/*
    * Copyright (C) 2012, Christian Halstrick <christian.halstrick@sap.com>
    * Copyright (C) 2011, Shawn O. Pearce <spearce@spearce.org>
    * 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.BITMAP_INDEX;
  import static org.eclipse.jgit.internal.storage.pack.PackExt.INDEX;
  
  import java.io.File;
  import java.io.FileOutputStream;
  import java.io.IOException;
  import java.io.OutputStream;
  import java.nio.channels.Channels;
  import java.nio.channels.FileChannel;
  import java.nio.file.DirectoryStream;
  import java.nio.file.Files;
  import java.nio.file.Path;
  import java.nio.file.Paths;
  import java.nio.file.StandardCopyOption;
  import java.text.MessageFormat;
  import java.text.ParseException;
  import java.util.ArrayList;
  import java.util.Collection;
  import java.util.Collections;
  import java.util.Comparator;
  import java.util.Date;
  import java.util.HashMap;
  import java.util.HashSet;
  import java.util.Iterator;
  import java.util.LinkedList;
  import java.util.List;
  import java.util.Map;
  import java.util.Objects;
  import java.util.Set;
  import java.util.TreeMap;
  import java.util.regex.Pattern;
  import java.util.stream.Collectors;
  import java.util.stream.Stream;
  
  import org.eclipse.jgit.annotations.NonNull;
  import org.eclipse.jgit.dircache.DirCacheIterator;
  import org.eclipse.jgit.errors.CorruptObjectException;
  import org.eclipse.jgit.errors.IncorrectObjectTypeException;
  import org.eclipse.jgit.errors.MissingObjectException;
  import org.eclipse.jgit.errors.NoWorkTreeException;
  import org.eclipse.jgit.internal.JGitText;
  import org.eclipse.jgit.internal.storage.pack.PackExt;
  import org.eclipse.jgit.internal.storage.pack.PackWriter;
  import org.eclipse.jgit.internal.storage.reftree.RefTreeNames;
  import org.eclipse.jgit.lib.ConfigConstants;
  import org.eclipse.jgit.lib.Constants;
  import org.eclipse.jgit.lib.FileMode;
  import org.eclipse.jgit.lib.NullProgressMonitor;
  import org.eclipse.jgit.lib.ObjectId;
  import org.eclipse.jgit.lib.ObjectIdSet;
  import org.eclipse.jgit.lib.ProgressMonitor;
  import org.eclipse.jgit.lib.Ref;
  import org.eclipse.jgit.lib.Ref.Storage;
  import org.eclipse.jgit.lib.RefDatabase;
 import org.eclipse.jgit.lib.ReflogEntry;
 import org.eclipse.jgit.lib.ReflogReader;
 import org.eclipse.jgit.revwalk.ObjectWalk;
 import org.eclipse.jgit.revwalk.RevObject;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.storage.pack.PackConfig;
 import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.jgit.treewalk.filter.TreeFilter;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.jgit.util.GitDateParser;
 import org.eclipse.jgit.util.SystemReader;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /**
  * A garbage collector for git {@link FileRepository}. Instances of this class
  * are not thread-safe. Don't use the same instance from multiple threads.
  *
  * This class started as a copy of DfsGarbageCollector from Shawn O. Pearce
  * adapted to FileRepositories.
  */
 public class GC {
 	private final static Logger LOG = LoggerFactory
 			.getLogger(GC.class);
 
 	private static final String PRUNE_EXPIRE_DEFAULT = "2.weeks.ago"; //$NON-NLS-1$
 
 	private static final String PRUNE_PACK_EXPIRE_DEFAULT = "1.hour.ago"; //$NON-NLS-1$
 
 	private static final Pattern PATTERN_LOOSE_OBJECT = Pattern
 			.compile("[0-9a-fA-F]{38}"); //$NON-NLS-1$
 
 	private static final String PACK_EXT = "." + PackExt.PACK.getExtension();//$NON-NLS-1$
 
 	private static final String BITMAP_EXT = "." //$NON-NLS-1$
 			+ PackExt.BITMAP_INDEX.getExtension();
 
 	private static final String INDEX_EXT = "." + PackExt.INDEX.getExtension(); //$NON-NLS-1$
 
 	private static final int DEFAULT_AUTOPACKLIMIT = 50;
 
 	private static final int DEFAULT_AUTOLIMIT = 6700;
 
 	private final FileRepository repo;
 
 	private ProgressMonitor pm;
 
 	private long expireAgeMillis = -1;
 
 	private Date expire;
 
 	private long packExpireAgeMillis = -1;
 
 	private Date packExpire;
 
 	private PackConfig pconfig = null;
 
 	/**
 	 * the refs which existed during the last call to {@link #repack()}. This is
 	 * needed during {@link #prune(Set)} where we can optimize by looking at the
 	 * difference between the current refs and the refs which existed during
 	 * last {@link #repack()}.
 	 */
 	private Collection<Ref> lastPackedRefs;
 
 	/**
 	 * Holds the starting time of the last repack() execution. This is needed in
 	 * prune() to inspect only those reflog entries which have been added since
 	 * last repack().
 	 */
 	private long lastRepackTime;
 
 	/**
 	 * Whether gc should do automatic housekeeping
 	 */
 	private boolean automatic;
 
 	/**
 	 * Creates a new garbage collector with default values. An expirationTime of
 	 * two weeks and <code>null</code> as progress monitor will be used.
 	 *
 	 * @param repo
 	 *            the repo to work on
 	 */
 	public GC(FileRepository repo) {
 		this.repo = repo;
 		this.pm = NullProgressMonitor.INSTANCE;
 	}
 
