conflict);
 		}
 	}
 
 	/**
 	 * Checks whether the subtree starting at a given path differs between Index and
 	 * workingtree.
 	 *
 	 * @param path
 	 * @return true if the subtrees differ
 	 * @throws CorruptObjectException
 	 * @throws IOException
 	 */
 	private boolean isModifiedSubtree_IndexWorkingtree(String path)
 			throws CorruptObjectException, IOException {
 		try (NameConflictTreeWalkTreeWalk.html#NameConflictTreeWalk">NameConflictTreeWalk tw = new NameConflictTreeWalk(repo)) {
 			int dciPos = tw.addTree(new DirCacheIterator(dc));
 			FileTreeIterator fti = new FileTreeIterator(repo);
 			tw.addTree(fti);
 			fti.setDirCacheIterator(tw, dciPos);
 			tw.setRecursive(true);
 			tw.setFilter(PathFilter.create(path));
 			DirCacheIterator dcIt;
 			WorkingTreeIterator wtIt;
 			while (tw.next()) {
 				dcIt = tw.getTree(0, DirCacheIterator.class);
 				wtIt = tw.getTree(1, WorkingTreeIterator.class);
 				if (dcIt == null || wtIt == null)
 					return true;
 				if (wtIt.isModified(dcIt.getDirCacheEntry(), true,
 						this.walk.getObjectReader())) {
 					return true;
 				}
 			}
 			return false;
 		}
 	}
 
 	private boolean isModified_IndexTree(String path, ObjectId iId,
 			FileMode iMode, ObjectIdrg/eclipse/jgit/lib/ObjectId.html#ObjectId">ObjectId tId, FileMode tMode, ObjectId rootTree)
 			throws CorruptObjectException, IOException {
 		if (iMode != tMode) {
 			return true;
 		}
 		if (FileMode.TREE.equals(iMode)
 				&& (iId == null || ObjectId.zeroId().equals(iId))) {
 			return isModifiedSubtree_IndexTree(path, rootTree);
 		}
 		return !equalIdAndMode(iId, iMode, tId, tMode);
 	}
 
 	/**
 	 * Checks whether the subtree starting at a given path differs between Index and
 	 * some tree.
 	 *
 	 * @param path
 	 * @param tree
 	 *            the tree to compare
 	 * @return true if the subtrees differ
 	 * @throws CorruptObjectException
 	 * @throws IOException
 	 */
 	private boolean isModifiedSubtree_IndexTree(String path, ObjectId tree)
 			throws CorruptObjectException, IOException {
 		try (NameConflictTreeWalkTreeWalk.html#NameConflictTreeWalk">NameConflictTreeWalk tw = new NameConflictTreeWalk(repo)) {
 			tw.addTree(new DirCacheIterator(dc));
 			tw.addTree(tree);
 			tw.setRecursive(true);
 			tw.setFilter(PathFilter.create(path));
 			while (tw.next()) {
 				AbstractTreeIterator dcIt = tw.getTree(0,
 						DirCacheIterator.class);
 				AbstractTreeIterator treeIt = tw.getTree(1,
 						AbstractTreeIterator.class);
 				if (dcIt == null || treeIt == null)
 					return true;
 				if (dcIt.getEntryRawMode() != treeIt.getEntryRawMode())
 					return true;
 				if (!dcIt.getEntryObjectId().equals(treeIt.getEntryObjectId()))
 					return true;
 			}
 			return false;
 		}
 	}
 
 	/**
 	 * Updates the file in the working tree with content and mode from an entry
 	 * in the index. The new content is first written to a new temporary file in
 	 * the same directory as the real file. Then that new file is renamed to the
 	 * final filename.
 	 *
 	 * <p>
 	 * <b>Note:</b> if the entry path on local file system exists as a non-empty
 	 * directory, and the target entry type is a link or file, the checkout will
 	 * fail with {@link java.io.IOException} since existing non-empty directory
 	 * cannot be renamed to file or link without deleting it recursively.
 	 * </p>
 	 *
 	 * <p>
 	 * TODO: this method works directly on File IO, we may need another
 	 * abstraction (like WorkingTreeIterator). This way we could tell e.g.
 	 * Eclipse that Files in the workspace got changed
 	 * </p>
 	 *
 	 * @param repo
 	 *            repository managing the destination work tree.
 	 * @param entry
 	 *            the entry containing new mode and content
 	 * @param or
 	 *            object reader to use for checkout
 	 * @throws java.io.IOException
 	 * @since 3.6
 	 * @deprecated since 5.1, use
 	 *             {@link #checkoutEntry(Repository, DirCacheEntry, ObjectReader, boolean, CheckoutMetadata)}
 	 *             instead
 	 */
 	@Deprecated
 	public static void checkoutEntry(Repository repo, DirCacheEntry entry,
 			ObjectReader or) throws IOException {
 		checkoutEntry(repo, entry, or, false, null);
 	}
 
