/*
    * Copyright (C) 2010, Stefan Lay <stefan.lay@sap.com>
    * Copyright (C) 2010, Christian Halstrick <christian.halstrick@sap.com>
    * 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.api;
  
  import static org.eclipse.jgit.util.FileUtils.RECURSIVE;
  import static org.junit.Assert.assertEquals;
  import static org.junit.Assert.assertTrue;
  import static org.junit.Assert.fail;
  
  import java.io.File;
  import java.io.FileInputStream;
  import java.io.IOException;
  import java.io.PrintWriter;
  import java.util.Set;
  
  import org.eclipse.jgit.api.errors.FilterFailedException;
  import org.eclipse.jgit.api.errors.GitAPIException;
  import org.eclipse.jgit.api.errors.NoFilepatternException;
  import org.eclipse.jgit.attributes.FilterCommandRegistry;
  import org.eclipse.jgit.dircache.DirCache;
  import org.eclipse.jgit.dircache.DirCacheBuilder;
  import org.eclipse.jgit.dircache.DirCacheEntry;
  import org.eclipse.jgit.junit.JGitTestUtil;
  import org.eclipse.jgit.junit.RepositoryTestCase;
  import org.eclipse.jgit.lfs.CleanFilter;
  import org.eclipse.jgit.lfs.SmudgeFilter;
  import org.eclipse.jgit.lib.ConfigConstants;
  import org.eclipse.jgit.lib.Constants;
  import org.eclipse.jgit.lib.FileMode;
  import org.eclipse.jgit.lib.ObjectId;
  import org.eclipse.jgit.lib.ObjectInserter;
  import org.eclipse.jgit.lib.Repository;
  import org.eclipse.jgit.lib.StoredConfig;
  import org.eclipse.jgit.revwalk.RevCommit;
  import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
  import org.eclipse.jgit.treewalk.TreeWalk;
  import org.eclipse.jgit.treewalk.WorkingTreeOptions;
  import org.eclipse.jgit.util.FS;
  import org.eclipse.jgit.util.FileUtils;
  import org.junit.Test;
  import org.junit.experimental.theories.DataPoints;
  import org.junit.experimental.theories.Theories;
  import org.junit.experimental.theories.Theory;
  import org.junit.runner.RunWith;
  
  @RunWith(Theories.class)
  public class AddCommandTest extends RepositoryTestCase {
  	@DataPoints
  	public static boolean[] sleepBeforeAddOptions = { true, false };
  
  
  	@Override
  	public void setUp() throws Exception {
  		CleanFilter.register();
  		SmudgeFilter.register();
  		super.setUp();
  	}
  
 	@Test
 	public void testAddNothing() throws GitAPIException {
 		try (Git git = new Git(db)) {
 			git.add().call();
 			fail("Expected IllegalArgumentException");
 		} catch (NoFilepatternException e) {
 			// expected
 		}
 
 	}
 
 	@Test
 	public void testAddNonExistingSingleFile() throws GitAPIException {
 		try (Git git = new Git(db)) {
 			DirCache dc = git.add().addFilepattern("a.txt").call();
 			assertEquals(0, dc.getEntryCount());
 		}
 	}
 
 	@Test
 	public void testAddExistingSingleFile() throws IOException, GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("content");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern("a.txt").call();
 
 			assertEquals(
 					"[a.txt, mode:100644, content:content]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testCleanFilter() throws IOException, GitAPIException {
 		writeTrashFile(".gitattributes", "*.txt filter=tstFilter");
 		writeTrashFile("src/a.tmp", "foo");
 		// Caution: we need a trailing '\n' since sed on mac always appends
 		// linefeeds if missing
 		writeTrashFile("src/a.txt", "foo\n");
 		File script = writeTempFile("sed s/o/e/g");
 
 		try (Git git = new Git(db)) {
 			StoredConfig config = git.getRepository().getConfig();
 			config.setString("filter", "tstFilter", "clean",
 					"sh " + slashify(script.getPath()));
 			config.save();
 
