Allow mutable object ids, improving commit parsing performance

[egit/zawir.git] / org.spearce.jgit / src / org / spearce / jgit / lib / Repository.java

/*
 *  Copyright (C) 2006  Shawn Pearce <spearce@spearce.org>
 *
 *  This library is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU General Public
 *  License, version 2, as published by the Free Software Foundation.
 *
 *  This library is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 *  General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public
 *  License along with this library; if not, write to the Free Software
 *  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301
 */
package org.spearce.jgit.lib;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FilenameFilter;
import java.io.IOException;
import java.lang.ref.Reference;
import java.lang.ref.SoftReference;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
import java.util.WeakHashMap;

import org.spearce.jgit.errors.IncorrectObjectTypeException;
import org.spearce.jgit.errors.ObjectWritingException;
import org.spearce.jgit.stgit.StGitPatch;

/**
 * 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>
 *
 * This implementation only handles a subtly undocumented subset of git features.
 *
 */
public class Repository {
        private static final String[] refSearchPaths = { "", "refs/", "refs/tags/",
                        "refs/heads/", "refs/remotes/" };

        private final File gitDir;

        private final File[] objectsDirs;

        private final File refsDir;

        private final RepositoryConfig config;

        private PackFile[] packs;

        private final WindowCache windows;

        private Map<ObjectId,Reference<Tree>> treeCache = new WeakHashMap<ObjectId,Reference<Tree>>(30000);
        private Map<ObjectId,Reference<Commit>> commitCache = new WeakHashMap<ObjectId,Reference<Commit>>(30000);

        private GitIndex index;

        /**
         * Construct a representation of this git repo managing a Git repository.
         *
         * @param d
         *            GIT_DIR
         * @throws IOException
         */
        public Repository(final File d) throws IOException {
                this(null, d);
        }

        /**
         * Construct a representation of a Git repository.
         * 
         * @param wc
         *            cache this repository's data will be cached through during
         *            access. May be shared with another repository, or null to
         *            indicate this repository should allocate its own private
         *            cache.
         * @param d
         *            GIT_DIR (the location of the repository metadata).
         * @throws IOException
         *             the repository appears to already exist but cannot be
         *             accessed.
         */
        public Repository(final WindowCache wc, final File d) throws IOException {
                gitDir = d.getAbsoluteFile();
                try {
                        objectsDirs = readObjectsDirs(new File(gitDir, "objects"), new ArrayList<File>()).toArray(new File[0]);
                } catch (IOException e) {
                        IOException ex = new IOException("Cannot find all object dirs for " + gitDir);
                        ex.initCause(e);
                        throw ex;
                }
                refsDir = new File(gitDir, "refs");
                packs = new PackFile[0];
                config = new RepositoryConfig(this);

                final boolean isExisting = objectsDirs[0].exists();
                if (isExisting) {
                        getConfig().load();
                        final String repositoryFormatVersion = getConfig().getString(
                                        "core", null, "repositoryFormatVersion");
                        if (!"0".equals(repositoryFormatVersion)) {
                                throw new IOException("Unknown repository format \""
                                                + repositoryFormatVersion + "\"; expected \"0\".");
                        }
                } else {
                        getConfig().create();
                }
                windows = wc != null ? wc : new WindowCache(getConfig());
                if (isExisting)
                        scanForPacks();
        }

        private Collection<File> readObjectsDirs(File objectsDir, Collection<File> ret) throws IOException {
                ret.add(objectsDir);
                File alternatesFile = new File(objectsDir,"info/alternates");
                if (alternatesFile.exists()) {
                        BufferedReader ar = new BufferedReader(new FileReader(alternatesFile));
                        for (String alt=ar.readLine(); alt!=null; alt=ar.readLine()) {
                                readObjectsDirs(new File(alt), ret);
                        }
                        ar.close();
                }
                return ret;
        }

