/*
    * Copyright (C) 2009, Google Inc.
    * 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.internal.storage.file;
  
  import static org.eclipse.jgit.internal.storage.pack.PackExt.INDEX;
  import static org.eclipse.jgit.internal.storage.pack.PackExt.PACK;
  
  import java.io.BufferedReader;
  import java.io.File;
  import java.io.FileInputStream;
  import java.io.FileNotFoundException;
  import java.io.FileReader;
  import java.io.IOException;
  import java.nio.file.AtomicMoveNotSupportedException;
  import java.nio.file.Files;
  import java.nio.file.StandardCopyOption;
  import java.text.MessageFormat;
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.Collection;
  import java.util.Collections;
  import java.util.HashMap;
  import java.util.HashSet;
  import java.util.List;
  import java.util.Map;
  import java.util.Set;
  import java.util.concurrent.atomic.AtomicReference;
  
  import org.eclipse.jgit.errors.CorruptObjectException;
  import org.eclipse.jgit.errors.PackInvalidException;
  import org.eclipse.jgit.errors.PackMismatchException;
  import org.eclipse.jgit.internal.JGitText;
  import org.eclipse.jgit.internal.storage.pack.ObjectToPack;
  import org.eclipse.jgit.internal.storage.pack.PackExt;
  import org.eclipse.jgit.internal.storage.pack.PackWriter;
  import org.eclipse.jgit.lib.AbbreviatedObjectId;
  import org.eclipse.jgit.lib.AnyObjectId;
  import org.eclipse.jgit.lib.Config;
  import org.eclipse.jgit.lib.ConfigConstants;
  import org.eclipse.jgit.lib.Constants;
  import org.eclipse.jgit.lib.ObjectDatabase;
  import org.eclipse.jgit.lib.ObjectId;
  import org.eclipse.jgit.lib.ObjectLoader;
  import org.eclipse.jgit.lib.RepositoryCache;
  import org.eclipse.jgit.lib.RepositoryCache.FileKey;
  import org.eclipse.jgit.util.FS;
  import org.eclipse.jgit.util.FileUtils;
  import org.slf4j.Logger;
  import org.slf4j.LoggerFactory;
  
  /**
   * Traditional file system based {@link ObjectDatabase}.
   * <p>
   * This is the classical object database representation for a Git repository,
   * where objects are stored loose by hashing them into directories by their
   * {@link ObjectId}, or are stored in compressed containers known as
   * {@link PackFile}s.
   * <p>
  * Optionally an object database can reference one or more alternates; other
  * ObjectDatabase instances that are searched in addition to the current
  * database.
  * <p>
  * Databases are divided into two halves: a half that is considered to be fast
  * to search (the {@code PackFile}s), and a half that is considered to be slow
  * to search (loose objects). When alternates are present the fast half is fully
  * searched (recursively through all alternates) before the slow half is
  * considered.
  */
 public class ObjectDirectory extends FileObjectDatabase {
 	private final static Logger LOG = LoggerFactory
 			.getLogger(ObjectDirectory.class);
 
 	private static final PackList NO_PACKS = new PackList(
 			FileSnapshot.DIRTY, new PackFile[0]);
 
 	/** Maximum number of candidates offered as resolutions of abbreviation. */
 	private static final int RESOLVE_ABBREV_LIMIT = 256;
 
 	private final Config config;
 
 	private final File objects;
 
 	private final File infoDirectory;
 
 	private final File packDirectory;
 
 	private final File alternatesFile;
 
 	private final AtomicReference<PackList> packList;
 
 	private final FS fs;
 
 	private final AtomicReference<AlternateHandle[]> alternates;
 
 	private final UnpackedObjectCache unpackedObjectCache;
 
 	private final File shallowFile;
 
 	private FileSnapshot shallowFileSnapshot = FileSnapshot.DIRTY;
 
 	private Set<ObjectId> shallowCommitsIds;
 
