/*
 * Copyright (C) 2007, Dave Watson <dwatson@mimvista.com>
 * Copyright (C) 2008-2010, Google Inc.
 * Copyright (C) 2006-2010, Robin Rosenberg <robin.rosenberg@dewire.com>
 * Copyright (C) 2006-2008, Shawn O. Pearce <spearce@spearce.org> and others
 *
 * This program and the accompanying materials are made available under the
 * terms of the Eclipse Distribution License v. 1.0 which is available at
 * https://www.eclipse.org/org/documents/edl-v10.php.
 *
 * SPDX-License-Identifier: BSD-3-Clause
 */

package org.eclipse.jgit.internal.storage.file;

import static java.util.stream.Collectors.toList;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.text.MessageFormat;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Objects;
import java.util.Set;

import org.eclipse.jgit.annotations.Nullable;
import org.eclipse.jgit.api.errors.JGitInternalException;
import org.eclipse.jgit.attributes.AttributesNode;
import org.eclipse.jgit.attributes.AttributesNodeProvider;
import org.eclipse.jgit.errors.ConfigInvalidException;
import org.eclipse.jgit.events.IndexChangedEvent;
import org.eclipse.jgit.internal.JGitText;
import org.eclipse.jgit.internal.storage.file.ObjectDirectory.AlternateHandle;
import org.eclipse.jgit.internal.storage.file.ObjectDirectory.AlternateRepository;
import org.eclipse.jgit.internal.storage.reftree.RefTreeDatabase;
import org.eclipse.jgit.lib.BaseRepositoryBuilder;
import org.eclipse.jgit.lib.BatchRefUpdate;
import org.eclipse.jgit.lib.ConfigConstants;
import org.eclipse.jgit.lib.Constants;
import org.eclipse.jgit.lib.CoreConfig.HideDotFiles;
import org.eclipse.jgit.lib.CoreConfig.SymLinks;
import org.eclipse.jgit.lib.NullProgressMonitor;
import org.eclipse.jgit.lib.ObjectId;
import org.eclipse.jgit.lib.ProgressMonitor;
import org.eclipse.jgit.lib.Ref;
import org.eclipse.jgit.lib.RefDatabase;
import org.eclipse.jgit.lib.RefUpdate;
import org.eclipse.jgit.lib.ReflogEntry;
import org.eclipse.jgit.lib.ReflogReader;
import org.eclipse.jgit.lib.Repository;
import org.eclipse.jgit.lib.StoredConfig;
import org.eclipse.jgit.revwalk.RevWalk;
import org.eclipse.jgit.storage.file.FileBasedConfig;
import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
import org.eclipse.jgit.storage.pack.PackConfig;
import org.eclipse.jgit.transport.ReceiveCommand;
import org.eclipse.jgit.util.FileUtils;
import org.eclipse.jgit.util.IO;
import org.eclipse.jgit.util.RawParseUtils;
import org.eclipse.jgit.util.StringUtils;
import org.eclipse.jgit.util.SystemReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

Represents a Git repository. A repository holds all objects and refs used for
managing source code (could by any type of file, but source code is what
SCM's are typically used for).
In Git terms all data is stored in GIT_DIR, typically a directory called
.git. A work tree is maintained unless the repository is a bare repository.
Typically the .git directory is located at the root of the work dir.

GIT_DIR
	

		
objects/ - objects
		
refs/ - tags and heads
		
config - configuration
		
info/ - more configurations
	



This class is thread-safe.

This implementation only handles a subtly undocumented subset of git features.
/**
 * Represents a Git repository. A repository holds all objects and refs used for
 * managing source code (could by any type of file, but source code is what
 * SCM's are typically used for).
 *
 * In Git terms all data is stored in GIT_DIR, typically a directory called
 * .git. A work tree is maintained unless the repository is a bare repository.
 * Typically the .git directory is located at the root of the work dir.
 *
 * <ul>
 * <li>GIT_DIR
 * 	<ul>
 * 		<li>objects/ - objects</li>
 * 		<li>refs/ - tags and heads</li>
 * 		<li>config - configuration</li>
 * 		<li>info/ - more configurations</li>
 * 	</ul>
 * </li>
 * </ul>
 * <p>
 * This class is thread-safe.
 * <p>
 * This implementation only handles a subtly undocumented subset of git features.
 */
public class FileRepository extends Repository {
	private static final Logger LOG = LoggerFactory
			.getLogger(FileRepository.class);
	private static final String UNNAMED = "Unnamed repository; edit this file to name it for gitweb."; //$NON-NLS-1$

	private final FileBasedConfig repoConfig;
	private RefDatabase refs;
	private final ObjectDirectory objectDatabase;

	private final Object snapshotLock = new Object();