        /**
         * Create a new Git repository initializing the necessary files and
         * directories.
         *
         * @throws IOException
         */
        public void create() throws IOException {
                if (gitDir.exists()) {
                        throw new IllegalStateException("Repository already exists: "
                                        + gitDir);
                }

                gitDir.mkdirs();

                objectsDirs[0].mkdirs();
                new File(objectsDirs[0], "pack").mkdir();
                new File(objectsDirs[0], "info").mkdir();

                refsDir.mkdir();
                new File(refsDir, "heads").mkdir();
                new File(refsDir, "tags").mkdir();

                new File(gitDir, "branches").mkdir();
                new File(gitDir, "remotes").mkdir();
                writeSymref("HEAD", "refs/heads/master");

                getConfig().create();
                getConfig().save();
        }

        /**
         * @return GIT_DIR
         */
        public File getDirectory() {
                return gitDir;
        }

        /**
         * @return the directory containg the objects owned by this repository.
         */
        public File getObjectsDirectory() {
                return objectsDirs[0];
        }

        /**
         * @return the configuration of this repository
         */
        public RepositoryConfig getConfig() {
                return config;
        }

        /**
         * @return the cache needed for accessing packed objects in this repository.
         */
        public WindowCache getWindowCache() {
                return windows;
        }

        /**
         * Construct a filename where the loose object having a specified SHA-1
         * should be stored. If the object is stored in a shared repository the path
         * to the alternative repo will be returned. If the object is not yet store
         * a usable path in this repo will be returned. It is assumed that callers
         * will look for objects in a pack first.
         *
         * @param objectId
         * @return suggested file name
         */
        public File toFile(final AnyObjectId objectId) {
                final String n = objectId.toString();
                String d=n.substring(0, 2);
                String f=n.substring(2);
                for (int i=0; i<objectsDirs.length; ++i) {
                        File ret = new File(new File(objectsDirs[i], d), f);
                        if (ret.exists())
                                return ret;
                }
                return new File(new File(objectsDirs[0], d), f);
        }

        /**
         * @param objectId
         * @return true if the specified object is stored in this repo or any of the
         *         known shared repositories.
         */
        public boolean hasObject(final AnyObjectId objectId) {
                int k = packs.length;
                if (k > 0) {
                        do {
                                if (packs[--k].hasObject(objectId))
                                        return true;
                        } while (k > 0);
                }
                return toFile(objectId).isFile();
        }

        /**
         * @param id
         *            SHA-1 of an object.
         * 
         * @return a {@link ObjectLoader} for accessing the data of the named
         *         object, or null if the object does not exist.
         * @throws IOException
         */
        public ObjectLoader openObject(final AnyObjectId id)
                        throws IOException {
                return openObject(new WindowCursor(),id);
        }

        /**
         * @param curs
         *            temporary working space associated with the calling thread.
         * @param id
         *            SHA-1 of an object.
         * 
         * @return a {@link ObjectLoader} for accessing the data of the named
         *         object, or null if the object does not exist.
         * @throws IOException
         */
        public ObjectLoader openObject(final WindowCursor curs, final AnyObjectId id)
                        throws IOException {
                int k = packs.length;
                if (k > 0) {
                        do {
                                try {
                                        final ObjectLoader ol = packs[--k].get(curs, id);
                                        if (ol != null)
                                                return ol;
                                } catch (IOException ioe) {
                                        // This shouldn't happen unless the pack was corrupted
                                        // after we opened it or the VM runs out of memory. This is
                                        // a know problem with memory mapped I/O in java and have
                                        // been noticed with JDK < 1.6. Tell the gc that now is a good
                                        // time to collect and try once more.
                                        try {
                                                curs.release();
                                                System.gc();
                                                final ObjectLoader ol = packs[k].get(curs, id);
                                                if (ol != null)
                                                        return ol;
                                        } catch (IOException ioe2) {
                                                ioe2.printStackTrace();
                                                ioe.printStackTrace();
                                                // Still fails.. that's BAD, maybe the pack has
                                                // been corrupted after all, or the gc didn't manage
                                                // to release enough previously mmaped areas.
                                        }
                                }
                        } while (k > 0);
                }
                try {
                        return new UnpackedObjectLoader(this, id.toObjectId());
                } catch (FileNotFoundException fnfe) {
                        return null;
                }
        }

        /**
         * @param id
         *            SHA'1 of a blob
         * @return an {@link ObjectLoader} for accessing the data of a named blob
         * @throws IOException
         */
        public ObjectLoader openBlob(final ObjectId id) throws IOException {
                return openObject(id);
        }

