/*
    * Copyright (C) 2008, Shawn O. Pearce <spearce@spearce.org>
    * Copyright (C) 2010, Christian Halstrick <christian.halstrick@sap.com>
    * Copyright (C) 2010, Matthias Sohn <matthias.sohn@sap.com>
    * Copyright (C) 2012-2013, Robin Rosenberg
    * 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.treewalk;
  
  import java.io.ByteArrayInputStream;
  import java.io.File;
  import java.io.FileInputStream;
  import java.io.FileNotFoundException;
  import java.io.IOException;
  import java.io.InputStream;
  import java.nio.ByteBuffer;
  import java.nio.CharBuffer;
  import java.nio.charset.CharacterCodingException;
  import java.nio.charset.CharsetEncoder;
  import java.security.MessageDigest;
  import java.text.MessageFormat;
  import java.util.Arrays;
  import java.util.Collections;
  import java.util.Comparator;
  
  import org.eclipse.jgit.api.errors.FilterFailedException;
  import org.eclipse.jgit.attributes.AttributesNode;
  import org.eclipse.jgit.attributes.AttributesRule;
  import org.eclipse.jgit.diff.RawText;
  import org.eclipse.jgit.dircache.DirCache;
  import org.eclipse.jgit.dircache.DirCacheEntry;
  import org.eclipse.jgit.dircache.DirCacheIterator;
  import org.eclipse.jgit.errors.CorruptObjectException;
  import org.eclipse.jgit.errors.MissingObjectException;
  import org.eclipse.jgit.errors.NoWorkTreeException;
  import org.eclipse.jgit.ignore.FastIgnoreRule;
  import org.eclipse.jgit.ignore.IgnoreNode;
  import org.eclipse.jgit.internal.JGitText;
  import org.eclipse.jgit.lib.Constants;
  import org.eclipse.jgit.lib.CoreConfig;
  import org.eclipse.jgit.lib.CoreConfig.CheckStat;
  import org.eclipse.jgit.lib.CoreConfig.EolStreamType;
  import org.eclipse.jgit.lib.CoreConfig.SymLinks;
  import org.eclipse.jgit.lib.FileMode;
  import org.eclipse.jgit.lib.ObjectId;
  import org.eclipse.jgit.lib.ObjectLoader;
  import org.eclipse.jgit.lib.ObjectReader;
  import org.eclipse.jgit.lib.Repository;
  import org.eclipse.jgit.submodule.SubmoduleWalk;
  import org.eclipse.jgit.treewalk.TreeWalk.OperationType;
  import org.eclipse.jgit.util.FS;
  import org.eclipse.jgit.util.FS.ExecutionResult;
  import org.eclipse.jgit.util.Holder;
  import org.eclipse.jgit.util.IO;
  import org.eclipse.jgit.util.Paths;
  import org.eclipse.jgit.util.RawParseUtils;
  import org.eclipse.jgit.util.io.AutoLFInputStream;
  import org.eclipse.jgit.util.io.EolStreamTypeUtil;
  
  /**
  * Walks a working directory tree as part of a {@link TreeWalk}.
  * <p>
  * Most applications will want to use the standard implementation of this
  * iterator, {@link FileTreeIterator}, as that does all IO through the standard
  * <code>java.io</code> package. Plugins for a Java based IDE may however wish
  * to create their own implementations of this class to allow traversal of the
  * IDE's project space, as well as benefit from any caching the IDE may have.
  *
  * @see FileTreeIterator
  */
 public abstract class WorkingTreeIterator extends AbstractTreeIterator {
 	private static final int MAX_EXCEPTION_TEXT_SIZE = 10 * 1024;
 
 	/** An empty entry array, suitable for {@link #init(Entry[])}. */
 	protected static final Entry[] EOF = {};
 
 	/** Size we perform file IO in if we have to read and hash a file. */
 	static final int BUFFER_SIZE = 2048;
 
 	/**
 	 * Maximum size of files which may be read fully into memory for performance
 	 * reasons.
 	 */
 	private static final long MAXIMUM_FILE_SIZE_TO_READ_FULLY = 65536;
 
 	/** Inherited state of this iterator, describing working tree, etc. */
 	private final IteratorState state;
 
 	/** The {@link #idBuffer()} for the current entry. */
 	private byte[] contentId;
 
 	/** Index within {@link #entries} that {@link #contentId} came from. */
 	private int contentIdFromPtr;
 
 	/** List of entries obtained from the subclass. */
 	private Entry[] entries;
 
 	/** Total number of entries in {@link #entries} that are valid. */
 	private int entryCnt;
 
 	/** Current position within {@link #entries}. */
 	private int ptr;
 
 	/** If there is a .gitignore file present, the parsed rules from it. */
 	private IgnoreNode ignoreNode;
 
 	/**
 	 * cached clean filter command. Use a Ref in order to distinguish between
 	 * the ref not cached yet and the value null
 	 */
 	private Holder<String> cleanFilterCommandHolder;
 
 	/**
 	 * cached eol stream type. Use a Ref in order to distinguish between the ref
 	 * not cached yet and the value null
 	 */
 	private Holder<EolStreamType> eolStreamTypeHolder;
 
 	/** Repository that is the root level being iterated over */
 	protected Repository repository;
 
 	/** Cached canonical length, initialized from {@link #idBuffer()} */
 	private long canonLen = -1;
 
 	/** The offset of the content id in {@link #idBuffer()} */
 	private int contentIdOffset;
 
 	/**
 	 * Create a new iterator with no parent.
 	 *
 	 * @param options
 	 *            working tree options to be used
 	 */
 	protected WorkingTreeIterator(WorkingTreeOptions options) {
 		super();
 		state = new IteratorState(options);
 	}
 