	// protected by snapshotLock
	private FileSnapshot snapshot;

	
Construct a representation of a Git repository.
 The work tree, object directory, alternate object directories and index file locations are deduced from the given git directory and the default rules by running FileRepositoryBuilder. This constructor is the same as saying: 
new FileRepositoryBuilder().setGitDir(gitDir).build()

Params:
gitDir – 
           GIT_DIR (the location of the repository metadata).
Throws:
IOException – 
            the repository appears to already exist but cannot be
            accessed.
See Also:
FileRepositoryBuilder/**
	 * Construct a representation of a Git repository.
	 * <p>
	 * The work tree, object directory, alternate object directories and index
	 * file locations are deduced from the given git directory and the default
	 * rules by running
	 * {@link org.eclipse.jgit.storage.file.FileRepositoryBuilder}. This
	 * constructor is the same as saying:
	 *
	 * <pre>
	 * new FileRepositoryBuilder().setGitDir(gitDir).build()
	 * </pre>
	 *
	 * @param gitDir
	 *            GIT_DIR (the location of the repository metadata).
	 * @throws java.io.IOException
	 *             the repository appears to already exist but cannot be
	 *             accessed.
	 * @see FileRepositoryBuilder
	 */
	public FileRepository(File gitDir) throws IOException {
		this(new FileRepositoryBuilder().setGitDir(gitDir).setup());
	}

	
A convenience API for FileRepository(File). 
Params:
gitDir – 
           GIT_DIR (the location of the repository metadata).
Throws:
IOException – 
            the repository appears to already exist but cannot be
            accessed.
See Also:
FileRepositoryBuilder/**
	 * A convenience API for {@link #FileRepository(File)}.
	 *
	 * @param gitDir
	 *            GIT_DIR (the location of the repository metadata).
	 * @throws java.io.IOException
	 *             the repository appears to already exist but cannot be
	 *             accessed.
	 * @see FileRepositoryBuilder
	 */
	public FileRepository(String gitDir) throws IOException {
		this(new File(gitDir));
	}

	
Create a repository using the local file system.
Params:
options – 
           description of the repository's important paths.
Throws:
IOException – 
            the user configuration file or repository configuration file
            cannot be accessed./**
	 * Create a repository using the local file system.
	 *
	 * @param options
	 *            description of the repository's important paths.
	 * @throws java.io.IOException
	 *             the user configuration file or repository configuration file
	 *             cannot be accessed.
	 */
	public FileRepository(BaseRepositoryBuilder options) throws IOException {
		super(options);
		StoredConfig userConfig = null;
		try {
			userConfig = SystemReader.getInstance().getUserConfig();
		} catch (ConfigInvalidException e) {
			LOG.error(e.getMessage(), e);
			throw new IOException(e.getMessage(), e);
		}
		repoConfig = new FileBasedConfig(userConfig, getFS().resolve(
				getDirectory(), Constants.CONFIG),
				getFS());
		loadRepoConfig();

		repoConfig.addChangeListener(this::fireEvent);

		final long repositoryFormatVersion = getConfig().getLong(
				ConfigConstants.CONFIG_CORE_SECTION, null,
				ConfigConstants.CONFIG_KEY_REPO_FORMAT_VERSION, 0);