        /**
         * @param id
         *            SHA'1 of a tree
         * @return an {@link ObjectLoader} for accessing the data of a named tree
         * @throws IOException
         */
        public ObjectLoader openTree(final ObjectId id) throws IOException {
                return openObject(id);
        }

        /**
         * Access a Commit object using a symbolic reference. This reference may
         * be a SHA-1 or ref in combination with a number of symbols translating
         * from one ref or SHA1-1 to another, such as HEAD^ etc.
         *
         * @param revstr a reference to a git commit object
         * @return a Commit named by the specified string
         * @throws IOException for I/O error or unexpected object type.
         *
         * @see #resolve(String)
         */
        public Commit mapCommit(final String revstr) throws IOException {
                final ObjectId id = resolve(revstr);
                return id != null ? mapCommit(id) : null;
        }

        /**
         * Access a Commit by SHA'1 id.
         * @param id
         * @return Commit or null
         * @throws IOException for I/O error or unexpected object type.
         */
        public Commit mapCommit(final ObjectId id) throws IOException {
                Reference<Commit> retr = commitCache.get(id);
                if (retr != null) {
                        Commit ret = retr.get();
                        if (ret != null)
                                return ret;
//                      System.out.println("Found a null id, size was "+commitCache.size());
                }

                final ObjectLoader or = openObject(id);
                if (or == null)
                        return null;
                final byte[] raw = or.getBytes();
                if (Constants.OBJ_COMMIT == or.getType()) {
                        Commit ret = new Commit(this, id, raw);
                        // The key must not be the referenced strongly
                        // by the value in WeakHashMaps
                        commitCache.put(id, new SoftReference<Commit>(ret));
                        return ret;
                }
                throw new IncorrectObjectTypeException(id, Constants.TYPE_COMMIT);
        }

        /**
         * Access a Tree object using a symbolic reference. This reference may
         * be a SHA-1 or ref in combination with a number of symbols translating
         * from one ref or SHA1-1 to another, such as HEAD^{tree} etc.
         *
         * @param revstr a reference to a git commit object
         * @return a Tree named by the specified string
         * @throws IOException
         *
         * @see #resolve(String)
         */
        public Tree mapTree(final String revstr) throws IOException {
                final ObjectId id = resolve(revstr);
                return id != null ? mapTree(id) : null;
        }

        /**
         * Access a Tree by SHA'1 id.
         * @param id
         * @return Tree or null
         * @throws IOException for I/O error or unexpected object type.
         */
        public Tree mapTree(final ObjectId id) throws IOException {
                Reference<Tree> wret = treeCache.get(id);
                if (wret != null) {
                        Tree ret = wret.get();
                        if (ret != null)
                                return ret;
                }

                final ObjectLoader or = openObject(id);
                if (or == null)
                        return null;
                final byte[] raw = or.getBytes();
                if (Constants.OBJ_TREE == or.getType()) {
                        Tree ret = new Tree(this, id, raw);
                        treeCache.put(id, new SoftReference<Tree>(ret));
                        return ret;
                }
                if (Constants.OBJ_COMMIT == or.getType())
                        return mapTree(ObjectId.fromString(raw, 5));
                throw new IncorrectObjectTypeException(id, Constants.TYPE_TREE);
        }

        /**
         * Access a tag by symbolic name.
         *
         * @param revstr
         * @return a Tag or null
         * @throws IOException on I/O error or unexpected type
         */
        public Tag mapTag(String revstr) throws IOException {
                final ObjectId id = resolve(revstr);
                return id != null ? mapTag(revstr, id) : null;
        }

        /**
         * Access a Tag by SHA'1 id
         * @param refName
         * @param id
         * @return Commit or null
         * @throws IOException for I/O error or unexpected object type.
         */
        public Tag mapTag(final String refName, final ObjectId id) throws IOException {
                final ObjectLoader or = openObject(id);
                if (or == null)
                        return null;
                final byte[] raw = or.getBytes();
                if (Constants.OBJ_TAG == or.getType())
                        return new Tag(this, id, refName, raw);
                return new Tag(this, id, refName, null);
        }

