/*
 * Copyright (C) 2008-2010, Google Inc.
 * Copyright (C) 2008, Shawn O. Pearce <spearce@spearce.org>
 * Copyright (C) 2011, Matthias Sohn <matthias.sohn@sap.com> and others
 *
 * This program and the accompanying materials are made available under the
 * terms of the Eclipse Distribution License v. 1.0 which is available at
 * https://www.eclipse.org/org/documents/edl-v10.php.
 *
 * SPDX-License-Identifier: BSD-3-Clause
 */

package org.eclipse.jgit.dircache;

import static java.nio.charset.StandardCharsets.ISO_8859_1;

import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.EOFException;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.security.DigestOutputStream;
import java.security.MessageDigest;
import java.text.MessageFormat;
import java.time.Instant;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;

import org.eclipse.jgit.errors.CorruptObjectException;
import org.eclipse.jgit.errors.IndexReadException;
import org.eclipse.jgit.errors.LockFailedException;
import org.eclipse.jgit.errors.UnmergedPathException;
import org.eclipse.jgit.events.IndexChangedEvent;
import org.eclipse.jgit.events.IndexChangedListener;
import org.eclipse.jgit.internal.JGitText;
import org.eclipse.jgit.internal.storage.file.FileSnapshot;
import org.eclipse.jgit.internal.storage.file.LockFile;
import org.eclipse.jgit.lib.AnyObjectId;
import org.eclipse.jgit.lib.Constants;
import org.eclipse.jgit.lib.ObjectId;
import org.eclipse.jgit.lib.ObjectInserter;
import org.eclipse.jgit.lib.ObjectReader;
import org.eclipse.jgit.lib.Repository;
import org.eclipse.jgit.treewalk.FileTreeIterator;
import org.eclipse.jgit.treewalk.TreeWalk;
import org.eclipse.jgit.treewalk.TreeWalk.OperationType;
import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
import org.eclipse.jgit.util.FS;
import org.eclipse.jgit.util.IO;
import org.eclipse.jgit.util.MutableInteger;
import org.eclipse.jgit.util.NB;
import org.eclipse.jgit.util.TemporaryBuffer;
import org.eclipse.jgit.util.io.SilentFileInputStream;

/**
 * Support for the Git dircache (aka index file).
 * <p>
 * The index file keeps track of which objects are currently checked out in the
 * working directory, and the last modified time of those working files. Changes
 * in the working directory can be detected by comparing the modification times
 * to the cached modification time within the index file.
 * <p>
 * Index files are also used during merges, where the merge happens within the
 * index file first, and the working directory is updated as a post-merge step.
 * Conflicts are stored in the index file to allow tool (and human) based
 * resolutions to be easily performed.
 */
public class DirCache {
	private static final byte[] SIG_DIRC = { 'D', 'I', 'R', 'C' };

	private static final int EXT_TREE = 0x54524545 /* 'TREE' */;

	private static final DirCacheEntry[] NO_ENTRIES = {};

	private static final byte[] NO_CHECKSUM = {};

	static final Comparator<DirCacheEntry> ENT_CMP = (DirCacheEntry o1,
			DirCacheEntry o2) -> {
		final int cr = cmp(o1, o2);
		if (cr != 0)
			return cr;
		return o1.getStage() - o2.getStage();
	};

	static int cmp(DirCacheEntry a, DirCacheEntry b) {
		return cmp(a.path, a.path.length, b);
	}

	static int cmp(byte[] aPath, int aLen, DirCacheEntry b) {
		return cmp(aPath, aLen, b.path, b.path.length);
	}

	static int cmp(final byte[] aPath, final int aLen, final byte[] bPath,
			final int bLen) {
		for (int cPos = 0; cPos < aLen && cPos < bLen; cPos++) {
			final int cmp = (aPath[cPos] & 0xff) - (bPath[cPos] & 0xff);
			if (cmp != 0)
				return cmp;
		}
		return aLen - bLen;
	}

	/**
	 * Create a new empty index which is never stored on disk.
	 *
	 * @return an empty cache which has no backing store file. The cache may not
	 *         be read or written, but it may be queried and updated (in
	 *         memory).
	 */
	public static DirCache newInCore() {
		return new DirCache(null, null);
	}

