Kill GitIndex

A few places were still using GitIndex. Replacing it was fairly
simple, but there is a difference in test outcome in
ReadTreeTest.testUntrackedConflicts. I believe the new behavior
is good, since we do not update neither the index, not the worktree.

Change-Id: I4be5357b7b3139dded17f77e07a140addb213ea7
Signed-off-by: Robin Rosenberg <robin.rosenberg@dewire.com>

4 files changed, 0 insertions, 1592 deletions

diff --git a/org.eclipse.jgit.test/exttst/org/eclipse/jgit/lib/T0007_GitIndexTest.java b/org.eclipse.jgit.test/exttst/org/eclipse/jgit/lib/T0007_GitIndexTest.java
deleted file mode 100644
index fac828822b..0000000000
--- a/org.eclipse.jgit.test/exttst/org/eclipse/jgit/lib/T0007_GitIndexTest.java
+++ /dev/null
@@ -1,481 +0,0 @@
-/*
- * Copyright (C) 2007, Robin Rosenberg <robin.rosenberg@dewire.com>
- * Copyright (C) 2008, Shawn O. Pearce <spearce@spearce.org>
- * and other copyright owners as documented in the project's IP log.
- *
- * This program and the accompanying materials are made available
- * under the terms of the Eclipse Distribution License v1.0 which
- * accompanies this distribution, is reproduced below, and is
- * available at http://www.eclipse.org/org/documents/edl-v10.php
- *
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or
- * without modification, are permitted provided that the following
- * conditions are met:
- *
- * - Redistributions of source code must retain the above copyright
- *   notice, this list of conditions and the following disclaimer.
- *
- * - Redistributions in binary form must reproduce the above
- *   copyright notice, this list of conditions and the following
- *   disclaimer in the documentation and/or other materials provided
- *   with the distribution.
- *
- * - Neither the name of the Eclipse Foundation, Inc. nor the
- *   names of its contributors may be used to endorse or promote
- *   products derived from this software without specific prior
- *   written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
- * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
- * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
- * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
- * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
- * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
- * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-package org.eclipse.jgit.lib;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-
-import org.eclipse.jgit.junit.LocalDiskRepositoryTestCase;
-import org.eclipse.jgit.lib.GitIndex.Entry;
-import org.eclipse.jgit.util.FS;
-import org.junit.Before;
-import org.junit.Test;
-
-public class T0007_GitIndexTest extends LocalDiskRepositoryTestCase {
-
-	static boolean canrungitstatus;
-	static {
-		try {
-			canrungitstatus = system(new File("."),"git --version") == 0;
-		} catch (IOException e) {
-			System.out.println("Warning: cannot invoke native git to validate index");
-		} catch (InterruptedException e) {
-			e.printStackTrace();
-		}
-	}
-
-	private static int system(File dir, String cmd) throws IOException,
-			InterruptedException {
-		final Process process = Runtime.getRuntime().exec(cmd, null, dir);
-		new Thread() {
-			public void run() {
-				try {
-					InputStream s = process.getErrorStream();
-					for (int c = s.read(); c != -1; c = s.read()) {
-						System.err.print((char) c);
-					}
-					s.close();
-				} catch (IOException e1) {
-					// TODO Auto-generated catch block
-					e1.printStackTrace();
-				}
-			}
-		}.start();
-		final Thread t2 = new Thread() {
-			public void run() {
-				synchronized (this) {
-					try {
-						InputStream e = process.getInputStream();
-						for (int c = e.read(); c != -1; c = e.read()) {
-							System.out.print((char) c);
-						}
-						e.close();
-					} catch (IOException e1) {
-						// TODO Auto-generated catch block
-						e1.printStackTrace();
-					}
-				}
-			}
-		};
-		t2.start();
-		process.getOutputStream().close();
-		int ret = process.waitFor();
-		synchronized (t2) {
-			return ret;
-		}
-	}
-
-	private Repository db;
-
-	private File trash;
-
-	@Override
-	@Before
-	public void setUp() throws Exception {
-		super.setUp();
-		db = createWorkRepository();
-		trash = db.getWorkTree();
-	}
-
-	@Test
-	public void testCreateEmptyIndex() throws Exception {
-		GitIndex index = new GitIndex(db);
-		index.write();
-// native git doesn't like an empty index
-// assertEquals(0,system(trash,"git status"));
-
-		GitIndex indexr = new GitIndex(db);
-		indexr.read();
-		assertEquals(0, indexr.getMembers().length);
-	}
-
-	@Test
-	public void testReadWithNoIndex() throws Exception {
-		GitIndex index = new GitIndex(db);
-		index.read();
-		assertEquals(0, index.getMembers().length);
-	}
-
-	@Test
-	public void testCreateSimpleSortTestIndex() throws Exception {
-		GitIndex index = new GitIndex(db);
-		writeTrashFile("a/b", "data:a/b");
-		writeTrashFile("a:b", "data:a:b");
-		writeTrashFile("a.b", "data:a.b");
-		index.add(trash, new File(trash, "a/b"));
-		index.add(trash, new File(trash, "a:b"));
-		index.add(trash, new File(trash, "a.b"));
-		index.write();
-
-		assertEquals("a/b", index.getEntry("a/b").getName());
-		assertEquals("a:b", index.getEntry("a:b").getName());
-		assertEquals("a.b", index.getEntry("a.b").getName());
-		assertNull(index.getEntry("a*b"));
-
-		// Repeat test for re-read index
-		GitIndex indexr = new GitIndex(db);
-		indexr.read();
-		assertEquals("a/b", indexr.getEntry("a/b").getName());
-		assertEquals("a:b", indexr.getEntry("a:b").getName());
-		assertEquals("a.b", indexr.getEntry("a.b").getName());
-		assertNull(indexr.getEntry("a*b"));
-
-		if (canrungitstatus)
-			assertEquals(0, system(trash, "git status"));
-	}
-
-	@Test
-	public void testUpdateSimpleSortTestIndex() throws Exception {
-		GitIndex index = new GitIndex(db);
-		writeTrashFile("a/b", "data:a/b");
-		writeTrashFile("a:b", "data:a:b");
-		writeTrashFile("a.b", "data:a.b");
-		index.add(trash, new File(trash, "a/b"));
-		index.add(trash, new File(trash, "a:b"));
