Package org.eclipse.jgit.dircache

Source Code of org.eclipse.jgit.dircache.DirCacheCheckout

/*
* 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 java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.text.MessageFormat;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

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.internal.JGitText;
import org.eclipse.jgit.lib.Constants;
import org.eclipse.jgit.lib.CoreConfig.AutoCRLF;
import org.eclipse.jgit.lib.CoreConfig.SymLinks;
import org.eclipse.jgit.lib.FileMode;
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.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.FileUtils;
import org.eclipse.jgit.util.RawParseUtils;
import org.eclipse.jgit.util.SystemReader;
import org.eclipse.jgit.util.io.AutoCRLFOutputStream;

/**
* This class handles checking out one or two trees merging with the index.
*/
public class DirCacheCheckout {
  private Repository repo;

  private HashMap<String, ObjectId> updated = new HashMap<String, ObjectId>();

  private ArrayList<String> conflicts = new ArrayList<String>();

  private ArrayList<String> removed = new ArrayList<String>();

  private ObjectId mergeCommitTree;

  private DirCache dc;

  private DirCacheBuilder builder;

  private NameConflictTreeWalk walk;

  private ObjectId headCommitTree;

  private WorkingTreeIterator workingTree;

  private boolean failOnConflict = true;

  private ArrayList<String> toBeDeleted = new ArrayList<String>();

  private boolean emptyDirCache;

  /**
   * @return a list of updated paths and objectIds
   */
  public Map<String, ObjectId> getUpdated() {
    return updated;
  }

  /**
   * @return a list of conflicts created by this checkout
   */
  public List<String> getConflicts() {
    return conflicts;
  }

  /**
   * @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 DirCacheCheckout}.
   */
  public List<String> getToBeDeleted() {
    return toBeDeleted;
  }

  /**
   * @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 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.emptyDirCache = (dc == null) || (dc.getEntryCount() == 0);
  }

  /**
   * 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 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 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 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 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 IOException
   */
  public DirCacheCheckout(Repository repo, DirCache dc,
      ObjectId mergeCommitTree) throws IOException {
    this(repo, null, dc, mergeCommitTree, new FileTreeIterator(repo));
  }

  /**
   * Scan head, index and merge tree. Used during normal checkout or merge
   * operations.
   *
   * @throws CorruptObjectException
   * @throws 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);
    walk.addTree(new DirCacheBuildIterator(builder));
    walk.addTree(workingTree);

    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 MissingObjectException
   * @throws IncorrectObjectTypeException
   * @throws CorruptObjectException
   * @throws 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);
    walk.addTree(new DirCacheBuildIterator(builder));
    walk.addTree(workingTree);

    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()) {
          // don't overwrite an untracked and not ignored file
          conflicts.add(walk.getPathString());
        } 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();
          if (entry.getLastModified() == 0)
            entry.setLastModified(f.getEntryLastModified());
          keep(entry);
        }
      } else
        // The index contains a folder
        keep(i.getDirCacheEntry());
    } 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()) {
          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
   *
   * @return <code>false</code> if this method could not delete all the files
   *         which should be deleted (e.g. because of 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 IOException
   */
  public boolean checkout() throws IOException {
    try {
      return doCheckout();
    } finally {
      dc.unlock();
    }
  }

  private boolean doCheckout() throws CorruptObjectException, IOException,
      MissingObjectException, IncorrectObjectTypeException,
      CheckoutConflictException, IndexWriteException {
    toBeDeleted.clear();
    ObjectReader objectReader = repo.getObjectDatabase().newReader();
    try {
      if (headCommitTree != null)
        preScanTwoTrees();
      else
        prescanOneTree();

      if (!conflicts.isEmpty()) {
        if (failOnConflict)
          throw new CheckoutConflictException(conflicts.toArray(new String[conflicts.size()]));
        else
          cleanUpConflicts();
      }

      // update our index
      builder.finish();

      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
      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))
            toBeDeleted.add(r);
        } else {
          if (last != null && !isSamePrefix(r, last))
            removeEmptyParents(new File(repo.getWorkTree(), last));
          last = r;
        }
      }
      if (file != null)
        removeEmptyParents(file);

      for (String path : updated.keySet()) {
        // ... create/overwrite this file ...
        file = new File(repo.getWorkTree(), path);
        if (!file.getParentFile().mkdirs()) {
          // ignore
        }

        DirCacheEntry entry = dc.getEntry(path);

        // submodules are handled with separate operations
        if (FileMode.GITLINK.equals(entry.getRawMode()))
          continue;

        checkoutEntry(repo, file, entry, objectReader);
      }

      // commit the index builder - a new index is persisted
      if (!builder.commit())
        throw new IndexWriteException();
    } finally {
      objectReader.release();
    }
    return toBeDeleted.size() == 0;
  }

  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(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 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(dce);
        break;
      case 0xF0D: // 18
        remove(name);
        break;
      case 0xDFF: // 5 5b 6 6b
        if (equalIdAndMode(iId, iMode, mId, mMode))
          keep(dce); // 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(dce);
        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(dce);
      }
      return;
    }