	/**
	 * Create a new in memory index read from the contents of a tree.
	 *
	 * @param reader
	 *            reader to access the tree objects from a repository.
	 * @param treeId
	 *            tree to read. Must identify a tree, not a tree-ish.
	 * @return a new cache which has no backing store file, but contains the
	 *         contents of {@code treeId}.
	 * @throws java.io.IOException
	 *             one or more trees not available from the ObjectReader.
	 * @since 4.2
	 */
	public static DirCache read(ObjectReader reader, AnyObjectId treeId)
			throws IOException {
		DirCache d = newInCore();
		DirCacheBuilder b = d.builder();
		b.addTree(null, DirCacheEntry.STAGE_0, reader, treeId);
		b.finish();
		return d;
	}

	/**
	 * Create a new in-core index representation and read an index from disk.
	 * <p>
	 * The new index will be read before it is returned to the caller. Read
	 * failures are reported as exceptions and therefore prevent the method from
	 * returning a partially populated index.
	 *
	 * @param repository
	 *            repository containing the index to read
	 * @return a cache representing the contents of the specified index file (if
	 *         it exists) or an empty cache if the file does not exist.
	 * @throws java.io.IOException
	 *             the index file is present but could not be read.
	 * @throws org.eclipse.jgit.errors.CorruptObjectException
	 *             the index file is using a format or extension that this
	 *             library does not support.
	 */
	public static DirCache read(Repository repository)
			throws CorruptObjectException, IOException {
		final DirCache c = read(repository.getIndexFile(), repository.getFS());
		c.repository = repository;
		return c;
	}

	/**
	 * Create a new in-core index representation and read an index from disk.
	 * <p>
	 * The new index will be read before it is returned to the caller. Read
	 * failures are reported as exceptions and therefore prevent the method from
	 * returning a partially populated index.
	 *
	 * @param indexLocation
	 *            location of the index file on disk.
	 * @param fs
	 *            the file system abstraction which will be necessary to perform
	 *            certain file system operations.
	 * @return a cache representing the contents of the specified index file (if
	 *         it exists) or an empty cache if the file does not exist.
	 * @throws java.io.IOException
	 *             the index file is present but could not be read.
	 * @throws org.eclipse.jgit.errors.CorruptObjectException
	 *             the index file is using a format or extension that this
	 *             library does not support.
	 */
	public static DirCache read(File indexLocation, FS fs)
			throws CorruptObjectException, IOException {
		final DirCache c = new DirCache(indexLocation, fs);
		c.read();
		return c;
	}

	/**
	 * Create a new in-core index representation, lock it, and read from disk.
	 * <p>
	 * The new index will be locked and then read before it is returned to the
	 * caller. Read failures are reported as exceptions and therefore prevent
	 * the method from returning a partially populated index. On read failure,
	 * the lock is released.
	 *
	 * @param indexLocation
	 *            location of the index file on disk.
	 * @param fs
	 *            the file system abstraction which will be necessary to perform
	 *            certain file system operations.
	 * @return a cache representing the contents of the specified index file (if
	 *         it exists) or an empty cache if the file does not exist.
	 * @throws java.io.IOException
	 *             the index file is present but could not be read, or the lock
	 *             could not be obtained.
	 * @throws org.eclipse.jgit.errors.CorruptObjectException
	 *             the index file is using a format or extension that this
	 *             library does not support.
	 */
	public static DirCache lock(File indexLocation, FS fs)
			throws CorruptObjectException, IOException {
		final DirCache c = new DirCache(indexLocation, fs);
		if (!c.lock())
			throw new LockFailedException(indexLocation);

		try {
			c.read();
		} catch (IOException | RuntimeException | Error e) {
			c.unlock();
			throw e;
		}