 	/**
 	 * Updates the file in the working tree with content and mode from an entry
 	 * in the index. The new content is first written to a new temporary file in
 	 * the same directory as the real file. Then that new file is renamed to the
 	 * final filename.
 	 *
 	 * <p>
 	 * <b>Note:</b> if the entry path on local file system exists as a file, it
 	 * will be deleted and if it exists as a directory, it will be deleted
 	 * recursively, independently if has any content.
 	 * </p>
 	 *
 	 * <p>
 	 * TODO: this method works directly on File IO, we may need another
 	 * abstraction (like WorkingTreeIterator). This way we could tell e.g.
 	 * Eclipse that Files in the workspace got changed
 	 * </p>
 	 *
 	 * @param repo
 	 *            repository managing the destination work tree.
 	 * @param entry
 	 *            the entry containing new mode and content
 	 * @param or
 	 *            object reader to use for checkout
 	 * @param deleteRecursive
 	 *            true to recursively delete final path if it exists on the file
 	 *            system
 	 * @param checkoutMetadata
 	 *            containing
 	 *            <ul>
 	 *            <li>smudgeFilterCommand to be run for smudging the entry to be
 	 *            checked out</li>
 	 *            <li>eolStreamType used for stream conversion</li>
 	 *            </ul>
 	 * @throws java.io.IOException
 	 * @since 4.2
 	 */
 	public static void checkoutEntry(Repository repo, DirCacheEntry entry,
 			ObjectReader or, boolean deleteRecursive,
 			CheckoutMetadata checkoutMetadata) throws IOException {
 		if (checkoutMetadata == null)
 			checkoutMetadata = CheckoutMetadata.EMPTY;
 		ObjectLoader ol = or.open(entry.getObjectId());
 		File f = new File(repo.getWorkTree(), entry.getPathString());
 		File parentDir = f.getParentFile();
 		if (parentDir.isFile()) {
 			FileUtils.delete(parentDir);
 		}
 		FileUtils.mkdirs(parentDir, true);
 		FS fs = repo.getFS();
 		WorkingTreeOptions opt = repo.getConfig().get(WorkingTreeOptions.KEY);
 		if (entry.getFileMode() == FileMode.SYMLINK
 				&& opt.getSymLinks() == SymLinks.TRUE) {
 			byte[] bytes = ol.getBytes();
 			String target = RawParseUtils.decode(bytes);
 			if (deleteRecursive && f.isDirectory()) {
 				FileUtils.delete(f, FileUtils.RECURSIVE);
 			}
 			fs.createSymLink(f, target);
 			entry.setLength(bytes.length);
 			entry.setLastModified(fs.lastModifiedInstant(f));
 			return;
 		}
 
 		String name = f.getName();
 		if (name.length() > 200) {
 			name = name.substring(0, 200);
 		}
 		File tmpFile = File.createTempFile(
 				"._" + name, null, parentDir); //$NON-NLS-1$
 
 		EolStreamType nonNullEolStreamType;
 		if (checkoutMetadata.eolStreamType != null) {
 			nonNullEolStreamType = checkoutMetadata.eolStreamType;
 		} else if (opt.getAutoCRLF() == AutoCRLF.TRUE) {
 			nonNullEolStreamType = EolStreamType.AUTO_CRLF;
 		} else {
 			nonNullEolStreamType = EolStreamType.DIRECT;
 		}
 		try (OutputStream channel = EolStreamTypeUtil.wrapOutputStream(
 				new FileOutputStream(tmpFile), nonNullEolStreamType)) {
 			if (checkoutMetadata.smudgeFilterCommand != null) {
 				if (FilterCommandRegistry
 						.isRegistered(checkoutMetadata.smudgeFilterCommand)) {
 					runBuiltinFilterCommand(repo, checkoutMetadata, ol,
 							channel);
 				} else {
 					runExternalFilterCommand(repo, entry, checkoutMetadata, ol,
 							fs, channel);
 				}
 			} else {
 				ol.copyTo(channel);
 			}
 		}
 		// The entry needs to correspond to the on-disk filesize. If the content
 		// was filtered (either by autocrlf handling or smudge filters) ask the
 		// filesystem again for the length. Otherwise the objectloader knows the
 		// size
 		if (checkoutMetadata.eolStreamType == EolStreamType.DIRECT
 				&& checkoutMetadata.smudgeFilterCommand == null) {
 			entry.setLength(ol.getSize());
 		} else {
 			entry.setLength(tmpFile.length());
 		}
 