		String reftype = repoConfig.getString(
				ConfigConstants.CONFIG_EXTENSIONS_SECTION, null,
				ConfigConstants.CONFIG_KEY_REF_STORAGE);
		if (repositoryFormatVersion >= 1 && reftype != null) {
			if (StringUtils.equalsIgnoreCase(reftype,
					ConfigConstants.CONFIG_REF_STORAGE_REFTABLE)) {
				refs = new FileReftableDatabase(this);
			} else if (StringUtils.equalsIgnoreCase(reftype,
					ConfigConstants.CONFIG_REFSTORAGE_REFTREE)) {
				refs = new RefTreeDatabase(this, new RefDirectory(this));
			} else {
				throw new IOException(JGitText.get().unknownRepositoryFormat);
			}
		} else {
			refs = new RefDirectory(this);
		}

		objectDatabase = new ObjectDirectory(repoConfig, //
				options.getObjectDirectory(), //
				options.getAlternateObjectDirectories(), //
				getFS(), //
				new File(getDirectory(), Constants.SHALLOW));

		if (objectDatabase.exists()) {
			if (repositoryFormatVersion > 1)
				throw new IOException(MessageFormat.format(
						JGitText.get().unknownRepositoryFormat2,
						Long.valueOf(repositoryFormatVersion)));
		}

		if (!isBare()) {
			snapshot = FileSnapshot.save(getIndexFile());
		}
	}

	private void loadRepoConfig() throws IOException {
		try {
			repoConfig.load();
		} catch (ConfigInvalidException e) {
			throw new IOException(JGitText.get().unknownRepositoryFormat, e);
		}
	}

	
{@inheritDoc}

Create a new Git repository initializing the necessary files and
directories.
/**
	 * {@inheritDoc}
	 * <p>
	 * Create a new Git repository initializing the necessary files and
	 * directories.
	 */
	@Override
	public void create(boolean bare) throws IOException {
		final FileBasedConfig cfg = getConfig();
		if (cfg.getFile().exists()) {
			throw new IllegalStateException(MessageFormat.format(
					JGitText.get().repositoryAlreadyExists, getDirectory()));
		}
		FileUtils.mkdirs(getDirectory(), true);
		HideDotFiles hideDotFiles = getConfig().getEnum(
				ConfigConstants.CONFIG_CORE_SECTION, null,
				ConfigConstants.CONFIG_KEY_HIDEDOTFILES,
				HideDotFiles.DOTGITONLY);
		if (hideDotFiles != HideDotFiles.FALSE && !isBare()
				&& getDirectory().getName().startsWith(".")) //$NON-NLS-1$
			getFS().setHidden(getDirectory(), true);
		refs.create();
		objectDatabase.create();

		FileUtils.mkdir(new File(getDirectory(), "branches")); //$NON-NLS-1$
		FileUtils.mkdir(new File(getDirectory(), "hooks")); //$NON-NLS-1$

		RefUpdate head = updateRef(Constants.HEAD);
		head.disableRefLog();
		head.link(Constants.R_HEADS + Constants.MASTER);

		final boolean fileMode;
		if (getFS().supportsExecute()) {
			File tmp = File.createTempFile("try", "execute", getDirectory()); //$NON-NLS-1$ //$NON-NLS-2$

			getFS().setExecute(tmp, true);
			final boolean on = getFS().canExecute(tmp);

			getFS().setExecute(tmp, false);
			final boolean off = getFS().canExecute(tmp);
			FileUtils.delete(tmp);