		return c;
	}

	/**
	 * Create a new in-core index representation, lock it, and read from disk.
	 * <p>
	 * The new index will be locked and then read before it is returned to the
	 * caller. Read failures are reported as exceptions and therefore prevent
	 * the method from returning a partially populated index. On read failure,
	 * the lock is released.
	 *
	 * @param repository
	 *            repository containing the index to lock and read
	 * @param indexChangedListener
	 *            listener to be informed when DirCache is committed
	 * @return a cache representing the contents of the specified index file (if
	 *         it exists) or an empty cache if the file does not exist.
	 * @throws java.io.IOException
	 *             the index file is present but could not be read, or the lock
	 *             could not be obtained.
	 * @throws org.eclipse.jgit.errors.CorruptObjectException
	 *             the index file is using a format or extension that this
	 *             library does not support.
	 * @since 2.0
	 */
	public static DirCache lock(final Repository repository,
			final IndexChangedListener indexChangedListener)
			throws CorruptObjectException, IOException {
		DirCache c = lock(repository.getIndexFile(), repository.getFS(),
				indexChangedListener);
		c.repository = repository;
		return c;
	}

	/**
	 * Create a new in-core index representation, lock it, and read from disk.
	 * <p>
	 * The new index will be locked and then read before it is returned to the
	 * caller. Read failures are reported as exceptions and therefore prevent
	 * the method from returning a partially populated index. On read failure,
	 * the lock is released.
	 *
	 * @param indexLocation
	 *            location of the index file on disk.
	 * @param fs
	 *            the file system abstraction which will be necessary to perform
	 *            certain file system operations.
	 * @param indexChangedListener
	 *            listener to be informed when DirCache is committed
	 * @return a cache representing the contents of the specified index file (if
	 *         it exists) or an empty cache if the file does not exist.
	 * @throws java.io.IOException
	 *             the index file is present but could not be read, or the lock
	 *             could not be obtained.
	 * @throws org.eclipse.jgit.errors.CorruptObjectException
	 *             the index file is using a format or extension that this
	 *             library does not support.
	 */
	public static DirCache lock(final File indexLocation, final FS fs,
			IndexChangedListener indexChangedListener)
			throws CorruptObjectException,
			IOException {
		DirCache c = lock(indexLocation, fs);
		c.registerIndexChangedListener(indexChangedListener);
		return c;
	}

	/** Location of the current version of the index file. */
	private final File liveFile;

	/** Individual file index entries, sorted by path name. */
	private DirCacheEntry[] sortedEntries;

	/** Number of positions within {@link #sortedEntries} that are valid. */
	private int entryCnt;

	/** Cache tree for this index; null if the cache tree is not available. */
	private DirCacheTree tree;

	/** Our active lock (if we hold it); null if we don't have it locked. */
	private LockFile myLock;

	/** Keep track of whether the index has changed or not */
	private FileSnapshot snapshot;

	/** index checksum when index was read from disk */
	private byte[] readIndexChecksum;

	/** index checksum when index was written to disk */
	private byte[] writeIndexChecksum;

	/** listener to be informed on commit */
	private IndexChangedListener indexChangedListener;

	/** Repository containing this index */
	private Repository repository;

	/**
	 * Create a new in-core index representation.
	 * <p>
	 * The new index will be empty. Callers may wish to read from the on disk
	 * file first with {@link #read()}.
	 *
	 * @param indexLocation
	 *            location of the index file on disk.
	 * @param fs
	 *            the file system abstraction which will be necessary to perform
	 *            certain file system operations.
	 */
	public DirCache(File indexLocation, FS fs) {
		liveFile = indexLocation;
		clear();
	}

	/**
	 * Create a new builder to update this cache.
	 * <p>
	 * Callers should add all entries to the builder, then use
	 * {@link org.eclipse.jgit.dircache.DirCacheBuilder#finish()} to update this
	 * instance.
	 *
	 * @return a new builder instance for this cache.
	 */
	public DirCacheBuilder builder() {
		return new DirCacheBuilder(this, entryCnt + 16);
	}

	/**
	 * Create a new editor to recreate this cache.
	 * <p>
	 * Callers should add commands to the editor, then use
	 * {@link org.eclipse.jgit.dircache.DirCacheEditor#finish()} to update this
	 * instance.
	 *
	 * @return a new builder instance for this cache.
	 */
	public DirCacheEditor editor() {
		return new DirCacheEditor(this, entryCnt + 16);
	}

	void replace(DirCacheEntry[] e, int cnt) {
		sortedEntries = e;
		entryCnt = cnt;
		tree = null;
	}

