@Override
protected void run () throws GitException {
    Repository repository = getRepository();
    
    try (TreeWalk walk = new TreeWalk(repository)) {
        walk.reset();
        walk.setRecursive(true);
        walk.addTree(Utils.findCommit(repository, revisionFirst).getTree());
        walk.addTree(Utils.findCommit(repository, revisionSecond).getTree());
        Collection<PathFilter> pathFilters = Utils.getPathFilters(repository.getWorkTree(), roots);
        if (pathFilters.isEmpty()) {
            walk.setFilter(AndTreeFilter.create(TreeFilter.ANY_DIFF, PathFilter.ANY_DIFF));
        } else {
            walk.setFilter(AndTreeFilter.create(new TreeFilter[] { 
                TreeFilter.ANY_DIFF,
                PathFilter.ANY_DIFF,
                PathFilterGroup.create(pathFilters)
            }));
        }
        List<GitRevisionInfo.GitFileInfo> infos = Utils.getDiffEntries(repository, walk, getClassFactory());
        for (GitRevisionInfo.GitFileInfo info : infos) {
            statuses.put(info.getFile(), info);
        }
    } catch (IOException ex) {
        throw new GitException(ex);
    }
}
 

private void mergeConflicts (List<String> conflicts, DirCache cache) throws GitException {
    DirCacheBuilder builder = cache.builder();
    DirCacheBuildIterator dci = new DirCacheBuildIterator(builder);
    ObjectDatabase od = null;
    DiffAlgorithm.SupportedAlgorithm diffAlg = getRepository().getConfig().getEnum(
                    ConfigConstants.CONFIG_DIFF_SECTION, null,
                    ConfigConstants.CONFIG_KEY_ALGORITHM,
                    DiffAlgorithm.SupportedAlgorithm.HISTOGRAM);
    MergeAlgorithm merger = new MergeAlgorithm(DiffAlgorithm.getAlgorithm(diffAlg));
    try (TreeWalk walk = new TreeWalk(getRepository());) {
        od = getRepository().getObjectDatabase();
        walk.addTree(dci);
        walk.setFilter(PathFilterGroup.create(Utils.getPathFilters(conflicts)));
        String lastPath = null;
        DirCacheEntry[] entries = new DirCacheEntry[3];
        walk.setRecursive(true);
        while (walk.next()) {
            DirCacheEntry e = walk.getTree(0, DirCacheIterator.class).getDirCacheEntry();
            String path = e.getPathString();
            if (lastPath != null && !lastPath.equals(path)) {
                resolveEntries(merger, lastPath, entries, od, builder);
            }
            if (e.getStage() == 0) {
                DirCacheIterator c = walk.getTree(0, DirCacheIterator.class);
                builder.add(c.getDirCacheEntry());
            } else {
                entries[e.getStage() - 1] = e;
                lastPath = path;
            }
        }
        resolveEntries(merger, lastPath, entries, od, builder);
        builder.commit();
    } catch (IOException ex) {
        throw new GitException(ex);
    } finally {
        if (od != null) {
            od.close();
        }
    }
}
 

public void checkout() throws IOException, GitException {
    try (ObjectReader od = repository.newObjectReader();
        TreeWalk treeWalk = new TreeWalk(repository);) {
        Collection<String> relativePaths = Utils.getRelativePaths(repository.getWorkTree(), roots);
        if (!relativePaths.isEmpty()) {
            treeWalk.setFilter(PathFilterGroup.createFromStrings(relativePaths));
        }
        treeWalk.setRecursive(true);
        treeWalk.reset();
        treeWalk.addTree(new DirCacheIterator(cache));
        treeWalk.addTree(new FileTreeIterator(repository));
        String lastAddedPath = null;
        while (treeWalk.next() && !monitor.isCanceled()) {
            File path = new File(repository.getWorkTree(), treeWalk.getPathString());
            if (treeWalk.getPathString().equals(lastAddedPath)) {
                // skip conflicts
                continue;
            } else {
                lastAddedPath = treeWalk.getPathString();
            }
            DirCacheIterator dit = treeWalk.getTree(0, DirCacheIterator.class);
            FileTreeIterator fit = treeWalk.getTree(1, FileTreeIterator.class);
            if (dit != null && (recursively || directChild(roots, repository.getWorkTree(), path)) && (fit == null || fit.isModified(dit.getDirCacheEntry(), checkContent, od))) {
                // update entry
                listener.notifyFile(path, treeWalk.getPathString());
                checkoutEntry(repository, path, dit.getDirCacheEntry(), od);
            }
        }
    }
}
 