 	/**
 	 * Initialize a reference to an on-disk object directory.
 	 *
 	 * @param cfg
 	 *            configuration this directory consults for write settings.
 	 * @param dir
 	 *            the location of the <code>objects</code> directory.
 	 * @param alternatePaths
 	 *            a list of alternate object directories
 	 * @param fs
 	 *            the file system abstraction which will be necessary to perform
 	 *            certain file system operations.
 	 * @param shallowFile
 	 *            file which contains IDs of shallow commits, null if shallow
 	 *            commits handling should be turned off
 	 * @throws IOException
 	 *             an alternate object cannot be opened.
 	 */
 	public ObjectDirectory(final Config cfg, final File dir,
 			File[] alternatePaths, FS fs, File shallowFile) throws IOException {
 		config = cfg;
 		objects = dir;
 		infoDirectory = new File(objects, "info"); //$NON-NLS-1$
 		packDirectory = new File(objects, "pack"); //$NON-NLS-1$
 		alternatesFile = new File(infoDirectory, "alternates"); //$NON-NLS-1$
 		packList = new AtomicReference<PackList>(NO_PACKS);
 		unpackedObjectCache = new UnpackedObjectCache();
 		this.fs = fs;
 		this.shallowFile = shallowFile;
 
 		alternates = new AtomicReference<AlternateHandle[]>();
 		if (alternatePaths != null) {
 			AlternateHandle[] alt;
 
 			alt = new AlternateHandle[alternatePaths.length];
 			for (int i = 0; i < alternatePaths.length; i++)
 				alt[i] = openAlternate(alternatePaths[i]);
 			alternates.set(alt);
 		}
 	}
 
 	/**
 	 * @return the location of the <code>objects</code> directory.
 	 */
 	public final File getDirectory() {
 		return objects;
 	}
 
 	@Override
 	public boolean exists() {
 		return fs.exists(objects);
 	}
 
 	@Override
 	public void create() throws IOException {
 		FileUtils.mkdirs(objects);
 		FileUtils.mkdir(infoDirectory);
 		FileUtils.mkdir(packDirectory);
 	}
 
 	@Override
 	public ObjectDirectoryInserter newInserter() {
 		return new ObjectDirectoryInserter(this, config);
 	}
 
 	@Override
 	public void close() {
 		unpackedObjectCache.clear();
 
 		final PackList packs = packList.get();
 		if (packs != NO_PACKS && packList.compareAndSet(packs, NO_PACKS)) {
 			for (PackFile p : packs.packs)
 				p.close();
 		}
 
 		// Fully close all loaded alternates and clear the alternate list.
 		AlternateHandle[] alt = alternates.get();
 		if (alt != null && alternates.compareAndSet(alt, null)) {
 			for(final AlternateHandle od : alt)
 				od.close();
 		}
 	}
 
 	/**
 	 * @return unmodifiable collection of all known pack files local to this
 	 *         directory. Most recent packs are presented first. Packs most
 	 *         likely to contain more recent objects appear before packs
 	 *         containing objects referenced by commits further back in the
 	 *         history of the repository.
 	 */
 	@Override
 	public Collection<PackFile> getPacks() {
 		PackList list = packList.get();
 		if (list == NO_PACKS)
 			list = scanPacks(list);
 		PackFile[] packs = list.packs;
 		return Collections.unmodifiableCollection(Arrays.asList(packs));
 	}
 
 	/**
 	 * Add a single existing pack to the list of available pack files.
 	 *
 	 * @param pack
 	 *            path of the pack file to open.
 	 * @return the pack that was opened and added to the database.
 	 * @throws IOException
 	 *             index file could not be opened, read, or is not recognized as
 	 *             a Git pack file index.
 	 */
 	public PackFile openPack(final File pack)
 			throws IOException {
 		final String p = pack.getName();
 		if (p.length() != 50 || !p.startsWith("pack-") || !p.endsWith(".pack")) //$NON-NLS-1$ //$NON-NLS-2$
 			throw new IOException(MessageFormat.format(JGitText.get().notAValidPack, pack));
 