			fileMode = on && !off;
		} else {
			fileMode = false;
		}

		SymLinks symLinks = SymLinks.FALSE;
		if (getFS().supportsSymlinks()) {
			File tmp = new File(getDirectory(), "tmplink"); //$NON-NLS-1$
			try {
				getFS().createSymLink(tmp, "target"); //$NON-NLS-1$
				symLinks = null;
				FileUtils.delete(tmp);
			} catch (IOException e) {
				// Normally a java.nio.file.FileSystemException
			}
		}
		if (symLinks != null)
			cfg.setString(ConfigConstants.CONFIG_CORE_SECTION, null,
					ConfigConstants.CONFIG_KEY_SYMLINKS, symLinks.name()
							.toLowerCase(Locale.ROOT));
		cfg.setInt(ConfigConstants.CONFIG_CORE_SECTION, null,
				ConfigConstants.CONFIG_KEY_REPO_FORMAT_VERSION, 0);
		cfg.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
				ConfigConstants.CONFIG_KEY_FILEMODE, fileMode);
		if (bare)
			cfg.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
					ConfigConstants.CONFIG_KEY_BARE, true);
		cfg.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
				ConfigConstants.CONFIG_KEY_LOGALLREFUPDATES, !bare);
		if (SystemReader.getInstance().isMacOS())
			// Java has no other way
			cfg.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
					ConfigConstants.CONFIG_KEY_PRECOMPOSEUNICODE, true);
		if (!bare) {
			File workTree = getWorkTree();
			if (!getDirectory().getParentFile().equals(workTree)) {
				cfg.setString(ConfigConstants.CONFIG_CORE_SECTION, null,
						ConfigConstants.CONFIG_KEY_WORKTREE, getWorkTree()
								.getAbsolutePath());
				LockFile dotGitLockFile = new LockFile(new File(workTree,
						Constants.DOT_GIT));
				try {
					if (dotGitLockFile.lock()) {
						dotGitLockFile.write(Constants.encode(Constants.GITDIR
								+ getDirectory().getAbsolutePath()));
						dotGitLockFile.commit();
					}
				} finally {
					dotGitLockFile.unlock();
				}
			}
		}
		cfg.save();
	}

	
Get the directory containing the objects owned by this repository
Returns:
the directory containing the objects owned by this repository./**
	 * Get the directory containing the objects owned by this repository
	 *
	 * @return the directory containing the objects owned by this repository.
	 */
	public File getObjectsDirectory() {
		return objectDatabase.getDirectory();
	}

	
{@inheritDoc} /** {@inheritDoc} */
	@Override
	public ObjectDirectory getObjectDatabase() {
		return objectDatabase;
	}

	
{@inheritDoc} /** {@inheritDoc} */
	@Override
	public RefDatabase getRefDatabase() {
		return refs;
	}

	
{@inheritDoc} /** {@inheritDoc} */
	@Override
	public String getIdentifier() {
		File directory = getDirectory();
		if (directory != null) {
			return directory.getPath();
		}
		throw new IllegalStateException();
	}

	
{@inheritDoc} /** {@inheritDoc} */
	@Override
	public FileBasedConfig getConfig() {
		try {
			SystemReader.getInstance().getUserConfig();
			if (repoConfig.isOutdated()) {
				loadRepoConfig();
			}
		} catch (IOException | ConfigInvalidException e) {
			throw new RuntimeException(e);
		}
		return repoConfig;
	}

	
{@inheritDoc} /** {@inheritDoc} */
	@Override
	@Nullable
	public String getGitwebDescription() throws IOException {
		String d;
		try {
			d = RawParseUtils.decode(IO.readFully(descriptionFile()));
		} catch (FileNotFoundException err) {
			return null;
		}
		if (d != null) {
			d = d.trim();
			if (d.isEmpty() || UNNAMED.equals(d)) {
				return null;
			}
		}
		return d;
	}

	
{@inheritDoc} /** {@inheritDoc} */
	@Override
	public void setGitwebDescription(@Nullable String description)
			throws IOException {
		String old = getGitwebDescription();
		if (Objects.equals(old, description)) {
			return;
		}

		File path = descriptionFile();
		LockFile lock = new LockFile(path);
		if (!lock.lock()) {
			throw new IOException(MessageFormat.format(JGitText.get().lockError,
					path.getAbsolutePath()));
		}
		try {
			String d = description;
			if (d != null) {
				d = d.trim();
				if (!d.isEmpty()) {
					d += '\n';
				}
			} else {
				d = ""; //$NON-NLS-1$
			}
			lock.write(Constants.encode(d));
			lock.commit();
		} finally {
			lock.unlock();
		}
	}

	private File descriptionFile() {
		return new File(getDirectory(), "description"); //$NON-NLS-1$
	}

	
{@inheritDoc}
 Objects known to exist but not expressed by #getAllRefs(). 