 	/**
 	 * Create a new iterator with no parent and a prefix.
 	 * <p>
 	 * The prefix path supplied is inserted in front of all paths generated by
 	 * this iterator. It is intended to be used when an iterator is being
 	 * created for a subsection of an overall repository and needs to be
 	 * combined with other iterators that are created to run over the entire
 	 * repository namespace.
 	 *
 	 * @param prefix
 	 *            position of this iterator in the repository tree. The value
 	 *            may be null or the empty string to indicate the prefix is the
 	 *            root of the repository. A trailing slash ('/') is
 	 *            automatically appended if the prefix does not end in '/'.
 	 * @param options
 	 *            working tree options to be used
 	 */
 	protected WorkingTreeIterator(final String prefix,
 			WorkingTreeOptions options) {
 		super(prefix);
 		state = new IteratorState(options);
 	}
 
 	/**
 	 * Create an iterator for a subtree of an existing iterator.
 	 *
 	 * @param p
 	 *            parent tree iterator.
 	 */
 	protected WorkingTreeIterator(final WorkingTreeIterator p) {
 		super(p);
 		state = p.state;
 		repository = p.repository;
 	}
 
 	/**
 	 * Initialize this iterator for the root level of a repository.
 	 * <p>
 	 * This method should only be invoked after calling {@link #init(Entry[])},
 	 * and only for the root iterator.
 	 *
 	 * @param repo
 	 *            the repository.
 	 */
 	protected void initRootIterator(Repository repo) {
 		repository = repo;
 		Entry entry;
 		if (ignoreNode instanceof PerDirectoryIgnoreNode)
 			entry = ((PerDirectoryIgnoreNode) ignoreNode).entry;
 		else
 			entry = null;
 		ignoreNode = new RootIgnoreNode(entry, repo);
 	}
 
 	/**
 	 * Define the matching {@link DirCacheIterator}, to optimize ObjectIds.
 	 *
 	 * Once the DirCacheIterator has been set this iterator must only be
 	 * advanced by the TreeWalk that is supplied, as it assumes that itself and
 	 * the corresponding DirCacheIterator are positioned on the same file path
 	 * whenever {@link #idBuffer()} is invoked.
 	 *
 	 * @param walk
 	 *            the walk that will be advancing this iterator.
 	 * @param treeId
 	 *            index of the matching {@link DirCacheIterator}.
 	 */
 	public void setDirCacheIterator(TreeWalk walk, int treeId) {
 		state.walk = walk;
 		state.dirCacheTree = treeId;
 	}
 
 	@Override
 	public boolean hasId() {
 		if (contentIdFromPtr == ptr)
 			return true;
 		return (mode & FileMode.TYPE_MASK) == FileMode.TYPE_FILE;
 	}
 
 	@Override
 	public byte[] idBuffer() {
 		if (contentIdFromPtr == ptr)
 			return contentId;
 
 		if (state.walk != null) {
 			// If there is a matching DirCacheIterator, we can reuse
 			// its idBuffer, but only if we appear to be clean against
 			// the cached index information for the path.
 			//
 			DirCacheIterator i = state.walk.getTree(state.dirCacheTree,
 							DirCacheIterator.class);
 			if (i != null) {
 				DirCacheEntry ent = i.getDirCacheEntry();
 				if (ent != null && compareMetadata(ent) == MetadataDiff.EQUAL) {
 					contentIdOffset = i.idOffset();
 					contentIdFromPtr = ptr;
 					return contentId = i.idBuffer();
 				}
 				contentIdOffset = 0;
 			} else {
 				contentIdOffset = 0;
 			}
 		}
 		switch (mode & FileMode.TYPE_MASK) {
 		case FileMode.TYPE_SYMLINK:
 		case FileMode.TYPE_FILE:
 			contentIdFromPtr = ptr;
 			return contentId = idBufferBlob(entries[ptr]);
 		case FileMode.TYPE_GITLINK:
 			contentIdFromPtr = ptr;
 			return contentId = idSubmodule(entries[ptr]);
 		}
 		return zeroid;
 	}
 
 	@Override
 	public boolean isWorkTree() {
 		return true;
 	}
 
 	/**
 	 * Get submodule id for given entry.
 	 *
 	 * @param e
 	 * @return non-null submodule id
 	 */
 	protected byte[] idSubmodule(Entry e) {
 		if (repository == null)
 			return zeroid;
 		File directory;
 		try {
 			directory = repository.getWorkTree();
 		} catch (NoWorkTreeException nwte) {
 			return zeroid;
 		}
 		return idSubmodule(directory, e);
 	}
 
 	/**
 	 * Get submodule id using the repository at the location of the entry
 	 * relative to the directory.
 	 *
 	 * @param directory
 	 * @param e
 	 * @return non-null submodule id
 	 */
 	protected byte[] idSubmodule(File directory, Entry e) {
 		final Repository submoduleRepo;
 		try {
 			submoduleRepo = SubmoduleWalk.getSubmoduleRepository(directory,
 					e.getName());
 		} catch (IOException exception) {
 			return zeroid;
 		}
 		if (submoduleRepo == null)
 			return zeroid;
 
 		final ObjectId head;
 		try {
 			head = submoduleRepo.resolve(Constants.HEAD);
 		} catch (IOException exception) {
 			return zeroid;
 		} finally {
 			submoduleRepo.close();
 		}
 		if (head == null)
 			return zeroid;
 		final byte[] id = new byte[Constants.OBJECT_ID_LENGTH];
 		head.copyRawTo(id, 0);
 		return id;
 	}
 
 	private static final byte[] digits = { '0', '1', '2', '3', '4', '5', '6',
 			'7', '8', '9' };
 
 	private static final byte[] hblob = Constants
 			.encodedTypeString(Constants.OBJ_BLOB);
 
 	private byte[] idBufferBlob(final Entry e) {
 		try {
 			final InputStream is = e.openInputStream();
 			if (is == null)
 				return zeroid;
 			try {
 				state.initializeDigestAndReadBuffer();
 
 				final long len = e.getLength();
 				InputStream filteredIs = possiblyFilteredInputStream(e, is, len,
 						OperationType.CHECKIN_OP);
 				return computeHash(filteredIs, canonLen);
 			} finally {
 				safeClose(is);
 			}
 		} catch (IOException err) {
 			// Can't read the file? Don't report the failure either.
 			return zeroid;
 		}
 	}
 
 	private InputStream possiblyFilteredInputStream(final Entry e,
 			final InputStream is, final long len) throws IOException {
 		return possiblyFilteredInputStream(e, is, len, null);
 