 		// The pack and index are assumed to exist. The existence of other
 		// extensions needs to be explicitly checked.
 		//
 		int extensions = PACK.getBit() | INDEX.getBit();
 		final String base = p.substring(0, p.length() - 4);
 		for (PackExt ext : PackExt.values()) {
 			if ((extensions & ext.getBit()) == 0) {
 				final String name = base + ext.getExtension();
 				if (new File(pack.getParentFile(), name).exists())
 					extensions |= ext.getBit();
 			}
 		}
 
 		PackFile res = new PackFile(pack, extensions);
 		insertPack(res);
 		return res;
 	}
 
 	@Override
 	public String toString() {
 		return "ObjectDirectory[" + getDirectory() + "]"; //$NON-NLS-1$ //$NON-NLS-2$
 	}
 
 	@Override
 	public boolean has(AnyObjectId objectId) {
 		return unpackedObjectCache.isUnpacked(objectId)
 				|| hasPackedInSelfOrAlternate(objectId)
 				|| hasLooseInSelfOrAlternate(objectId);
 	}
 
 	private boolean hasPackedInSelfOrAlternate(AnyObjectId objectId) {
 		if (hasPackedObject(objectId))
 			return true;
 		for (AlternateHandle alt : myAlternates()) {
 			if (alt.db.hasPackedInSelfOrAlternate(objectId))
 				return true;
 		}
 		return false;
 	}
 
 	private boolean hasLooseInSelfOrAlternate(AnyObjectId objectId) {
 		if (fileFor(objectId).exists())
 			return true;
 		for (AlternateHandle alt : myAlternates()) {
 			if (alt.db.hasLooseInSelfOrAlternate(objectId))
 				return true;
 		}
 		return false;
 	}
 
 	boolean hasPackedObject(AnyObjectId objectId) {
 		PackList pList;
 		do {
 			pList = packList.get();
 			for (PackFile p : pList.packs) {
 				try {
 					if (p.hasObject(objectId))
 						return true;
 				} catch (IOException e) {
 					// The hasObject call should have only touched the index,
 					// so any failure here indicates the index is unreadable
 					// by this process, and the pack is likewise not readable.
 					removePack(p);
 				}
 			}
 		} while (searchPacksAgain(pList));
 		return false;
 	}
 
 	@Override
 	void resolve(Set<ObjectId> matches, AbbreviatedObjectId id)
 			throws IOException {
 		// Go through the packs once. If we didn't find any resolutions
 		// scan for new packs and check once more.
 		int oldSize = matches.size();
 		PackList pList;
 		do {
 			pList = packList.get();
 			for (PackFile p : pList.packs) {
 				try {
 					p.resolve(matches, id, RESOLVE_ABBREV_LIMIT);
 				} catch (IOException e) {
 					handlePackError(e, p);
 				}
 				if (matches.size() > RESOLVE_ABBREV_LIMIT)
 					return;
 			}
 		} while (matches.size() == oldSize && searchPacksAgain(pList));
 
 		String fanOut = id.name().substring(0, 2);
 		String[] entries = new File(getDirectory(), fanOut).list();
 		if (entries != null) {
 			for (String e : entries) {
 				if (e.length() != Constants.OBJECT_ID_STRING_LENGTH - 2)
 					continue;
 				try {
 					ObjectId entId = ObjectId.fromString(fanOut + e);
 					if (id.prefixCompare(entId) == 0)
 						matches.add(entId);
 				} catch (IllegalArgumentException notId) {
 					continue;
 				}
 				if (matches.size() > RESOLVE_ABBREV_LIMIT)
 					return;
 			}
 		}
 
 		for (AlternateHandle alt : myAlternates()) {
 			alt.db.resolve(matches, id);
 			if (matches.size() > RESOLVE_ABBREV_LIMIT)
 				return;
 		}
 	}
 