	/**
	 * Read the index from disk, if it has changed on disk.
	 * <p>
	 * This method tries to avoid loading the index if it has not changed since
	 * the last time we consulted it. A missing index file will be treated as
	 * though it were present but had no file entries in it.
	 *
	 * @throws java.io.IOException
	 *             the index file is present but could not be read. This
	 *             DirCache instance may not be populated correctly.
	 * @throws org.eclipse.jgit.errors.CorruptObjectException
	 *             the index file is using a format or extension that this
	 *             library does not support.
	 */
	public void read() throws IOException, CorruptObjectException {
		if (liveFile == null)
			throw new IOException(JGitText.get().dirCacheDoesNotHaveABackingFile);
		if (!liveFile.exists())
			clear();
		else if (snapshot == null || snapshot.isModified(liveFile)) {
			try (SilentFileInputStream inStream = new SilentFileInputStream(
					liveFile)) {
				clear();
				readFrom(inStream);
			} catch (FileNotFoundException fnfe) {
				if (liveFile.exists()) {
					// Panic: the index file exists but we can't read it
					throw new IndexReadException(
							MessageFormat.format(JGitText.get().cannotReadIndex,
									liveFile.getAbsolutePath(), fnfe));
				}
				// Someone must have deleted it between our exists test
				// and actually opening the path. That's fine, its empty.
				//
				clear();
			}
			snapshot = FileSnapshot.save(liveFile);
		}
	}

	/**
	 * Whether the memory state differs from the index file
	 *
	 * @return {@code true} if the memory state differs from the index file
	 * @throws java.io.IOException
	 */
	public boolean isOutdated() throws IOException {
		if (liveFile == null || !liveFile.exists())
			return false;
		return snapshot == null || snapshot.isModified(liveFile);
	}

	/**
	 * Empty this index, removing all entries.
	 */
	public void clear() {
		snapshot = null;
		sortedEntries = NO_ENTRIES;
		entryCnt = 0;
		tree = null;
		readIndexChecksum = NO_CHECKSUM;
	}

	private void readFrom(InputStream inStream) throws IOException,
			CorruptObjectException {
		final BufferedInputStream in = new BufferedInputStream(inStream);
		final MessageDigest md = Constants.newMessageDigest();

		// Read the index header and verify we understand it.
		//
		final byte[] hdr = new byte[20];
		IO.readFully(in, hdr, 0, 12);
		md.update(hdr, 0, 12);
		if (!is_DIRC(hdr))
			throw new CorruptObjectException(JGitText.get().notADIRCFile);
		final int ver = NB.decodeInt32(hdr, 4);
		boolean extended = false;
		if (ver == 3)
			extended = true;
		else if (ver != 2)
			throw new CorruptObjectException(MessageFormat.format(
					JGitText.get().unknownDIRCVersion, Integer.valueOf(ver)));
		entryCnt = NB.decodeInt32(hdr, 8);
		if (entryCnt < 0)
			throw new CorruptObjectException(JGitText.get().DIRCHasTooManyEntries);

		snapshot = FileSnapshot.save(liveFile);
		Instant smudge = snapshot.lastModifiedInstant();

		// Load the individual file entries.
		//
		final int infoLength = DirCacheEntry.getMaximumInfoLength(extended);
		final byte[] infos = new byte[infoLength * entryCnt];
		sortedEntries = new DirCacheEntry[entryCnt];

		final MutableInteger infoAt = new MutableInteger();
		for (int i = 0; i < entryCnt; i++) {
			sortedEntries[i] = new DirCacheEntry(infos, infoAt, in, md, smudge);
		}