 	}
 
 	private InputStream possiblyFilteredInputStream(final Entry e,
 			final InputStream is, final long len, OperationType opType)
 			throws IOException {
 		if (getCleanFilterCommand() == null
 				&& getEolStreamType(opType) == EolStreamType.DIRECT) {
 			canonLen = len;
 			return is;
 		}
 
 		if (len <= MAXIMUM_FILE_SIZE_TO_READ_FULLY) {
 			ByteBuffer rawbuf = IO.readWholeStream(is, (int) len);
 			byte[] raw = rawbuf.array();
 			int n = rawbuf.limit();
 			if (!isBinary(raw, n)) {
 				rawbuf = filterClean(raw, n, opType);
 				raw = rawbuf.array();
 				n = rawbuf.limit();
 			}
 			canonLen = n;
 			return new ByteArrayInputStream(raw, 0, n);
 		}
 
 		if (getCleanFilterCommand() == null && isBinary(e)) {
 				canonLen = len;
 				return is;
 			}
 
 		final InputStream lenIs = filterClean(e.openInputStream(),
 				opType);
 		try {
 			canonLen = computeLength(lenIs);
 		} finally {
 			safeClose(lenIs);
 		}
 		return filterClean(is, opType);
 	}
 
 	private static void safeClose(final InputStream in) {
 		try {
 			in.close();
 		} catch (IOException err2) {
 			// Suppress any error related to closing an input
 			// stream. We don't care, we should not have any
 			// outstanding data to flush or anything like that.
 		}
 	}
 
 	private static boolean isBinary(byte[] content, int sz) {
 		return RawText.isBinary(content, sz);
 	}
 
 	private static boolean isBinary(Entry entry) throws IOException {
 		InputStream in = entry.openInputStream();
 		try {
 			return RawText.isBinary(in);
 		} finally {
 			safeClose(in);
 		}
 	}
 
 	private ByteBuffer filterClean(byte[] src, int n, OperationType opType)
 			throws IOException {
 		InputStream in = new ByteArrayInputStream(src);
 		try {
 			return IO.readWholeStream(filterClean(in, opType), n);
 		} finally {
 			safeClose(in);
 		}
 	}
 
 	private InputStream filterClean(InputStream in) throws IOException {
 		return filterClean(in, null);
 	}
 
 	private InputStream filterClean(InputStream in, OperationType opType)
 			throws IOException {
 		in = handleAutoCRLF(in, opType);
 		String filterCommand = getCleanFilterCommand();
 		if (filterCommand != null) {
 			FS fs = repository.getFS();
 			ProcessBuilder filterProcessBuilder = fs.runInShell(filterCommand,
 					new String[0]);
 			filterProcessBuilder.directory(repository.getWorkTree());
 			filterProcessBuilder.environment().put(Constants.GIT_DIR_KEY,
 					repository.getDirectory().getAbsolutePath());
 			ExecutionResult result;
 			try {
 				result = fs.execute(filterProcessBuilder, in);
 			} catch (IOException | InterruptedException e) {
 				throw new IOException(new FilterFailedException(e,
 						filterCommand, getEntryPathString()));
 			}
 			int rc = result.getRc();
 			if (rc != 0) {
 				throw new IOException(new FilterFailedException(rc,
 						filterCommand, getEntryPathString(),
 						result.getStdout().toByteArray(MAX_EXCEPTION_TEXT_SIZE),
 						RawParseUtils.decode(result.getStderr()
 								.toByteArray(MAX_EXCEPTION_TEXT_SIZE))));
 			}
 			return result.getStdout().openInputStream();
 		}
 		return in;
 	}
 
 	private InputStream handleAutoCRLF(InputStream in, OperationType opType)
 			throws IOException {
 		return EolStreamTypeUtil.wrapInputStream(in, getEolStreamType(opType));
 	}
 
 	/**
 	 * Returns the working tree options used by this iterator.
 	 *
 	 * @return working tree options
 	 */
 	public WorkingTreeOptions getOptions() {
 		return state.options;
 	}
 
 	@Override
 	public int idOffset() {
 		return contentIdOffset;
 	}
 
 	@Override
 	public void reset() {
 		if (!first()) {
 			ptr = 0;
 			if (!eof())
 				parseEntry();
 		}
 	}
 
 	@Override
 	public boolean first() {
 		return ptr == 0;
 	}
 
 	@Override
 	public boolean eof() {
 		return ptr == entryCnt;
 	}
 
 	@Override
 	public void next(final int delta) throws CorruptObjectException {
 		ptr += delta;
 		if (!eof()) {
 			parseEntry();
 		}
 	}
 