 	@Override
 	ObjectLoader openObject(WindowCursor curs, AnyObjectId objectId)
 			throws IOException {
 		if (unpackedObjectCache.isUnpacked(objectId)) {
 			ObjectLoader ldr = openLooseObject(curs, objectId);
 			if (ldr != null)
 				return ldr;
 		}
 		ObjectLoader ldr = openPackedFromSelfOrAlternate(curs, objectId);
 		if (ldr != null)
 			return ldr;
 		return openLooseFromSelfOrAlternate(curs, objectId);
 	}
 
 	private ObjectLoader openPackedFromSelfOrAlternate(WindowCursor curs,
 			AnyObjectId objectId) {
 		ObjectLoader ldr = openPackedObject(curs, objectId);
 		if (ldr != null)
 			return ldr;
 		for (AlternateHandle alt : myAlternates()) {
 			ldr = alt.db.openPackedFromSelfOrAlternate(curs, objectId);
 			if (ldr != null)
 				return ldr;
 		}
 		return null;
 	}
 
 	private ObjectLoader openLooseFromSelfOrAlternate(WindowCursor curs,
 			AnyObjectId objectId) throws IOException {
 		ObjectLoader ldr = openLooseObject(curs, objectId);
 		if (ldr != null)
 			return ldr;
 		for (AlternateHandle alt : myAlternates()) {
 			ldr = alt.db.openLooseFromSelfOrAlternate(curs, objectId);
 			if (ldr != null)
 				return ldr;
 		}
 		return null;
 	}
 
 	ObjectLoader openPackedObject(WindowCursor curs, AnyObjectId objectId) {
 		PackList pList;
 		do {
 			SEARCH: for (;;) {
 				pList = packList.get();
 				for (PackFile p : pList.packs) {
 					try {
 						ObjectLoader ldr = p.get(curs, objectId);
 						if (ldr != null)
 							return ldr;
 					} catch (PackMismatchException e) {
 						// Pack was modified; refresh the entire pack list.
 						if (searchPacksAgain(pList))
 							continue SEARCH;
 					} catch (IOException e) {
 						handlePackError(e, p);
 					}
 				}
 				break SEARCH;
 			}
 		} while (searchPacksAgain(pList));
 		return null;
 	}
 
 	ObjectLoader openLooseObject(WindowCursor curs, AnyObjectId id)
 			throws IOException {
 		File path = fileFor(id);
 		try (FileInputStream in = new FileInputStream(path)) {
 			unpackedObjectCache.add(id);
 			return UnpackedObject.open(in, path, id, curs);
 		} catch (FileNotFoundException noFile) {
 			if (path.exists()) {
 				throw noFile;
 			}
 			unpackedObjectCache.remove(id);
 			return null;
 		}
 	}
 
 	long getObjectSize(WindowCursor curs, AnyObjectId id)
 			throws IOException {
 		if (unpackedObjectCache.isUnpacked(id)) {
 			long len = getLooseObjectSize(curs, id);
 			if (0 <= len)
 				return len;
 		}
 		long len = getPackedSizeFromSelfOrAlternate(curs, id);
 		if (0 <= len)
 			return len;
 		return getLooseSizeFromSelfOrAlternate(curs, id);
 	}
 
 	private long getPackedSizeFromSelfOrAlternate(WindowCursor curs,
 			AnyObjectId id) {
 		long len = getPackedObjectSize(curs, id);
 		if (0 <= len)
 			return len;
 		for (AlternateHandle alt : myAlternates()) {
 			len = alt.db.getPackedSizeFromSelfOrAlternate(curs, id);
 			if (0 <= len)
 				return len;
 		}
 		return -1;
 	}
 
 	private long getLooseSizeFromSelfOrAlternate(WindowCursor curs,
 			AnyObjectId id) throws IOException {
 		long len = getLooseObjectSize(curs, id);
 		if (0 <= len)
 			return len;
 		for (AlternateHandle alt : myAlternates()) {
 			len = alt.db.getLooseSizeFromSelfOrAlternate(curs, id);
 			if (0 <= len)
 				return len;
 		}
 		return -1;
 	}
 
 	private long getPackedObjectSize(WindowCursor curs, AnyObjectId id) {
 		PackList pList;
 		do {
 			SEARCH: for (;;) {
 				pList = packList.get();
 				for (PackFile p : pList.packs) {
 					try {
 						long len = p.getObjectSize(curs, id);
 						if (0 <= len)
 							return len;
 					} catch (PackMismatchException e) {
 						// Pack was modified; refresh the entire pack list.
 						if (searchPacksAgain(pList))
 							continue SEARCH;
 					} catch (IOException e) {
 						handlePackError(e, p);
 					}
 				}
 				break SEARCH;
 			}
 		} while (searchPacksAgain(pList));
 		return -1;
 	}
 