 	/**
 	 * Runs a garbage collector on a {@link FileRepository}. It will
 	 * <ul>
 	 * <li>pack loose references into packed-refs</li>
 	 * <li>repack all reachable objects into new pack files and delete the old
 	 * pack files</li>
 	 * <li>prune all loose objects which are now reachable by packs</li>
 	 * </ul>
 	 *
 	 * If {@link #setAuto(boolean)} was set to {@code true} {@code gc} will
 	 * first check whether any housekeeping is required; if not, it exits
 	 * without performing any work.
 	 *
 	 * @return the collection of {@link PackFile}'s which are newly created
 	 * @throws IOException
 	 * @throws ParseException
 	 *             If the configuration parameter "gc.pruneexpire" couldn't be
 	 *             parsed
 	 */
 	public Collection<PackFile> gc() throws IOException, ParseException {
 		if (automatic && !needGc()) {
 			return Collections.emptyList();
 		}
 		pm.start(6 /* tasks */);
 		packRefs();
 		// TODO: implement reflog_expire(pm, repo);
 		Collection<PackFile> newPacks = repack();
 		prune(Collections.<ObjectId> emptySet());
 		// TODO: implement rerere_gc(pm);
 		return newPacks;
 	}
 
 	/**
 	 * Delete old pack files. What is 'old' is defined by specifying a set of
 	 * old pack files and a set of new pack files. Each pack file contained in
 	 * old pack files but not contained in new pack files will be deleted. If an
 	 * expirationDate is set then pack files which are younger than the
 	 * expirationDate will not be deleted.
 	 *
 	 * @param oldPacks
 	 * @param newPacks
 	 * @throws ParseException
 	 * @throws IOException
 	 */
 	private void deleteOldPacks(Collection<PackFile> oldPacks,
 			Collection<PackFile> newPacks) throws ParseException, IOException {
 		long packExpireDate = getPackExpireDate();
 		oldPackLoop: for (PackFile oldPack : oldPacks) {
 			String oldName = oldPack.getPackName();
 			// check whether an old pack file is also among the list of new
 			// pack files. Then we must not delete it.
 			for (PackFile newPack : newPacks)
 				if (oldName.equals(newPack.getPackName()))
 					continue oldPackLoop;
 
 			if (!oldPack.shouldBeKept()
 					&& repo.getFS().lastModified(
 							oldPack.getPackFile()) < packExpireDate) {
 				oldPack.close();
 				prunePack(oldName);
 			}
 		}
 		// close the complete object database. Thats my only chance to force
 		// rescanning and to detect that certain pack files are now deleted.
 		repo.getObjectDatabase().close();
 	}
 
 	/**
 	 * Delete files associated with a single pack file. First try to delete the
 	 * ".pack" file because on some platforms the ".pack" file may be locked and
 	 * can't be deleted. In such a case it is better to detect this early and
 	 * give up on deleting files for this packfile. Otherwise we may delete the
 	 * ".index" file and when failing to delete the ".pack" file we are left
 	 * with a ".pack" file without a ".index" file.
 	 *
 	 * @param packName
 	 */
 	private void prunePack(String packName) {
 		PackExt[] extensions = PackExt.values();
 		try {
 			// Delete the .pack file first and if this fails give up on deleting
 			// the other files
 			int deleteOptions = FileUtils.RETRY | FileUtils.SKIP_MISSING;
 			for (PackExt ext : extensions)
 				if (PackExt.PACK.equals(ext)) {
 					File f = nameFor(packName, "." + ext.getExtension()); //$NON-NLS-1$
 					FileUtils.delete(f, deleteOptions);
 					break;
 				}
 			// The .pack file has been deleted. Delete as many as the other
 			// files as you can.
 			deleteOptions |= FileUtils.IGNORE_ERRORS;
 			for (PackExt ext : extensions) {
 				if (!PackExt.PACK.equals(ext)) {
 					File f = nameFor(packName, "." + ext.getExtension()); //$NON-NLS-1$
 					FileUtils.delete(f, deleteOptions);
 				}
 			}
 		} catch (IOException e) {
 			// Deletion of the .pack file failed. Silently return.
 		}
 	}
 
 	/**
 	 * Like "git prune-packed" this method tries to prune all loose objects
 	 * which can be found in packs. If certain objects can't be pruned (e.g.
 	 * because the filesystem delete operation fails) this is silently ignored.
 	 *
 	 * @throws IOException
 	 */
 	public void prunePacked() throws IOException {
 		ObjectDirectory objdb = repo.getObjectDatabase();
 		Collection<PackFile> packs = objdb.getPacks();
 		File objects = repo.getObjectsDirectory();
 		String[] fanout = objects.list();
 
 		if (fanout != null && fanout.length > 0) {
 			pm.beginTask(JGitText.get().pruneLoosePackedObjects, fanout.length);
 			try {
 				for (String d : fanout) {
 					pm.update(1);
 					if (d.length() != 2)
 						continue;
 					String[] entries = new File(objects, d).list();
 					if (entries == null)
 						continue;
 					for (String e : entries) {
 						if (e.length() != Constants.OBJECT_ID_STRING_LENGTH - 2)
 							continue;
 						ObjectId id;
 						try {
 							id = ObjectId.fromString(d + e);
 						} catch (IllegalArgumentException notAnObject) {
 							// ignoring the file that does not represent loose
 							// object
 							continue;
 						}
 						boolean found = false;
 						for (PackFile p : packs)
 							if (p.hasObject(id)) {
 								found = true;
 								break;
 							}
 						if (found)
 							FileUtils.delete(objdb.fileFor(id), FileUtils.RETRY
 									| FileUtils.SKIP_MISSING
 									| FileUtils.IGNORE_ERRORS);
 					}
 				}
 			} finally {
 				pm.endTask();
 			}
 		}
 	}
 
 	/**
 	 * Like "git prune" this method tries to prune all loose objects which are
 	 * unreferenced. If certain objects can't be pruned (e.g. because the
 	 * filesystem delete operation fails) this is silently ignored.
 	 *
 	 * @param objectsToKeep
 	 *            a set of objects which should explicitly not be pruned
 	 *
 	 * @throws IOException
 	 * @throws ParseException
 	 *             If the configuration parameter "gc.pruneexpire" couldn't be
 	 *             parsed
 	 */
 	public void prune(Set<ObjectId> objectsToKeep) throws IOException,
 			ParseException {
 		long expireDate = getExpireDate();
 