		// After the file entries are index extensions, and then a footer.
		//
		for (;;) {
			in.mark(21);
			IO.readFully(in, hdr, 0, 20);
			if (in.read() < 0) {
				// No extensions present; the file ended where we expected.
				//
				break;
			}

			in.reset();
			md.update(hdr, 0, 8);
			IO.skipFully(in, 8);

			long sz = NB.decodeUInt32(hdr, 4);
			switch (NB.decodeInt32(hdr, 0)) {
			case EXT_TREE: {
				if (Integer.MAX_VALUE < sz) {
					throw new CorruptObjectException(MessageFormat.format(
							JGitText.get().DIRCExtensionIsTooLargeAt,
							formatExtensionName(hdr), Long.valueOf(sz)));
				}
				final byte[] raw = new byte[(int) sz];
				IO.readFully(in, raw, 0, raw.length);
				md.update(raw, 0, raw.length);
				tree = new DirCacheTree(raw, new MutableInteger(), null);
				break;
			}
			default:
				if (hdr[0] >= 'A' && hdr[0] <= 'Z') {
					// The extension is optional and is here only as
					// a performance optimization. Since we do not
					// understand it, we can safely skip past it, after
					// we include its data in our checksum.
					//
					skipOptionalExtension(in, md, hdr, sz);
				} else {
					// The extension is not an optimization and is
					// _required_ to understand this index format.
					// Since we did not trap it above we must abort.
					//
					throw new CorruptObjectException(MessageFormat.format(JGitText.get().DIRCExtensionNotSupportedByThisVersion
							, formatExtensionName(hdr)));
				}
			}
		}

		readIndexChecksum = md.digest();
		if (!Arrays.equals(readIndexChecksum, hdr)) {
			throw new CorruptObjectException(JGitText.get().DIRCChecksumMismatch);
		}
	}

	private void skipOptionalExtension(final InputStream in,
			final MessageDigest md, final byte[] hdr, long sz)
			throws IOException {
		final byte[] b = new byte[4096];
		while (0 < sz) {
			int n = in.read(b, 0, (int) Math.min(b.length, sz));
			if (n < 0) {
				throw new EOFException(
						MessageFormat.format(
								JGitText.get().shortReadOfOptionalDIRCExtensionExpectedAnotherBytes,
								formatExtensionName(hdr), Long.valueOf(sz)));
			}
			md.update(b, 0, n);
			sz -= n;
		}
	}

	private static String formatExtensionName(byte[] hdr) {
		return "'" + new String(hdr, 0, 4, ISO_8859_1) + "'"; //$NON-NLS-1$ //$NON-NLS-2$
	}

	private static boolean is_DIRC(byte[] hdr) {
		if (hdr.length < SIG_DIRC.length)
			return false;
		for (int i = 0; i < SIG_DIRC.length; i++)
			if (hdr[i] != SIG_DIRC[i])
				return false;
		return true;
	}

	/**
	 * Try to establish an update lock on the cache file.
	 *
	 * @return true if the lock is now held by the caller; false if it is held
	 *         by someone else.
	 * @throws java.io.IOException
	 *             the output file could not be created. The caller does not
	 *             hold the lock.
	 */
	public boolean lock() throws IOException {
		if (liveFile == null)
			throw new IOException(JGitText.get().dirCacheDoesNotHaveABackingFile);
		final LockFile tmp = new LockFile(liveFile);
		if (tmp.lock()) {
			tmp.setNeedStatInformation(true);
			myLock = tmp;
			return true;
		}
		return false;
	}

	/**
	 * Write the entry records from memory to disk.
	 * <p>
	 * The cache must be locked first by calling {@link #lock()} and receiving
	 * true as the return value. Applications are encouraged to lock the index,
	 * then invoke {@link #read()} to ensure the in-memory data is current,
	 * prior to updating the in-memory entries.
	 * <p>
	 * Once written the lock is closed and must be either committed with
	 * {@link #commit()} or rolled back with {@link #unlock()}.
	 *
	 * @throws java.io.IOException
	 *             the output file could not be created. The caller no longer
	 *             holds the lock.
	 */
	public void write() throws IOException {
		final LockFile tmp = myLock;
		requireLocked(tmp);
		try (OutputStream o = tmp.getOutputStream();
				OutputStream bo = new BufferedOutputStream(o)) {
			writeTo(liveFile.getParentFile(), bo);
		} catch (IOException | RuntimeException | Error err) {
			tmp.unlock();
			throw err;
		}
	}

	void writeTo(File dir, OutputStream os) throws IOException {
		final MessageDigest foot = Constants.newMessageDigest();
		final DigestOutputStream dos = new DigestOutputStream(os, foot);

		boolean extended = false;
		for (int i = 0; i < entryCnt; i++) {
			if (sortedEntries[i].isExtended()) {
				extended = true;
				break;
			}
		}