 	private long getLooseObjectSize(WindowCursor curs, AnyObjectId id)
 			throws IOException {
 		File f = fileFor(id);
 		try (FileInputStream in = new FileInputStream(f)) {
 			unpackedObjectCache.add(id);
 			return UnpackedObject.getSize(in, id, curs);
 		} catch (FileNotFoundException noFile) {
 			if (f.exists()) {
 				throw noFile;
 			}
 			unpackedObjectCache.remove(id);
 			return -1;
 		}
 	}
 
 	@Override
 	void selectObjectRepresentation(PackWriter packer, ObjectToPack otp,
 			WindowCursor curs) throws IOException {
 		PackList pList = packList.get();
 		SEARCH: for (;;) {
 			for (final PackFile p : pList.packs) {
 				try {
 					LocalObjectRepresentation rep = p.representation(curs, otp);
 					if (rep != null)
 						packer.select(otp, rep);
 				} catch (PackMismatchException e) {
 					// Pack was modified; refresh the entire pack list.
 					//
 					pList = scanPacks(pList);
 					continue SEARCH;
 				} catch (IOException e) {
 					handlePackError(e, p);
 				}
 			}
 			break SEARCH;
 		}
 
 		for (AlternateHandle h : myAlternates())
 			h.db.selectObjectRepresentation(packer, otp, curs);
 	}
 
 	private void handlePackError(IOException e, PackFile p) {
 		String warnTmpl = null;
 		if ((e instanceof CorruptObjectException)
 				|| (e instanceof PackInvalidException)) {
 			warnTmpl = JGitText.get().corruptPack;
 			// Assume the pack is corrupted, and remove it from the list.
 			removePack(p);
 		} else if (e instanceof FileNotFoundException) {
 			if (p.getPackFile().exists()) {
 				warnTmpl = JGitText.get().packInaccessible;
 			} else {
 				warnTmpl = JGitText.get().packWasDeleted;
 			}
 			removePack(p);
 		} else if (FileUtils.isStaleFileHandle(e)) {
 			warnTmpl = JGitText.get().packHandleIsStale;
 			removePack(p);
 		}
 		if (warnTmpl != null) {
 			if (LOG.isDebugEnabled()) {
 				LOG.debug(MessageFormat.format(warnTmpl,
 						p.getPackFile().getAbsolutePath()), e);
 			} else {
 				LOG.warn(MessageFormat.format(warnTmpl,
 						p.getPackFile().getAbsolutePath()));
 			}
 		} else {
 			// Don't remove the pack from the list, as the error may be
 			// transient.
 			LOG.error(MessageFormat.format(
 					JGitText.get().exceptionWhileReadingPack, p.getPackFile()
 							.getAbsolutePath()), e);
 		}
 	}
 
 	@Override
 	InsertLooseObjectResult insertUnpackedObject(File tmp, ObjectId id,
 			boolean createDuplicate) throws IOException {
 		// If the object is already in the repository, remove temporary file.
 		//
 		if (unpackedObjectCache.isUnpacked(id)) {
 			FileUtils.delete(tmp, FileUtils.RETRY);
 			return InsertLooseObjectResult.EXISTS_LOOSE;
 		}
 		if (!createDuplicate && has(id)) {
 			FileUtils.delete(tmp, FileUtils.RETRY);
 			return InsertLooseObjectResult.EXISTS_PACKED;
 		}
 
 		final File dst = fileFor(id);
 		if (dst.exists()) {
 			// We want to be extra careful and avoid replacing an object
 			// that already exists. We can't be sure renameTo() would
 			// fail on all platforms if dst exists, so we check first.
 			//
 			FileUtils.delete(tmp, FileUtils.RETRY);
 			return InsertLooseObjectResult.EXISTS_LOOSE;
 		}
 		try {
 			Files.move(tmp.toPath(), dst.toPath(),
 					StandardCopyOption.ATOMIC_MOVE);
 			dst.setReadOnly();
 			unpackedObjectCache.add(id);
 			return InsertLooseObjectResult.INSERTED;
 		} catch (AtomicMoveNotSupportedException e) {
 			LOG.error(e.getMessage(), e);
 		} catch (IOException e) {
 			// ignore
 		}
 