 	@Override
 	public void back(final int delta) throws CorruptObjectException {
 		ptr -= delta;
 		parseEntry();
 	}
 
 	private void parseEntry() {
 		final Entry e = entries[ptr];
 		mode = e.getMode().getBits();
 
 		final int nameLen = e.encodedNameLen;
 		ensurePathCapacity(pathOffset + nameLen, pathOffset);
 		System.arraycopy(e.encodedName, 0, path, pathOffset, nameLen);
 		pathLen = pathOffset + nameLen;
 		canonLen = -1;
 		cleanFilterCommandHolder = null;
 		eolStreamTypeHolder = null;
 	}
 
 	/**
 	 * Get the raw byte length of this entry.
 	 *
 	 * @return size of this file, in bytes.
 	 */
 	public long getEntryLength() {
 		return current().getLength();
 	}
 
 	/**
 	 * Get the filtered input length of this entry
 	 *
 	 * @return size of the content, in bytes
 	 * @throws IOException
 	 */
 	public long getEntryContentLength() throws IOException {
 		if (canonLen == -1) {
 			long rawLen = getEntryLength();
 			if (rawLen == 0)
 				canonLen = 0;
 			InputStream is = current().openInputStream();
 			try {
 				// canonLen gets updated here
 				possiblyFilteredInputStream(current(), is, current()
 						.getLength());
 			} finally {
 				safeClose(is);
 			}
 		}
 		return canonLen;
 	}
 
 	/**
 	 * Get the last modified time of this entry.
 	 *
 	 * @return last modified time of this file, in milliseconds since the epoch
 	 *         (Jan 1, 1970 UTC).
 	 */
 	public long getEntryLastModified() {
 		return current().getLastModified();
 	}
 
 	/**
 	 * Obtain an input stream to read the file content.
 	 * <p>
 	 * Efficient implementations are not required. The caller will usually
 	 * obtain the stream only once per entry, if at all.
 	 * <p>
 	 * The input stream should not use buffering if the implementation can avoid
 	 * it. The caller will buffer as necessary to perform efficient block IO
 	 * operations.
 	 * <p>
 	 * The caller will close the stream once complete.
 	 *
 	 * @return a stream to read from the file.
 	 * @throws IOException
 	 *             the file could not be opened for reading.
 	 */
 	public InputStream openEntryStream() throws IOException {
 		InputStream rawis = current().openInputStream();
 		if (getCleanFilterCommand() == null
 				&& getEolStreamType() == EolStreamType.DIRECT)
 			return rawis;
 		else
 			return filterClean(rawis);
 	}
 
 	/**
 	 * Determine if the current entry path is ignored by an ignore rule.
 	 *
 	 * @return true if the entry was ignored by an ignore rule file.
 	 * @throws IOException
 	 *             a relevant ignore rule file exists but cannot be read.
 	 */
 	public boolean isEntryIgnored() throws IOException {
 		return isEntryIgnored(pathLen);
 	}
 
 	/**
 	 * Determine if the entry path is ignored by an ignore rule.
 	 *
 	 * @param pLen
 	 *            the length of the path in the path buffer.
 	 * @return true if the entry is ignored by an ignore rule.
 	 * @throws IOException
 	 *             a relevant ignore rule file exists but cannot be read.
 	 */
 	protected boolean isEntryIgnored(final int pLen) throws IOException {
 		return isEntryIgnored(pLen, mode, false);
 	}
 
 	/**
 	 * Determine if the entry path is ignored by an ignore rule. Consider
 	 * possible rule negation from child iterator.
 	 *
 	 * @param pLen
 	 *            the length of the path in the path buffer.
 	 * @param fileMode
 	 *            the original iterator file mode
 	 * @param negatePrevious
 	 *            true if the previous matching iterator rule was negation
 	 * @return true if the entry is ignored by an ignore rule.
 	 * @throws IOException
 	 *             a relevant ignore rule file exists but cannot be read.
 	 */
 	private boolean isEntryIgnored(final int pLen, int fileMode,
 			boolean negatePrevious)
 			throws IOException {
 		IgnoreNode rules = getIgnoreNode();
 		if (rules != null) {
 			// The ignore code wants path to start with a '/' if possible.
 			// If we have the '/' in our path buffer because we are inside
 			// a subdirectory include it in the range we convert to string.
 			//
 			int pOff = pathOffset;
 			if (0 < pOff)
 				pOff--;
 			String p = TreeWalk.pathOf(path, pOff, pLen);
 			switch (rules.isIgnored(p, FileMode.TREE.equals(fileMode),
 					negatePrevious)) {
 			case IGNORED:
 				return true;
 			case NOT_IGNORED:
 				return false;
 			case CHECK_PARENT:
 				negatePrevious = false;
 				break;
 			case CHECK_PARENT_NEGATE_FIRST_MATCH:
 				negatePrevious = true;
 				break;
 			}
 		}
 		if (parent instanceof WorkingTreeIterator)
 			return ((WorkingTreeIterator) parent).isEntryIgnored(pLen, fileMode,
 					negatePrevious);
 		return false;
 	}
 
 	private IgnoreNode getIgnoreNode() throws IOException {
 		if (ignoreNode instanceof PerDirectoryIgnoreNode)
 			ignoreNode = ((PerDirectoryIgnoreNode) ignoreNode).load();
 		return ignoreNode;
 	}
 
 	/**
 	 * Retrieves the {@link AttributesNode} for the current entry.
 	 *
 	 * @return {@link AttributesNode} for the current entry.
 	 * @throws IOException
 	 *             if an error is raised while parsing the .gitattributes file
 	 * @since 3.7
 	 */
 	public AttributesNode getEntryAttributesNode() throws IOException {
 		if (attributesNode instanceof PerDirectoryAttributesNode)
 			attributesNode = ((PerDirectoryAttributesNode) attributesNode)
 					.load();
 		return attributesNode;
 	}
 
 	private static final Comparator<Entry> ENTRY_CMP = new Comparator<Entry>() {
 		public int compare(Entry a, Entry b) {
 			return Paths.compare(
 					a.encodedName, 0, a.encodedNameLen, a.getMode().getBits(),
 					b.encodedName, 0, b.encodedNameLen, b.getMode().getBits());
 		}
 	};
 