When a repository borrows objects from another repository, it can
advertise that it safely has that other repository's references, without
exposing any other details about the other repository. This may help a
client trying to push changes avoid pushing more than it needs to.
/**
	 * {@inheritDoc}
	 * <p>
	 * Objects known to exist but not expressed by {@code #getAllRefs()}.
	 * <p>
	 * When a repository borrows objects from another repository, it can
	 * advertise that it safely has that other repository's references, without
	 * exposing any other details about the other repository. This may help a
	 * client trying to push changes avoid pushing more than it needs to.
	 */
	@Override
	public Set<ObjectId> getAdditionalHaves() {
		return getAdditionalHaves(null);
	}

	
Objects known to exist but not expressed by #getAllRefs(). 

When a repository borrows objects from another repository, it can
advertise that it safely has that other repository's references, without
exposing any other details about the other repository. This may help a
client trying to push changes avoid pushing more than it needs to.
Params:
skips – 
           Set of AlternateHandle Ids already seen
Returns:
unmodifiable collection of other known objects./**
	 * Objects known to exist but not expressed by {@code #getAllRefs()}.
	 * <p>
	 * When a repository borrows objects from another repository, it can
	 * advertise that it safely has that other repository's references, without
	 * exposing any other details about the other repository. This may help a
	 * client trying to push changes avoid pushing more than it needs to.
	 *
	 * @param skips
	 *            Set of AlternateHandle Ids already seen
	 *
	 * @return unmodifiable collection of other known objects.
	 */
	private Set<ObjectId> getAdditionalHaves(Set<AlternateHandle.Id> skips) {
		HashSet<ObjectId> r = new HashSet<>();
		skips = objectDatabase.addMe(skips);
		for (AlternateHandle d : objectDatabase.myAlternates()) {
			if (d instanceof AlternateRepository && !skips.contains(d.getId())) {
				FileRepository repo;

				repo = ((AlternateRepository) d).repository;
				for (Ref ref : repo.getAllRefs().values()) {
					if (ref.getObjectId() != null)
						r.add(ref.getObjectId());
					if (ref.getPeeledObjectId() != null)
						r.add(ref.getPeeledObjectId());
				}
				r.addAll(repo.getAdditionalHaves(skips));
			}
		}
		return r;
	}

	
Add a single existing pack to the list of available pack files.
Params:
pack – 
           path of the pack file to open.
Throws:
IOException – 
            index file could not be opened, read, or is not recognized as
            a Git pack file index./**
	 * Add a single existing pack to the list of available pack files.
	 *
	 * @param pack
	 *            path of the pack file to open.
	 * @throws java.io.IOException
	 *             index file could not be opened, read, or is not recognized as
	 *             a Git pack file index.
	 */
	public void openPack(File pack) throws IOException {
		objectDatabase.openPack(pack);
	}

	
{@inheritDoc} /** {@inheritDoc} */
	@Override
	public void scanForRepoChanges() throws IOException {
		getRefDatabase().getRefs(); // This will look for changes to refs
		detectIndexChanges();
	}

	
Detect index changes. /** Detect index changes. */
	private void detectIndexChanges() {
		if (isBare()) {
			return;
		}

		File indexFile = getIndexFile();
		synchronized (snapshotLock) {
			if (snapshot == null) {
				snapshot = FileSnapshot.save(indexFile);
				return;
			}
			if (!snapshot.isModified(indexFile)) {
				return;
			}
		}
		notifyIndexChanged(false);
	}

	
{@inheritDoc} /** {@inheritDoc} */
	@Override
	public void notifyIndexChanged(boolean internal) {
		synchronized (snapshotLock) {
			snapshot = FileSnapshot.save(getIndexFile());
		}
		fireEvent(new IndexChangedEvent(internal));
	}

	
{@inheritDoc} /** {@inheritDoc} */
	@Override
	public ReflogReader getReflogReader(String refName) throws IOException {
		if (refs instanceof FileReftableDatabase) {
			// Cannot use findRef: reftable stores log data for deleted or renamed
			// branches.
			return ((FileReftableDatabase)refs).getReflogReader(refName);
		}

		// TODO: use exactRef here, which offers more predictable and therefore preferable
		// behavior.
		Ref ref = findRef(refName);
		if (ref == null) {
			return null;
		}
		return new ReflogReaderImpl(this, ref.getName());
	}