 			git.add().addFilepattern("src/a.txt").addFilepattern("src/a.tmp")
 					.call();
 
 			assertEquals(
 					"[src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:fee\n]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Theory
 	public void testBuiltinFilters(boolean sleepBeforeAdd)
 			throws IOException,
 			GitAPIException, InterruptedException {
 		writeTrashFile(".gitattributes", "*.txt filter=lfs");
 		writeTrashFile("src/a.tmp", "foo");
 		// Caution: we need a trailing '\n' since sed on mac always appends
 		// linefeeds if missing
 		File script = writeTempFile("sed s/o/e/g");
 		File f = writeTrashFile("src/a.txt", "foo\n");
 
 		try (Git git = new Git(db)) {
 			if (!sleepBeforeAdd) {
 				fsTick(f);
 			}
 			git.add().addFilepattern(".gitattributes").call();
 			StoredConfig config = git.getRepository().getConfig();
 			config.setString("filter", "lfs", "clean",
 					"sh " + slashify(script.getPath()));
 			config.setString("filter", "lfs", "smudge",
 					"sh " + slashify(script.getPath()));
 			config.setBoolean("filter", "lfs", "useJGitBuiltin", true);
 			config.save();
 
 			if (!sleepBeforeAdd) {
 				fsTick(f);
 			}
 			git.add().addFilepattern("src/a.txt").addFilepattern("src/a.tmp")
 					.addFilepattern(".gitattributes").call();
 
 			assertEquals(
 					"[.gitattributes, mode:100644, content:*.txt filter=lfs][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:version https://git-lfs.github.com/spec/v1\noid sha256:b5bb9d8014a0f9b1d61e21e796d78dccdf1352f23cd32812f4850b878ae4944c\nsize 4\n]",
 					indexState(CONTENT));
 
 			RevCommit c1 = git.commit().setMessage("c1").call();
 			assertTrue(git.status().call().isClean());
 			f = writeTrashFile("src/a.txt", "foobar\n");
 			if (!sleepBeforeAdd) {
 				fsTick(f);
 			}
 			git.add().addFilepattern("src/a.txt").call();
 			git.commit().setMessage("c2").call();
 			assertTrue(git.status().call().isClean());
 			assertEquals(
 					"[.gitattributes, mode:100644, content:*.txt filter=lfs][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:version https://git-lfs.github.com/spec/v1\noid sha256:aec070645fe53ee3b3763059376134f058cc337247c978add178b6ccdfb0019f\nsize 7\n]",
 					indexState(CONTENT));
 			assertEquals("foobar\n", read("src/a.txt"));
 			git.checkout().setName(c1.getName()).call();
 			assertEquals(
 					"[.gitattributes, mode:100644, content:*.txt filter=lfs][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:version https://git-lfs.github.com/spec/v1\noid sha256:b5bb9d8014a0f9b1d61e21e796d78dccdf1352f23cd32812f4850b878ae4944c\nsize 4\n]",
 					indexState(CONTENT));
 			assertEquals(
 					"foo\n", read("src/a.txt"));
 		}
 	}
 
 	@Theory
 	public void testBuiltinCleanFilter(boolean sleepBeforeAdd)
 			throws IOException, GitAPIException, InterruptedException {
 		writeTrashFile(".gitattributes", "*.txt filter=lfs");
 		writeTrashFile("src/a.tmp", "foo");
 		// Caution: we need a trailing '\n' since sed on mac always appends
 		// linefeeds if missing
 		File script = writeTempFile("sed s/o/e/g");
 		File f = writeTrashFile("src/a.txt", "foo\n");
 