 	/**
 	 * Constructor helper.
 	 *
 	 * @param list
 	 *            files in the subtree of the work tree this iterator operates
 	 *            on
 	 */
 	protected void init(final Entry[] list) {
 		// Filter out nulls, . and .. as these are not valid tree entries,
 		// also cache the encoded forms of the path names for efficient use
 		// later on during sorting and iteration.
 		//
 		entries = list;
 		int i, o;
 
 		final CharsetEncoder nameEncoder = state.nameEncoder;
 		for (i = 0, o = 0; i < entries.length; i++) {
 			final Entry e = entries[i];
 			if (e == null)
 				continue;
 			final String name = e.getName();
 			if (".".equals(name) || "..".equals(name)) //$NON-NLS-1$ //$NON-NLS-2$
 				continue;
 			if (Constants.DOT_GIT.equals(name))
 				continue;
 			if (Constants.DOT_GIT_IGNORE.equals(name))
 				ignoreNode = new PerDirectoryIgnoreNode(e);
 			if (Constants.DOT_GIT_ATTRIBUTES.equals(name))
 				attributesNode = new PerDirectoryAttributesNode(e);
 			if (i != o)
 				entries[o] = e;
 			e.encodeName(nameEncoder);
 			o++;
 		}
 		entryCnt = o;
 		Arrays.sort(entries, 0, entryCnt, ENTRY_CMP);
 
 		contentIdFromPtr = -1;
 		ptr = 0;
 		if (!eof())
 			parseEntry();
 		else if (pathLen == 0) // see bug 445363
 			pathLen = pathOffset;
 	}
 
 	/**
 	 * Obtain the current entry from this iterator.
 	 *
 	 * @return the currently selected entry.
 	 */
 	protected Entry current() {
 		return entries[ptr];
 	}
 
 	/**
 	 * The result of a metadata-comparison between the current entry and a
 	 * {@link DirCacheEntry}
 	 */
 	public enum MetadataDiff {
 		/**
 		 * The entries are equal by metaData (mode, length,
 		 * modification-timestamp) or the <code>assumeValid</code> attribute of
 		 * the index entry is set
 		 */
 		EQUAL,
 
 		/**
 		 * The entries are not equal by metaData (mode, length) or the
 		 * <code>isUpdateNeeded</code> attribute of the index entry is set
 		 */
 		DIFFER_BY_METADATA,
 
 		/** index entry is smudged - can't use that entry for comparison */
 		SMUDGED,
 
 		/**
 		 * The entries are equal by metaData (mode, length) but differ by
 		 * modification-timestamp.
 		 */
 		DIFFER_BY_TIMESTAMP
 	}
 
 	/**
 	 * Is the file mode of the current entry different than the given raw mode?
 	 *
 	 * @param rawMode
 	 * @return true if different, false otherwise
 	 */
 	public boolean isModeDifferent(final int rawMode) {
 		// Determine difference in mode-bits of file and index-entry. In the
 		// bitwise presentation of modeDiff we'll have a '1' when the two modes
 		// differ at this position.
 		int modeDiff = getEntryRawMode() ^ rawMode;
 
 		if (modeDiff == 0)
 			return false;
 
 		// Do not rely on filemode differences in case of symbolic links
 		if (getOptions().getSymLinks() == SymLinks.FALSE)
 			if (FileMode.SYMLINK.equals(rawMode))
 				return false;
 
 		// Ignore the executable file bits if WorkingTreeOptions tell me to
 		// do so. Ignoring is done by setting the bits representing a
 		// EXECUTABLE_FILE to '0' in modeDiff
 		if (!state.options.isFileMode())
 			modeDiff &= ~FileMode.EXECUTABLE_FILE.getBits();
 		return modeDiff != 0;
 	}
 
 	/**
 	 * Compare the metadata (mode, length, modification-timestamp) of the
 	 * current entry and a {@link DirCacheEntry}
 	 *
 	 * @param entry
 	 *            the {@link DirCacheEntry} to compare with
 	 * @return a {@link MetadataDiff} which tells whether and how the entries
 	 *         metadata differ
 	 */
 	public MetadataDiff compareMetadata(DirCacheEntry entry) {
 		if (entry.isAssumeValid())
 			return MetadataDiff.EQUAL;
 
 		if (entry.isUpdateNeeded())
 			return MetadataDiff.DIFFER_BY_METADATA;
 
 		if (!entry.isSmudged() && entry.getLength() != (int) getEntryLength())
 			return MetadataDiff.DIFFER_BY_METADATA;
 
 		if (isModeDifferent(entry.getRawMode()))
 			return MetadataDiff.DIFFER_BY_METADATA;
 
 		// Git under windows only stores seconds so we round the timestamp
 		// Java gives us if it looks like the timestamp in index is seconds
 		// only. Otherwise we compare the timestamp at millisecond precision,
 		// unless core.checkstat is set to "minimal", in which case we only
 		// compare the whole second part.
 		long cacheLastModified = entry.getLastModified();
 		long fileLastModified = getEntryLastModified();
 		long lastModifiedMillis = fileLastModified % 1000;
 		long cacheMillis = cacheLastModified % 1000;
 		if (getOptions().getCheckStat() == CheckStat.MINIMAL) {
 			fileLastModified = fileLastModified - lastModifiedMillis;
 			cacheLastModified = cacheLastModified - cacheMillis;
 		} else if (cacheMillis == 0)
 			fileLastModified = fileLastModified - lastModifiedMillis;
 		// Some Java version on Linux return whole seconds only even when
 		// the file systems supports more precision.
 		else if (lastModifiedMillis == 0)
 			cacheLastModified = cacheLastModified - cacheMillis;
 
 		if (fileLastModified != cacheLastModified)
 			return MetadataDiff.DIFFER_BY_TIMESTAMP;
 		else if (!entry.isSmudged())
 			// The file is clean when you look at timestamps.
 			return MetadataDiff.EQUAL;
 		else
 			return MetadataDiff.SMUDGED;
 	}
 