-		index.add(trash, new File(trash, "a.b"));
-		writeTrashFile("a/b", "data:a/b modified");
-		index.add(trash, new File(trash, "a/b"));
-		index.write();
-		if (canrungitstatus)
-			assertEquals(0, system(trash, "git status"));
-	}
-
-	@Test
-	public void testWriteTree() throws Exception {
-		GitIndex index = new GitIndex(db);
-		writeTrashFile("a/b", "data:a/b");
-		writeTrashFile("a:b", "data:a:b");
-		writeTrashFile("a.b", "data:a.b");
-		index.add(trash, new File(trash, "a/b"));
-		index.add(trash, new File(trash, "a:b"));
-		index.add(trash, new File(trash, "a.b"));
-		index.write();
-
-		ObjectId id = index.writeTree();
-		assertEquals("c696abc3ab8e091c665f49d00eb8919690b3aec3", id.name());
-
-		writeTrashFile("a/b", "data:a/b");
-		index.add(trash, new File(trash, "a/b"));
-
-		if (canrungitstatus)
-			assertEquals(0, system(trash, "git status"));
-	}
-
-	@Test
-	public void testReadTree() throws Exception {
-		// Prepare tree
-		GitIndex index = new GitIndex(db);
-		writeTrashFile("a/b", "data:a/b");
-		writeTrashFile("a:b", "data:a:b");
-		writeTrashFile("a.b", "data:a.b");
-		index.add(trash, new File(trash, "a/b"));
-		index.add(trash, new File(trash, "a:b"));
-		index.add(trash, new File(trash, "a.b"));
-		index.write();
-
-		ObjectId id = index.writeTree();
-		System.out.println("wrote id " + id);
-		assertEquals("c696abc3ab8e091c665f49d00eb8919690b3aec3", id.name());
-		GitIndex index2 = new GitIndex(db);
-
-		index2.readTree(mapTree("c696abc3ab8e091c665f49d00eb8919690b3aec3"));
-		Entry[] members = index2.getMembers();
-		assertEquals(3, members.length);
-		assertEquals("a.b", members[0].getName());
-		assertEquals("a/b", members[1].getName());
-		assertEquals("a:b", members[2].getName());
-		assertEquals(3, members.length);
-
-		GitIndex indexr = new GitIndex(db);
-		indexr.read();
-		Entry[] membersr = indexr.getMembers();
-		assertEquals(3, membersr.length);
-		assertEquals("a.b", membersr[0].getName());
-		assertEquals("a/b", membersr[1].getName());
-		assertEquals("a:b", membersr[2].getName());
-		assertEquals(3, membersr.length);
-
-		if (canrungitstatus)
-			assertEquals(0, system(trash, "git status"));
-	}
-
-	@Test
-	public void testReadTree2() throws Exception {
-		// Prepare a larger tree to test some odd cases in tree writing
-		GitIndex index = new GitIndex(db);
-		File f1 = writeTrashFile("a/a/a/a", "data:a/a/a/a");
-		File f2 = writeTrashFile("a/c/c", "data:a/c/c");
-		File f3 = writeTrashFile("a/b", "data:a/b");
-		File f4 = writeTrashFile("a:b", "data:a:b");
-		File f5 = writeTrashFile("a/d", "data:a/d");
-		File f6 = writeTrashFile("a.b", "data:a.b");
-		index.add(trash, f1);
-		index.add(trash, f2);
-		index.add(trash, f3);
-		index.add(trash, f4);
-		index.add(trash, f5);
-		index.add(trash, f6);
-		index.write();
-		ObjectId id = index.writeTree();
-		System.out.println("wrote id " + id);
-		assertEquals("ba78e065e2c261d4f7b8f42107588051e87e18e9", id.name());
-		GitIndex index2 = new GitIndex(db);
-
-		index2.readTree(mapTree("ba78e065e2c261d4f7b8f42107588051e87e18e9"));
-		Entry[] members = index2.getMembers();
-		assertEquals(6, members.length);
-		assertEquals("a.b", members[0].getName());
-		assertEquals("a/a/a/a", members[1].getName());
-		assertEquals("a/b", members[2].getName());
-		assertEquals("a/c/c", members[3].getName());
-		assertEquals("a/d", members[4].getName());
-		assertEquals("a:b", members[5].getName());
-
-		// reread and test
-		GitIndex indexr = new GitIndex(db);
-		indexr.read();
-		Entry[] membersr = indexr.getMembers();
-		assertEquals(6, membersr.length);
-		assertEquals("a.b", membersr[0].getName());
-		assertEquals("a/a/a/a", membersr[1].getName());
-		assertEquals("a/b", membersr[2].getName());
-		assertEquals("a/c/c", membersr[3].getName());
-		assertEquals("a/d", membersr[4].getName());
-		assertEquals("a:b", membersr[5].getName());
-	}
-
-	@Test
-	public void testDelete() throws Exception {
-		GitIndex index = new GitIndex(db);
-		writeTrashFile("a/b", "data:a/b");
-		writeTrashFile("a:b", "data:a:b");
-		writeTrashFile("a.b", "data:a.b");
-		index.add(trash, new File(trash, "a/b"));
-		index.add(trash, new File(trash, "a:b"));
-		index.add(trash, new File(trash, "a.b"));
-		index.write();
-		index.writeTree();
-		index.remove(trash, new File(trash, "a:b"));
-		index.write();
-		assertEquals("a.b", index.getMembers()[0].getName());
-		assertEquals("a/b", index.getMembers()[1].getName());
-
-		GitIndex indexr = new GitIndex(db);
-		indexr.read();
-		assertEquals("a.b", indexr.getMembers()[0].getName());
-		assertEquals("a/b", indexr.getMembers()[1].getName());
-
-		if (canrungitstatus)
-			assertEquals(0, system(trash, "git status"));
-	}
-
-	@Test
-	public void testCheckout() throws Exception {
-		// Prepare tree, remote it and checkout
-		GitIndex index = new GitIndex(db);
-		File aslashb = writeTrashFile("a/b", "data:a/b");
-		File acolonb = writeTrashFile("a:b", "data:a:b");
-		File adotb = writeTrashFile("a.b", "data:a.b");
-		index.add(trash, aslashb);
-		index.add(trash, acolonb);
-		index.add(trash, adotb);
-		index.write();
-		index.writeTree();
-		delete(aslashb);
-		delete(acolonb);
-		delete(adotb);
-		delete(aslashb.getParentFile());
-
-		GitIndex index2 = new GitIndex(db);
-		assertEquals(0, index2.getMembers().length);
-
-		index2.readTree(mapTree("c696abc3ab8e091c665f49d00eb8919690b3aec3"));
-
-		index2.checkout(trash);
-		assertEquals("data:a/b", read(aslashb));
-		assertEquals("data:a:b", read(acolonb));
-		assertEquals("data:a.b", read(adotb));
-
-		if (canrungitstatus)
-			assertEquals(0, system(trash, "git status"));
-	}
-
-	@Test
-	public void test030_executeBit_coreModeTrue() throws IllegalArgumentException, IllegalAccessException, InvocationTargetException, Error, Exception {
-		if (!FS.DETECTED.supportsExecute()) {
-			System.err.println("Test ignored since platform FS does not support the execute permission");
-			return;
-		}
-		try {
-			// coremode true is the default, typically set to false
-			// by git init (but not jgit!)