 		// unregister the smudge filter. Only clean filter should be builtin
 		FilterCommandRegistry.unregister(
 				org.eclipse.jgit.lib.Constants.BUILTIN_FILTER_PREFIX
 						+ "lfs/smudge");
 
 		try (Git git = new Git(db)) {
 			if (!sleepBeforeAdd) {
 				fsTick(f);
 			}
 			git.add().addFilepattern(".gitattributes").call();
 			StoredConfig config = git.getRepository().getConfig();
 			config.setString("filter", "lfs", "clean",
 					"sh " + slashify(script.getPath()));
 			config.setString("filter", "lfs", "smudge",
 					"sh " + slashify(script.getPath()));
 			config.setBoolean("filter", "lfs", "useJGitBuiltin", true);
 			config.save();
 
 			if (!sleepBeforeAdd) {
 				fsTick(f);
 			}
 			git.add().addFilepattern("src/a.txt").addFilepattern("src/a.tmp")
 					.addFilepattern(".gitattributes").call();
 
 			assertEquals(
 					"[.gitattributes, mode:100644, content:*.txt filter=lfs][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:version https://git-lfs.github.com/spec/v1\noid sha256:b5bb9d8014a0f9b1d61e21e796d78dccdf1352f23cd32812f4850b878ae4944c\nsize 4\n]",
 					indexState(CONTENT));
 
 			RevCommit c1 = git.commit().setMessage("c1").call();
 			assertTrue(git.status().call().isClean());
 			f = writeTrashFile("src/a.txt", "foobar\n");
 			if (!sleepBeforeAdd) {
 				fsTick(f);
 			}
 			git.add().addFilepattern("src/a.txt").call();
 			git.commit().setMessage("c2").call();
 			assertTrue(git.status().call().isClean());
 			assertEquals(
 					"[.gitattributes, mode:100644, content:*.txt filter=lfs][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:version https://git-lfs.github.com/spec/v1\noid sha256:aec070645fe53ee3b3763059376134f058cc337247c978add178b6ccdfb0019f\nsize 7\n]",
 					indexState(CONTENT));
 			assertEquals("foobar\n", read("src/a.txt"));
 			git.checkout().setName(c1.getName()).call();
 			assertEquals(
 					"[.gitattributes, mode:100644, content:*.txt filter=lfs][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:version https://git-lfs.github.com/spec/v1\noid sha256:b5bb9d8014a0f9b1d61e21e796d78dccdf1352f23cd32812f4850b878ae4944c\nsize 4\n]",
 					indexState(CONTENT));
 			// due to lfs clean filter but dummy smudge filter we expect strange
 			// content. The smudge filter converts from real content to pointer
 			// file content (starting with "version ") but the smudge filter
 			// replaces 'o' by 'e' which results in a text starting with
 			// "versien "
 			assertEquals(
 					"versien https://git-lfs.github.cem/spec/v1\neid sha256:b5bb9d8014a0f9b1d61e21e796d78dccdf1352f23cd32812f4850b878ae4944c\nsize 4\n",
 					read("src/a.txt"));
 		}
 	}
 
 	@Test
 	public void testAttributesWithTreeWalkFilter()
 			throws IOException, GitAPIException {
 		writeTrashFile(".gitattributes", "*.txt filter=lfs");
 		writeTrashFile("src/a.tmp", "foo");
 		writeTrashFile("src/a.txt", "foo\n");
 		File script = writeTempFile("sed s/o/e/g");
 
 		try (Git git = new Git(db)) {
 			StoredConfig config = git.getRepository().getConfig();
 			config.setString("filter", "lfs", "clean",
 					"sh " + slashify(script.getPath()));
 			config.save();
 
 			git.add().addFilepattern(".gitattributes").call();
 			git.commit().setMessage("attr").call();
 			git.add().addFilepattern("src/a.txt").addFilepattern("src/a.tmp")
 					.addFilepattern(".gitattributes").call();
 			git.commit().setMessage("c1").call();
 			assertTrue(git.status().call().isClean());
 		}
 	}
 