 	/**
 	 * Checks whether this entry differs from a given entry from the
 	 * {@link DirCache}.
 	 *
 	 * File status information is used and if status is same we consider the
 	 * file identical to the state in the working directory. Native git uses
 	 * more stat fields than we have accessible in Java.
 	 *
 	 * @param entry
 	 *            the entry from the dircache we want to compare against
 	 * @param forceContentCheck
 	 *            True if the actual file content should be checked if
 	 *            modification time differs.
 	 * @param reader
 	 *            access to repository objects if necessary. Should not be null.
 	 * @return true if content is most likely different.
 	 * @throws IOException
 	 * @since 3.3
 	 */
 	public boolean isModified(DirCacheEntry entry, boolean forceContentCheck,
 			ObjectReader reader) throws IOException {
 		if (entry == null)
 			return !FileMode.MISSING.equals(getEntryFileMode());
 		MetadataDiff diff = compareMetadata(entry);
 		switch (diff) {
 		case DIFFER_BY_TIMESTAMP:
 			if (forceContentCheck)
 				// But we are told to look at content even though timestamps
 				// tell us about modification
 				return contentCheck(entry, reader);
 			else
 				// We are told to assume a modification if timestamps differs
 				return true;
 		case SMUDGED:
 			// The file is clean by timestamps but the entry was smudged.
 			// Lets do a content check
 			return contentCheck(entry, reader);
 		case EQUAL:
 			return false;
 		case DIFFER_BY_METADATA:
 			if (mode == FileMode.SYMLINK.getBits())
 				return contentCheck(entry, reader);
 			return true;
 		default:
 			throw new IllegalStateException(MessageFormat.format(
 					JGitText.get().unexpectedCompareResult, diff.name()));
 		}
 	}
 
 	/**
 	 * Get the file mode to use for the current entry when it is to be updated
 	 * in the index.
 	 *
 	 * @param indexIter
 	 *            {@link DirCacheIterator} positioned at the same entry as this
 	 *            iterator or null if no {@link DirCacheIterator} is available
 	 *            at this iterator's current entry
 	 * @return index file mode
 	 */
 	public FileMode getIndexFileMode(final DirCacheIterator indexIter) {
 		final FileMode wtMode = getEntryFileMode();
 		if (indexIter == null) {
 			return wtMode;
 		}
 		final FileMode iMode = indexIter.getEntryFileMode();
 		if (getOptions().isFileMode() && iMode != FileMode.GITLINK && iMode != FileMode.TREE) {
 			return wtMode;
 		}
 		if (!getOptions().isFileMode()) {
 			if (FileMode.REGULAR_FILE == wtMode
 					&& FileMode.EXECUTABLE_FILE == iMode) {
 				return iMode;
 			}
 			if (FileMode.EXECUTABLE_FILE == wtMode
 					&& FileMode.REGULAR_FILE == iMode) {
 				return iMode;
 			}
 		}
 		if (FileMode.GITLINK == iMode
 				&& FileMode.TREE == wtMode) {
 			return iMode;
 		}
 		if (FileMode.TREE == iMode
 				&& FileMode.GITLINK == wtMode) {
 			return iMode;
 		}
 		return wtMode;
 	}
 
 	/**
 	 * Compares the entries content with the content in the filesystem.
 	 * Unsmudges the entry when it is detected that it is clean.
 	 *
 	 * @param entry
 	 *            the entry to be checked
 	 * @param reader
 	 *            acccess to repository data if necessary
 	 * @return <code>true</code> if the content doesn't match,
 	 *         <code>false</code> if it matches
 	 * @throws IOException
 	 */
 	private boolean contentCheck(DirCacheEntry entry, ObjectReader reader)
 			throws IOException {
 		if (getEntryObjectId().equals(entry.getObjectId())) {
 			// Content has not changed
 
 			// We know the entry can't be racily clean because it's still clean.
 			// Therefore we unsmudge the entry!
 			// If by any chance we now unsmudge although we are still in the
 			// same time-slot as the last modification to the index file the
 			// next index write operation will smudge again.
 			// Caution: we are unsmudging just by setting the length of the
 			// in-memory entry object. It's the callers task to detect that we
 			// have modified the entry and to persist the modified index.
 			entry.setLength((int) getEntryLength());
 
 			return false;
 		} else {
 			if (mode == FileMode.SYMLINK.getBits())
 				return !new File(readContentAsNormalizedString(current()))
 						.equals(new File((readContentAsNormalizedString(entry,
 								reader))));
 			// Content differs: that's a real change, perhaps
 			if (reader == null) // deprecated use, do no further checks
 				return true;
 
 			switch (getEolStreamType()) {
 			case DIRECT:
 				return true;
 			default:
 				try {
 					ObjectLoader loader = reader.open(entry.getObjectId());
 					if (loader == null)
 						return true;
 