	
{@inheritDoc} /** {@inheritDoc} */
	@Override
	public AttributesNodeProvider createAttributesNodeProvider() {
		return new AttributesNodeProviderImpl(this);
	}

	
Implementation a AttributesNodeProvider for a FileRepository. 
Author:
Arthur Daussy/**
	 * Implementation a {@link AttributesNodeProvider} for a
	 * {@link FileRepository}.
	 *
	 * @author <a href="mailto:arthur.daussy@obeo.fr">Arthur Daussy</a>
	 *
	 */
	static class AttributesNodeProviderImpl implements
			AttributesNodeProvider {

		private AttributesNode infoAttributesNode;

		private AttributesNode globalAttributesNode;

		
Constructor.
Params:
repo –  Repository that will provide the attribute nodes./**
		 * Constructor.
		 *
		 * @param repo
		 *            {@link Repository} that will provide the attribute nodes.
		 */
		protected AttributesNodeProviderImpl(Repository repo) {
			infoAttributesNode = new InfoAttributesNode(repo);
			globalAttributesNode = new GlobalAttributesNode(repo);
		}

		@Override
		public AttributesNode getInfoAttributesNode() throws IOException {
			if (infoAttributesNode instanceof InfoAttributesNode)
				infoAttributesNode = ((InfoAttributesNode) infoAttributesNode)
						.load();
			return infoAttributesNode;
		}

		@Override
		public AttributesNode getGlobalAttributesNode() throws IOException {
			if (globalAttributesNode instanceof GlobalAttributesNode)
				globalAttributesNode = ((GlobalAttributesNode) globalAttributesNode)
						.load();
			return globalAttributesNode;
		}

		static void loadRulesFromFile(AttributesNode r, File attrs)
				throws FileNotFoundException, IOException {
			if (attrs.exists()) {
				try (FileInputStream in = new FileInputStream(attrs)) {
					r.parse(in);
				}
			}
		}

	}

	private boolean shouldAutoDetach() {
		return getConfig().getBoolean(ConfigConstants.CONFIG_GC_SECTION,
				ConfigConstants.CONFIG_KEY_AUTODETACH, true);
	}

	
{@inheritDoc} /** {@inheritDoc} */
	@Override
	public void autoGC(ProgressMonitor monitor) {
		GC gc = new GC(this);
		gc.setPackConfig(new PackConfig(this));
		gc.setProgressMonitor(monitor);
		gc.setAuto(true);
		gc.setBackground(shouldAutoDetach());
		try {
			gc.gc();
		} catch (ParseException | IOException e) {
			throw new JGitInternalException(JGitText.get().gcFailed, e);
		}
	}

	
Converts the RefDatabase from reftable to RefDirectory. This operation is
not atomic.
Params:
writeLogs – 
           whether to write reflogs
backup –  whether to rename or delete the old storage files. If set to true, the reftable list is left in refs.old, and the reftable/ dir is left alone. If set to false, the reftable/ dir is removed, and refs file is removed.
Throws:
IOException – 
            on IO problem/**
	 * Converts the RefDatabase from reftable to RefDirectory. This operation is
	 * not atomic.
	 *
	 * @param writeLogs
	 *            whether to write reflogs
	 * @param backup
	 *            whether to rename or delete the old storage files. If set to
	 *            {@code true}, the reftable list is left in {@code refs.old},
	 *            and the {@code reftable/} dir is left alone. If set to
	 *            {@code false}, the {@code reftable/} dir is removed, and
	 *            {@code refs} file is removed.
	 * @throws IOException
	 *             on IO problem
	 */
	void convertToPackedRefs(boolean writeLogs, boolean backup) throws IOException {
		List<Ref> all = refs.getRefs();
		File packedRefs = new File(getDirectory(), Constants.PACKED_REFS);
		if (packedRefs.exists()) {
			throw new IOException(MessageFormat.format(JGitText.get().fileAlreadyExists,
				packedRefs.getName()));
		}