 	@Test
 	public void testCleanFilterEnvironment()
 			throws IOException, GitAPIException {
 		writeTrashFile(".gitattributes", "*.txt filter=tstFilter");
 		writeTrashFile("src/a.txt", "foo");
 		File script = writeTempFile("echo $GIT_DIR; echo 1 >xyz");
 
 		try (Git git = new Git(db)) {
 			StoredConfig config = git.getRepository().getConfig();
 			config.setString("filter", "tstFilter", "clean",
 					"sh " + slashify(script.getPath()));
 			config.save();
 			git.add().addFilepattern("src/a.txt").call();
 
 			String gitDir = db.getDirectory().getAbsolutePath();
 			assertEquals("[src/a.txt, mode:100644, content:" + gitDir
 					+ "\n]", indexState(CONTENT));
 			assertTrue(new File(db.getWorkTree(), "xyz").exists());
 		}
 	}
 
 	@Test
 	public void testMultipleCleanFilter() throws IOException, GitAPIException {
 		writeTrashFile(".gitattributes",
 				"*.txt filter=tstFilter\n*.tmp filter=tstFilter2");
 		// Caution: we need a trailing '\n' since sed on mac always appends
 		// linefeeds if missing
 		writeTrashFile("src/a.tmp", "foo\n");
 		writeTrashFile("src/a.txt", "foo\n");
 		File script = writeTempFile("sed s/o/e/g");
 		File script2 = writeTempFile("sed s/f/x/g");
 
 		try (Git git = new Git(db)) {
 			StoredConfig config = git.getRepository().getConfig();
 			config.setString("filter", "tstFilter", "clean",
 					"sh " + slashify(script.getPath()));
 			config.setString("filter", "tstFilter2", "clean",
 					"sh " + slashify(script2.getPath()));
 			config.save();
 
 			git.add().addFilepattern("src/a.txt").addFilepattern("src/a.tmp")
 					.call();
 
 			assertEquals(
 					"[src/a.tmp, mode:100644, content:xoo\n][src/a.txt, mode:100644, content:fee\n]",
 					indexState(CONTENT));
 
 			// TODO: multiple clean filters for one file???
 		}
 	}
 
 	/**
 	 * The path of an added file name contains ';' and afterwards malicious
 	 * commands. Make sure when calling filter commands to properly escape the
 	 * filenames
 	 *
 	 * @throws IOException
 	 * @throws GitAPIException
 	 */
 	@Test
 	public void testCommandInjection() throws IOException, GitAPIException {
 		// Caution: we need a trailing '\n' since sed on mac always appends
 		// linefeeds if missing
 		writeTrashFile("; echo virus", "foo\n");
 		File script = writeTempFile("sed s/o/e/g");
 
 		try (Git git = new Git(db)) {
 			StoredConfig config = git.getRepository().getConfig();
 			config.setString("filter", "tstFilter", "clean",
 					"sh " + slashify(script.getPath()) + " %f");
 			writeTrashFile(".gitattributes", "* filter=tstFilter");
 
 			git.add().addFilepattern("; echo virus").call();
 			// Without proper escaping the content would be "feovirus". The sed
 			// command and the "echo virus" would contribute to the content
 			assertEquals("[; echo virus, mode:100644, content:fee\n]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testBadCleanFilter() throws IOException, GitAPIException {
 		writeTrashFile("a.txt", "foo");
 		File script = writeTempFile("sedfoo s/o/e/g");
 
 		try (Git git = new Git(db)) {
 			StoredConfig config = git.getRepository().getConfig();
 			config.setString("filter", "tstFilter", "clean",
 					"sh " + script.getPath());
 			config.save();
 			writeTrashFile(".gitattributes", "*.txt filter=tstFilter");
 
 			try {
 				git.add().addFilepattern("a.txt").call();
 				fail("Didn't received the expected exception");
 			} catch (FilterFailedException e) {
 				assertEquals(127, e.getReturnCode());
 			}
 		}
 	}
 