 		// Collect all loose objects which are old enough, not referenced from
 		// the index and not in objectsToKeep
 		Map<ObjectId, File> deletionCandidates = new HashMap<ObjectId, File>();
 		Set<ObjectId> indexObjects = null;
 		File objects = repo.getObjectsDirectory();
 		String[] fanout = objects.list();
 		if (fanout == null || fanout.length == 0) {
 			return;
 		}
 		pm.beginTask(JGitText.get().pruneLooseUnreferencedObjects,
 				fanout.length);
 		try {
 			for (String d : fanout) {
 				pm.update(1);
 				if (d.length() != 2)
 					continue;
 				File[] entries = new File(objects, d).listFiles();
 				if (entries == null)
 					continue;
 				for (File f : entries) {
 					String fName = f.getName();
 					if (fName.length() != Constants.OBJECT_ID_STRING_LENGTH - 2)
 						continue;
 					if (repo.getFS().lastModified(f) >= expireDate)
 						continue;
 					try {
 						ObjectId id = ObjectId.fromString(d + fName);
 						if (objectsToKeep.contains(id))
 							continue;
 						if (indexObjects == null)
 							indexObjects = listNonHEADIndexObjects();
 						if (indexObjects.contains(id))
 							continue;
 						deletionCandidates.put(id, f);
 					} catch (IllegalArgumentException notAnObject) {
 						// ignoring the file that does not represent loose
 						// object
 						continue;
 					}
 				}
 			}
 		} finally {
 			pm.endTask();
 		}
 
 		if (deletionCandidates.isEmpty()) {
 			return;
 		}
 
 		// From the set of current refs remove all those which have been handled
 		// during last repack(). Only those refs will survive which have been
 		// added or modified since the last repack. Only these can save existing
 		// loose refs from being pruned.
 		Collection<Ref> newRefs;
 		if (lastPackedRefs == null || lastPackedRefs.isEmpty())
 			newRefs = getAllRefs();
 		else {
 			Map<String, Ref> last = new HashMap<>();
 			for (Ref r : lastPackedRefs) {
 				last.put(r.getName(), r);
 			}
 			newRefs = new ArrayList<>();
 			for (Ref r : getAllRefs()) {
 				Ref old = last.get(r.getName());
 				if (!equals(r, old)) {
 					newRefs.add(r);
 				}
 			}
 		}
 
 		if (!newRefs.isEmpty()) {
 			// There are new/modified refs! Check which loose objects are now
 			// referenced by these modified refs (or their reflogentries).
 			// Remove these loose objects
 			// from the deletionCandidates. When the last candidate is removed
 			// leave this method.
 			ObjectWalk w = new ObjectWalk(repo);
 			try {
 				for (Ref cr : newRefs)
 					w.markStart(w.parseAny(cr.getObjectId()));
 				if (lastPackedRefs != null)
 					for (Ref lpr : lastPackedRefs)
 						w.markUninteresting(w.parseAny(lpr.getObjectId()));
 				removeReferenced(deletionCandidates, w);
 			} finally {
 				w.dispose();
 			}
 		}
 
 		if (deletionCandidates.isEmpty())
 			return;
 
 		// Since we have not left the method yet there are still
 		// deletionCandidates. Last chance for these objects not to be pruned is
 		// that they are referenced by reflog entries. Even refs which currently
 		// point to the same object as during last repack() may have
 		// additional reflog entries not handled during last repack()
 		ObjectWalk w = new ObjectWalk(repo);
 		try {
 			for (Ref ar : getAllRefs())
 				for (ObjectId id : listRefLogObjects(ar, lastRepackTime))
 					w.markStart(w.parseAny(id));
 			if (lastPackedRefs != null)
 				for (Ref lpr : lastPackedRefs)
 					w.markUninteresting(w.parseAny(lpr.getObjectId()));
 			removeReferenced(deletionCandidates, w);
 		} finally {
 			w.dispose();
 		}
 
 		if (deletionCandidates.isEmpty())
 			return;
 
 		// delete all candidates which have survived: these are unreferenced
 		// loose objects. Make a last check, though, to avoid deleting objects
 		// that could have been referenced while the candidates list was being
 		// built (by an incoming push, for example).
 		Set<File> touchedFanout = new HashSet<>();
 		for (File f : deletionCandidates.values()) {
 			if (f.lastModified() < expireDate) {
 				f.delete();
 				touchedFanout.add(f.getParentFile());
 			}
 		}
 
 		for (File f : touchedFanout) {
 			FileUtils.delete(f,
 					FileUtils.EMPTY_DIRECTORIES_ONLY | FileUtils.IGNORE_ERRORS);
 		}
 
 		repo.getObjectDatabase().close();
 	}
 
 	private long getExpireDate() throws ParseException {
 		long expireDate = Long.MAX_VALUE;
 
 		if (expire == null && expireAgeMillis == -1) {
 			String pruneExpireStr = repo.getConfig().getString(
 					ConfigConstants.CONFIG_GC_SECTION, null,
 					ConfigConstants.CONFIG_KEY_PRUNEEXPIRE);
 			if (pruneExpireStr == null)
 				pruneExpireStr = PRUNE_EXPIRE_DEFAULT;
 			expire = GitDateParser.parse(pruneExpireStr, null, SystemReader
 					.getInstance().getLocale());
 			expireAgeMillis = -1;
 		}
 		if (expire != null)
 			expireDate = expire.getTime();
 		if (expireAgeMillis != -1)
 			expireDate = System.currentTimeMillis() - expireAgeMillis;
 		return expireDate;
 	}
 
 	private long getPackExpireDate() throws ParseException {
 		long packExpireDate = Long.MAX_VALUE;
 
 		if (packExpire == null && packExpireAgeMillis == -1) {
 			String prunePackExpireStr = repo.getConfig().getString(
 					ConfigConstants.CONFIG_GC_SECTION, null,
 					ConfigConstants.CONFIG_KEY_PRUNEPACKEXPIRE);
 			if (prunePackExpireStr == null)
 				prunePackExpireStr = PRUNE_PACK_EXPIRE_DEFAULT;
 			packExpire = GitDateParser.parse(prunePackExpireStr, null,
 					SystemReader.getInstance().getLocale());
 			packExpireAgeMillis = -1;
 		}
 		if (packExpire != null)
 			packExpireDate = packExpire.getTime();
 		if (packExpireAgeMillis != -1)
 			packExpireDate = System.currentTimeMillis() - packExpireAgeMillis;
 		return packExpireDate;
 	}
 