public Commit(URI cloneLocation, Repository db, RevCommit revCommit, String pattern) {
	super(cloneLocation, db);
	this.revCommit = revCommit;
	if (revCommit.getParentCount() == 0) {
		this.revCommit = parseCommit(revCommit);
	}
	this.pattern = pattern;
	if (pattern != null && !pattern.isEmpty()) {
		filter = AndTreeFilter.create(PathFilterGroup.createFromStrings(Collections.singleton(pattern)), TreeFilter.ANY_DIFF);
		isRoot = false;
	}
}
 

@Override
  protected void run() throws GitException {
      Repository repository = getRepository();
      String workTreePath = repository.getWorkTree().getAbsolutePath();
      try (DiffFormatter formatter = new DiffFormatter(out);
          ObjectReader or = repository.newObjectReader()) {
          formatter.setRepository(repository);
          Collection<PathFilter> pathFilters = Utils.getPathFilters(repository.getWorkTree(), roots);
          if (!pathFilters.isEmpty()) {
              formatter.setPathFilter(PathFilterGroup.create(pathFilters));
          }
          if (repository.getConfig().get(WorkingTreeOptions.KEY).getAutoCRLF() != CoreConfig.AutoCRLF.FALSE) {
              // work-around for autocrlf
              formatter.setDiffComparator(new AutoCRLFComparator());
          }
          AbstractTreeIterator firstTree = getIterator(firstCommit, or);
          AbstractTreeIterator secondTree = getIterator(secondCommit, or);
          List<DiffEntry> diffEntries;
          if (secondTree instanceof WorkingTreeIterator) {
              // remote when fixed in JGit, see ExportDiffTest.testDiffRenameDetectionProblem
              formatter.setDetectRenames(false);
              diffEntries = formatter.scan(firstTree, secondTree);
              formatter.setDetectRenames(true);
              RenameDetector detector = formatter.getRenameDetector();
              detector.reset();
              detector.addAll(diffEntries);
diffEntries = detector.compute(new ContentSource.Pair(ContentSource.create(or), ContentSource.create((WorkingTreeIterator) secondTree)), NullProgressMonitor.INSTANCE);
          } else {
              formatter.setDetectRenames(true);
              diffEntries = formatter.scan(firstTree, secondTree);
          }
          for (DiffEntry ent : diffEntries) {
              if (monitor.isCanceled()) {
                  break;
              }
              listener.notifyFile(new File(workTreePath + File.separator + ent.getNewPath()), ent.getNewPath());
              formatter.format(ent);
          }
          formatter.flush();
      } catch (IOException ex) {
          throw new GitException(ex);
      }
  }
 

private void applyCriteria (RevWalk walk, SearchCriteria criteria,
        final RevFlag partOfResultFlag, DiffConfig diffConfig) {
    File[] files = criteria.getFiles();
    if (files.length > 0) {
        Collection<PathFilter> pathFilters = Utils.getPathFilters(getRepository().getWorkTree(), files);
        if (!pathFilters.isEmpty()) {
            if (criteria.isFollow() && pathFilters.size() == 1) {
                walk.setTreeFilter(FollowFilter.create(pathFilters.iterator().next().getPath(), diffConfig));
            } else {
                walk.setTreeFilter(AndTreeFilter.create(TreeFilter.ANY_DIFF, PathFilterGroup.create(pathFilters)));
            }
        }
    }
    RevFilter filter;
    if (criteria.isIncludeMerges()) {
        filter = RevFilter.ALL;
    } else {
        filter = RevFilter.NO_MERGES;
    }
    filter = AndRevFilter.create(filter, new CancelRevFilter(monitor));
    filter = AndRevFilter.create(filter, new RevFilter() {