 					// We need to compute the length, but only if it is not
 					// a binary stream.
 					long dcInLen;
 					try (InputStream dcIn = new AutoLFInputStream(
 							loader.openStream(), true,
 							true /* abort if binary */)) {
 						dcInLen = computeLength(dcIn);
 					} catch (AutoLFInputStream.IsBinaryException e) {
 						return true;
 					}
 
 					try (InputStream dcIn = new AutoLFInputStream(
 							loader.openStream(), true)) {
 						byte[] autoCrLfHash = computeHash(dcIn, dcInLen);
 						boolean changed = getEntryObjectId()
 								.compareTo(autoCrLfHash, 0) != 0;
 						return changed;
 					}
 				} catch (IOException e) {
 					return true;
 				}
 			}
 		}
 	}
 
 	private static String readContentAsNormalizedString(DirCacheEntry entry,
 			ObjectReader reader) throws MissingObjectException, IOException {
 		ObjectLoader open = reader.open(entry.getObjectId());
 		byte[] cachedBytes = open.getCachedBytes();
 		return FS.detect().normalize(RawParseUtils.decode(cachedBytes));
 	}
 
 	private static String readContentAsNormalizedString(Entry entry) throws IOException {
 		long length = entry.getLength();
 		byte[] content = new byte[(int) length];
 		InputStream is = entry.openInputStream();
 		IO.readFully(is, content, 0, (int) length);
 		return FS.detect().normalize(RawParseUtils.decode(content));
 	}
 
 	private static long computeLength(InputStream in) throws IOException {
 		// Since we only care about the length, use skip. The stream
 		// may be able to more efficiently wade through its data.
 		//
 		long length = 0;
 		for (;;) {
 			long n = in.skip(1 << 20);
 			if (n <= 0)
 				break;
 			length += n;
 		}
 		return length;
 	}
 
 	private byte[] computeHash(InputStream in, long length) throws IOException {
 		final MessageDigest contentDigest = state.contentDigest;
 		final byte[] contentReadBuffer = state.contentReadBuffer;
 
 		contentDigest.reset();
 		contentDigest.update(hblob);
 		contentDigest.update((byte) ' ');
 
 		long sz = length;
 		if (sz == 0) {
 			contentDigest.update((byte) '0');
 		} else {
 			final int bufn = contentReadBuffer.length;
 			int p = bufn;
 			do {
 				contentReadBuffer[--p] = digits[(int) (sz % 10)];
 				sz /= 10;
 			} while (sz > 0);
 			contentDigest.update(contentReadBuffer, p, bufn - p);
 		}
 		contentDigest.update((byte) 0);
 
 		for (;;) {
 			final int r = in.read(contentReadBuffer);
 			if (r <= 0)
 				break;
 			contentDigest.update(contentReadBuffer, 0, r);
 			sz += r;
 		}
 		if (sz != length)
 			return zeroid;
 		return contentDigest.digest();
 	}
 
 	/** A single entry within a working directory tree. */
 	protected static abstract class Entry {
 		byte[] encodedName;
 
 		int encodedNameLen;
 
 		void encodeName(final CharsetEncoder enc) {
 			final ByteBuffer b;
 			try {
 				b = enc.encode(CharBuffer.wrap(getName()));
 			} catch (CharacterCodingException e) {
 				// This should so never happen.
 				throw new RuntimeException(MessageFormat.format(
 						JGitText.get().unencodeableFile, getName()));
 			}
 
 			encodedNameLen = b.limit();
 			if (b.hasArray() && b.arrayOffset() == 0)
 				encodedName = b.array();
 			else
 				b.get(encodedName = new byte[encodedNameLen]);
 		}
 
 		public String toString() {
 			return getMode().toString() + " " + getName(); //$NON-NLS-1$
 		}
 
 		/**
 		 * Get the type of this entry.
 		 * <p>
 		 * <b>Note: Efficient implementation required.</b>
 		 * <p>
 		 * The implementation of this method must be efficient. If a subclass
 		 * needs to compute the value they should cache the reference within an
 		 * instance member instead.
 		 *
 		 * @return a file mode constant from {@link FileMode}.
 		 */
 		public abstract FileMode getMode();
 
 		/**
 		 * Get the byte length of this entry.
 		 * <p>
 		 * <b>Note: Efficient implementation required.</b>
 		 * <p>
 		 * The implementation of this method must be efficient. If a subclass
 		 * needs to compute the value they should cache the reference within an
 		 * instance member instead.
 		 *
 		 * @return size of this file, in bytes.
 		 */
 		public abstract long getLength();
 
 		/**
 		 * Get the last modified time of this entry.
 		 * <p>
 		 * <b>Note: Efficient implementation required.</b>
 		 * <p>
 		 * The implementation of this method must be efficient. If a subclass
 		 * needs to compute the value they should cache the reference within an
 		 * instance member instead.
 		 *
 		 * @return time since the epoch (in ms) of the last change.
 		 */
 		public abstract long getLastModified();
 
 		/**
 		 * Get the name of this entry within its directory.
 		 * <p>
 		 * Efficient implementations are not required. The caller will obtain
 		 * the name only once and cache it once obtained.
 		 *
 		 * @return name of the entry.
 		 */
 		public abstract String getName();
 
 		/**
 		 * Obtain an input stream to read the file content.
 		 * <p>
 		 * Efficient implementations are not required. The caller will usually
 		 * obtain the stream only once per entry, if at all.
 		 * <p>
 		 * The input stream should not use buffering if the implementation can
 		 * avoid it. The caller will buffer as necessary to perform efficient
 		 * block IO operations.
 		 * <p>
 		 * The caller will close the stream once complete.
 		 *
 		 * @return a stream to read from the file.
 		 * @throws IOException
 		 *             the file could not be opened for reading.
 		 */
 		public abstract InputStream openInputStream() throws IOException;
 	}
 
 	/** Magic type indicating we know rules exist, but they aren't loaded. */
 	private static class PerDirectoryIgnoreNode extends IgnoreNode {
 		final Entry entry;
 
 		PerDirectoryIgnoreNode(Entry entry) {
 			super(Collections.<FastIgnoreRule> emptyList());
 			this.entry = entry;
 		}
 
