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1   /*
2    * Copyright (C) 2007, Dave Watson <dwatson@mimvista.com>
3    * Copyright (C) 2008-2010, Google Inc.
4    * Copyright (C) 2006-2010, Robin Rosenberg <robin.rosenberg@dewire.com>
5    * Copyright (C) 2006-2008, Shawn O. Pearce <spearce@spearce.org> and others
6    *
7    * This program and the accompanying materials are made available under the
8    * terms of the Eclipse Distribution License v. 1.0 which is available at
9    * https://www.eclipse.org/org/documents/edl-v10.php.
10   *
11   * SPDX-License-Identifier: BSD-3-Clause
12   */
13  
14  package org.eclipse.jgit.internal.storage.file;
15  
16  import static java.util.stream.Collectors.toList;
17  
18  import java.io.File;
19  import java.io.FileInputStream;
20  import java.io.FileNotFoundException;
21  import java.io.FileOutputStream;
22  import java.io.IOException;
23  import java.io.OutputStream;
24  import java.text.MessageFormat;
25  import java.text.ParseException;
26  import java.util.ArrayList;
27  import java.util.Collections;
28  import java.util.HashSet;
29  import java.util.List;
30  import java.util.Locale;
31  import java.util.Objects;
32  import java.util.Set;
33  
34  import org.eclipse.jgit.annotations.Nullable;
35  import org.eclipse.jgit.api.errors.JGitInternalException;
36  import org.eclipse.jgit.attributes.AttributesNode;
37  import org.eclipse.jgit.attributes.AttributesNodeProvider;
38  import org.eclipse.jgit.errors.ConfigInvalidException;
39  import org.eclipse.jgit.events.IndexChangedEvent;
40  import org.eclipse.jgit.internal.JGitText;
41  import org.eclipse.jgit.internal.storage.file.ObjectDirectory.AlternateHandle;
42  import org.eclipse.jgit.internal.storage.file.ObjectDirectory.AlternateRepository;
43  import org.eclipse.jgit.lib.BaseRepositoryBuilder;
44  import org.eclipse.jgit.lib.BatchRefUpdate;
45  import org.eclipse.jgit.lib.ConfigConstants;
46  import org.eclipse.jgit.lib.Constants;
47  import org.eclipse.jgit.lib.CoreConfig.HideDotFiles;
48  import org.eclipse.jgit.lib.CoreConfig.SymLinks;
49  import org.eclipse.jgit.lib.NullProgressMonitor;
50  import org.eclipse.jgit.lib.ObjectId;
51  import org.eclipse.jgit.lib.ProgressMonitor;
52  import org.eclipse.jgit.lib.Ref;
53  import org.eclipse.jgit.lib.RefDatabase;
54  import org.eclipse.jgit.lib.RefUpdate;
55  import org.eclipse.jgit.lib.ReflogEntry;
56  import org.eclipse.jgit.lib.ReflogReader;
57  import org.eclipse.jgit.lib.Repository;
58  import org.eclipse.jgit.lib.StoredConfig;
59  import org.eclipse.jgit.revwalk.RevWalk;
60  import org.eclipse.jgit.storage.file.FileBasedConfig;
61  import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
62  import org.eclipse.jgit.storage.pack.PackConfig;
63  import org.eclipse.jgit.transport.ReceiveCommand;
64  import org.eclipse.jgit.util.FileUtils;
65  import org.eclipse.jgit.util.IO;
66  import org.eclipse.jgit.util.RawParseUtils;
67  import org.eclipse.jgit.util.StringUtils;
68  import org.eclipse.jgit.util.SystemReader;
69  import org.slf4j.Logger;
70  import org.slf4j.LoggerFactory;
71  
72  /**
73   * Represents a Git repository. A repository holds all objects and refs used for
74   * managing source code (could by any type of file, but source code is what
75   * SCM's are typically used for).
76   *
77   * In Git terms all data is stored in GIT_DIR, typically a directory called
78   * .git. A work tree is maintained unless the repository is a bare repository.
79   * Typically the .git directory is located at the root of the work dir.