-			Method canExecute = File.class.getMethod("canExecute", (Class[])null);
-			Method setExecute = File.class.getMethod("setExecutable", new Class[] { Boolean.TYPE });
-			File execFile = writeTrashFile("exec","exec");
-			if (!((Boolean)setExecute.invoke(execFile, new Object[] { Boolean.TRUE })).booleanValue())
-				throw new Error("could not set execute bit on "+execFile.getAbsolutePath()+"for test");
-			File nonexecFile = writeTrashFile("nonexec","nonexec");
-			if (!((Boolean)setExecute.invoke(nonexecFile, new Object[] { Boolean.FALSE })).booleanValue())
-				throw new Error("could not clear execute bit on "+nonexecFile.getAbsolutePath()+"for test");
-
-			GitIndex index = new GitIndex(db);
-			index.filemode = Boolean.TRUE; // TODO: we need a way to set this using config
-			index.add(trash, execFile);
-			index.add(trash, nonexecFile);
-			Tree tree = mapTree(index.writeTree().name());
-			assertEquals(FileMode.EXECUTABLE_FILE, tree.findBlobMember(execFile.getName()).getMode());
-			assertEquals(FileMode.REGULAR_FILE, tree.findBlobMember(nonexecFile.getName()).getMode());
-
-			index.write();
-
-			if (!execFile.delete())
-				throw new Error("Problem in test, cannot delete test file "+execFile.getAbsolutePath());
-			if (!nonexecFile.delete())
-				throw new Error("Problem in test, cannot delete test file "+nonexecFile.getAbsolutePath());
-			GitIndex index2 = new GitIndex(db);
-			index2.filemode = Boolean.TRUE; // TODO: we need a way to set this using config
-			index2.read();
-			index2.checkout(trash);
-			assertTrue(((Boolean)canExecute.invoke(execFile,(Object[])null)).booleanValue());
-			assertFalse(((Boolean)canExecute.invoke(nonexecFile,(Object[])null)).booleanValue());
-
-			assertFalse(index2.getEntry(execFile.getName()).isModified(trash));
-			assertFalse(index2.getEntry(nonexecFile.getName()).isModified(trash));
-
-			if (!((Boolean)setExecute.invoke(execFile, new Object[] { Boolean.FALSE })).booleanValue())
-				throw new Error("could not clear set execute bit on "+execFile.getAbsolutePath()+"for test");
-			if (!((Boolean)setExecute.invoke(nonexecFile, new Object[] { Boolean.TRUE })).booleanValue())
-				throw new Error("could set execute bit on "+nonexecFile.getAbsolutePath()+"for test");
-
-			assertTrue(index2.getEntry(execFile.getName()).isModified(trash));
-			assertTrue(index2.getEntry(nonexecFile.getName()).isModified(trash));
-
-		} catch (NoSuchMethodException e) {
-			System.err.println("Test ignored when running under JDK < 1.6");
-			return;
-		}
-	}
-
-	@Test
-	public void test031_executeBit_coreModeFalse() throws IllegalArgumentException, IllegalAccessException, InvocationTargetException, Error, Exception {
-		if (!FS.DETECTED.supportsExecute()) {
-			System.err.println("Test ignored since platform FS does not support the execute permission");
-			return;
-		}
-		try {
-			// coremode true is the default, typically set to false
-			// by git init (but not jgit!)
-			Method canExecute = File.class.getMethod("canExecute", (Class[])null);
-			Method setExecute = File.class.getMethod("setExecutable", new Class[] { Boolean.TYPE });
-			File execFile = writeTrashFile("exec","exec");
-			if (!((Boolean)setExecute.invoke(execFile, new Object[] { Boolean.TRUE })).booleanValue())
-				throw new Error("could not set execute bit on "+execFile.getAbsolutePath()+"for test");
-			File nonexecFile = writeTrashFile("nonexec","nonexec");
-			if (!((Boolean)setExecute.invoke(nonexecFile, new Object[] { Boolean.FALSE })).booleanValue())
-				throw new Error("could not clear execute bit on "+nonexecFile.getAbsolutePath()+"for test");
-
-			GitIndex index = new GitIndex(db);
-			index.filemode = Boolean.FALSE; // TODO: we need a way to set this using config
-			index.add(trash, execFile);
-			index.add(trash, nonexecFile);
-			Tree tree = mapTree(index.writeTree().name());
-			assertEquals(FileMode.REGULAR_FILE, tree.findBlobMember(execFile.getName()).getMode());
-			assertEquals(FileMode.REGULAR_FILE, tree.findBlobMember(nonexecFile.getName()).getMode());
-
-			index.write();
-
-			if (!execFile.delete())
-				throw new Error("Problem in test, cannot delete test file "+execFile.getAbsolutePath());
-			if (!nonexecFile.delete())
-				throw new Error("Problem in test, cannot delete test file "+nonexecFile.getAbsolutePath());
-			GitIndex index2 = new GitIndex(db);
-			index2.filemode = Boolean.FALSE; // TODO: we need a way to set this using config
-			index2.read();
-			index2.checkout(trash);
-			assertFalse(((Boolean)canExecute.invoke(execFile,(Object[])null)).booleanValue());
-			assertFalse(((Boolean)canExecute.invoke(nonexecFile,(Object[])null)).booleanValue());
-
-			assertFalse(index2.getEntry(execFile.getName()).isModified(trash));
-			assertFalse(index2.getEntry(nonexecFile.getName()).isModified(trash));
-
-			if (!((Boolean)setExecute.invoke(execFile, new Object[] { Boolean.FALSE })).booleanValue())
-				throw new Error("could not clear set execute bit on "+execFile.getAbsolutePath()+"for test");
-			if (!((Boolean)setExecute.invoke(nonexecFile, new Object[] { Boolean.TRUE })).booleanValue())
-				throw new Error("could set execute bit on "+nonexecFile.getAbsolutePath()+"for test");
-
-			// no change since we ignore the execute bit
-			assertFalse(index2.getEntry(execFile.getName()).isModified(trash));
-			assertFalse(index2.getEntry(nonexecFile.getName()).isModified(trash));
-
-		} catch (NoSuchMethodException e) {
-			System.err.println("Test ignored when running under JDK < 1.6");
-			return;
-		}
-	}
-
-	private void delete(File f) throws IOException {
-		if (!f.delete())
-			throw new IOException("Failed to delete f");
-	}
-
-	private File writeTrashFile(String name, String body) throws IOException {
-		final File path = new File(trash, name);
-		write(path, body);
-		return path;
-	}
-
-	private Tree mapTree(String name) throws IOException {
-		ObjectId id = db.resolve(name + "^{tree}");
-		return new Tree(db, id, db.open(id).getCachedBytes());
-	}
-}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/GitIndex.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/GitIndex.java
deleted file mode 100644
index 56a98bdcd6..0000000000
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/GitIndex.java
+++ /dev/null
@@ -1,1072 +0,0 @@
-/*
- * Copyright (C) 2007, Dave Watson <dwatson@mimvista.com>
- * Copyright (C) 2007, Robin Rosenberg <me@lathund.dewire.com>
- * Copyright (C) 2007-2009, Robin Rosenberg <robin.rosenberg@dewire.com>
- * Copyright (C) 2008, Roger C. Soares <rogersoares@intelinet.com.br>
- * Copyright (C) 2008, Shawn O. Pearce <spearce@spearce.org>
- * and other copyright owners as documented in the project's IP log.