 	/**
 	 * Remove all entries from a map which key is the id of an object referenced
 	 * by the given ObjectWalk
 	 *
 	 * @param id2File
 	 * @param w
 	 * @throws MissingObjectException
 	 * @throws IncorrectObjectTypeException
 	 * @throws IOException
 	 */
 	private void removeReferenced(Map<ObjectId, File> id2File,
 			ObjectWalk w) throws MissingObjectException,
 			IncorrectObjectTypeException, IOException {
 		RevObject ro = w.next();
 		while (ro != null) {
 			if (id2File.remove(ro.getId()) != null)
 				if (id2File.isEmpty())
 					return;
 			ro = w.next();
 		}
 		ro = w.nextObject();
 		while (ro != null) {
 			if (id2File.remove(ro.getId()) != null)
 				if (id2File.isEmpty())
 					return;
 			ro = w.nextObject();
 		}
 	}
 
 	private static boolean equals(Ref r1, Ref r2) {
 		if (r1 == null || r2 == null)
 			return false;
 		if (r1.isSymbolic()) {
 			if (!r2.isSymbolic())
 				return false;
 			return r1.getTarget().getName().equals(r2.getTarget().getName());
 		} else {
 			if (r2.isSymbolic()) {
 				return false;
 			}
 			return Objects.equals(r1.getObjectId(), r2.getObjectId());
 		}
 	}
 
 	/**
 	 * Packs all non-symbolic, loose refs into packed-refs.
 	 *
 	 * @throws IOException
 	 */
 	public void packRefs() throws IOException {
 		Collection<Ref> refs = repo.getRefDatabase().getRefs(Constants.R_REFS).values();
 		List<String> refsToBePacked = new ArrayList<String>(refs.size());
 		pm.beginTask(JGitText.get().packRefs, refs.size());
 		try {
 			for (Ref ref : refs) {
 				if (!ref.isSymbolic() && ref.getStorage().isLoose())
 					refsToBePacked.add(ref.getName());
 				pm.update(1);
 			}
 			((RefDirectory) repo.getRefDatabase()).pack(refsToBePacked);
 		} finally {
 			pm.endTask();
 		}
 	}
 
 	/**
 	 * Packs all objects which reachable from any of the heads into one pack
 	 * file. Additionally all objects which are not reachable from any head but
 	 * which are reachable from any of the other refs (e.g. tags), special refs
 	 * (e.g. FETCH_HEAD) or index are packed into a separate pack file. Objects
 	 * included in pack files which have a .keep file associated are never
 	 * repacked. All old pack files which existed before are deleted.
 	 *
 	 * @return a collection of the newly created pack files
 	 * @throws IOException
 	 *             when during reading of refs, index, packfiles, objects,
 	 *             reflog-entries or during writing to the packfiles
 	 *             {@link IOException} occurs
 	 */
 	public Collection<PackFile> repack() throws IOException {
 		Collection<PackFile> toBeDeleted = repo.getObjectDatabase().getPacks();
 
 		long time = System.currentTimeMillis();
 		Collection<Ref> refsBefore = getAllRefs();
 
 		Set<ObjectId> allHeads = new HashSet<ObjectId>();
 		Set<ObjectId> nonHeads = new HashSet<ObjectId>();
 		Set<ObjectId> txnHeads = new HashSet<ObjectId>();
 		Set<ObjectId> tagTargets = new HashSet<ObjectId>();
 		Set<ObjectId> indexObjects = listNonHEADIndexObjects();
 		RefDatabase refdb = repo.getRefDatabase();
 
 		for (Ref ref : refsBefore) {
 			nonHeads.addAll(listRefLogObjects(ref, 0));
 			if (ref.isSymbolic() || ref.getObjectId() == null)
 				continue;
 			if (ref.getName().startsWith(Constants.R_HEADS))
 				allHeads.add(ref.getObjectId());
 			else if (RefTreeNames.isRefTree(refdb, ref.getName()))
 				txnHeads.add(ref.getObjectId());
 			else
 				nonHeads.add(ref.getObjectId());
 			if (ref.getPeeledObjectId() != null)
 				tagTargets.add(ref.getPeeledObjectId());
 		}
 
 		List<ObjectIdSet> excluded = new LinkedList<ObjectIdSet>();
 		for (final PackFile f : repo.getObjectDatabase().getPacks())
 			if (f.shouldBeKept())
 				excluded.add(f.getIndex());
 
 		tagTargets.addAll(allHeads);
 		nonHeads.addAll(indexObjects);
 