80   *
81   * <ul>
82   * <li>GIT_DIR
83   * 	<ul>
84   * 		<li>objects/ - objects</li>
85   * 		<li>refs/ - tags and heads</li>
86   * 		<li>config - configuration</li>
87   * 		<li>info/ - more configurations</li>
88   * 	</ul>
89   * </li>
90   * </ul>
91   * <p>
92   * This class is thread-safe.
93   * <p>
94   * This implementation only handles a subtly undocumented subset of git features.
95   */
96  public class FileRepository extends Repository {
97  	private static final Logger LOG = LoggerFactory
98  			.getLogger(FileRepository.class);
99  	private static final String UNNAMED = "Unnamed repository; edit this file to name it for gitweb."; //$NON-NLS-1$
100 
101 	private final FileBasedConfig repoConfig;
102 	private RefDatabase refs;
103 	private final ObjectDirectory objectDatabase;
104 
105 	private final Object snapshotLock = new Object();
106 
107 	// protected by snapshotLock
108 	private FileSnapshot snapshot;
109 
110 	/**
111 	 * Construct a representation of a Git repository.
112 	 * <p>
113 	 * The work tree, object directory, alternate object directories and index
114 	 * file locations are deduced from the given git directory and the default
115 	 * rules by running
116 	 * {@link org.eclipse.jgit.storage.file.FileRepositoryBuilder}. This
117 	 * constructor is the same as saying:
118 	 *
119 	 * <pre>
120 	 * new FileRepositoryBuilder().setGitDir(gitDir).build()
121 	 * </pre>
122 	 *
123 	 * @param gitDir
124 	 *            GIT_DIR (the location of the repository metadata).
125 	 * @throws java.io.IOException
126 	 *             the repository appears to already exist but cannot be
127 	 *             accessed.
128 	 * @see FileRepositoryBuilder
129 	 */
130 	public FileRepository(File gitDir) throws IOException {
131 		this(new FileRepositoryBuilder().setGitDir(gitDir).setup());
132 	}
133 
134 	/**
135 	 * A convenience API for {@link #FileRepository(File)}.
136 	 *
137 	 * @param gitDir
138 	 *            GIT_DIR (the location of the repository metadata).
139 	 * @throws java.io.IOException
140 	 *             the repository appears to already exist but cannot be
141 	 *             accessed.
142 	 * @see FileRepositoryBuilder
143 	 */
144 	public FileRepository(String gitDir) throws IOException {
145 		this(new File(gitDir));
146 	}
147 
148 	/**
149 	 * Create a repository using the local file system.
150 	 *
151 	 * @param options
152 	 *            description of the repository's important paths.
153 	 * @throws java.io.IOException
154 	 *             the user configuration file or repository configuration file
155 	 *             cannot be accessed.
156 	 */
157 	public FileRepository(BaseRepositoryBuilder options) throws IOException {
158 		super(options);
159 		StoredConfig userConfig = null;
160 		try {
161 			userConfig = SystemReader.getInstance().getUserConfig();
162 		} catch (ConfigInvalidException e) {
163 			LOG.error(e.getMessage(), e);
164 			throw new IOException(e.getMessage(), e);
165 		}
166 		repoConfig = new FileBasedConfig(userConfig, getFS().resolve(
167 				getDirectory(), Constants.CONFIG),
168 				getFS());
169 		loadRepoConfig();
170 
171 		repoConfig.addChangeListener(this::fireEvent);
172 
173 		final long repositoryFormatVersion = getConfig().getLong(
174 				ConfigConstants.CONFIG_CORE_SECTION, null,
175 				ConfigConstants.CONFIG_KEY_REPO_FORMAT_VERSION, 0);
176 
177 		String reftype = repoConfig.getString(
178 				ConfigConstants.CONFIG_EXTENSIONS_SECTION, null,
179 				ConfigConstants.CONFIG_KEY_REF_STORAGE);
180 		if (repositoryFormatVersion >= 1 && reftype != null) {
181 			if (StringUtils.equalsIgnoreCase(reftype,
182 					ConfigConstants.CONFIG_REF_STORAGE_REFTABLE)) {
183 				refs = new FileReftableDatabase(this);
184 			} else {
185 				throw new IOException(JGitText.get().unknownRepositoryFormat);
186 			}
187 		} else {
188 			refs = new RefDirectory(this);
189 		}
190 
191 		objectDatabase = new ObjectDirectory(repoConfig, //
192 				options.getObjectDirectory(), //
193 				options.getAlternateObjectDirectories(), //
194 				getFS(), //
195 				new File(getDirectory(), Constants.SHALLOW));
196 
197 		if (objectDatabase.exists()) {
198 			if (repositoryFormatVersion > 1)
199 				throw new IOException(MessageFormat.format(
200 						JGitText.get().unknownRepositoryFormat2,
201 						Long.valueOf(repositoryFormatVersion)));
202 		}
203 
204 		if (!isBare()) {
205 			snapshot = FileSnapshot.save(getIndexFile());
206 		}
207 	}
208 
209 	private void loadRepoConfig() throws IOException {
210 		try {
211 			repoConfig.load();
212 		} catch (ConfigInvalidException e) {
213 			throw new IOException(JGitText.get().unknownRepositoryFormat, e);
214 		}
215 	}
216 
217 	/**
218 	 * {@inheritDoc}
219 	 * <p>
220 	 * Create a new Git repository initializing the necessary files and
221 	 * directories.