- *
- * This program and the accompanying materials are made available
- * under the terms of the Eclipse Distribution License v1.0 which
- * accompanies this distribution, is reproduced below, and is
- * available at http://www.eclipse.org/org/documents/edl-v10.php
- *
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or
- * without modification, are permitted provided that the following
- * conditions are met:
- *
- * - Redistributions of source code must retain the above copyright
- *   notice, this list of conditions and the following disclaimer.
- *
- * - Redistributions in binary form must reproduce the above
- *   copyright notice, this list of conditions and the following
- *   disclaimer in the documentation and/or other materials provided
- *   with the distribution.
- *
- * - Neither the name of the Eclipse Foundation, Inc. nor the
- *   names of its contributors may be used to endorse or promote
- *   products derived from this software without specific prior
- *   written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
- * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
- * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
- * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
- * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
- * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
- * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-package org.eclipse.jgit.lib;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.RandomAccessFile;
-import java.io.UnsupportedEncodingException;
-import java.nio.ByteBuffer;
-import java.nio.ByteOrder;
-import java.nio.channels.FileChannel;
-import java.security.MessageDigest;
-import java.text.MessageFormat;
-import java.util.Comparator;
-import java.util.Date;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Stack;
-import java.util.TreeMap;
-
-import org.eclipse.jgit.JGitText;
-import org.eclipse.jgit.dircache.DirCache;
-import org.eclipse.jgit.errors.CorruptObjectException;
-import org.eclipse.jgit.errors.NotSupportedException;
-import org.eclipse.jgit.events.IndexChangedEvent;
-import org.eclipse.jgit.util.FileUtils;
-import org.eclipse.jgit.util.RawParseUtils;
-
-/**
- * A representation of the Git index.
- *
- * The index points to the objects currently checked out or in the process of
- * being prepared for committing or objects involved in an unfinished merge.
- *
- * The abstract format is:<br/> path stage flags statdata SHA-1
- * <ul>
- * <li>Path is the relative path in the workdir</li>
- * <li>stage is 0 (normally), but when
- * merging 1 is the common ancestor version, 2 is 'our' version and 3 is 'their'
- * version. A fully resolved merge only contains stage 0.</li>
- * <li>flags is the object type and information of validity</li>
- * <li>statdata is the size of this object and some other file system specifics,
- * some of it ignored by JGit</li>
- * <li>SHA-1 represents the content of the references object</li>
- * </ul>
- *
- * An index can also contain a tree cache which we ignore for now. We drop the
- * tree cache when writing the index.
- *
- * @deprecated Use {@link DirCache} instead.
- */
-public class GitIndex {
-
-	/** Stage 0 represents merged entries. */
-	public static final int STAGE_0 = 0;
-
-	private RandomAccessFile cache;
-
-	private File cacheFile;
-
-	// Index is modified
-	private boolean changed;
-
-	// Stat information updated
-	private boolean statDirty;
-
-	private Header header;
-
-	private long lastCacheTime;
-
-	private final Repository db;
-
-	private Map<byte[], Entry> entries = new TreeMap<byte[], Entry>(new Comparator<byte[]>() {
-		public int compare(byte[] o1, byte[] o2) {
-			for (int i = 0; i < o1.length && i < o2.length; ++i) {
-				int c = (o1[i] & 0xff) - (o2[i] & 0xff);
-				if (c != 0)
-					return c;
-			}
-			if (o1.length < o2.length)
-				return -1;
-			else if (o1.length > o2.length)
-				return 1;
-			return 0;
-		}
-	});
-
-	/**
-	 * Construct a Git index representation.
-	 * @param db
-	 */
-	public GitIndex(Repository db) {
-		this.db = db;
-		this.cacheFile = db.getIndexFile();
-	}
-
-	/**
-	 * @return true if we have modified the index in memory since reading it from disk
-	 */
-	public boolean isChanged() {
-		return changed || statDirty;
-	}
-
-	/**
-	 * Reread index data from disk if the index file has been changed
-	 * @throws IOException
-	 */
-	public void rereadIfNecessary() throws IOException {
-		if (cacheFile.exists() && cacheFile.lastModified() != lastCacheTime) {
-			read();
-			db.fireEvent(new IndexChangedEvent());
-		}
-	}
-
-	/**
-	 * Add the content of a file to the index.
-	 *
-	 * @param wd workdir
-	 * @param f the file
-	 * @return a new or updated index entry for the path represented by f
-	 * @throws IOException
-	 */
-	public Entry add(File wd, File f) throws IOException {
-		byte[] key = makeKey(wd, f);
-		Entry e = entries.get(key);
-		if (e == null) {
-			e = new Entry(key, f, 0);
-			entries.put(key, e);
-		} else {
-			e.update(f);
-		}
-		return e;
-	}
-
-	/**
-	 * Add the content of a file to the index.
-	 *
-	 * @param wd
-	 *            workdir
-	 * @param f
-	 *            the file
-	 * @param content
-	 *            content of the file
-	 * @return a new or updated index entry for the path represented by f
-	 * @throws IOException
-	 */
-	public Entry add(File wd, File f, byte[] content) throws IOException {
-		byte[] key = makeKey(wd, f);
-		Entry e = entries.get(key);
-		if (e == null) {
-			e = new Entry(key, f, 0, content);
-			entries.put(key, e);
-		} else {
-			e.update(f, content);
-		}
-		return e;
-	}
-
-	/**
-	 * Remove a path from the index.
-	 *
-	 * @param wd
-	 *            workdir
-	 * @param f
-	 *            the file whose path shall be removed.
-	 * @return true if such a path was found (and thus removed)
-	 * @throws IOException
-	 */
-	public boolean remove(File wd, File f) throws IOException {
-		byte[] key = makeKey(wd, f);
-		return entries.remove(key) != null;
-	}
-
-	/**
-	 * Read the cache file into memory.