		// Write the header.
		//
		final byte[] tmp = new byte[128];
		System.arraycopy(SIG_DIRC, 0, tmp, 0, SIG_DIRC.length);
		NB.encodeInt32(tmp, 4, extended ? 3 : 2);
		NB.encodeInt32(tmp, 8, entryCnt);
		dos.write(tmp, 0, 12);

		// Write the individual file entries.

		Instant smudge;
		if (myLock != null) {
			// For new files we need to smudge the index entry
			// if they have been modified "now". Ideally we'd
			// want the timestamp when we're done writing the index,
			// so we use the current timestamp as a approximation.
			myLock.createCommitSnapshot();
			snapshot = myLock.getCommitSnapshot();
			smudge = snapshot.lastModifiedInstant();
		} else {
			// Used in unit tests only
			smudge = Instant.EPOCH;
		}

		// Check if tree is non-null here since calling updateSmudgedEntries
		// will automatically build it via creating a DirCacheIterator
		final boolean writeTree = tree != null;

		if (repository != null && entryCnt > 0)
			updateSmudgedEntries();

		for (int i = 0; i < entryCnt; i++) {
			final DirCacheEntry e = sortedEntries[i];
			if (e.mightBeRacilyClean(smudge)) {
				e.smudgeRacilyClean();
			}
			e.write(dos);
		}

		if (writeTree) {
			@SuppressWarnings("resource") // Explicitly closed in try block, and
											// destroyed in finally
			TemporaryBuffer bb = new TemporaryBuffer.LocalFile(dir, 5 << 20);
			try {
				tree.write(tmp, bb);
				bb.close();

				NB.encodeInt32(tmp, 0, EXT_TREE);
				NB.encodeInt32(tmp, 4, (int) bb.length());
				dos.write(tmp, 0, 8);
				bb.writeTo(dos, null);
			} finally {
				bb.destroy();
			}
		}
		writeIndexChecksum = foot.digest();
		os.write(writeIndexChecksum);
		os.close();
	}

	/**
	 * Commit this change and release the lock.
	 * <p>
	 * If this method fails (returns false) the lock is still released.
	 *
	 * @return true if the commit was successful and the file contains the new
	 *         data; false if the commit failed and the file remains with the
	 *         old data.
	 * @throws java.lang.IllegalStateException
	 *             the lock is not held.
	 */
	public boolean commit() {
		final LockFile tmp = myLock;
		requireLocked(tmp);
		myLock = null;
		if (!tmp.commit()) {
			return false;
		}
		snapshot = tmp.getCommitSnapshot();
		if (indexChangedListener != null
				&& !Arrays.equals(readIndexChecksum, writeIndexChecksum)) {
			indexChangedListener.onIndexChanged(new IndexChangedEvent(true));
		}
		return true;
	}

	private void requireLocked(LockFile tmp) {
		if (liveFile == null)
			throw new IllegalStateException(JGitText.get().dirCacheIsNotLocked);
		if (tmp == null)
			throw new IllegalStateException(MessageFormat.format(JGitText.get().dirCacheFileIsNotLocked
					, liveFile.getAbsolutePath()));
	}

	/**
	 * Unlock this file and abort this change.
	 * <p>
	 * The temporary file (if created) is deleted before returning.
	 */
	public void unlock() {
		final LockFile tmp = myLock;
		if (tmp != null) {
			myLock = null;
			tmp.unlock();
		}
	}

	/**
	 * Locate the position a path's entry is at in the index. For details refer
	 * to #findEntry(byte[], int).
	 *
	 * @param path
	 *            the path to search for.
	 * @return if &gt;= 0 then the return value is the position of the entry in
	 *         the index; pass to {@link #getEntry(int)} to obtain the entry
	 *         information. If &lt; 0 the entry does not exist in the index.
	 */
	public int findEntry(String path) {
		final byte[] p = Constants.encode(path);
		return findEntry(p, p.length);
	}