222 	 */
223 	@Override
224 	public void create(boolean bare) throws IOException {
225 		final FileBasedConfig cfg = getConfig();
226 		if (cfg.getFile().exists()) {
227 			throw new IllegalStateException(MessageFormat.format(
228 					JGitText.get().repositoryAlreadyExists, getDirectory()));
229 		}
230 		FileUtils.mkdirs(getDirectory(), true);
231 		HideDotFiles hideDotFiles = getConfig().getEnum(
232 				ConfigConstants.CONFIG_CORE_SECTION, null,
233 				ConfigConstants.CONFIG_KEY_HIDEDOTFILES,
234 				HideDotFiles.DOTGITONLY);
235 		if (hideDotFiles != HideDotFiles.FALSE && !isBare()
236 				&& getDirectory().getName().startsWith(".")) //$NON-NLS-1$
237 			getFS().setHidden(getDirectory(), true);
238 		refs.create();
239 		objectDatabase.create();
240 
241 		FileUtils.mkdir(new File(getDirectory(), "branches")); //$NON-NLS-1$
242 		FileUtils.mkdir(new File(getDirectory(), "hooks")); //$NON-NLS-1$
243 
244 		RefUpdate head = updateRef(Constants.HEAD);
245 		head.disableRefLog();
246 		head.link(Constants.R_HEADS + getInitialBranch());
247 
248 		final boolean fileMode;
249 		if (getFS().supportsExecute()) {
250 			File tmp = File.createTempFile("try", "execute", getDirectory()); //$NON-NLS-1$ //$NON-NLS-2$
251 
252 			getFS().setExecute(tmp, true);
253 			final boolean on = getFS().canExecute(tmp);
254 
255 			getFS().setExecute(tmp, false);
256 			final boolean off = getFS().canExecute(tmp);
257 			FileUtils.delete(tmp);
258 
259 			fileMode = on && !off;
260 		} else {
261 			fileMode = false;
262 		}
263 
264 		SymLinks symLinks = SymLinks.FALSE;
265 		if (getFS().supportsSymlinks()) {
266 			File tmp = new File(getDirectory(), "tmplink"); //$NON-NLS-1$
267 			try {
268 				getFS().createSymLink(tmp, "target"); //$NON-NLS-1$
269 				symLinks = null;
270 				FileUtils.delete(tmp);
271 			} catch (IOException e) {
272 				// Normally a java.nio.file.FileSystemException
273 			}
274 		}
275 		if (symLinks != null)
276 			cfg.setString(ConfigConstants.CONFIG_CORE_SECTION, null,
277 					ConfigConstants.CONFIG_KEY_SYMLINKS, symLinks.name()
278 							.toLowerCase(Locale.ROOT));
279 		cfg.setInt(ConfigConstants.CONFIG_CORE_SECTION, null,
280 				ConfigConstants.CONFIG_KEY_REPO_FORMAT_VERSION, 0);
281 		cfg.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
282 				ConfigConstants.CONFIG_KEY_FILEMODE, fileMode);
283 		if (bare)
284 			cfg.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
285 					ConfigConstants.CONFIG_KEY_BARE, true);
286 		cfg.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
287 				ConfigConstants.CONFIG_KEY_LOGALLREFUPDATES, !bare);
288 		if (SystemReader.getInstance().isMacOS())
289 			// Java has no other way
290 			cfg.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
291 					ConfigConstants.CONFIG_KEY_PRECOMPOSEUNICODE, true);
292 		if (!bare) {
293 			File workTree = getWorkTree();
294 			if (!getDirectory().getParentFile().equals(workTree)) {
295 				cfg.setString(ConfigConstants.CONFIG_CORE_SECTION, null,
296 						ConfigConstants.CONFIG_KEY_WORKTREE, getWorkTree()