 		List<PackFile> ret = new ArrayList<PackFile>(2);
 		PackFile heads = null;
 		if (!allHeads.isEmpty()) {
 			heads = writePack(allHeads, Collections.<ObjectId> emptySet(),
 					tagTargets, excluded);
 			if (heads != null) {
 				ret.add(heads);
 				excluded.add(0, heads.getIndex());
 			}
 		}
 		if (!nonHeads.isEmpty()) {
 			PackFile rest = writePack(nonHeads, allHeads, tagTargets, excluded);
 			if (rest != null)
 				ret.add(rest);
 		}
 		if (!txnHeads.isEmpty()) {
 			PackFile txn = writePack(txnHeads, PackWriter.NONE, null, excluded);
 			if (txn != null)
 				ret.add(txn);
 		}
 		try {
 			deleteOldPacks(toBeDeleted, ret);
 		} catch (ParseException e) {
 			// TODO: the exception has to be wrapped into an IOException because
 			// throwing the ParseException directly would break the API, instead
 			// we should throw a ConfigInvalidException
 			throw new IOException(e);
 		}
 		prunePacked();
 		deleteOrphans();
 
 		lastPackedRefs = refsBefore;
 		lastRepackTime = time;
 		return ret;
 	}
 
 	/**
 	 * Deletes orphans
 	 * <p>
 	 * A file is considered an orphan if it is either a "bitmap" or an index
 	 * file, and its corresponding pack file is missing in the list.
 	 * </p>
 	 */
 	private void deleteOrphans() {
 		Path packDir = Paths.get(repo.getObjectsDirectory().getAbsolutePath(),
 				"pack"); //$NON-NLS-1$
 		List<String> fileNames = null;
 		try (Stream<Path> files = Files.list(packDir)) {
 			fileNames = files.map(path -> path.getFileName().toString())
 					.filter(name -> {
 						return (name.endsWith(PACK_EXT)
 								|| name.endsWith(BITMAP_EXT)
 								|| name.endsWith(INDEX_EXT));
 					}).sorted(Collections.reverseOrder())
 					.collect(Collectors.toList());
 		} catch (IOException e1) {
 			// ignore
 		}
 		if (fileNames == null) {
 			return;
 		}
 
 		String base = null;
 		for (String n : fileNames) {
 			if (n.endsWith(PACK_EXT)) {
 				base = n.substring(0, n.lastIndexOf('.'));
 			} else {
 				if (base == null || !n.startsWith(base)) {
 					try {
 						Files.delete(new File(packDir.toFile(), n).toPath());
 					} catch (IOException e) {
 						LOG.error(e.getMessage(), e);
 					}
 				}
 			}
 		}
 	}
 
 	/**
 	 * @param ref
 	 *            the ref which log should be inspected
 	 * @param minTime only reflog entries not older then this time are processed
 	 * @return the {@link ObjectId}s contained in the reflog
 	 * @throws IOException
 	 */
 	private Set<ObjectId> listRefLogObjects(Ref ref, long minTime) throws IOException {
 		ReflogReader reflogReader = repo.getReflogReader(ref.getName());
 		if (reflogReader == null) {
 			return Collections.emptySet();
 		}
 		List<ReflogEntry> rlEntries = reflogReader
 				.getReverseEntries();
 		if (rlEntries == null || rlEntries.isEmpty())
 			return Collections.<ObjectId> emptySet();
 		Set<ObjectId> ret = new HashSet<ObjectId>();
 		for (ReflogEntry e : rlEntries) {
 			if (e.getWho().getWhen().getTime() < minTime)
 				break;
 			ObjectId newId = e.getNewId();
 			if (newId != null && !ObjectId.zeroId().equals(newId))
 				ret.add(newId);
 			ObjectId oldId = e.getOldId();
 			if (oldId != null && !ObjectId.zeroId().equals(oldId))
 				ret.add(oldId);
 		}
 		return ret;
 	}
 
 	/**
 	 * Returns a collection of all refs and additional refs.
 	 *
 	 * Additional refs which don't start with "refs/" are not returned because
 	 * they should not save objects from being garbage collected. Examples for
 	 * such references are ORIG_HEAD, MERGE_HEAD, FETCH_HEAD and
 	 * CHERRY_PICK_HEAD.
 	 *
 	 * @return a collection of refs pointing to live objects.
 	 * @throws IOException
 	 */
 	private Collection<Ref> getAllRefs() throws IOException {
 		RefDatabase refdb = repo.getRefDatabase();
 		Collection<Ref> refs = refdb.getRefs(RefDatabase.ALL).values();
 		List<Ref> addl = refdb.getAdditionalRefs();
 		if (!addl.isEmpty()) {
 			List<Ref> all = new ArrayList<>(refs.size() + addl.size());
 			all.addAll(refs);
 			// add additional refs which start with refs/
 			for (Ref r : addl) {
 				if (r.getName().startsWith(Constants.R_REFS)) {
 					all.add(r);
 				}
 			}
 			return all;
 		}
 		return refs;
 	}
 
 	/**
 	 * Return a list of those objects in the index which differ from whats in
 	 * HEAD
 	 *
 	 * @return a set of ObjectIds of changed objects in the index
 	 * @throws IOException
 	 * @throws CorruptObjectException
 	 * @throws NoWorkTreeException
 	 */
 	private Set<ObjectId> listNonHEADIndexObjects()
 			throws CorruptObjectException, IOException {
 		if (repo.isBare()) {
 			return Collections.emptySet();
 		}
 		try (TreeWalk treeWalk = new TreeWalk(repo)) {
 			treeWalk.addTree(new DirCacheIterator(repo.readDirCache()));
 			ObjectId headID = repo.resolve(Constants.HEAD);
 			if (headID != null) {
 				try (RevWalk revWalk = new RevWalk(repo)) {
 					treeWalk.addTree(revWalk.parseTree(headID));
 				}
 			}
 
 			treeWalk.setFilter(TreeFilter.ANY_DIFF);
 			treeWalk.setRecursive(true);
 			Set<ObjectId> ret = new HashSet<ObjectId>();
 
 			while (treeWalk.next()) {
 				ObjectId objectId = treeWalk.getObjectId(0);
 				switch (treeWalk.getRawMode(0) & FileMode.TYPE_MASK) {
 				case FileMode.TYPE_MISSING:
 				case FileMode.TYPE_GITLINK:
 					continue;
 				case FileMode.TYPE_TREE:
 				case FileMode.TYPE_FILE:
 				case FileMode.TYPE_SYMLINK:
 					ret.add(objectId);
 					continue;
 				default:
 					throw new IOException(MessageFormat.format(
 							JGitText.get().corruptObjectInvalidMode3,
 							String.format("%o", //$NON-NLS-1$
 									Integer.valueOf(treeWalk.getRawMode(0))),
 							(objectId == null) ? "null" : objectId.name(), //$NON-NLS-1$
 							treeWalk.getPathString(), //
 							repo.getIndexFile()));
 				}
 			}
 			return ret;
 		}
 	}
 