 		// Maybe the directory doesn't exist yet as the object
 		// directories are always lazily created. Note that we
 		// try the rename first as the directory likely does exist.
 		//
 		FileUtils.mkdir(dst.getParentFile(), true);
 		try {
 			Files.move(tmp.toPath(), dst.toPath(),
 					StandardCopyOption.ATOMIC_MOVE);
 			dst.setReadOnly();
 			unpackedObjectCache.add(id);
 			return InsertLooseObjectResult.INSERTED;
 		} catch (AtomicMoveNotSupportedException e) {
 			LOG.error(e.getMessage(), e);
 		} catch (IOException e) {
 			LOG.debug(e.getMessage(), e);
 		}
 
 		if (!createDuplicate && has(id)) {
 			FileUtils.delete(tmp, FileUtils.RETRY);
 			return InsertLooseObjectResult.EXISTS_PACKED;
 		}
 
 		// The object failed to be renamed into its proper
 		// location and it doesn't exist in the repository
 		// either. We really don't know what went wrong, so
 		// fail.
 		//
 		FileUtils.delete(tmp, FileUtils.RETRY);
 		return InsertLooseObjectResult.FAILURE;
 	}
 
 	private boolean searchPacksAgain(PackList old) {
 		// Whether to trust the pack folder's modification time. If set
 		// to false we will always scan the .git/objects/pack folder to
 		// check for new pack files. If set to true (default) we use the
 		// lastmodified attribute of the folder and assume that no new
 		// pack files can be in this folder if his modification time has
 		// not changed.
 		boolean trustFolderStat = config.getBoolean(
 				ConfigConstants.CONFIG_CORE_SECTION,
 				ConfigConstants.CONFIG_KEY_TRUSTFOLDERSTAT, true);
 
 		return ((!trustFolderStat) || old.snapshot.isModified(packDirectory))
 				&& old != scanPacks(old);
 	}
 
 	Config getConfig() {
 		return config;
 	}
 
 	@Override
 	FS getFS() {
 		return fs;
 	}
 
 	@Override
 	Set<ObjectId> getShallowCommits() throws IOException {
 		if (shallowFile == null || !shallowFile.isFile())
 			return Collections.emptySet();
 
 		if (shallowFileSnapshot == null
 				|| shallowFileSnapshot.isModified(shallowFile)) {
 			shallowCommitsIds = new HashSet<ObjectId>();
 
 			final BufferedReader reader = open(shallowFile);
 			try {
 				String line;
 				while ((line = reader.readLine()) != null)
 					shallowCommitsIds.add(ObjectId.fromString(line));
 			} finally {
 				reader.close();
 			}
 
 			shallowFileSnapshot = FileSnapshot.save(shallowFile);
 		}
 
 		return shallowCommitsIds;
 	}
 
 	private void insertPack(final PackFile pf) {
 		PackList o, n;
 		do {
 			o = packList.get();
 
 			// If the pack in question is already present in the list
 			// (picked up by a concurrent thread that did a scan?) we
 			// do not want to insert it a second time.
 			//
 			final PackFile[] oldList = o.packs;
 			final String name = pf.getPackFile().getName();
 			for (PackFile p : oldList) {
 				if (PackFile.SORT.compare(pf, p) < 0)
 					break;
 				if (name.equals(p.getPackFile().getName()))
 					return;
 			}
 
 			final PackFile[] newList = new PackFile[1 + oldList.length];
 			newList[0] = pf;
 			System.arraycopy(oldList, 0, newList, 1, oldList.length);
 			n = new PackList(o.snapshot, newList);
 		} while (!packList.compareAndSet(o, n));
 	}
 