297 								.getAbsolutePath());
298 				LockFile dotGitLockFile = new LockFile(new File(workTree,
299 						Constants.DOT_GIT));
300 				try {
301 					if (dotGitLockFile.lock()) {
302 						dotGitLockFile.write(Constants.encode(Constants.GITDIR
303 								+ getDirectory().getAbsolutePath()));
304 						dotGitLockFile.commit();
305 					}
306 				} finally {
307 					dotGitLockFile.unlock();
308 				}
309 			}
310 		}
311 		cfg.save();
312 	}
313 
314 	/**
315 	 * Get the directory containing the objects owned by this repository
316 	 *
317 	 * @return the directory containing the objects owned by this repository.
318 	 */
319 	public File getObjectsDirectory() {
320 		return objectDatabase.getDirectory();
321 	}
322 
323 	/** {@inheritDoc} */
324 	@Override
325 	public ObjectDirectory getObjectDatabase() {
326 		return objectDatabase;
327 	}
328 
329 	/** {@inheritDoc} */
330 	@Override
331 	public RefDatabase getRefDatabase() {
332 		return refs;
333 	}
334 
335 	/** {@inheritDoc} */
336 	@Override
337 	public String getIdentifier() {
338 		File directory = getDirectory();
339 		if (directory != null) {
340 			return directory.getPath();
341 		}
342 		throw new IllegalStateException();
343 	}
344 
345 	/** {@inheritDoc} */
346 	@Override
347 	public FileBasedConfig getConfig() {
348 		try {
349 			SystemReader.getInstance().getUserConfig();
350 			if (repoConfig.isOutdated()) {
351 				loadRepoConfig();
352 			}
353 		} catch (IOException | ConfigInvalidException e) {
354 			throw new RuntimeException(e);
355 		}
356 		return repoConfig;
357 	}
358 
359 	/** {@inheritDoc} */
360 	@Override
361 	@Nullable
362 	public String getGitwebDescription() throws IOException {
363 		String d;
364 		try {
365 			d = RawParseUtils.decode(IO.readFully(descriptionFile()));
366 		} catch (FileNotFoundException err) {
367 			return null;
368 		}
369 		if (d != null) {
370 			d = d.trim();
371 			if (d.isEmpty() || UNNAMED.equals(d)) {
372 				return null;
373 			}
374 		}
375 		return d;
376 	}
377 
378 	/** {@inheritDoc} */
379 	@Override
380 	public void setGitwebDescription(@Nullable String description)
381 			throws IOException {
382 		String old = getGitwebDescription();
383 		if (Objects.equals(old, description)) {
384 			return;
385 		}
386 
387 		File path = descriptionFile();
388 		LockFile lock = new LockFile(path);
389 		if (!lock.lock()) {
390 			throw new IOException(MessageFormat.format(JGitText.get().lockError,
391 					path.getAbsolutePath()));
392 		}
393 		try {
394 			String d = description;
395 			if (d != null) {
396 				d = d.trim();
397 				if (!d.isEmpty()) {
398 					d += '\n';
399 				}
400 			} else {
401 				d = ""; //$NON-NLS-1$
402 			}
403 			lock.write(Constants.encode(d));
404 			lock.commit();
405 		} finally {
406 			lock.unlock();
407 		}
408 	}
409 
410 	private File descriptionFile() {
411 		return new File(getDirectory(), "description"); //$NON-NLS-1$
412 	}
413 
414 	/**
415 	 * {@inheritDoc}
416 	 * <p>
417 	 * Objects known to exist but not expressed by {@code #getAllRefs()}.