-	 *
-	 * @throws IOException
-	 */
-	public void read() throws IOException {
-		changed = false;
-		statDirty = false;
-		if (!cacheFile.exists()) {
-			header = null;
-			entries.clear();
-			lastCacheTime = 0;
-			return;
-		}
-		cache = new RandomAccessFile(cacheFile, "r");
-		try {
-			FileChannel channel = cache.getChannel();
-			ByteBuffer buffer = ByteBuffer.allocateDirect((int) cacheFile.length());
-			buffer.order(ByteOrder.BIG_ENDIAN);
-			int j = channel.read(buffer);
-			if (j != buffer.capacity())
-				throw new IOException(MessageFormat.format(JGitText.get().couldNotReadIndexInOneGo
-						, j, buffer.capacity()));
-			buffer.flip();
-			header = new Header(buffer);
-			entries.clear();
-			for (int i = 0; i < header.entries; ++i) {
-				Entry entry = new Entry(buffer);
-				final GitIndex.Entry existing = entries.get(entry.name);
-				entries.put(entry.name, entry);
-				if (existing != null) {
-					entry.stages |= existing.stages;
-				}
-			}
-			lastCacheTime = cacheFile.lastModified();
-		} finally {
-			cache.close();
-		}
-	}
-
-	/**
-	 * Write content of index to disk.
-	 *
-	 * @throws IOException
-	 */
-	public void write() throws IOException {
-		checkWriteOk();
-		File tmpIndex = new File(cacheFile.getAbsoluteFile() + ".tmp");
-		File lock = new File(cacheFile.getAbsoluteFile() + ".lock");
-		if (!lock.createNewFile())
-			throw new IOException(JGitText.get().indexFileIsInUse);
-		try {
-			FileOutputStream fileOutputStream = new FileOutputStream(tmpIndex);
-			FileChannel fc = fileOutputStream.getChannel();
-			ByteBuffer buf = ByteBuffer.allocate(4096);
-			MessageDigest newMessageDigest = Constants.newMessageDigest();
-			header = new Header(entries);
-			header.write(buf);
-			buf.flip();
-			newMessageDigest
-					.update(buf.array(), buf.arrayOffset(), buf.limit());
-			fc.write(buf);
-			buf.flip();
-			buf.clear();
-			for (Iterator i = entries.values().iterator(); i.hasNext();) {
-				Entry e = (Entry) i.next();
-				e.write(buf);
-				buf.flip();
-				newMessageDigest.update(buf.array(), buf.arrayOffset(), buf
-						.limit());
-				fc.write(buf);
-				buf.flip();
-				buf.clear();
-			}
-			buf.put(newMessageDigest.digest());
-			buf.flip();
-			fc.write(buf);
-			fc.close();
-			fileOutputStream.close();
-			if (cacheFile.exists()) {
-				if (db.getFS().retryFailedLockFileCommit()) {
-					// file deletion fails on windows if another
-					// thread is reading the file concurrently
-					// So let's try 10 times...
-					boolean deleted = false;
-					for (int i = 0; i < 10; i++) {
-						if (cacheFile.delete()) {
-							deleted = true;
-							break;
-						}
-						try {
-							Thread.sleep(100);
-						} catch (InterruptedException e) {
-							// ignore
-						}
-					}
-					if (!deleted)
-						throw new IOException(
-								JGitText.get().couldNotRenameDeleteOldIndex);
-				} else {
-					if (!cacheFile.delete())
-						throw new IOException(
-								JGitText.get().couldNotRenameDeleteOldIndex);
-				}
-			}
-			if (!tmpIndex.renameTo(cacheFile))
-				throw new IOException(
-						JGitText.get().couldNotRenameTemporaryIndexFileToIndex);
-			changed = false;
-			statDirty = false;
-			lastCacheTime = cacheFile.lastModified();
-			db.fireEvent(new IndexChangedEvent());
-		} finally {
-			if (!lock.delete())
-				throw new IOException(
-						JGitText.get().couldNotDeleteLockFileShouldNotHappen);
-			if (tmpIndex.exists() && !tmpIndex.delete())
-				throw new IOException(
-						JGitText.get().couldNotDeleteTemporaryIndexFileShouldNotHappen);
-		}
-	}
-
-	private void checkWriteOk() throws IOException {
-		for (Iterator i = entries.values().iterator(); i.hasNext();) {
-			Entry e = (Entry) i.next();
-			if (e.getStage() != 0) {
-				throw new NotSupportedException(JGitText.get().cannotWorkWithOtherStagesThanZeroRightNow);
-			}
-		}
-	}
-
-	private boolean File_canExecute(File f){
-		return db.getFS().canExecute(f);
-	}
-
-	private boolean File_setExecute(File f, boolean value) {
-		return db.getFS().setExecute(f, value);
-	}
-
-	private boolean File_hasExecute() {
-		return db.getFS().supportsExecute();
-	}
-
-	static byte[] makeKey(File wd, File f) {
-		if (!f.getPath().startsWith(wd.getPath()))
-			throw new Error(JGitText.get().pathIsNotInWorkingDir);
-		String relName = Repository.stripWorkDir(wd, f);
-		return Constants.encode(relName);
-	}
-
-	Boolean filemode;
-	private boolean config_filemode() {
-		// temporary til we can actually set parameters. We need to be able
-		// to change this for testing.
-		if (filemode != null)
-			return filemode.booleanValue();
-		Config config = db.getConfig();
-		filemode = Boolean.valueOf(config.getBoolean("core", null, "filemode", true));
-		return filemode.booleanValue();
-	}
-
-	/**
-	 * An index entry
-	 *
-	 * @deprecated Use {@link org.eclipse.jgit.dircache.DirCacheEntry}.