 	private PackFile writePack(@NonNull Set<? extends ObjectId> want,
 			@NonNull Set<? extends ObjectId> have, Set<ObjectId> tagTargets,
 			List<ObjectIdSet> excludeObjects) throws IOException {
 		File tmpPack = null;
 		Map<PackExt, File> tmpExts = new TreeMap<PackExt, File>(
 				new Comparator<PackExt>() {
 					public int compare(PackExt o1, PackExt o2) {
 						// INDEX entries must be returned last, so the pack
 						// scanner does pick up the new pack until all the
 						// PackExt entries have been written.
 						if (o1 == o2)
 							return 0;
 						if (o1 == PackExt.INDEX)
 							return 1;
 						if (o2 == PackExt.INDEX)
 							return -1;
 						return Integer.signum(o1.hashCode() - o2.hashCode());
 					}
 
 				});
 		try (PackWriter pw = new PackWriter(
 				(pconfig == null) ? new PackConfig(repo) : pconfig,
 				repo.newObjectReader())) {
 			// prepare the PackWriter
 			pw.setDeltaBaseAsOffset(true);
 			pw.setReuseDeltaCommits(false);
 			if (tagTargets != null)
 				pw.setTagTargets(tagTargets);
 			if (excludeObjects != null)
 				for (ObjectIdSet idx : excludeObjects)
 					pw.excludeObjects(idx);
 			pw.preparePack(pm, want, have);
 			if (pw.getObjectCount() == 0)
 				return null;
 
 			// create temporary files
 			String id = pw.computeName().getName();
 			File packdir = new File(repo.getObjectsDirectory(), "pack"); //$NON-NLS-1$
 			tmpPack = File.createTempFile("gc_", ".pack_tmp", packdir); //$NON-NLS-1$ //$NON-NLS-2$
 			final String tmpBase = tmpPack.getName()
 					.substring(0, tmpPack.getName().lastIndexOf('.'));
 			File tmpIdx = new File(packdir, tmpBase + ".idx_tmp"); //$NON-NLS-1$
 			tmpExts.put(INDEX, tmpIdx);
 
 			if (!tmpIdx.createNewFile())
 				throw new IOException(MessageFormat.format(
 						JGitText.get().cannotCreateIndexfile, tmpIdx.getPath()));
 
 			// write the packfile
 			FileOutputStream fos = new FileOutputStream(tmpPack);
 			FileChannel channel = fos.getChannel();
 			OutputStream channelStream = Channels.newOutputStream(channel);
 			try {
 				pw.writePack(pm, pm, channelStream);
 			} finally {
 				channel.force(true);
 				channelStream.close();
 				fos.close();
 			}
 
 			// write the packindex
 			fos = new FileOutputStream(tmpIdx);
 			FileChannel idxChannel = fos.getChannel();
 			OutputStream idxStream = Channels.newOutputStream(idxChannel);
 			try {
 				pw.writeIndex(idxStream);
 			} finally {
 				idxChannel.force(true);
 				idxStream.close();
 				fos.close();
 			}
 
 			if (pw.prepareBitmapIndex(pm)) {
 				File tmpBitmapIdx = new File(packdir, tmpBase + ".bitmap_tmp"); //$NON-NLS-1$
 				tmpExts.put(BITMAP_INDEX, tmpBitmapIdx);
 
 				if (!tmpBitmapIdx.createNewFile())
 					throw new IOException(MessageFormat.format(
 							JGitText.get().cannotCreateIndexfile,
 							tmpBitmapIdx.getPath()));
 
 				fos = new FileOutputStream(tmpBitmapIdx);
 				idxChannel = fos.getChannel();
 				idxStream = Channels.newOutputStream(idxChannel);
 				try {
 					pw.writeBitmapIndex(idxStream);
 				} finally {
 					idxChannel.force(true);
 					idxStream.close();
 					fos.close();
 				}
 			}
 
 			// rename the temporary files to real files
 			File realPack = nameFor(id, ".pack"); //$NON-NLS-1$
 
 			// if the packfile already exists (because we are rewriting a
 			// packfile for the same set of objects maybe with different
 			// PackConfig) then make sure we get rid of all handles on the file.
 			// Windows will not allow for rename otherwise.
 			if (realPack.exists())
 				for (PackFile p : repo.getObjectDatabase().getPacks())
 					if (realPack.getPath().equals(p.getPackFile().getPath())) {
 						p.close();
 						break;
 					}
 			tmpPack.setReadOnly();
 
 			FileUtils.rename(tmpPack, realPack, StandardCopyOption.ATOMIC_MOVE);
 			for (Map.Entry<PackExt, File> tmpEntry : tmpExts.entrySet()) {
 				File tmpExt = tmpEntry.getValue();
 				tmpExt.setReadOnly();
 
 				File realExt = nameFor(id,
 						"." + tmpEntry.getKey().getExtension()); //$NON-NLS-1$
 				try {
 					FileUtils.rename(tmpExt, realExt,
 							StandardCopyOption.ATOMIC_MOVE);
 				} catch (IOException e) {
 					File newExt = new File(realExt.getParentFile(),
 							realExt.getName() + ".new"); //$NON-NLS-1$
 					try {
 						FileUtils.rename(tmpExt, newExt,
 								StandardCopyOption.ATOMIC_MOVE);
 					} catch (IOException e2) {
 						newExt = tmpExt;
 						e = e2;
 					}
 					throw new IOException(MessageFormat.format(
 							JGitText.get().panicCantRenameIndexFile, newExt,
 							realExt), e);
 				}
 			}
 
 			return repo.getObjectDatabase().openPack(realPack);
 		} finally {
 			if (tmpPack != null && tmpPack.exists())
 				tmpPack.delete();
 			for (File tmpExt : tmpExts.values()) {
 				if (tmpExt.exists())
 					tmpExt.delete();
 			}
 		}
 	}
 
 	private File nameFor(String name, String ext) {
 		File packdir = new File(repo.getObjectsDirectory(), "pack"); //$NON-NLS-1$
 		return new File(packdir, "pack-" + name + ext); //$NON-NLS-1$
 	}
 