418 	 * <p>
419 	 * When a repository borrows objects from another repository, it can
420 	 * advertise that it safely has that other repository's references, without
421 	 * exposing any other details about the other repository. This may help a
422 	 * client trying to push changes avoid pushing more than it needs to.
423 	 *
424 	 * @throws IOException
425 	 */
426 	@Override
427 	public Set<ObjectId> getAdditionalHaves() throws IOException {
428 		return getAdditionalHaves(null);
429 	}
430 
431 	/**
432 	 * Objects known to exist but not expressed by {@code #getAllRefs()}.
433 	 * <p>
434 	 * When a repository borrows objects from another repository, it can
435 	 * advertise that it safely has that other repository's references, without
436 	 * exposing any other details about the other repository. This may help a
437 	 * client trying to push changes avoid pushing more than it needs to.
438 	 *
439 	 * @param skips
440 	 *            Set of AlternateHandle Ids already seen
441 	 *
442 	 * @return unmodifiable collection of other known objects.
443 	 * @throws IOException
444 	 *             if getting refs hits an IO error
445 	 */
446 	private Set<ObjectId> getAdditionalHaves(Set<AlternateHandle.Id> skips)
447 			throws IOException {
448 		HashSet<ObjectId> r = new HashSet<>();
449 		skips = objectDatabase.addMe(skips);
450 		for (AlternateHandle d : objectDatabase.myAlternates()) {
451 			if (d instanceof AlternateRepository && !skips.contains(d.getId())) {
452 				FileRepository repo;
453 
454 				repo = ((AlternateRepository) d).repository;
455 				for (Ref ref : repo.getRefDatabase().getRefs()) {
456 					if (ref.getObjectId() != null)
457 						r.add(ref.getObjectId());
458 					if (ref.getPeeledObjectId() != null)
459 						r.add(ref.getPeeledObjectId());
460 				}
461 				r.addAll(repo.getAdditionalHaves(skips));
462 			}
463 		}
464 		return r;
465 	}
466 
467 	/**
468 	 * Add a single existing pack to the list of available pack files.
469 	 *
470 	 * @param pack
471 	 *            path of the pack file to open.
472 	 * @throws java.io.IOException
473 	 *             index file could not be opened, read, or is not recognized as
474 	 *             a Git pack file index.
475 	 */
476 	public void openPack(File pack) throws IOException {
477 		objectDatabase.openPack(pack);
478 	}
479 
480 	/** {@inheritDoc} */
481 	@Override
482 	public void scanForRepoChanges() throws IOException {
483 		getRefDatabase().getRefs(); // This will look for changes to refs
484 		detectIndexChanges();
485 	}
486 
487 	/** Detect index changes. */
488 	private void detectIndexChanges() {
489 		if (isBare()) {
490 			return;
491 		}
492 
493 		File indexFile = getIndexFile();
494 		synchronized (snapshotLock) {
495 			if (snapshot == null) {
496 				snapshot = FileSnapshot.save(indexFile);
497 				return;
498 			}
499 			if (!snapshot.isModified(indexFile)) {
500 				return;
501 			}
502 		}
503 		notifyIndexChanged(false);
504 	}
505 
506 	/** {@inheritDoc} */
507 	@Override
508 	public void notifyIndexChanged(boolean internal) {
509 		synchronized (snapshotLock) {
510 			snapshot = FileSnapshot.save(getIndexFile());
511 		}
512 		fireEvent(new IndexChangedEvent(internal));
513 	}
514 
515 	/** {@inheritDoc} */
516 	@Override
517 	public ReflogReader getReflogReader(String refName) throws IOException {
518 		if (refs instanceof FileReftableDatabase) {
519 			// Cannot use findRef: reftable stores log data for deleted or renamed
520 			// branches.
521 			return ((FileReftableDatabase)refs).getReflogReader(refName);
522 		}
523 
524 		// TODO: use exactRef here, which offers more predictable and therefore preferable
525 		// behavior.
526 		Ref ref = findRef(refName);
527 		if (ref == null) {
528 			return null;
529 		}
530 		return new ReflogReaderImpl(this, ref.getName());
531 	}
532 
533 	/** {@inheritDoc} */
534 	@Override
535 	public AttributesNodeProvider createAttributesNodeProvider() {
536 		return new AttributesNodeProviderImpl(this);
537 	}
538 
539 	/**
540 	 * Implementation a {@link AttributesNodeProvider} for a
541 	 * {@link FileRepository}.