-	 */
-	@Deprecated
-	public class Entry {
-		private long ctime;
-
-		private long mtime;
-
-		private int dev;
-
-		private int ino;
-
-		private int mode;
-
-		private int uid;
-
-		private int gid;
-
-		private int size;
-
-		private ObjectId sha1;
-
-		private short flags;
-
-		private byte[] name;
-
-		private int stages;
-
-		Entry(byte[] key, File f, int stage)
-				throws IOException {
-			ctime = f.lastModified() * 1000000L;
-			mtime = ctime; // we use same here
-			dev = -1;
-			ino = -1;
-			if (config_filemode() && File_canExecute(f))
-				mode = FileMode.EXECUTABLE_FILE.getBits();
-			else
-				mode = FileMode.REGULAR_FILE.getBits();
-			uid = -1;
-			gid = -1;
-			size = (int) f.length();
-			ObjectInserter inserter = db.newObjectInserter();
-			try {
-				InputStream in = new FileInputStream(f);
-				try {
-					sha1 = inserter.insert(Constants.OBJ_BLOB, f.length(), in);
-				} finally {
-					in.close();
-				}
-				inserter.flush();
-			} finally {
-				inserter.release();
-			}
-			name = key;
-			flags = (short) ((stage << 12) | name.length); // TODO: fix flags
-			stages = (1 >> getStage());
-		}
-
-		Entry(byte[] key, File f, int stage, byte[] newContent)
-				throws IOException {
-			ctime = f.lastModified() * 1000000L;
-			mtime = ctime; // we use same here
-			dev = -1;
-			ino = -1;
-			if (config_filemode() && File_canExecute(f))
-				mode = FileMode.EXECUTABLE_FILE.getBits();
-			else
-				mode = FileMode.REGULAR_FILE.getBits();
-			uid = -1;
-			gid = -1;
-			size = newContent.length;
-			ObjectInserter inserter = db.newObjectInserter();
-			try {
-				InputStream in = new FileInputStream(f);
-				try {
-					sha1 = inserter.insert(Constants.OBJ_BLOB, newContent);
-				} finally {
-					in.close();
-				}
-				inserter.flush();
-			} finally {
-				inserter.release();
-			}
-			name = key;
-			flags = (short) ((stage << 12) | name.length); // TODO: fix flags
-			stages = (1 >> getStage());
-		}
-
-		Entry(TreeEntry f, int stage) {
-			ctime = -1; // hmm
-			mtime = -1;
-			dev = -1;
-			ino = -1;
-			mode = f.getMode().getBits();
-			uid = -1;
-			gid = -1;
-			try {
-				size = (int) db.open(f.getId(), Constants.OBJ_BLOB).getSize();
-			} catch (IOException e) {
-				e.printStackTrace();
-				size = -1;
-			}
-			sha1 = f.getId();
-			name = Constants.encode(f.getFullName());
-			flags = (short) ((stage << 12) | name.length); // TODO: fix flags
-			stages = (1 >> getStage());
-		}
-
-		Entry(ByteBuffer b) {
-			int startposition = b.position();
-			ctime = b.getInt() * 1000000000L + (b.getInt() % 1000000000L);
-			mtime = b.getInt() * 1000000000L + (b.getInt() % 1000000000L);
-			dev = b.getInt();
-			ino = b.getInt();
-			mode = b.getInt();
-			uid = b.getInt();
-			gid = b.getInt();
-			size = b.getInt();
-			byte[] sha1bytes = new byte[Constants.OBJECT_ID_LENGTH];
-			b.get(sha1bytes);
-			sha1 = ObjectId.fromRaw(sha1bytes);
-			flags = b.getShort();
-			stages = (1 << getStage());
-			name = new byte[flags & 0xFFF];
-			b.get(name);
-			b
-					.position(startposition
-							+ ((8 + 8 + 4 + 4 + 4 + 4 + 4 + 4 + 20 + 2
-									+ name.length + 8) & ~7));
-		}
-
-		/**
-		 * Update this index entry with stat and SHA-1 information if it looks
-		 * like the file has been modified in the workdir.
-		 *
-		 * @param f
-		 *            file in work dir
-		 * @return true if a change occurred
-		 * @throws IOException
-		 */
-		public boolean update(File f) throws IOException {
-			long lm = f.lastModified() * 1000000L;
-			boolean modified = mtime != lm;
-			mtime = lm;
-			if (size != f.length())
-				modified = true;
-			if (config_filemode()) {
-				if (File_canExecute(f) != FileMode.EXECUTABLE_FILE.equals(mode)) {
-					mode = FileMode.EXECUTABLE_FILE.getBits();
-					modified = true;
-				}
-			}
-			if (modified) {
-				size = (int) f.length();
-				ObjectInserter oi = db.newObjectInserter();
-				try {
-					InputStream in = new FileInputStream(f);
-					try {
-						ObjectId newsha1 = oi.insert(Constants.OBJ_BLOB, f
-								.length(), in);
-						oi.flush();
-						if (!newsha1.equals(sha1))
-							modified = true;
-						sha1 = newsha1;
-					} finally {
-						in.close();
-					}
-				} finally {
-					oi.release();
-				}
-			}
-			return modified;
-		}
-
-		/**
-		 * Update this index entry with stat and SHA-1 information if it looks
-		 * like the file has been modified in the workdir.
-		 *
-		 * @param f
-		 *            file in work dir
-		 * @param newContent
-		 *            the new content of the file
-		 * @return true if a change occurred
-		 * @throws IOException
-		 */
-		public boolean update(File f, byte[] newContent) throws IOException {
-			boolean modified = false;
-			size = newContent.length;
-			ObjectInserter oi = db.newObjectInserter();
-			try {
-				ObjectId newsha1 = oi.insert(Constants.OBJ_BLOB, newContent);
-				oi.flush();
-				if (!newsha1.equals(sha1))
-					modified = true;
-				sha1 = newsha1;
-			} finally {
-				oi.release();
-			}
-			return modified;
-		}
-
-		void write(ByteBuffer buf) {
-			int startposition = buf.position();
-			buf.putInt((int) (ctime / 1000000000L));
-			buf.putInt((int) (ctime % 1000000000L));
-			buf.putInt((int) (mtime / 1000000000L));
-			buf.putInt((int) (mtime % 1000000000L));
-			buf.putInt(dev);
-			buf.putInt(ino);
-			buf.putInt(mode);
-			buf.putInt(uid);
-			buf.putInt(gid);
-			buf.putInt(size);
-			sha1.copyRawTo(buf);
-			buf.putShort(flags);
-			buf.put(name);
-			int end = startposition
-					+ ((8 + 8 + 4 + 4 + 4 + 4 + 4 + 4 + 20 + 2 + name.length + 8) & ~7);
-			int remain = end - buf.position();
-			while (remain-- > 0)
-				buf.put((byte) 0);
-		}
-
-		/**
-		 * Check if an entry's content is different from the cache,
-		 *
-		 * File status information is used and 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 wd working directory to compare content with
-		 * @return true if content is most likely different.
-		 */
-		public boolean isModified(File wd) {
-			return isModified(wd, false);
-		}
-
-		/**
-		 * Check if an entry's content is different from the cache,
-		 *
-		 * File status information is used and 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 wd working directory to compare content with
-		 * @param forceContentCheck True if the actual file content
-		 * should be checked if modification time differs.
-		 *
-		 * @return true if content is most likely different.
-		 */
-		public boolean isModified(File wd, boolean forceContentCheck) {
-
-			if (isAssumedValid())
-				return false;
-
-			if (isUpdateNeeded())
-				return true;
-
-			File file = getFile(wd);
-			long length = file.length();
-			if (length == 0) {
-				if (!file.exists())
-					return true;
-			}
-			if (length != size)
-				return true;
-
-			// JDK1.6 has file.canExecute
-			// if (file.canExecute() != FileMode.EXECUTABLE_FILE.equals(mode))
-			// return true;
-			final int exebits = FileMode.EXECUTABLE_FILE.getBits()
-					^ FileMode.REGULAR_FILE.getBits();
-
-			if (config_filemode() && FileMode.EXECUTABLE_FILE.equals(mode)) {
-				if (!File_canExecute(file)&& File_hasExecute())
-					return true;
-			} else {
-				if (FileMode.REGULAR_FILE.equals(mode&~exebits)) {
-					if (!file.isFile())
-						return true;
-					if (config_filemode() && File_canExecute(file) && File_hasExecute())
-						return true;
-				} else {
-					if (FileMode.SYMLINK.equals(mode)) {
-						return true;
-					} else {
-						if (FileMode.TREE.equals(mode)) {
-							if (!file.isDirectory())
-								return true;
-						} else {
-							System.out.println(MessageFormat.format(JGitText.get().doesNotHandleMode
-									, mode, file));
-							return true;
-						}
-					}
-				}
-			}
-
-			// 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 prevision.