        @Override
        public boolean include (RevWalk walker, RevCommit cmit) {
            return cmit.has(partOfResultFlag);
        }

        @Override
        public RevFilter clone () {
            return this;
        }

        @Override
        public boolean requiresCommitBody () {
            return false;
        }
    });

    String username = criteria.getUsername();
    if (username != null && !(username = username.trim()).isEmpty()) {
        filter = AndRevFilter.create(filter, OrRevFilter.create(CommitterRevFilter.create(username), AuthorRevFilter.create(username)));
    }
    String message = criteria.getMessage();
    if (message != null && !(message = message.trim()).isEmpty()) {
        filter = AndRevFilter.create(filter, MessageRevFilter.create(message));
    }
    Date from  = criteria.getFrom();
    Date to  = criteria.getTo();
    if (from != null && to != null) {
        filter = AndRevFilter.create(filter, CommitTimeRevFilter.between(from, to));
    } else if (from != null) {
        filter = AndRevFilter.create(filter, CommitTimeRevFilter.after(from));
    } else if (to != null) {
        filter = AndRevFilter.create(filter, CommitTimeRevFilter.before(to));
    }
    // this must be at the end, limit filter must apply as the last
    if (criteria.getLimit() != -1) {
        filter = AndRevFilter.create(filter, MaxCountRevFilter.create(criteria.getLimit()));
    }
    walk.setRevFilter(filter);
}
 

public void testAddMixedLineEndings () throws Exception {
    File f = new File(workDir, "f");
    String content = "";
    for (int i = 0; i < 10000; ++i) {
        content += i + "\r\n";
    }
    write(f, content);
    File[] files = new File[] { f };
    GitClient client = getClient(workDir);
    client.add(files, NULL_PROGRESS_MONITOR);
    client.commit(files, "commit", null, null, NULL_PROGRESS_MONITOR);
    
    Map<File, GitStatus> statuses = client.getStatus(files, NULL_PROGRESS_MONITOR);
    assertEquals(1, statuses.size());
    assertStatus(statuses, workDir, f, true, Status.STATUS_NORMAL, Status.STATUS_NORMAL, Status.STATUS_NORMAL, false);
    
    // lets turn autocrlf on
    StoredConfig cfg = repository.getConfig();
    cfg.setString(ConfigConstants.CONFIG_CORE_SECTION, null, ConfigConstants.CONFIG_KEY_AUTOCRLF, "true");
    cfg.save();
    
    // when this starts failing, remove the work around
    ObjectInserter inserter = repository.newObjectInserter();
    TreeWalk treeWalk = new TreeWalk(repository);
    treeWalk.setFilter(PathFilterGroup.createFromStrings("f"));
    treeWalk.setRecursive(true);
    treeWalk.reset();
    treeWalk.addTree(new FileTreeIterator(repository));
    while (treeWalk.next()) {
        String path = treeWalk.getPathString();
        assertEquals("f", path);
        WorkingTreeIterator fit = treeWalk.getTree(0, WorkingTreeIterator.class);
        try (InputStream in = fit.openEntryStream()) {
            inserter.insert(Constants.OBJ_BLOB, fit.getEntryLength(), in);
            fail("this should fail, remove the work around");
        } catch (EOFException ex) {
            assertEquals("Input did not match supplied length. 10.000 bytes are missing.", ex.getMessage());
        } finally {
            inserter.close();
        }
        break;
    }
    