542 	 *
543 	 * @author <a href="mailto:arthur.daussy@obeo.fr">Arthur Daussy</a>
544 	 *
545 	 */
546 	static class AttributesNodeProviderImpl implements
547 			AttributesNodeProvider {
548 
549 		private AttributesNode infoAttributesNode;
550 
551 		private AttributesNode globalAttributesNode;
552 
553 		/**
554 		 * Constructor.
555 		 *
556 		 * @param repo
557 		 *            {@link Repository} that will provide the attribute nodes.
558 		 */
559 		protected AttributesNodeProviderImpl(Repository repo) {
560 			infoAttributesNode = new InfoAttributesNode(repo);
561 			globalAttributesNode = new GlobalAttributesNode(repo);
562 		}
563 
564 		@Override
565 		public AttributesNode getInfoAttributesNode() throws IOException {
566 			if (infoAttributesNode instanceof InfoAttributesNode)
567 				infoAttributesNode = ((InfoAttributesNode) infoAttributesNode)
568 						.load();
569 			return infoAttributesNode;
570 		}
571 
572 		@Override
573 		public AttributesNode getGlobalAttributesNode() throws IOException {
574 			if (globalAttributesNode instanceof GlobalAttributesNode)
575 				globalAttributesNode = ((GlobalAttributesNode) globalAttributesNode)
576 						.load();
577 			return globalAttributesNode;
578 		}
579 
580 		static void loadRulesFromFile(AttributesNode r, File attrs)
581 				throws FileNotFoundException, IOException {
582 			if (attrs.exists()) {
583 				try (FileInputStream in = new FileInputStream(attrs)) {
584 					r.parse(in);
585 				}
586 			}
587 		}
588 
589 	}
590 
591 	private boolean shouldAutoDetach() {
592 		return getConfig().getBoolean(ConfigConstants.CONFIG_GC_SECTION,
593 				ConfigConstants.CONFIG_KEY_AUTODETACH, true);
594 	}
595 
596 	/** {@inheritDoc} */
597 	@Override
598 	public void autoGC(ProgressMonitor monitor) {
599 		GC gc = new GC(this);
600 		gc.setPackConfig(new PackConfig(this));
601 		gc.setProgressMonitor(monitor);
602 		gc.setAuto(true);
603 		gc.setBackground(shouldAutoDetach());
604 		try {
605 			gc.gc();
606 		} catch (ParseException | IOException e) {
607 			throw new JGitInternalException(JGitText.get().gcFailed, e);
608 		}
609 	}
610 
611 	/**
612 	 * Converts the RefDatabase from reftable to RefDirectory. This operation is
613 	 * not atomic.
614 	 *
615 	 * @param writeLogs
616 	 *            whether to write reflogs
617 	 * @param backup
618 	 *            whether to rename or delete the old storage files. If set to
619 	 *            {@code true}, the reftable list is left in {@code refs.old},
620 	 *            and the {@code reftable/} dir is left alone. If set to
621 	 *            {@code false}, the {@code reftable/} dir is removed, and
622 	 *            {@code refs} file is removed.
623 	 * @throws IOException
624 	 *             on IO problem
625 	 */
626 	void convertToPackedRefs(boolean writeLogs, boolean backup) throws IOException {
627 		List<Ref> all = refs.getRefs();
628 		File packedRefs = new File(getDirectory(), Constants.PACKED_REFS);
629 		if (packedRefs.exists()) {
630 			throw new IOException(MessageFormat.format(JGitText.get().fileAlreadyExists,
631 				packedRefs.getName()));
632 		}
633 
634 		File refsFile = new File(getDirectory(), "refs"); //$NON-NLS-1$
635 		File refsHeadsFile = new File(refsFile, "heads");//$NON-NLS-1$
636 		File headFile = new File(getDirectory(), Constants.HEAD);
637 		FileReftableDatabase oldDb = (FileReftableDatabase) refs;
638 
639 		// Remove the dummy files that ensure compatibility with older git
640 		// versions (see convertToReftable). First make room for refs/heads/
641 		refsHeadsFile.delete();
642 		// RefDirectory wants to create the refs/ directory from scratch, so
643 		// remove that too.