-			long javamtime = mtime / 1000000L;
-			long lastm = file.lastModified();
-			if (javamtime % 1000 == 0)
-				lastm = lastm - lastm % 1000;
-			if (lastm != javamtime) {
-				if (!forceContentCheck)
-					return true;
-
-				try {
-					InputStream is = new FileInputStream(file);
-					try {
-						ObjectId newId = new ObjectInserter.Formatter().idFor(
-								Constants.OBJ_BLOB, file.length(), is);
-						return !newId.equals(sha1);
-					} catch (IOException e) {
-						e.printStackTrace();
-					} finally {
-						try {
-							is.close();
-						} catch (IOException e) {
-							// can't happen, but if it does we ignore it
-							e.printStackTrace();
-						}
-					}
-				} catch (FileNotFoundException e) {
-					// should not happen because we already checked this
-					e.printStackTrace();
-					throw new Error(e);
-				}
-			}
-			return false;
-		}
-
-		/**
-		 * Returns the stages in which the entry's file is recorded in the index.
-		 * The stages are bit-encoded: bit N is set if the file is present
-		 * in stage N. In particular, the N-th bit will be set if this entry
-		 * itself is in stage N (see getStage()).
-		 *
-		 * @return flags denoting stages
-		 * @see #getStage()
-		 */
-		public int getStages() {
-			return stages;
-		}
-
-		// for testing
-		void forceRecheck() {
-			mtime = -1;
-		}
-
-		private File getFile(File wd) {
-			return new File(wd, getName());
-		}
-
-		public String toString() {
-			return getName() + "/SHA-1(" + sha1.name() + ")/M:"
-					+ new Date(ctime / 1000000L) + "/C:"
-					+ new Date(mtime / 1000000L) + "/d" + dev + "/i" + ino
-					+ "/m" + Integer.toString(mode, 8) + "/u" + uid + "/g"
-					+ gid + "/s" + size + "/f" + flags + "/@" + getStage();
-		}
-
-		/**
-		 * @return path name for this entry
-		 */
-		public String getName() {
-			return RawParseUtils.decode(name);
-		}
-
-		/**
-		 * @return path name for this entry as byte array, hopefully UTF-8 encoded
-		 */
-		public byte[] getNameUTF8() {
-			return name;
-		}
-
-		/**
-		 * @return SHA-1 of the entry managed by this index
-		 */
-		public ObjectId getObjectId() {
-			return sha1;
-		}
-
-		/**
-		 * @return the stage this entry is in
-		 */
-		public int getStage() {
-			return (flags & 0x3000) >> 12;
-		}
-
-		/**
-		 * @return size of disk object
-		 */
-		public int getSize() {
-			return size;
-		}
-
-		/**
-		 * @return true if this entry shall be assumed valid
-		 */
-		public boolean isAssumedValid() {
-			return (flags & 0x8000) != 0;
-		}
-
-		/**
-		 * @return true if this entry should be checked for changes
-		 */
-		public boolean isUpdateNeeded() {
-			return (flags & 0x4000) != 0;
-		}
-
-		/**
-		 * Set whether to always assume this entry valid
-		 *
-		 * @param assumeValid true to ignore changes
-		 */
-		public void setAssumeValid(boolean assumeValid) {
-			if (assumeValid)
-				flags |= 0x8000;
-			else
-				flags &= ~0x8000;
-		}
-
-		/**
-		 * Set whether this entry must be checked
-		 *
-		 * @param updateNeeded
-		 */
-		public void setUpdateNeeded(boolean updateNeeded) {
-			if (updateNeeded)
-				flags |= 0x4000;
-			else
-				flags &= ~0x4000;
-		}
-
-		/**
-		 * Return raw file mode bits. See {@link FileMode}
-		 * @return file mode bits
-		 */
-		public int getModeBits() {
-			return mode;
-		}
-	}
-
-	static class Header {
-		private int signature;
-
-		private int version;
-
-		int entries;
-
-		Header(ByteBuffer map) throws CorruptObjectException {
-			read(map);
-		}
-
-		private void read(ByteBuffer buf) throws CorruptObjectException {
-			signature = buf.getInt();
-			version = buf.getInt();
-			entries = buf.getInt();
-			if (signature != 0x44495243)
-				throw new CorruptObjectException(MessageFormat.format(
-						JGitText.get().indexSignatureIsInvalid, signature));
-			if (version != 2)
-				throw new CorruptObjectException(MessageFormat.format(
-						JGitText.get().unknownIndexVersionOrCorruptIndex, version));
-		}
-
-		void write(ByteBuffer buf) {
-			buf.order(ByteOrder.BIG_ENDIAN);
-			buf.putInt(signature);
-			buf.putInt(version);
-			buf.putInt(entries);
-		}
-
-		Header(Map entryset) {
-			signature = 0x44495243;
-			version = 2;
-			entries = entryset.size();
-		}
-	}
-
-	/**
-	 * Read a Tree recursively into the index
-	 *
-	 * @param t The tree to read
-	 *
-	 * @throws IOException
-	 */
-	public void readTree(Tree t) throws IOException {
-		entries.clear();
-		readTree("", t);
-	}
-
-	void readTree(String prefix, Tree t) throws IOException {
-		TreeEntry[] members = t.members();
-		for (int i = 0; i < members.length; ++i) {
-			TreeEntry te = members[i];
-			String name;
-			if (prefix.length() > 0)
-				name = prefix + "/" + te.getName();
-			else
-				name = te.getName();
-			if (te instanceof Tree) {
-				readTree(name, (Tree) te);
-			} else {
-				Entry e = new Entry(te, 0);
-				entries.put(Constants.encode(name), e);
-			}
-		}
-	}
-
-	/**
-	 * Add tree entry to index
-	 * @param te tree entry
-	 * @return new or modified index entry
-	 * @throws IOException
-	 */
-	public Entry addEntry(TreeEntry te) throws IOException {
-		byte[] key = Constants.encode(te.getFullName());
-		Entry e = new Entry(te, 0);
-		entries.put(key, e);
-		return e;
-	}
-
-	/**
-	 * Check out content of the content represented by the index
-	 *
-	 * @param wd
-	 *            workdir
-	 * @throws IOException
-	 */
-	public void checkout(File wd) throws IOException {
-		for (Entry e : entries.values()) {
-			if (e.getStage() != 0)
-				continue;
-			checkoutEntry(wd, e);
-		}
-	}
-
-	/**
-	 * Check out content of the specified index entry
-	 *
-	 * @param wd workdir
-	 * @param e index entry
-	 * @throws IOException
-	 */
-	public void checkoutEntry(File wd, Entry e) throws IOException {
-		ObjectLoader ol = db.open(e.sha1, Constants.OBJ_BLOB);
-		File file = new File(wd, e.getName());
-		file.delete();
-		FileUtils.mkdirs(file.getParentFile(), true);
-		FileOutputStream dst = new FileOutputStream(file);
-		try {
-			ol.copyTo(dst);
-		} finally {
-			dst.close();
-		}
-		if (config_filemode() && File_hasExecute()) {
-			if (FileMode.EXECUTABLE_FILE.equals(e.mode)) {
-				if (!File_canExecute(file))
-					File_setExecute(file, true);
-			} else {
-				if (File_canExecute(file))
-					File_setExecute(file, false);
-			}
-		}
-		e.mtime = file.lastModified() * 1000000L;
-		e.ctime = e.mtime;
-	}
-
-	/**
-	 * Construct and write tree out of index.