		File refsFile = new File(getDirectory(), "refs"); //$NON-NLS-1$
		File refsHeadsFile = new File(refsFile, "heads");//$NON-NLS-1$
		File headFile = new File(getDirectory(), Constants.HEAD);
		FileReftableDatabase oldDb = (FileReftableDatabase) refs;

		// Remove the dummy files that ensure compatibility with older git
		// versions (see convertToReftable). First make room for refs/heads/
		refsHeadsFile.delete();
		// RefDirectory wants to create the refs/ directory from scratch, so
		// remove that too.
		refsFile.delete();
		// remove HEAD so its previous invalid value doesn't cause issues.
		headFile.delete();

		// This is not atomic, but there is no way to instantiate a RefDirectory
		// that is disconnected from the current repo.
		RefDirectory refDir = new RefDirectory(this);
		refs = refDir;
		refs.create();

		ReflogWriter logWriter = refDir.newLogWriter(true);
		List<Ref> symrefs = new ArrayList<>();
		BatchRefUpdate bru = refs.newBatchUpdate();
		for (Ref r : all) {
			if (r.isSymbolic()) {
				symrefs.add(r);
			} else {
				bru.addCommand(new ReceiveCommand(ObjectId.zeroId(),
						r.getObjectId(), r.getName()));
			}

			if (writeLogs) {
				List<ReflogEntry> logs = oldDb.getReflogReader(r.getName())
					.getReverseEntries();
				Collections.reverse(logs);
				for (ReflogEntry e : logs) {
					logWriter.log(r.getName(), e);
				}
			}
		}

		try (RevWalk rw = new RevWalk(this)) {
			bru.execute(rw, NullProgressMonitor.INSTANCE);
		}

		List<String> failed = new ArrayList<>();
		for (ReceiveCommand cmd : bru.getCommands()) {
			if (cmd.getResult() != ReceiveCommand.Result.OK) {
				failed.add(cmd.getRefName() + ": " + cmd.getResult()); //$NON-NLS-1$
			}
		}

		if (!failed.isEmpty()) {
			throw new IOException(String.format("%s: %s", //$NON-NLS-1$
					JGitText.get().failedToConvert,
					StringUtils.join(failed, ", "))); //$NON-NLS-1$
		}

		for (Ref s : symrefs) {
			RefUpdate up = refs.newUpdate(s.getName(), false);
			up.setForceUpdate(true);
			RefUpdate.Result res = up.link(s.getTarget().getName());
			if (res != RefUpdate.Result.NEW
					&& res != RefUpdate.Result.NO_CHANGE) {
				throw new IOException(
						String.format("ref %s: %s", s.getName(), res)); //$NON-NLS-1$
			}
		}

		if (!backup) {
			File reftableDir = new File(getDirectory(), Constants.REFTABLE);
			FileUtils.delete(reftableDir,
					FileUtils.RECURSIVE | FileUtils.IGNORE_ERRORS);
		}
		repoConfig.unset(ConfigConstants.CONFIG_EXTENSIONS_SECTION, null,
				ConfigConstants.CONFIG_KEY_REF_STORAGE);
		repoConfig.save();
	}

	
Converts the RefDatabase from RefDirectory to reftable. This operation is
not atomic.
Params:
writeLogs – 
           whether to write reflogs
backup –  whether to rename or delete the old storage files. If set to true, the loose refs are left in refs.old, the packed-refs in packed-refs.old and reflogs in refs.old/. HEAD is left in HEAD.old and also .log is appended to additional refs. If set to false, the refs/ and logs/ directories and HEAD and additional symbolic refs are removed.
Throws:
IOException – 
            on IO problem/**
	 * Converts the RefDatabase from RefDirectory to reftable. This operation is
	 * not atomic.
	 *
	 * @param writeLogs
	 *            whether to write reflogs
	 * @param backup
	 *            whether to rename or delete the old storage files. If set to
	 *            {@code true}, the loose refs are left in {@code refs.old}, the
	 *            packed-refs in {@code packed-refs.old} and reflogs in
	 *            {@code refs.old/}. HEAD is left in {@code HEAD.old} and also
	 *            {@code .log} is appended to additional refs. If set to
	 *            {@code false}, the {@code refs/} and {@code logs/} directories
	 *            and {@code HEAD} and additional symbolic refs are removed.
	 * @throws IOException
	 *             on IO problem
	 */
	@SuppressWarnings("nls")
	void convertToReftable(boolean writeLogs, boolean backup)
			throws IOException {
		File reftableDir = new File(getDirectory(), Constants.REFTABLE);
		File headFile = new File(getDirectory(), Constants.HEAD);
		if (reftableDir.exists() && reftableDir.listFiles().length > 0) {
			throw new IOException(JGitText.get().reftableDirExists);
		}