 	@Test
 	public void testBadCleanFilter2() throws IOException, GitAPIException {
 		writeTrashFile("a.txt", "foo");
 		File script = writeTempFile("sed s/o/e/g");
 
 		try (Git git = new Git(db)) {
 			StoredConfig config = git.getRepository().getConfig();
 			config.setString("filter", "tstFilter", "clean",
 					"shfoo " + script.getPath());
 			config.save();
 			writeTrashFile(".gitattributes", "*.txt filter=tstFilter");
 
 			try {
 				git.add().addFilepattern("a.txt").call();
 				fail("Didn't received the expected exception");
 			} catch (FilterFailedException e) {
 				assertEquals(127, e.getReturnCode());
 			}
 		}
 	}
 
 	@Test
 	public void testCleanFilterReturning12() throws IOException,
 			GitAPIException {
 		writeTrashFile("a.txt", "foo");
 		File script = writeTempFile("exit 12");
 
 		try (Git git = new Git(db)) {
 			StoredConfig config = git.getRepository().getConfig();
 			config.setString("filter", "tstFilter", "clean",
 					"sh " + slashify(script.getPath()));
 			config.save();
 			writeTrashFile(".gitattributes", "*.txt filter=tstFilter");
 
 			try {
 				git.add().addFilepattern("a.txt").call();
 				fail("Didn't received the expected exception");
 			} catch (FilterFailedException e) {
 				assertEquals(12, e.getReturnCode());
 			}
 		}
 	}
 
 	@Test
 	public void testNotApplicableFilter() throws IOException, GitAPIException {
 		writeTrashFile("a.txt", "foo");
 		File script = writeTempFile("sed s/o/e/g");
 
 		try (Git git = new Git(db)) {
 			StoredConfig config = git.getRepository().getConfig();
 			config.setString("filter", "tstFilter", "something",
 					"sh " + script.getPath());
 			config.save();
 			writeTrashFile(".gitattributes", "*.txt filter=tstFilter");
 
 			git.add().addFilepattern("a.txt").call();
 
 			assertEquals("[a.txt, mode:100644, content:foo]",
 					indexState(CONTENT));
 		}
 	}
 
 	private File writeTempFile(String body) throws IOException {
 		File f = File.createTempFile("AddCommandTest_", "");
 		JGitTestUtil.write(f, body);
 		return f;
 	}
 
 	@Test
 	public void testAddExistingSingleSmallFileWithNewLine() throws IOException,
 			GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("row1\r\nrow2");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			db.getConfig().setString("core", null, "autocrlf", "false");
 			git.add().addFilepattern("a.txt").call();
 			assertEquals("[a.txt, mode:100644, content:row1\r\nrow2]",
 					indexState(CONTENT));
 			db.getConfig().setString("core", null, "autocrlf", "true");
 			git.add().addFilepattern("a.txt").call();
 			assertEquals("[a.txt, mode:100644, content:row1\nrow2]",
 					indexState(CONTENT));
 			db.getConfig().setString("core", null, "autocrlf", "input");
 			git.add().addFilepattern("a.txt").call();
 			assertEquals("[a.txt, mode:100644, content:row1\nrow2]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testAddExistingSingleMediumSizeFileWithNewLine()
 			throws IOException, GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		StringBuilder data = new StringBuilder();
 		for (int i = 0; i < 1000; ++i) {
 			data.append("row1\r\nrow2");
 		}
 		String crData = data.toString();
 		PrintWriter writer = new PrintWriter(file);
 		writer.print(crData);
 		writer.close();
 		String lfData = data.toString().replaceAll("\r", "");
 		try (Git git = new Git(db)) {
 			db.getConfig().setString("core", null, "autocrlf", "false");
 			git.add().addFilepattern("a.txt").call();
 			assertEquals("[a.txt, mode:100644, content:" + data + "]",
 					indexState(CONTENT));
 			db.getConfig().setString("core", null, "autocrlf", "true");
 			git.add().addFilepattern("a.txt").call();
 			assertEquals("[a.txt, mode:100644, content:" + lfData + "]",
 					indexState(CONTENT));
 			db.getConfig().setString("core", null, "autocrlf", "input");
 			git.add().addFilepattern("a.txt").call();
 			assertEquals("[a.txt, mode:100644, content:" + lfData + "]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testAddExistingSingleBinaryFile() throws IOException,
 			GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("row1\r\nrow2\u0000");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			db.getConfig().setString("core", null, "autocrlf", "false");
 			git.add().addFilepattern("a.txt").call();
 			assertEquals("[a.txt, mode:100644, content:row1\r\nrow2\u0000]",
 					indexState(CONTENT));
 			db.getConfig().setString("core", null, "autocrlf", "true");
 			git.add().addFilepattern("a.txt").call();
 			assertEquals("[a.txt, mode:100644, content:row1\r\nrow2\u0000]",
 					indexState(CONTENT));
 			db.getConfig().setString("core", null, "autocrlf", "input");
 			git.add().addFilepattern("a.txt").call();
 			assertEquals("[a.txt, mode:100644, content:row1\r\nrow2\u0000]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testAddExistingSingleFileInSubDir() throws IOException,
 			GitAPIException {
 		FileUtils.mkdir(new File(db.getWorkTree(), "sub"));
 		File file = new File(db.getWorkTree(), "sub/a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("content");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern("sub/a.txt").call();
 