 		if (opt.isFileMode() && fs.supportsExecute()) {
 			if (FileMode.EXECUTABLE_FILE.equals(entry.getRawMode())) {
 				if (!fs.canExecute(tmpFile))
 					fs.setExecute(tmpFile, true);
 			} else {
 				if (fs.canExecute(tmpFile))
 					fs.setExecute(tmpFile, false);
 			}
 		}
 		try {
 			if (deleteRecursive && f.isDirectory()) {
 				FileUtils.delete(f, FileUtils.RECURSIVE);
 			}
 			FileUtils.rename(tmpFile, f, StandardCopyOption.ATOMIC_MOVE);
 		} catch (IOException e) {
 			throw new IOException(
 					MessageFormat.format(JGitText.get().renameFileFailed,
 							tmpFile.getPath(), f.getPath()),
 					e);
 		} finally {
 			if (tmpFile.exists()) {
 				FileUtils.delete(tmpFile);
 			}
 		}
 		entry.setLastModified(fs.lastModifiedInstant(f));
 	}
 
 	// Run an external filter command
 	private static void runExternalFilterCommand(Repository repo,
 			DirCacheEntry entry,
 			CheckoutMetadata checkoutMetadata, ObjectLoader ol, FS fs,
 			OutputStream channel) throws IOException {
 		ProcessBuilder filterProcessBuilder = fs.runInShell(
 				checkoutMetadata.smudgeFilterCommand, new String[0]);
 		filterProcessBuilder.directory(repo.getWorkTree());
 		filterProcessBuilder.environment().put(Constants.GIT_DIR_KEY,
 				repo.getDirectory().getAbsolutePath());
 		ExecutionResult result;
 		int rc;
 		try {
 			// TODO: wire correctly with AUTOCRLF
 			result = fs.execute(filterProcessBuilder, ol.openStream());
 			rc = result.getRc();
 			if (rc == 0) {
 				result.getStdout().writeTo(channel,
 						NullProgressMonitor.INSTANCE);
 			}
 		} catch (IOException | InterruptedException e) {
 			throw new IOException(new FilterFailedException(e,
 					checkoutMetadata.smudgeFilterCommand,
 					entry.getPathString()));
 		}
 		if (rc != 0) {
 			throw new IOException(new FilterFailedException(rc,
 					checkoutMetadata.smudgeFilterCommand,
 					entry.getPathString(),
 					result.getStdout().toByteArray(MAX_EXCEPTION_TEXT_SIZE),
 					RawParseUtils.decode(result.getStderr()
 							.toByteArray(MAX_EXCEPTION_TEXT_SIZE))));
 		}
 	}
 
 	// Run a builtin filter command
 	private static void runBuiltinFilterCommand(Repository repo,
 			CheckoutMetadata checkoutMetadata, ObjectLoader ol,
 			OutputStream channel) throws MissingObjectException, IOException {
 		boolean isMandatory = repo.getConfig().getBoolean(
 				ConfigConstants.CONFIG_FILTER_SECTION,
 				ConfigConstants.CONFIG_SECTION_LFS,
 				ConfigConstants.CONFIG_KEY_REQUIRED, false);
 		FilterCommand command = null;
 		try {
 			command = FilterCommandRegistry.createFilterCommand(
 					checkoutMetadata.smudgeFilterCommand, repo, ol.openStream(),
 					channel);
 		} catch (IOException e) {
 			LOG.error(JGitText.get().failedToDetermineFilterDefinition, e);
 			if (!isMandatory) {
 				// In case an IOException occurred during creating of the
 				// command then proceed as if there would not have been a
 				// builtin filter (only if the filter is not mandatory).
 				ol.copyTo(channel);
 			} else {
 				throw e;
 			}
 		}
 		if (command != null) {
 			while (command.run() != -1) {
 				// loop as long as command.run() tells there is work to do
 			}
 		}
 	}
 
 	@SuppressWarnings("deprecation")
 	private static void checkValidPath(CanonicalTreeParser t)
 			throws InvalidPathException {
 		ObjectChecker chk = new ObjectChecker()
 			.setSafeForWindows(SystemReader.getInstance().isWindows())
 			.setSafeForMacOS(SystemReader.getInstance().isMacOS());
 		for (CanonicalTreeParser i = t; i != null; i = i.getParent())
 			checkValidPathSegment(chk, i);
 	}
 
 	private static void checkValidPathSegment(ObjectChecker chk,
 			CanonicalTreeParser t) throws InvalidPathException {
 		try {
 			int ptr = t.getNameOffset();
 			int end = ptr + t.getNameLength();
 			chk.checkPathSegment(t.getEntryPathBuffer(), ptr, end);
 		} catch (CorruptObjectException err) {
 			String path = t.getEntryPathString();
 			InvalidPathException i = new InvalidPathException(path);
 			i.initCause(err);
 			throw i;
 		}
 	}
 }