	/**
	 * Locate the position a path's entry is at in the index.
	 * <p>
	 * If there is at least one entry in the index for this path the position of
	 * the lowest stage is returned. Subsequent stages can be identified by
	 * testing consecutive entries until the path differs.
	 * <p>
	 * If no path matches the entry -(position+1) is returned, where position is
	 * the location it would have gone within the index.
	 *
	 * @param p
	 *            the byte array starting with the path to search for.
	 * @param pLen
	 *            the length of the path in bytes
	 * @return if &gt;= 0 then the return value is the position of the entry in
	 *         the index; pass to {@link #getEntry(int)} to obtain the entry
	 *         information. If &lt; 0 the entry does not exist in the index.
	 * @since 3.4
	 */
	public int findEntry(byte[] p, int pLen) {
		return findEntry(0, p, pLen);
	}

	int findEntry(int low, byte[] p, int pLen) {
		int high = entryCnt;
		while (low < high) {
			int mid = (low + high) >>> 1;
			final int cmp = cmp(p, pLen, sortedEntries[mid]);
			if (cmp < 0)
				high = mid;
			else if (cmp == 0) {
				while (mid > 0 && cmp(p, pLen, sortedEntries[mid - 1]) == 0)
					mid--;
				return mid;
			} else
				low = mid + 1;
		}
		return -(low + 1);
	}

	/**
	 * Determine the next index position past all entries with the same name.
	 * <p>
	 * As index entries are sorted by path name, then stage number, this method
	 * advances the supplied position to the first position in the index whose
	 * path name does not match the path name of the supplied position's entry.
	 *
	 * @param position
	 *            entry position of the path that should be skipped.
	 * @return position of the next entry whose path is after the input.
	 */
	public int nextEntry(int position) {
		DirCacheEntry last = sortedEntries[position];
		int nextIdx = position + 1;
		while (nextIdx < entryCnt) {
			final DirCacheEntry next = sortedEntries[nextIdx];
			if (cmp(last, next) != 0)
				break;
			last = next;
			nextIdx++;
		}
		return nextIdx;
	}

	int nextEntry(byte[] p, int pLen, int nextIdx) {
		while (nextIdx < entryCnt) {
			final DirCacheEntry next = sortedEntries[nextIdx];
			if (!DirCacheTree.peq(p, next.path, pLen))
				break;
			nextIdx++;
		}
		return nextIdx;
	}

	/**
	 * Total number of file entries stored in the index.
	 * <p>
	 * This count includes unmerged stages for a file entry if the file is
	 * currently conflicted in a merge. This means the total number of entries
	 * in the index may be up to 3 times larger than the number of files in the
	 * working directory.
	 * <p>
	 * Note that this value counts only <i>files</i>.
	 *
	 * @return number of entries available.
	 * @see #getEntry(int)
	 */
	public int getEntryCount() {
		return entryCnt;
	}

	/**
	 * Get a specific entry.
	 *
	 * @param i
	 *            position of the entry to get.
	 * @return the entry at position <code>i</code>.
	 */
	public DirCacheEntry getEntry(int i) {
		return sortedEntries[i];
	}

	/**
	 * Get a specific entry.
	 *
	 * @param path
	 *            the path to search for.
	 * @return the entry for the given <code>path</code>.
	 */
	public DirCacheEntry getEntry(String path) {
		final int i = findEntry(path);
		return i < 0 ? null : sortedEntries[i];
	}