 			assertEquals(
 					"[sub/a.txt, mode:100644, content:content]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testAddExistingSingleFileTwice() throws IOException,
 			GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("content");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			DirCache dc = git.add().addFilepattern("a.txt").call();
 
 			dc.getEntry(0).getObjectId();
 
 			writer = new PrintWriter(file);
 			writer.print("other content");
 			writer.close();
 
 			dc = git.add().addFilepattern("a.txt").call();
 
 			assertEquals(
 					"[a.txt, mode:100644, content:other content]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testAddExistingSingleFileTwiceWithCommit() throws Exception {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("content");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			DirCache dc = git.add().addFilepattern("a.txt").call();
 
 			dc.getEntry(0).getObjectId();
 
 			git.commit().setMessage("commit a.txt").call();
 
 			writer = new PrintWriter(file);
 			writer.print("other content");
 			writer.close();
 
 			dc = git.add().addFilepattern("a.txt").call();
 
 			assertEquals(
 					"[a.txt, mode:100644, content:other content]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testAddRemovedFile() throws Exception {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("content");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			DirCache dc = git.add().addFilepattern("a.txt").call();
 
 			dc.getEntry(0).getObjectId();
 			FileUtils.delete(file);
 
 			// is supposed to do nothing
 			dc = git.add().addFilepattern("a.txt").call();
 
 			assertEquals(
 					"[a.txt, mode:100644, content:content]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testAddRemovedCommittedFile() throws Exception {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("content");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			DirCache dc = git.add().addFilepattern("a.txt").call();
 
 			git.commit().setMessage("commit a.txt").call();
 
 			dc.getEntry(0).getObjectId();
 			FileUtils.delete(file);
 
 			// is supposed to do nothing
 			dc = git.add().addFilepattern("a.txt").call();
 
 			assertEquals(
 					"[a.txt, mode:100644, content:content]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testAddWithConflicts() throws Exception {
 		// prepare conflict
 
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("content");
 		writer.close();
 
 		File file2 = new File(db.getWorkTree(), "b.txt");
 		FileUtils.createNewFile(file2);
 		writer = new PrintWriter(file2);
 		writer.print("content b");
 		writer.close();
 