        /**
         * Get a locked handle to a ref suitable for updating or creating.
         *
         * @param ref name to lock
         * @return a locked ref
         * @throws IOException
         */
        public RefLock lockRef(final String ref) throws IOException {
                final Ref r = readRef(ref, true);
                final RefLock l = new RefLock(new File(gitDir, r.getName()));
                return l.lock() ? l : null;
        }

        /**
         * Parse a git revision string and return an object id.
         *
         * Currently supported is combinations of these.
         * <ul>
         *  <li>SHA-1 - a SHA-1</li>
         *  <li>refs/... - a ref name</li>
         *  <li>ref^n - nth parent reference</li>
         *  <li>ref~n - distance via parent reference</li>
         *  <li>ref@{n} - nth version of ref</li>
         *  <li>ref^{tree} - tree references by ref</li>
         *  <li>ref^{commit} - commit references by ref</li>
         * </ul>
         *
         * Not supported is
         * <ul>
         * <li>timestamps in reflogs, ref@{full or relative timestamp}</li>
         * <li>abbreviated SHA-1's</li>
         * </ul>
         *
         * @param revstr A git object references expression
         * @return an ObjectId
         * @throws IOException on serious errors
         */
        public ObjectId resolve(final String revstr) throws IOException {
                char[] rev = revstr.toCharArray();
                ObjectId ret = null;
                Commit ref = null;
                for (int i = 0; i < rev.length; ++i) {
                        switch (rev[i]) {
                        case '^':
                                if (ref == null) {
                                        String refstr = new String(rev,0,i);
                                        ObjectId refId = resolveSimple(refstr);
                                        ref = mapCommit(refId);
                                }
                                if (i + 1 < rev.length) {
                                        switch (rev[i + 1]) {
                                        case '0':
                                        case '1':
                                        case '2':
                                        case '3':
                                        case '4':
                                        case '5':
                                        case '6':
                                        case '7':
                                        case '8':
                                        case '9':
                                                int j;
                                                for (j=i+1; j<rev.length; ++j) {
                                                        if (!Character.isDigit(rev[j]))
                                                                break;
                                                }
                                                String parentnum = new String(rev, i+1, j-i-1);
                                                int pnum = Integer.parseInt(parentnum);
                                                if (pnum != 0)
                                                        ref = mapCommit(ref.getParentIds()[pnum - 1]);
                                                i = j - 1;
                                                break;
                                        case '{':
                                                int k;
                                                String item = null;
                                                for (k=i+2; k<rev.length; ++k) {
                                                        if (rev[k] == '}') {
                                                                item = new String(rev, i+2, k-i-2);
                                                                break;
                                                        }
                                                }
                                                i = k;
                                                if (item != null)
                                                        if (item.equals("tree"))
                                                                ret = ref.getTreeId();
                                                        else if (item.equals("commit"))
                                                                ; // just reference self
                                                        else
                                                                return null; // invalid
                                                else
                                                        return null; // invalid
                                                break;
                                        default:
                                                ref = mapCommit(ref.getParentIds()[0]);
                                        }
                                } else {
                                        ref = mapCommit(ref.getParentIds()[0]);
                                }
                                break;
                        case '~':
                                if (ref == null) {
                                        String refstr = new String(rev,0,i);
                                        ObjectId refId = resolveSimple(refstr);
                                        ref = mapCommit(refId);
                                }
                                int l;
                                for (l = i + 1; l < rev.length; ++l) {
                                        if (!Character.isDigit(rev[l]))
                                                break;
                                }
                                String distnum = new String(rev, i+1, l-i-1);
                                int dist = Integer.parseInt(distnum);
                                while (dist >= 0) {
                                        ref = mapCommit(ref.getParentIds()[0]);
                                        --dist;
                                }
                                i = l - 1;
                                break;
                        case '@':
                                int m;
                                String time = null;
                                for (m=i+2; m<rev.length; ++m) {
                                        if (rev[m] == '}') {
                                                time = new String(rev, i+2, m-i-2);
                                                break;
                                        }
                                }
                                if (time != null)
                                        throw new IllegalArgumentException("reflogs not yet supprted");
                                i = m - 1;
                                break;
                        default:
                                if (ref != null)
                                        return null; // cannot parse, return null
                        }
                }
                if (ret == null)
                        if (ref != null)
                                ret = ref.getCommitId();
                        else
                                ret = resolveSimple(revstr);
                return ret;
        }

        private ObjectId resolveSimple(final String revstr) throws IOException {
                if (ObjectId.isId(revstr))
                        return ObjectId.fromString(revstr);
                final Ref r = readRef(revstr, false);
                if (r != null) {
                        return r.getObjectId();
                }
                return null;
        }