 	/**
 	 * A class holding statistical data for a FileRepository regarding how many
 	 * objects are stored as loose or packed objects
 	 */
 	public static class RepoStatistics {
 		/**
 		 * The number of objects stored in pack files. If the same object is
 		 * stored in multiple pack files then it is counted as often as it
 		 * occurs in pack files.
 		 */
 		public long numberOfPackedObjects;
 
 		/**
 		 * The number of pack files
 		 */
 		public long numberOfPackFiles;
 
 		/**
 		 * The number of objects stored as loose objects.
 		 */
 		public long numberOfLooseObjects;
 
 		/**
 		 * The sum of the sizes of all files used to persist loose objects.
 		 */
 		public long sizeOfLooseObjects;
 
 		/**
 		 * The sum of the sizes of all pack files.
 		 */
 		public long sizeOfPackedObjects;
 
 		/**
 		 * The number of loose refs.
 		 */
 		public long numberOfLooseRefs;
 
 		/**
 		 * The number of refs stored in pack files.
 		 */
 		public long numberOfPackedRefs;
 
 		/**
 		 * The number of bitmaps in the bitmap indices.
 		 */
 		public long numberOfBitmaps;
 
 		public String toString() {
 			final StringBuilder b = new StringBuilder();
 			b.append("numberOfPackedObjects=").append(numberOfPackedObjects); //$NON-NLS-1$
 			b.append(", numberOfPackFiles=").append(numberOfPackFiles); //$NON-NLS-1$
 			b.append(", numberOfLooseObjects=").append(numberOfLooseObjects); //$NON-NLS-1$
 			b.append(", numberOfLooseRefs=").append(numberOfLooseRefs); //$NON-NLS-1$
 			b.append(", numberOfPackedRefs=").append(numberOfPackedRefs); //$NON-NLS-1$
 			b.append(", sizeOfLooseObjects=").append(sizeOfLooseObjects); //$NON-NLS-1$
 			b.append(", sizeOfPackedObjects=").append(sizeOfPackedObjects); //$NON-NLS-1$
 			b.append(", numberOfBitmaps=").append(numberOfBitmaps); //$NON-NLS-1$
 			return b.toString();
 		}
 	}
 
 	/**
 	 * Returns information about objects and pack files for a FileRepository.
 	 *
 	 * @return information about objects and pack files for a FileRepository
 	 * @throws IOException
 	 */
 	public RepoStatistics getStatistics() throws IOException {
 		RepoStatistics ret = new RepoStatistics();
 		Collection<PackFile> packs = repo.getObjectDatabase().getPacks();
 		for (PackFile f : packs) {
 			ret.numberOfPackedObjects += f.getIndex().getObjectCount();
 			ret.numberOfPackFiles++;
 			ret.sizeOfPackedObjects += f.getPackFile().length();
 			if (f.getBitmapIndex() != null)
 				ret.numberOfBitmaps += f.getBitmapIndex().getBitmapCount();
 		}
 		File objDir = repo.getObjectsDirectory();
 		String[] fanout = objDir.list();
 		if (fanout != null && fanout.length > 0) {
 			for (String d : fanout) {
 				if (d.length() != 2)
 					continue;
 				File[] entries = new File(objDir, d).listFiles();
 				if (entries == null)
 					continue;
 				for (File f : entries) {
 					if (f.getName().length() != Constants.OBJECT_ID_STRING_LENGTH - 2)
 						continue;
 					ret.numberOfLooseObjects++;
 					ret.sizeOfLooseObjects += f.length();
 				}
 			}
 		}
 
 		RefDatabase refDb = repo.getRefDatabase();
 		for (Ref r : refDb.getRefs(RefDatabase.ALL).values()) {
 			Storage storage = r.getStorage();
 			if (storage == Storage.LOOSE || storage == Storage.LOOSE_PACKED)
 				ret.numberOfLooseRefs++;
 			if (storage == Storage.PACKED || storage == Storage.LOOSE_PACKED)
 				ret.numberOfPackedRefs++;
 		}
 
 		return ret;
 	}
 
 	/**
 	 * Set the progress monitor used for garbage collection methods.
 	 *
 	 * @param pm
 	 * @return this
 	 */
 	public GC setProgressMonitor(ProgressMonitor pm) {
 		this.pm = (pm == null) ? NullProgressMonitor.INSTANCE : pm;
 		return this;
 	}
 
 	/**
 	 * During gc() or prune() each unreferenced, loose object which has been
 	 * created or modified in the last <code>expireAgeMillis</code> milliseconds
 	 * will not be pruned. Only older objects may be pruned. If set to 0 then
 	 * every object is a candidate for pruning.
 	 *
 	 * @param expireAgeMillis
 	 *            minimal age of objects to be pruned in milliseconds.
 	 */
 	public void setExpireAgeMillis(long expireAgeMillis) {
 		this.expireAgeMillis = expireAgeMillis;
 		expire = null;
 	}
 
 	/**
 	 * During gc() or prune() packfiles which are created or modified in the
 	 * last <code>packExpireAgeMillis</code> milliseconds will not be deleted.
 	 * Only older packfiles may be deleted. If set to 0 then every packfile is a
 	 * candidate for deletion.
 	 *
 	 * @param packExpireAgeMillis
 	 *            minimal age of packfiles to be deleted in milliseconds.
 	 */
 	public void setPackExpireAgeMillis(long packExpireAgeMillis) {
 		this.packExpireAgeMillis = packExpireAgeMillis;
 		expire = null;
 	}
 