		// Ignore return value, as it is tied to temporary newRefs file.
		FileReftableDatabase.convertFrom(this, writeLogs);

		File refsFile = new File(getDirectory(), "refs");

		// non-atomic: remove old data.
		File packedRefs = new File(getDirectory(), Constants.PACKED_REFS);
		File logsDir = new File(getDirectory(), Constants.LOGS);

		List<String> additional = getRefDatabase().getAdditionalRefs().stream()
				.map(Ref::getName).collect(toList());
		additional.add(Constants.HEAD);
		if (backup) {
			FileUtils.rename(refsFile, new File(getDirectory(), "refs.old"));
			if (packedRefs.exists()) {
				FileUtils.rename(packedRefs, new File(getDirectory(),
						Constants.PACKED_REFS + ".old"));
			}
			if (logsDir.exists()) {
				FileUtils.rename(logsDir,
						new File(getDirectory(), Constants.LOGS + ".old"));
			}
			for (String r : additional) {
				FileUtils.rename(new File(getDirectory(), r),
					new File(getDirectory(), r + ".old"));
			}
		} else {
			FileUtils.delete(packedRefs, FileUtils.SKIP_MISSING);
			FileUtils.delete(headFile);
			FileUtils.delete(logsDir, FileUtils.RECURSIVE);
			FileUtils.delete(refsFile, FileUtils.RECURSIVE);
			for (String r : additional) {
				new File(getDirectory(), r).delete();
			}
		}

		FileUtils.mkdir(refsFile, true);

		// By putting in a dummy HEAD, old versions of Git still detect a repo
		// (that they can't read)
		try (OutputStream os = new FileOutputStream(headFile)) {
			os.write(Constants.encodeASCII("ref: refs/heads/.invalid"));
		}

		// Some tools might write directly into .git/refs/heads/BRANCH. By
		// putting a file here, this fails spectacularly.
		FileUtils.createNewFile(new File(refsFile, "heads"));

		repoConfig.setString(ConfigConstants.CONFIG_EXTENSIONS_SECTION, null,
				ConfigConstants.CONFIG_KEY_REF_STORAGE,
				ConfigConstants.CONFIG_REF_STORAGE_REFTABLE);
		repoConfig.setLong(ConfigConstants.CONFIG_CORE_SECTION, null,
				ConfigConstants.CONFIG_KEY_REPO_FORMAT_VERSION, 1);
		repoConfig.save();
		refs.close();
		refs = new FileReftableDatabase(this);
	}

	
Converts between ref storage formats.
Params:
format – 
           the format to convert to, either "reftable" or "refdir"
writeLogs – 
           whether to write reflogs
backup – 
           whether to make a backup of the old data
Throws:
IOException – 
            on I/O problems./**
	 * Converts between ref storage formats.
	 *
	 * @param format
	 *            the format to convert to, either "reftable" or "refdir"
	 * @param writeLogs
	 *            whether to write reflogs
	 * @param backup
	 *            whether to make a backup of the old data
	 * @throws IOException
	 *             on I/O problems.
	 */
	public void convertRefStorage(String format, boolean writeLogs,
			boolean backup) throws IOException {
		if (format.equals("reftable")) { //$NON-NLS-1$
			if (refs instanceof RefDirectory) {
				convertToReftable(writeLogs, backup);
			}
		} else if (format.equals("refdir")) {//$NON-NLS-1$
			if (refs instanceof FileReftableDatabase) {
				convertToPackedRefs(writeLogs, backup);
			}
		} else {
			throw new IOException(MessageFormat
					.format(JGitText.get().unknownRefStorageFormat, format));
		}
	}
}