	/**
	 * Recursively get all entries within a subtree.
	 *
	 * @param path
	 *            the subtree path to get all entries within.
	 * @return all entries recursively contained within the subtree.
	 */
	public DirCacheEntry[] getEntriesWithin(String path) {
		if (path.length() == 0) {
			DirCacheEntry[] r = new DirCacheEntry[entryCnt];
			System.arraycopy(sortedEntries, 0, r, 0, entryCnt);
			return r;
		}
		if (!path.endsWith("/")) //$NON-NLS-1$
			path += "/"; //$NON-NLS-1$
		final byte[] p = Constants.encode(path);
		final int pLen = p.length;

		int eIdx = findEntry(p, pLen);
		if (eIdx < 0)
			eIdx = -(eIdx + 1);
		final int lastIdx = nextEntry(p, pLen, eIdx);
		final DirCacheEntry[] r = new DirCacheEntry[lastIdx - eIdx];
		System.arraycopy(sortedEntries, eIdx, r, 0, r.length);
		return r;
	}

	void toArray(final int i, final DirCacheEntry[] dst, final int off,
			final int cnt) {
		System.arraycopy(sortedEntries, i, dst, off, cnt);
	}

	/**
	 * Obtain (or build) the current cache tree structure.
	 * <p>
	 * This method can optionally recreate the cache tree, without flushing the
	 * tree objects themselves to disk.
	 *
	 * @param build
	 *            if true and the cache tree is not present in the index it will
	 *            be generated and returned to the caller.
	 * @return the cache tree; null if there is no current cache tree available
	 *         and <code>build</code> was false.
	 */
	public DirCacheTree getCacheTree(boolean build) {
		if (build) {
			if (tree == null)
				tree = new DirCacheTree();
			tree.validate(sortedEntries, entryCnt, 0, 0);
		}
		return tree;
	}

	/**
	 * Write all index trees to the object store, returning the root tree.
	 *
	 * @param ow
	 *            the writer to use when serializing to the store. The caller is
	 *            responsible for flushing the inserter before trying to use the
	 *            returned tree identity.
	 * @return identity for the root tree.
	 * @throws org.eclipse.jgit.errors.UnmergedPathException
	 *             one or more paths contain higher-order stages (stage &gt; 0),
	 *             which cannot be stored in a tree object.
	 * @throws java.lang.IllegalStateException
	 *             one or more paths contain an invalid mode which should never
	 *             appear in a tree object.
	 * @throws java.io.IOException
	 *             an unexpected error occurred writing to the object store.
	 */
	public ObjectId writeTree(ObjectInserter ow)
			throws UnmergedPathException, IOException {
		return getCacheTree(true).writeTree(sortedEntries, 0, 0, ow);
	}

	/**
	 * Tells whether this index contains unmerged paths.
	 *
	 * @return {@code true} if this index contains unmerged paths. Means: at
	 *         least one entry is of a stage different from 0. {@code false}
	 *         will be returned if all entries are of stage 0.
	 */
	public boolean hasUnmergedPaths() {
		for (int i = 0; i < entryCnt; i++) {
			if (sortedEntries[i].getStage() > 0) {
				return true;
			}
		}
		return false;
	}

	private void registerIndexChangedListener(IndexChangedListener listener) {
		this.indexChangedListener = listener;
	}

	/**
	 * Update any smudged entries with information from the working tree.
	 *
	 * @throws IOException
	 */
	private void updateSmudgedEntries() throws IOException {
		List<String> paths = new ArrayList<>(128);
		try (TreeWalk walk = new TreeWalk(repository)) {
			walk.setOperationType(OperationType.CHECKIN_OP);
			for (int i = 0; i < entryCnt; i++)
				if (sortedEntries[i].isSmudged())
					paths.add(sortedEntries[i].getPathString());
			if (paths.isEmpty())
				return;
			walk.setFilter(PathFilterGroup.createFromStrings(paths));

			DirCacheIterator iIter = new DirCacheIterator(this);
			FileTreeIterator fIter = new FileTreeIterator(repository);
			walk.addTree(iIter);
			walk.addTree(fIter);
			fIter.setDirCacheIterator(walk, 0);
			walk.setRecursive(true);
			while (walk.next()) {
				iIter = walk.getTree(0, DirCacheIterator.class);
				if (iIter == null)
					continue;
				fIter = walk.getTree(1, FileTreeIterator.class);
				if (fIter == null)
					continue;
				DirCacheEntry entry = iIter.getDirCacheEntry();
				if (entry.isSmudged() && iIter.idEqual(fIter)) {
					entry.setLength(fIter.getEntryLength());
					entry.setLastModified(fIter.getEntryLastModifiedInstant());
				}
			}
		}
	}
}