 	/**
 	 * Set the PackConfig used when (re-)writing packfiles. This allows to
 	 * influence how packs are written and to implement something similar to
 	 * "git gc --aggressive"
 	 *
 	 * @since 3.6
 	 * @param pconfig
 	 *            the {@link PackConfig} used when writing packs
 	 */
 	public void setPackConfig(PackConfig pconfig) {
 		this.pconfig = pconfig;
 	}
 
 	/**
 	 * During gc() or prune() each unreferenced, loose object which has been
 	 * created or modified after or at <code>expire</code> will not be pruned.
 	 * Only older objects may be pruned. If set to null then every object is a
 	 * candidate for pruning.
 	 *
 	 * @param expire
 	 *            instant in time which defines object expiration
 	 *            objects with modification time before this instant are expired
 	 *            objects with modification time newer or equal to this instant
 	 *            are not expired
 	 */
 	public void setExpire(Date expire) {
 		this.expire = expire;
 		expireAgeMillis = -1;
 	}
 
 	/**
 	 * During gc() or prune() packfiles which are created or modified after or
 	 * at <code>packExpire</code> will not be deleted. Only older packfiles may
 	 * be deleted. If set to null then every packfile is a candidate for
 	 * deletion.
 	 *
 	 * @param packExpire
 	 *            instant in time which defines packfile expiration
 	 */
 	public void setPackExpire(Date packExpire) {
 		this.packExpire = packExpire;
 		packExpireAgeMillis = -1;
 	}
 
 	/**
 	 * Set the {@code gc --auto} option.
 	 *
 	 * With this option, gc checks whether any housekeeping is required; if not,
 	 * it exits without performing any work. Some JGit commands run
 	 * {@code gc --auto} after performing operations that could create many
 	 * loose objects.
 	 * <p/>
 	 * Housekeeping is required if there are too many loose objects or too many
 	 * packs in the repository. If the number of loose objects exceeds the value
 	 * of the gc.auto option JGit GC consolidates all existing packs into a
 	 * single pack (equivalent to {@code -A} option), whereas git-core would
 	 * combine all loose objects into a single pack using {@code repack -d -l}.
 	 * Setting the value of {@code gc.auto} to 0 disables automatic packing of
 	 * loose objects.
 	 * <p/>
 	 * If the number of packs exceeds the value of {@code gc.autoPackLimit},
 	 * then existing packs (except those marked with a .keep file) are
 	 * consolidated into a single pack by using the {@code -A} option of repack.
 	 * Setting {@code gc.autoPackLimit} to 0 disables automatic consolidation of
 	 * packs.
 	 * <p/>
 	 * Like git the following jgit commands run auto gc:
 	 * <ul>
 	 * <li>fetch</li>
 	 * <li>merge</li>
 	 * <li>rebase</li>
 	 * <li>receive-pack</li>
 	 * </ul>
 	 * The auto gc for receive-pack can be suppressed by setting the config
 	 * option {@code receive.autogc = false}
 	 *
 	 * @param auto
 	 *            defines whether gc should do automatic housekeeping
 	 * @since 4.5
 	 */
 	public void setAuto(boolean auto) {
 		this.automatic = auto;
 	}
 
 	private boolean needGc() {
 		if (tooManyPacks()) {
 			addRepackAllOption();
 		} else if (!tooManyLooseObjects()) {
 			return false;
 		}
 		// TODO run pre-auto-gc hook, if it fails return false
 		return true;
 	}
 
 	private void addRepackAllOption() {
 		// TODO: if JGit GC is enhanced to support repack's option -l this
 		// method needs to be implemented
 	}
 
 	/**
 	 * @return {@code true} if number of packs > gc.autopacklimit (default 50)
 	 */
 	boolean tooManyPacks() {
 		int autopacklimit = repo.getConfig().getInt(
 				ConfigConstants.CONFIG_GC_SECTION,
 				ConfigConstants.CONFIG_KEY_AUTOPACKLIMIT,
 				DEFAULT_AUTOPACKLIMIT);
 		if (autopacklimit <= 0) {
 			return false;
 		}
 		// JGit always creates two packfiles, one for the objects reachable from
 		// branches, and another one for the rest
 		return repo.getObjectDatabase().getPacks().size() > (autopacklimit + 1);
 	}
 
 	/**
 	 * Quickly estimate number of loose objects, SHA1 is distributed evenly so
 	 * counting objects in one directory (bucket 17) is sufficient
 	 *
 	 * @return {@code true} if number of loose objects > gc.auto (default 6700)
 	 */
 	boolean tooManyLooseObjects() {
 		int auto = repo.getConfig().getInt(ConfigConstants.CONFIG_GC_SECTION,
 				ConfigConstants.CONFIG_KEY_AUTO, DEFAULT_AUTOLIMIT);
 		if (auto <= 0) {
 			return false;
 		}
 		int n = 0;
 		int threshold = (auto + 255) / 256;
 		Path dir = repo.getObjectsDirectory().toPath().resolve("17"); //$NON-NLS-1$
 		if (!Files.exists(dir)) {
 			return false;
 		}
 		try (DirectoryStream<Path> stream = Files.newDirectoryStream(dir,
 				new DirectoryStream.Filter<Path>() {
 
 					public boolean accept(Path file) throws IOException {
 						return Files.isRegularFile(file) && PATTERN_LOOSE_OBJECT
 								.matcher(file.getFileName().toString())
 								.matches();
 					}
 				})) {
 			for (Iterator<Path> iter = stream.iterator(); iter.hasNext();
 					iter.next()) {
 				if (++n > threshold) {
 					return true;
 				}
 			}
 		} catch (IOException e) {
 			LOG.error(e.getMessage(), e);
 		}
 		return false;
 	}
 }