644 			refsFile.delete();
645 		// remove HEAD so its previous invalid value doesn't cause issues.
646 		headFile.delete();
647 
648 		// This is not atomic, but there is no way to instantiate a RefDirectory
649 		// that is disconnected from the current repo.
650 		RefDirectory refDir = new RefDirectory(this);
651 		refs = refDir;
652 		refs.create();
653 
654 		ReflogWriter logWriter = refDir.newLogWriter(true);
655 		List<Ref> symrefs = new ArrayList<>();
656 		BatchRefUpdate bru = refs.newBatchUpdate();
657 		for (Ref r : all) {
658 			if (r.isSymbolic()) {
659 				symrefs.add(r);
660 			} else {
661 				bru.addCommand(new ReceiveCommand(ObjectId.zeroId(),
662 						r.getObjectId(), r.getName()));
663 			}
664 
665 			if (writeLogs) {
666 				List<ReflogEntry> logs = oldDb.getReflogReader(r.getName())
667 					.getReverseEntries();
668 				Collections.reverse(logs);
669 				for (ReflogEntry e : logs) {
670 					logWriter.log(r.getName(), e);
671 				}
672 		}
673 		}
674 
675 		try (RevWalk rw = new RevWalk(this)) {
676 			bru.execute(rw, NullProgressMonitor.INSTANCE);
677 		}
678 
679 		List<String> failed = new ArrayList<>();
680 		for (ReceiveCommand cmd : bru.getCommands()) {
681 			if (cmd.getResult() != ReceiveCommand.Result.OK) {
682 				failed.add(cmd.getRefName() + ": " + cmd.getResult()); //$NON-NLS-1$
683 			}
684 		}
685 
686 		if (!failed.isEmpty()) {
687 			throw new IOException(String.format("%s: %s", //$NON-NLS-1$
688 					JGitText.get().failedToConvert,
689 					StringUtils.join(failed, ", "))); //$NON-NLS-1$
690 		}
691 
692 		for (Ref s : symrefs) {
693 			RefUpdate up = refs.newUpdate(s.getName(), false);
694 			up.setForceUpdate(true);
695 			RefUpdate.Result res = up.link(s.getTarget().getName());
696 			if (res != RefUpdate.Result.NEW
697 					&& res != RefUpdate.Result.NO_CHANGE) {
698 				throw new IOException(
699 						String.format("ref %s: %s", s.getName(), res)); //$NON-NLS-1$
700 			}
701 		}
702 
703 		if (!backup) {
704 			File reftableDir = new File(getDirectory(), Constants.REFTABLE);
705 			FileUtils.delete(reftableDir,
706 					FileUtils.RECURSIVE | FileUtils.IGNORE_ERRORS);
707 		}
708 		repoConfig.unset(ConfigConstants.CONFIG_EXTENSIONS_SECTION, null,
709 				ConfigConstants.CONFIG_KEY_REF_STORAGE);
710 		repoConfig.save();
711 	}
712 
713 	/**
714 	 * Converts the RefDatabase from RefDirectory to reftable. This operation is
715 	 * not atomic.
716 	 *
717 	 * @param writeLogs
718 	 *            whether to write reflogs
719 	 * @param backup
720 	 *            whether to rename or delete the old storage files. If set to
721 	 *            {@code true}, the loose refs are left in {@code refs.old}, the
722 	 *            packed-refs in {@code packed-refs.old} and reflogs in
723 	 *            {@code refs.old/}. HEAD is left in {@code HEAD.old} and also
724 	 *            {@code .log} is appended to additional refs. If set to
725 	 *            {@code false}, the {@code refs/} and {@code logs/} directories
726 	 *            and {@code HEAD} and additional symbolic refs are removed.