-	 *
-	 * @return SHA-1 of the constructed tree
-	 *
-	 * @throws IOException
-	 */
-	public ObjectId writeTree() throws IOException {
-		checkWriteOk();
-		ObjectInserter inserter = db.newObjectInserter();
-			try {
-			Tree current = new Tree(db);
-			Stack<Tree> trees = new Stack<Tree>();
-			trees.push(current);
-			String[] prevName = new String[0];
-			for (Entry e : entries.values()) {
-				if (e.getStage() != 0)
-					continue;
-				String[] newName = splitDirPath(e.getName());
-				int c = longestCommonPath(prevName, newName);
-				while (c < trees.size() - 1) {
-					current.setId(inserter.insert(Constants.OBJ_TREE, current.format()));
-					trees.pop();
-					current = trees.isEmpty() ? null : (Tree) trees.peek();
-				}
-				while (trees.size() < newName.length) {
-					if (!current.existsTree(newName[trees.size() - 1])) {
-						current = new Tree(current, Constants.encode(newName[trees.size() - 1]));
-						current.getParent().addEntry(current);
-						trees.push(current);
-					} else {
-						current = (Tree) current.findTreeMember(newName[trees
-								.size() - 1]);
-						trees.push(current);
-					}
-				}
-				FileTreeEntry ne = new FileTreeEntry(current, e.sha1,
-						Constants.encode(newName[newName.length - 1]),
-						(e.mode & FileMode.EXECUTABLE_FILE.getBits()) == FileMode.EXECUTABLE_FILE.getBits());
-				current.addEntry(ne);
-			}
-			while (!trees.isEmpty()) {
-				current.setId(inserter.insert(Constants.OBJ_TREE, current.format()));
-				trees.pop();
-				if (!trees.isEmpty())
-					current = trees.peek();
-			}
-			inserter.flush();
-			return current.getId();
-		} finally {
-			inserter.release();
-		}
-	}
-
-	String[] splitDirPath(String name) {
-		String[] tmp = new String[name.length() / 2 + 1];
-		int p0 = -1;
-		int p1;
-		int c = 0;
-		while ((p1 = name.indexOf('/', p0 + 1)) != -1) {
-			tmp[c++] = name.substring(p0 + 1, p1);
-			p0 = p1;
-		}
-		tmp[c++] = name.substring(p0 + 1);
-		String[] ret = new String[c];
-		for (int i = 0; i < c; ++i) {
-			ret[i] = tmp[i];
-		}
-		return ret;
-	}
-
-	int longestCommonPath(String[] a, String[] b) {
-		int i;
-		for (i = 0; i < a.length && i < b.length; ++i)
-			if (!a[i].equals(b[i]))
-				return i;
-		return i;
-	}
-
-	/**
-	 * Return the members of the index sorted by the unsigned byte
-	 * values of the path names.
-	 *
-	 * Small beware: Unaccounted for are unmerged entries. You may want
-	 * to abort if members with stage != 0 are found if you are doing
-	 * any updating operations. All stages will be found after one another
-	 * here later. Currently only one stage per name is returned.
-	 *
-	 * @return The index entries sorted
-	 */
-	public Entry[] getMembers() {
-		return entries.values().toArray(new Entry[entries.size()]);
-	}
-
-	/**
-	 * Look up an entry with the specified path.
-	 *
-	 * @param path
-	 * @return index entry for the path or null if not in index.
-	 * @throws UnsupportedEncodingException
-	 */
-	public Entry getEntry(String path) throws UnsupportedEncodingException {
-		return entries.get(Repository.gitInternalSlash(Constants.encode(path)));
-	}
-
-	/**
-	 * @return The repository holding this index.
-	 */
-	public Repository getRepository() {
-		return db;
-	}
-}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
index b1c4c78e65..f6e0b13a9a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
@@ -109,8 +109,6 @@ public abstract class Repository {
 	/** File abstraction used to resolve paths. */
 	private final FS fs;
 
-	private GitIndex index;
-
 	private final ListenerList myListeners = new ListenerList();
 
 	/** If not bare, the top level directory of the working files. */
@@ -809,28 +807,6 @@ public abstract class Repository {
 	}
 
 	/**
-	 * @return a representation of the index associated with this
-	 *         {@link Repository}
-	 * @throws IOException
-	 *             if the index can not be read
-	 * @throws NoWorkTreeException
-	 *             if this is bare, which implies it has no working directory.
-	 *             See {@link #isBare()}.
-	 * @deprecated Use {@link #readDirCache()} instead
-	 */
-	public GitIndex getIndex() throws IOException, NoWorkTreeException {
-		if (isBare())
-			throw new NoWorkTreeException();
-		if (index == null) {
-			index = new GitIndex(this);
-			index.read();
-		} else {
-			index.rereadIfNecessary();
-		}
-		return index;
-	}
-
-	/**
 	 * @return the index file location
 	 * @throws NoWorkTreeException
 	 *             if this is bare, which implies it has no working directory.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/TreeEntry.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/TreeEntry.java
index 6f47db675e..a1ffa68056 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/TreeEntry.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/TreeEntry.java
@@ -46,7 +46,6 @@ package org.eclipse.jgit.lib;
 
 import java.io.IOException;
 
-import org.eclipse.jgit.lib.GitIndex.Entry;
 import org.eclipse.jgit.util.RawParseUtils;
 
 /**
@@ -237,20 +236,6 @@ public abstract class TreeEntry implements Comparable {
 	}
 
 	/**
-	 * Helper for accessing tree/blob/index methods.
-	 *
-	 * @param i
-	 * @return '/' for Tree entries and NUL for non-treeish objects
-	 * @deprecated since it depends on deprecated GitIndex, and internal
-	 */
-	final public static int lastChar(Entry i) {
-		// FIXME, gitlink etc. Currently Trees cannot appear in the
-		// index so '\0' is always returned, except maybe for submodules
-		// which we do not support yet.
-		return FileMode.TREE.equals(i.getModeBits()) ? '/' : '\0';
-	}
-
-	/**
 	 * @return mode (type of object)
 	 */
 	public abstract FileMode getMode();