        /**
         * Close all resources used by this repository
         */
        public void close() {
                closePacks();
        }

        void closePacks() {
                for (int k = packs.length - 1; k >= 0; k--) {
                        packs[k].close();
                }
                packs = new PackFile[0];
        }

        /**
         * Scan the object dirs, including alternates for packs
         * to use.
         */
        public void scanForPacks() {
                final ArrayList<PackFile> p = new ArrayList<PackFile>();
                for (int i=0; i<objectsDirs.length; ++i)
                        scanForPacks(new File(objectsDirs[i], "pack"), p);
                final PackFile[] arr = new PackFile[p.size()];
                p.toArray(arr);
                packs = arr;
        }

        private void scanForPacks(final File packDir, Collection<PackFile> packList) {
                final String[] idxList = packDir.list(new FilenameFilter() {
                        public boolean accept(final File baseDir, final String n) {
                                // Must match "pack-[0-9a-f]{40}.idx" to be an index.
                                return n.length() == 49 && n.endsWith(".idx")
                                                && n.startsWith("pack-");
                        }
                });
                if (idxList != null) {
                        for (final String indexName : idxList) {
                                final String n = indexName.substring(0, indexName.length() - 4);
                                final File idxFile = new File(packDir, n + ".idx");
                                final File packFile = new File(packDir, n + ".pack");
                                try {
                                        packList.add(new PackFile(this, idxFile, packFile));
                                } catch (IOException ioe) {
                                        // Whoops. That's not a pack!
                                        //
                                        ioe.printStackTrace();
                                }
                        }
                }
        }

    /**
     * Writes a symref (e.g. HEAD) to disk
     *
     * @param name symref name
     * @param target pointed to ref
     * @throws IOException
     */
    public void writeSymref(final String name, final String target)
                        throws IOException {
                final byte[] content = ("ref: " + target + "\n").getBytes("UTF-8");
                final RefLock lck = new RefLock(new File(gitDir, name));
                if (!lck.lock())
                        throw new ObjectWritingException("Unable to lock " + name);
                try {
                        lck.write(content);
                } catch (IOException ioe) {
                        throw new ObjectWritingException("Unable to write " + name, ioe);
                }
                if (!lck.commit())
                        throw new ObjectWritingException("Unable to write " + name);
        }

        private Ref readRef(final String revstr, final boolean missingOk)
                        throws IOException {
                refreshPackedRefsCache();
                for (int k = 0; k < refSearchPaths.length; k++) {
                        final Ref r = readRefBasic(refSearchPaths[k] + revstr);
                        if (missingOk || r.getObjectId() != null) {
                                return r;
                        }
                }
                return null;
        }

        private Ref readRefBasic(String name) throws IOException {
                int depth = 0;
                REF_READING: do {
                        // prefer unpacked ref to packed ref
                        final File f = new File(getDirectory(), name);
                        if (!f.isFile()) {
                                // look for packed ref, since this one doesn't exist
                                ObjectId id = packedRefs.get(name);
                                if (id != null)
                                        return new Ref(name, id);
                                
                                // no packed ref found, return blank one
                                return new Ref(name, null);
                        }

                        final BufferedReader br = new BufferedReader(new FileReader(f));
                        try {
                                final String line = br.readLine();
                                if (line == null || line.length() == 0)
                                        return new Ref(name, null);
                                else if (line.startsWith("ref: ")) {
                                        name = line.substring("ref: ".length());
                                        continue REF_READING;
                                } else if (ObjectId.isId(line))
                                        return new Ref(name, ObjectId.fromString(line));
                                throw new IOException("Not a ref: " + name + ": " + line);
                        } finally {
                                br.close();
                        }
                } while (depth++ < 5);
                throw new IOException("Exceed maximum ref depth.  Circular reference?");
        }

        public String toString() {
                return "Repository[" + getDirectory() + "]";
        }