    // no err should occur
    write(f, content + "hello");
    statuses = client.getStatus(files, NULL_PROGRESS_MONITOR);
    assertEquals(1, statuses.size());
    assertStatus(statuses, workDir, f, true, Status.STATUS_NORMAL, Status.STATUS_MODIFIED, Status.STATUS_MODIFIED, false);
    client.add(files, NULL_PROGRESS_MONITOR);
    statuses = client.getStatus(files, NULL_PROGRESS_MONITOR);
    assertEquals(1, statuses.size());
    assertStatus(statuses, workDir, f, true, Status.STATUS_MODIFIED, Status.STATUS_NORMAL, Status.STATUS_MODIFIED, false);
    client.commit(files, "message", null, null, NULL_PROGRESS_MONITOR);
    statuses = client.getStatus(files, NULL_PROGRESS_MONITOR);
    assertEquals(1, statuses.size());
    assertStatus(statuses, workDir, f, true, Status.STATUS_NORMAL, Status.STATUS_NORMAL, Status.STATUS_NORMAL, false);
}
 

/**
 * Executes the {@code Log} command with all the options and parameters collected by the setter methods (e.g. {@link #add(AnyObjectId)},
 * {@link #not(AnyObjectId)}, ..) of this class. Each instance of this class should only be used for one invocation of the command. Don't call this method
 * twice on an instance.
 *
 * @return an iteration over RevCommits
 * @throws NoHeadException
 *             of the references ref cannot be resolved
 */
@Override
public Iterable<RevCommit> call() throws GitAPIException, NoHeadException {
	checkCallable();
	ArrayList<RevFilter> filters = new ArrayList<RevFilter>();

	if (pathFilters.size() > 0)
		walk.setTreeFilter(AndTreeFilter.create(PathFilterGroup.create(pathFilters), TreeFilter.ANY_DIFF));

	if (msgFilter != null)
		filters.add(msgFilter);
	if (authorFilter != null)
		filters.add(authorFilter);
	if (committerFilter != null)
		filters.add(committerFilter);
	if (sha1Filter != null)
		filters.add(sha1Filter);
	if (dateFilter != null)
		filters.add(dateFilter);
	if (skip > -1)
		filters.add(SkipRevFilter.create(skip));
	if (maxCount > -1)
		filters.add(MaxCountRevFilter.create(maxCount));
	RevFilter filter = null;
	if (filters.size() > 1) {
		filter = AndRevFilter.create(filters);
	} else if (filters.size() == 1) {
		filter = filters.get(0);
	}

	if (filter != null)
		walk.setRevFilter(filter);

	if (!startSpecified) {
		try {
			ObjectId headId = repo.resolve(Constants.HEAD);
			if (headId == null)
				throw new NoHeadException(JGitText.get().noHEADExistsAndNoExplicitStartingRevisionWasSpecified);
			add(headId);
		} catch (IOException e) {
			// all exceptions thrown by add() shouldn't occur and represent
			// severe low-level exception which are therefore wrapped
			throw new JGitInternalException(JGitText.get().anExceptionOccurredWhileTryingToAddTheIdOfHEAD, e);
		}
	}
	setCallable(false);
	return walk;
}
 

@Nonnull
public static List<RevCommit> getFileRevisions(String path, AnyObjectId start, int skip, int limit, ObjectReader reader) throws IOException {
  path = normalizeNodePath(path);
  TreeFilter filter = AndTreeFilter.create(PathFilterGroup.createFromStrings(path), ANY_DIFF);
  return getHistory(start, skip, limit, filter, reader);
}
 

@Nonnull
public static List<RevCommit> getFileRevisions(String path, AnyObjectId start, int skip, int limit, ObjectReader reader) throws IOException {
  path = normalizeNodePath(path);
  TreeFilter filter = AndTreeFilter.create(PathFilterGroup.createFromStrings(path), ANY_DIFF);
  return getHistory(start, skip, limit, filter, reader);
}