 	private void removePack(final PackFile deadPack) {
 		PackList o, n;
 		do {
 			o = packList.get();
 
 			final PackFile[] oldList = o.packs;
 			final int j = indexOf(oldList, deadPack);
 			if (j < 0)
 				break;
 
 			final PackFile[] newList = new PackFile[oldList.length - 1];
 			System.arraycopy(oldList, 0, newList, 0, j);
 			System.arraycopy(oldList, j + 1, newList, j, newList.length - j);
 			n = new PackList(o.snapshot, newList);
 		} while (!packList.compareAndSet(o, n));
 		deadPack.close();
 	}
 
 	private static int indexOf(final PackFile[] list, final PackFile pack) {
 		for (int i = 0; i < list.length; i++) {
 			if (list[i] == pack)
 				return i;
 		}
 		return -1;
 	}
 
 	private PackList scanPacks(final PackList original) {
 		synchronized (packList) {
 			PackList o, n;
 			do {
 				o = packList.get();
 				if (o != original) {
 					// Another thread did the scan for us, while we
 					// were blocked on the monitor above.
 					//
 					return o;
 				}
 				n = scanPacksImpl(o);
 				if (n == o)
 					return n;
 			} while (!packList.compareAndSet(o, n));
 			return n;
 		}
 	}
 
 	private PackList scanPacksImpl(final PackList old) {
 		final Map<String, PackFile> forReuse = reuseMap(old);
 		final FileSnapshot snapshot = FileSnapshot.save(packDirectory);
 		final Set<String> names = listPackDirectory();
 		final List<PackFile> list = new ArrayList<PackFile>(names.size() >> 2);
 		boolean foundNew = false;
 		for (final String indexName : names) {
 			// Must match "pack-[0-9a-f]{40}.idx" to be an index.
 			//
 			if (indexName.length() != 49 || !indexName.endsWith(".idx")) //$NON-NLS-1$
 				continue;
 
 			final String base = indexName.substring(0, indexName.length() - 3);
 			int extensions = 0;
 			for (PackExt ext : PackExt.values()) {
 				if (names.contains(base + ext.getExtension()))
 					extensions |= ext.getBit();
 			}
 
 			if ((extensions & PACK.getBit()) == 0) {
 				// Sometimes C Git's HTTP fetch transport leaves a
 				// .idx file behind and does not download the .pack.
 				// We have to skip over such useless indexes.
 				//
 				continue;
 			}
 
 			final String packName = base + PACK.getExtension();
 			final PackFile oldPack = forReuse.remove(packName);
 			if (oldPack != null) {
 				list.add(oldPack);
 				continue;
 			}
 
 			final File packFile = new File(packDirectory, packName);
 			list.add(new PackFile(packFile, extensions));
 			foundNew = true;
 		}
 
 		// If we did not discover any new files, the modification time was not
 		// changed, and we did not remove any files, then the set of files is
 		// the same as the set we were given. Instead of building a new object
 		// return the same collection.
 		//
 		if (!foundNew && forReuse.isEmpty() && snapshot.equals(old.snapshot)) {
 			old.snapshot.setClean(snapshot);
 			return old;
 		}
 
 		for (final PackFile p : forReuse.values()) {
 			p.close();
 		}
 
 		if (list.isEmpty())
 			return new PackList(snapshot, NO_PACKS.packs);
 
 		final PackFile[] r = list.toArray(new PackFile[list.size()]);
 		Arrays.sort(r, PackFile.SORT);
 		return new PackList(snapshot, r);
 	}
 
 	private static Map<String, PackFile> reuseMap(final PackList old) {
 		final Map<String, PackFile> forReuse = new HashMap<String, PackFile>();
 		for (final PackFile p : old.packs) {
 			if (p.invalid()) {
 				// The pack instance is corrupted, and cannot be safely used
 				// again. Do not include it in our reuse map.
 				//
 				p.close();
 				continue;
 			}
 