        /**
         * @return name of topmost Stacked Git patch.
         * @throws IOException
         */
        public String getPatch() throws IOException {
                final File ptr = new File(getDirectory(),"patches/"+getBranch()+"/applied");
                final BufferedReader br = new BufferedReader(new FileReader(ptr));
                String last=null;
                try {
                        String line;
                        while ((line=br.readLine())!=null) {
                                last = line;
                        }
                } finally {
                        br.close();
                }
                return last;
        }

        /**
         * @return name of current branch
         * @throws IOException
         */
        public String getFullBranch() throws IOException {
                final File ptr = new File(getDirectory(),"HEAD");
                final BufferedReader br = new BufferedReader(new FileReader(ptr));
                String ref;
                try {
                        ref = br.readLine();
                } finally {
                        br.close();
                }
                if (ref.startsWith("ref: "))
                        ref = ref.substring(5);
                return ref;
        }
        
        /**
         * @return name of current branch.
         * @throws IOException
         */
        public String getBranch() throws IOException {
                try {
                        final File ptr = new File(getDirectory(),"HEAD");
                        final BufferedReader br = new BufferedReader(new FileReader(ptr));
                        String ref;
                        try {
                                ref = br.readLine();
                        } finally {
                                br.close();
                        }
                        if (ref.startsWith("ref: "))
                                ref = ref.substring(5);
                        if (ref.startsWith("refs/heads/"))
                                ref = ref.substring(11);
                        return ref;
                } catch (FileNotFoundException e) {
                        final File ptr = new File(getDirectory(),"head-name");
                        final BufferedReader br = new BufferedReader(new FileReader(ptr));
                        String ref;
                        try {
                                ref = br.readLine();
                        } finally {
                                br.close();
                        }
                        return ref;
                }
        }

        /**
         * @return names of all local branches
         */
        public Collection<String> getBranches() {
                return listRefs("heads");
        }
        
        /**
         * @return the names of all refs (local and remotes branches, tags)
         */
        public Collection<String> getAllRefs() {
                return listRefs("");
        }
        
        private Collection<String> listRefs(String refSubDir) {
                // add / to end, unless empty
                if (refSubDir.length() > 0 && refSubDir.charAt(refSubDir.length() -1 ) != '/')
                        refSubDir += "/";
                
                Collection<String> branchesRaw = listFilesRecursively(new File(refsDir, refSubDir), null);
                ArrayList<String> branches = new ArrayList<String>();
                for (String b : branchesRaw) {
                        branches.add("refs/" + refSubDir + b);
                }
                
                refreshPackedRefsCache();
                Set<String> keySet = packedRefs.keySet();
                for (String s : keySet)
                        if (s.startsWith("refs/" + refSubDir) && !branches.contains(s))
                                branches.add(s);
                return branches;
        }

        /**
         * @return all git tags
         */
        public Collection<String> getTags() {
                return listRefs("tags");
        }

        private Map<String,ObjectId> packedRefs = new HashMap<String,ObjectId>();
        private long packedrefstime = 0;

        private void refreshPackedRefsCache() {
                File file = new File(gitDir, "packed-refs");
                if (!file.exists()) {
                        if (packedRefs.size() > 0)
                                packedRefs = new HashMap<String,ObjectId>();
                        return;
                }
                if (file.lastModified() == packedrefstime)
                        return;
                Map<String,ObjectId> newPackedRefs = new HashMap<String,ObjectId>();
                FileReader fileReader = null;
                try {
                        fileReader = new FileReader(file);
                        BufferedReader b=new BufferedReader(fileReader);
                        String p;
                        while ((p = b.readLine()) != null) {
                                if (p.charAt(0) == '#')
                                        continue;
                                if (p.charAt(0) == '^') {
                                        continue;
                                }
                                int spos = p.indexOf(' ');
                                ObjectId id = ObjectId.fromString(p.substring(0,spos));
                                String name = p.substring(spos+1);
                                newPackedRefs.put(name, id);
                        }
                } catch (IOException e) {
                        throw new Error("Cannot read packed refs",e);
                } finally {
                        if (fileReader != null) {
                                try {
                                        fileReader.close();
                                } catch (IOException e) {
                                        // Cannot do anything more here
                                        e.printStackTrace();
                                }
                        }
                }
                packedRefs = newPackedRefs;
        }