    // if we have no file at all then there is nothing to do
    if ((ffMask & 0x222) == 0
        && (f == null || FileMode.TREE.equals(f.getEntryFileMode())))
      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 (emptyDirCache)
            update(name, mId, mMode);
          else
            keep(dce);
        } 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(dce);
        } 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;
              else
                // -> 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(dce);
        }
      }
    }
  }

  /**
   * 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 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(DirCacheEntry e) {
    if (e != null && !FileMode.TREE.equals(e.getFileMode()))
      builder.add(e);
  }

  private void remove(String path) {
    removed.add(path);
  }

  private void update(String path, ObjectId mId, FileMode mode) {
    if (!FileMode.TREE.equals(mode)) {
      updated.put(path, mId);
      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 CheckoutConflictException}. If
   * <code>false</code>, it will silently deal with the problem.
   *
   * @param failOnConflict
   */
  public void setFailOnConflict(boolean failOnConflict) {
    this.failOnConflict = failOnConflict;
  }

  /**
   * 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);
    }
    for (String r : removed) {
      File file = new File(repo.getWorkTree(), r);
      if (!file.delete())
        throw new CheckoutConflictException(
            MessageFormat.format(JGitText.get().cannotDeleteFile,
                file.getAbsolutePath()));
      removeEmptyParents(file);
    }
  }

  /**
   * 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 {
    NameConflictTreeWalk tw = new NameConflictTreeWalk(repo);
    try {
      tw.addTree(new DirCacheIterator(dc));
      tw.addTree(new FileTreeIterator(repo));
      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;
    } finally {
      tw.release();
    }
  }

  private boolean isModified_IndexTree(String path, ObjectId iId,
      FileMode iMode, 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);
    else
      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 {
    NameConflictTreeWalk tw = new NameConflictTreeWalk(repo);
    try {
      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;
    } finally {
      tw.release();
    }
  }

  /**
   * 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. Use this method only for checkout of a single entry.
   * Otherwise use
   * {@code checkoutEntry(Repository, File f, DirCacheEntry, ObjectReader)}
   * instead which allows to reuse one {@code ObjectReader} for multiple
   * entries.
   *
   * <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 repository
   * @param f
   *            the file to be modified. The parent directory for this file
   *            has to exist already
   * @param entry
   *            the entry containing new mode and content
   * @throws IOException
   */
  public static void checkoutEntry(final Repository repository, File f,
      DirCacheEntry entry) throws IOException {
    ObjectReader or = repository.newObjectReader();
    try {
      checkoutEntry(repository, f, entry, repository.newObjectReader());
    } finally {
      or.release();
    }
  }

  /**
   * 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>
   * 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
   * @param f
   *            the file to be modified. The parent directory for this file
   *            has to exist already
   * @param entry
   *            the entry containing new mode and content
   * @param or
   *            object reader to use for checkout
   * @throws IOException
   */
  public static void checkoutEntry(final Repository repo, File f,
      DirCacheEntry entry, ObjectReader or) throws IOException {
    ObjectLoader ol = or.open(entry.getObjectId());
    File parentDir = f.getParentFile();
    parentDir.mkdirs();
    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);
      fs.createSymLink(f, target);
      entry.setLength(bytes.length);
      entry.setLastModified(fs.lastModified(f));
    } else {
      File tmpFile = File.createTempFile(
          "._" + f.getName(), null, parentDir); //$NON-NLS-1$
      FileOutputStream rawChannel = new FileOutputStream(tmpFile);
      OutputStream channel;
      if (opt.getAutoCRLF() == AutoCRLF.TRUE)
        channel = new AutoCRLFOutputStream(rawChannel);
      else
        channel = rawChannel;
      try {
        ol.copyTo(channel);
      } finally {
        channel.close();
      }
      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 {
        FileUtils.rename(tmpFile, f);
      } catch (IOException e) {
        throw new IOException(MessageFormat.format(
            JGitText.get().renameFileFailed, tmpFile.getPath(),
            f.getPath()));
      }
    }
    entry.setLastModified(f.lastModified());
    if (opt.getAutoCRLF() != AutoCRLF.FALSE)
      entry.setLength(f.length()); // AutoCRLF wants on-disk-size
    else
      entry.setLength((int) ol.getSize());
  }

  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);
  }

  /**
   * Check if path is a valid path for a checked out file name or ref name.
   *
   * @param path
   * @throws InvalidPathException
   *             if the path is invalid
   * @since 3.3
   */
  public static void checkValidPath(String path) throws InvalidPathException {
    ObjectChecker chk = new ObjectChecker()
      .setSafeForWindows(SystemReader.getInstance().isWindows())
      .setSafeForMacOS(SystemReader.getInstance().isMacOS());

    byte[] bytes = Constants.encode(path);
    int segmentStart = 0;
    try {
      for (int i = 0; i < bytes.length; i++) {
        if (bytes[i] == '/') {
          chk.checkPathSegment(bytes, segmentStart, i);
          segmentStart = i + 1;
        }
      }
      chk.checkPathSegment(bytes, segmentStart, bytes.length);
    } catch (CorruptObjectException e) {
      throw new InvalidPathException(e.getMessage());
    }
  }

  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;
    }
  }
}
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