727 	 * @throws IOException
728 	 *             on IO problem
729 	 */
730 	@SuppressWarnings("nls")
731 	void convertToReftable(boolean writeLogs, boolean backup)
732 			throws IOException {
733 		File reftableDir = new File(getDirectory(), Constants.REFTABLE);
734 		File headFile = new File(getDirectory(), Constants.HEAD);
735 		if (reftableDir.exists() && FileUtils.hasFiles(reftableDir.toPath())) {
736 			throw new IOException(JGitText.get().reftableDirExists);
737 		}
738 
739 		// Ignore return value, as it is tied to temporary newRefs file.
740 		FileReftableDatabase.convertFrom(this, writeLogs);
741 
742 		File refsFile = new File(getDirectory(), "refs");
743 
744 		// non-atomic: remove old data.
745 		File packedRefs = new File(getDirectory(), Constants.PACKED_REFS);
746 		File logsDir = new File(getDirectory(), Constants.LOGS);
747 
748 		List<String> additional = getRefDatabase().getAdditionalRefs().stream()
749 				.map(Ref::getName).collect(toList());
750 		additional.add(Constants.HEAD);
751 		if (backup) {
752 			FileUtils.rename(refsFile, new File(getDirectory(), "refs.old"));
753 			if (packedRefs.exists()) {
754 				FileUtils.rename(packedRefs, new File(getDirectory(),
755 						Constants.PACKED_REFS + ".old"));
756 			}
757 			if (logsDir.exists()) {
758 				FileUtils.rename(logsDir,
759 						new File(getDirectory(), Constants.LOGS + ".old"));
760 			}
761 			for (String r : additional) {
762 				FileUtils.rename(new File(getDirectory(), r),
763 					new File(getDirectory(), r + ".old"));
764 			}
765 		} else {
766 			FileUtils.delete(packedRefs, FileUtils.SKIP_MISSING);
767 			FileUtils.delete(headFile, FileUtils.SKIP_MISSING);
768 			FileUtils.delete(logsDir,
769 					FileUtils.RECURSIVE | FileUtils.SKIP_MISSING);
770 			FileUtils.delete(refsFile,
771 					FileUtils.RECURSIVE | FileUtils.SKIP_MISSING);
772 			for (String r : additional) {
773 				new File(getDirectory(), r).delete();
774 			}
775 		}
776 
777 		FileUtils.mkdir(refsFile, true);
778 
779 		// By putting in a dummy HEAD, old versions of Git still detect a repo
780 		// (that they can't read)
781 		try (OutputStream os = new FileOutputStream(headFile)) {
782 			os.write(Constants.encodeASCII("ref: refs/heads/.invalid"));
783 		}
784 
785 		// Some tools might write directly into .git/refs/heads/BRANCH. By
786 		// putting a file here, this fails spectacularly.
787 		FileUtils.createNewFile(new File(refsFile, "heads"));
788 
789 		repoConfig.setString(ConfigConstants.CONFIG_EXTENSIONS_SECTION, null,
790 				ConfigConstants.CONFIG_KEY_REF_STORAGE,
791 				ConfigConstants.CONFIG_REF_STORAGE_REFTABLE);
792 		repoConfig.setLong(ConfigConstants.CONFIG_CORE_SECTION, null,
793 				ConfigConstants.CONFIG_KEY_REPO_FORMAT_VERSION, 1);
794 		repoConfig.save();
795 		refs.close();
796 		refs = new FileReftableDatabase(this);
797 	}
798 
799 	/**
800 	 * Converts between ref storage formats.
801 	 *
802 	 * @param format
803 	 *            the format to convert to, either "reftable" or "refdir"
804 	 * @param writeLogs
805 	 *            whether to write reflogs
806 	 * @param backup
807 	 *            whether to make a backup of the old data
808 	 * @throws IOException
809 	 *             on I/O problems.
810 	 */
811 	public void convertRefStorage(String format, boolean writeLogs,
812 			boolean backup) throws IOException {
813 		if (format.equals("reftable")) { //$NON-NLS-1$
814 			if (refs instanceof RefDirectory) {
815 				convertToReftable(writeLogs, backup);
816 			}
817 		} else if (format.equals("refdir")) {//$NON-NLS-1$
818 			if (refs instanceof FileReftableDatabase) {
819 				convertToPackedRefs(writeLogs, backup);
820 			}
821 		} else {
822 			throw new IOException(MessageFormat
823 					.format(JGitText.get().unknownRefStorageFormat, format));
824 		}
825 	}
826 }