        /**
         * @return true if HEAD points to a StGit patch.
         */
        public boolean isStGitMode() {
                try {
                        File file = new File(getDirectory(), "HEAD");
                        BufferedReader reader = new BufferedReader(new FileReader(file));
                        String string = reader.readLine();
                        if (!string.startsWith("ref: refs/heads/"))
                                return false;
                        String branch = string.substring("ref: refs/heads/".length());
                        File currentPatches = new File(new File(new File(getDirectory(),
                                        "patches"), branch), "applied");
                        if (!currentPatches.exists())
                                return false;
                        if (currentPatches.length() == 0)
                                return false;
                        return true;

                } catch (IOException e) {
                        e.printStackTrace();
                        return false;
                }
        }

        /**
         * @return applied patches in a map indexed on current commit id
         * @throws IOException
         */
        public Map<ObjectId,StGitPatch> getAppliedPatches() throws IOException {
                Map<ObjectId,StGitPatch> ret = new HashMap<ObjectId,StGitPatch>();
                if (isStGitMode()) {
                        File patchDir = new File(new File(getDirectory(),"patches"),getBranch());
                        BufferedReader apr = new BufferedReader(new FileReader(new File(patchDir,"applied")));
                        for (String patchName=apr.readLine(); patchName!=null; patchName=apr.readLine()) {
                                File topFile = new File(new File(new File(patchDir,"patches"), patchName), "top");
                                BufferedReader tfr = new BufferedReader(new FileReader(topFile));
                                String objectId = tfr.readLine();
                                ObjectId id = ObjectId.fromString(objectId);
                                ret.put(id, new StGitPatch(patchName, id));
                                tfr.close();
                        }
                        apr.close();
                }
                return ret;
        }

        private Collection<String> listFilesRecursively(File root, File start) {
                if (start == null)
                        start = root;
                Collection<String> ret = new ArrayList<String>();
                File[] files = start.listFiles();
                for (int i = 0; i < files.length; ++i) {
                        if (files[i].isDirectory())
                                ret.addAll(listFilesRecursively(root, files[i]));
                        else if (files[i].length() == 41) {
                                String name = files[i].toString().substring(
                                                root.toString().length() + 1);
                                if (File.separatorChar != '/')
                                        name = name.replace(File.separatorChar, '/');
                                ret.add(name);
                        }
                }
                return ret;
        }
        
        /** Clean up stale caches */
        public void refreshFromDisk() {
                packedRefs = null;
        }

        /**
         * @return a representation of the index associated with this repo
         * @throws IOException
         */
        public GitIndex getIndex() throws IOException {
                if (index == null) {
                        index = new GitIndex(this);
                        index.read();
                } else {
                        index.rereadIfNecessary();
                }
                return index;
        }

        static byte[] gitInternalSlash(byte[] bytes) {
                if (File.separatorChar == '/')
                        return bytes;
                for (int i=0; i<bytes.length; ++i)
                        if (bytes[i] == File.separatorChar)
                                bytes[i] = '/';
                return bytes;
        }

        /**
         * @return an important state
         */
        public RepositoryState getRepositoryState() {
                if (new File(gitDir.getParentFile(), ".dotest").exists())
                        return RepositoryState.REBASING;
                if (new File(gitDir,".dotest-merge").exists())
                        return RepositoryState.REBASING_INTERACTIVE;
                if (new File(gitDir,"MERGE_HEAD").exists())
                        return RepositoryState.MERGING;
                if (new File(gitDir,"BISECT_LOG").exists())
                        return RepositoryState.BISECTING;
                return RepositoryState.SAFE;
        }

        /**
         * String work dir and return normalized repository path
         *
         * @param wd Work dir
         * @param f File whose path shall be stripp off it's workdir
         * @return normalized repository relative path
         */
        public static String stripWorkDir(File wd, File f) {
                String relName = f.getPath().substring(wd.getPath().length() + 1);
                relName = relName.replace(File.separatorChar, '/');
                return relName;
        }
}