 		IgnoreNode load() throws IOException {
 			IgnoreNode r = new IgnoreNode();
 			InputStream in = entry.openInputStream();
 			try {
 				r.parse(in);
 			} finally {
 				in.close();
 			}
 			return r.getRules().isEmpty() ? null : r;
 		}
 	}
 
 	/** Magic type indicating there may be rules for the top level. */
 	private static class RootIgnoreNode extends PerDirectoryIgnoreNode {
 		final Repository repository;
 
 		RootIgnoreNode(Entry entry, Repository repository) {
 			super(entry);
 			this.repository = repository;
 		}
 
 		@Override
 		IgnoreNode load() throws IOException {
 			IgnoreNode r;
 			if (entry != null) {
 				r = super.load();
 				if (r == null)
 					r = new IgnoreNode();
 			} else {
 				r = new IgnoreNode();
 			}
 
 			FS fs = repository.getFS();
 			String path = repository.getConfig().get(CoreConfig.KEY)
 					.getExcludesFile();
 			if (path != null) {
 				File excludesfile;
 				if (path.startsWith("~/")) //$NON-NLS-1$
 					excludesfile = fs.resolve(fs.userHome(), path.substring(2));
 				else
 					excludesfile = fs.resolve(null, path);
 				loadRulesFromFile(r, excludesfile);
 			}
 
 			File exclude = fs.resolve(repository.getDirectory(),
 					Constants.INFO_EXCLUDE);
 			loadRulesFromFile(r, exclude);
 
 			return r.getRules().isEmpty() ? null : r;
 		}
 
 		private static void loadRulesFromFile(IgnoreNode r, File exclude)
 				throws FileNotFoundException, IOException {
 			if (FS.DETECTED.exists(exclude)) {
 				FileInputStream in = new FileInputStream(exclude);
 				try {
 					r.parse(in);
 				} finally {
 					in.close();
 				}
 			}
 		}
 	}
 
 	/** Magic type indicating we know rules exist, but they aren't loaded. */
 	private static class PerDirectoryAttributesNode extends AttributesNode {
 		final Entry entry;
 
 		PerDirectoryAttributesNode(Entry entry) {
 			super(Collections.<AttributesRule> emptyList());
 			this.entry = entry;
 		}
 
 		AttributesNode load() throws IOException {
 			AttributesNode r = new AttributesNode();
 			InputStream in = entry.openInputStream();
 			try {
 				r.parse(in);
 			} finally {
 				in.close();
 			}
 			return r.getRules().isEmpty() ? null : r;
 		}
 	}
 
 
 	private static final class IteratorState {
 		/** Options used to process the working tree. */
 		final WorkingTreeOptions options;
 
 		/** File name character encoder. */
 		final CharsetEncoder nameEncoder;
 
 		/** Digest computer for {@link #contentId} computations. */
 		MessageDigest contentDigest;
 
 		/** Buffer used to perform {@link #contentId} computations. */
 		byte[] contentReadBuffer;
 
 		/** TreeWalk with a (supposedly) matching DirCacheIterator. */
 		TreeWalk walk;
 
 		/** Position of the matching {@link DirCacheIterator}. */
 		int dirCacheTree;
 
 		IteratorState(WorkingTreeOptions options) {
 			this.options = options;
 			this.nameEncoder = Constants.CHARSET.newEncoder();
 		}
 
 		void initializeDigestAndReadBuffer() {
 			if (contentDigest == null) {
 				contentDigest = Constants.newMessageDigest();
 				contentReadBuffer = new byte[BUFFER_SIZE];
 			}
 		}
 	}
 
 	/**
 	 * @return the clean filter command for the current entry or
 	 *         <code>null</code> if no such command is defined
 	 * @throws IOException
 	 * @since 4.2
 	 */
 	public String getCleanFilterCommand() throws IOException {
 		if (cleanFilterCommandHolder == null) {
 			String cmd = null;
 			if (state.walk != null) {
 				cmd = state.walk
 						.getFilterCommand(Constants.ATTR_FILTER_TYPE_CLEAN);
 			}
 			cleanFilterCommandHolder = new Holder<String>(cmd);
 		}
 		return cleanFilterCommandHolder.get();
 	}
 
 	/**
 	 * @return the eol stream type for the current entry or <code>null</code> if
 	 *         it cannot be determined. When state or state.walk is null or the
 	 *         {@link TreeWalk} is not based on a {@link Repository} then null
 	 *         is returned.
 	 * @throws IOException
 	 * @since 4.3
 	 */
 	public EolStreamType getEolStreamType() throws IOException {
 		return getEolStreamType(null);
 	}
 
 	/**
 	 * @param opType
 	 *            The operationtype (checkin/checkout) which should be used
 	 * @return the eol stream type for the current entry or <code>null</code> if
 	 *         it cannot be determined. When state or state.walk is null or the
 	 *         {@link TreeWalk} is not based on a {@link Repository} then null
 	 *         is returned.
 	 * @throws IOException
 	 */
 	private EolStreamType getEolStreamType(OperationType opType)
 			throws IOException {
 		if (eolStreamTypeHolder == null) {
 			EolStreamType type=null;
 			if (state.walk != null) {
 				if (opType != null) {
 					type = state.walk.getEolStreamType(opType);
 				} else {
 					type=state.walk.getEolStreamType();
 				}
 			} else {
 				switch (getOptions().getAutoCRLF()) {
 				case FALSE:
 					type = EolStreamType.DIRECT;
 					break;
 				case TRUE:
 				case INPUT:
 					type = EolStreamType.AUTO_LF;
 					break;
 				}
 			}
 			eolStreamTypeHolder = new Holder<EolStreamType>(type);
 		}
 		return eolStreamTypeHolder.get();
 	}
 }