 			final PackFile prior = forReuse.put(p.getPackFile().getName(), p);
 			if (prior != null) {
 				// This should never occur. It should be impossible for us
 				// to have two pack files with the same name, as all of them
 				// came out of the same directory. If it does, we promised to
 				// close any PackFiles we did not reuse, so close the second,
 				// readers are likely to be actively using the first.
 				//
 				forReuse.put(prior.getPackFile().getName(), prior);
 				p.close();
 			}
 		}
 		return forReuse;
 	}
 
 	private Set<String> listPackDirectory() {
 		final String[] nameList = packDirectory.list();
 		if (nameList == null)
 			return Collections.emptySet();
 		final Set<String> nameSet = new HashSet<String>(nameList.length << 1);
 		for (final String name : nameList) {
 			if (name.startsWith("pack-")) //$NON-NLS-1$
 				nameSet.add(name);
 		}
 		return nameSet;
 	}
 
 	AlternateHandle[] myAlternates() {
 		AlternateHandle[] alt = alternates.get();
 		if (alt == null) {
 			synchronized (alternates) {
 				alt = alternates.get();
 				if (alt == null) {
 					try {
 						alt = loadAlternates();
 					} catch (IOException e) {
 						alt = new AlternateHandle[0];
 					}
 					alternates.set(alt);
 				}
 			}
 		}
 		return alt;
 	}
 
 	private AlternateHandle[] loadAlternates() throws IOException {
 		final List<AlternateHandle> l = new ArrayList<AlternateHandle>(4);
 		final BufferedReader br = open(alternatesFile);
 		try {
 			String line;
 			while ((line = br.readLine()) != null) {
 				l.add(openAlternate(line));
 			}
 		} finally {
 			br.close();
 		}
 		return l.toArray(new AlternateHandle[l.size()]);
 	}
 
 	private static BufferedReader open(final File f)
 			throws FileNotFoundException {
 		return new BufferedReader(new FileReader(f));
 	}
 
 	private AlternateHandle openAlternate(final String location)
 			throws IOException {
 		final File objdir = fs.resolve(objects, location);
 		return openAlternate(objdir);
 	}
 
 	private AlternateHandle openAlternate(File objdir) throws IOException {
 		final File parent = objdir.getParentFile();
 		if (FileKey.isGitRepository(parent, fs)) {
 			FileKey key = FileKey.exact(parent, fs);
 			FileRepository db = (FileRepository) RepositoryCache.open(key);
 			return new AlternateRepository(db);
 		}
 
 		ObjectDirectory db = new ObjectDirectory(config, objdir, null, fs, null);
 		return new AlternateHandle(db);
 	}
 
 	/**
 	 * Compute the location of a loose object file.
 	 *
 	 * @param objectId
 	 *            identity of the loose object to map to the directory.
 	 * @return location of the object, if it were to exist as a loose object.
 	 */
 	public File fileFor(AnyObjectId objectId) {
 		String n = objectId.name();
 		String d = n.substring(0, 2);
 		String f = n.substring(2);
 		return new File(new File(getDirectory(), d), f);
 	}
 
 	private static final class PackList {
 		/** State just before reading the pack directory. */
 		final FileSnapshot snapshot;
 
 		/** All known packs, sorted by {@link PackFile#SORT}. */
 		final PackFile[] packs;
 
 		PackList(final FileSnapshot monitor, final PackFile[] packs) {
 			this.snapshot = monitor;
 			this.packs = packs;
 		}
 	}
 
 	static class AlternateHandle {
 		final ObjectDirectory db;
 
 		AlternateHandle(ObjectDirectory db) {
 			this.db = db;
 		}
 
 		void close() {
 			db.close();
 		}
 	}
 
 	static class AlternateRepository extends AlternateHandle {
 		final FileRepository repository;
 
 		AlternateRepository(FileRepository r) {
 			super(r.getObjectDatabase());
 			repository = r;
 		}
 
 		void close() {
 			repository.close();
 		}
 	}
 
 	@Override
 	public ObjectDatabase newCachedDatabase() {
 		return newCachedFileObjectDatabase();
 	}
 
 	CachedObjectDirectory newCachedFileObjectDatabase() {
 		return new CachedObjectDirectory(this);
 	}
 }