 		ObjectInserter newObjectInserter = db.newObjectInserter();
 		DirCache dc = db.lockDirCache();
 		DirCacheBuilder builder = dc.builder();
 
 		addEntryToBuilder("b.txt", file2, newObjectInserter, builder, 0);
 		addEntryToBuilder("a.txt", file, newObjectInserter, builder, 1);
 
 		writer = new PrintWriter(file);
 		writer.print("other content");
 		writer.close();
 		addEntryToBuilder("a.txt", file, newObjectInserter, builder, 3);
 
 		writer = new PrintWriter(file);
 		writer.print("our content");
 		writer.close();
 		addEntryToBuilder("a.txt", file, newObjectInserter, builder, 2)
 				.getObjectId();
 
 		builder.commit();
 
 		assertEquals(
 				"[a.txt, mode:100644, stage:1, content:content]" +
 				"[a.txt, mode:100644, stage:2, content:our content]" +
 				"[a.txt, mode:100644, stage:3, content:other content]" +
 				"[b.txt, mode:100644, content:content b]",
 				indexState(CONTENT));
 
 		// now the test begins
 
 		try (Git git = new Git(db)) {
 			dc = git.add().addFilepattern("a.txt").call();
 
 			assertEquals(
 					"[a.txt, mode:100644, content:our content]" +
 					"[b.txt, mode:100644, content:content b]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testAddTwoFiles() throws Exception  {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("content");
 		writer.close();
 
 		File file2 = new File(db.getWorkTree(), "b.txt");
 		FileUtils.createNewFile(file2);
 		writer = new PrintWriter(file2);
 		writer.print("content b");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern("a.txt").addFilepattern("b.txt").call();
 			assertEquals(
 					"[a.txt, mode:100644, content:content]" +
 					"[b.txt, mode:100644, content:content b]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testAddFolder() throws Exception  {
 		FileUtils.mkdir(new File(db.getWorkTree(), "sub"));
 		File file = new File(db.getWorkTree(), "sub/a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("content");
 		writer.close();
 
 		File file2 = new File(db.getWorkTree(), "sub/b.txt");
 		FileUtils.createNewFile(file2);
 		writer = new PrintWriter(file2);
 		writer.print("content b");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern("sub").call();
 			assertEquals(
 					"[sub/a.txt, mode:100644, content:content]" +
 					"[sub/b.txt, mode:100644, content:content b]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testAddIgnoredFile() throws Exception  {
 		FileUtils.mkdir(new File(db.getWorkTree(), "sub"));
 		File file = new File(db.getWorkTree(), "sub/a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("content");
 		writer.close();
 
 		File ignoreFile = new File(db.getWorkTree(), ".gitignore");
 		FileUtils.createNewFile(ignoreFile);
 		writer = new PrintWriter(ignoreFile);
 		writer.print("sub/b.txt");
 		writer.close();
 
 		File file2 = new File(db.getWorkTree(), "sub/b.txt");
 		FileUtils.createNewFile(file2);
 		writer = new PrintWriter(file2);
 		writer.print("content b");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern("sub").call();
 
 			assertEquals(
 					"[sub/a.txt, mode:100644, content:content]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testAddWholeRepo() throws Exception  {
 		FileUtils.mkdir(new File(db.getWorkTree(), "sub"));
 		File file = new File(db.getWorkTree(), "sub/a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("content");
 		writer.close();
 
 		File file2 = new File(db.getWorkTree(), "sub/b.txt");
 		FileUtils.createNewFile(file2);
 		writer = new PrintWriter(file2);
 		writer.print("content b");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern(".").call();
 			assertEquals(
 					"[sub/a.txt, mode:100644, content:content]" +
 					"[sub/b.txt, mode:100644, content:content b]",
 					indexState(CONTENT));
 		}
 	}
 
 	// the same three cases as in testAddWithParameterUpdate
 	// file a exists in workdir and in index -> added
 	// file b exists not in workdir but in index -> unchanged
 	// file c exists in workdir but not in index -> added
 	@Test
 	public void testAddWithoutParameterUpdate() throws Exception {
 		FileUtils.mkdir(new File(db.getWorkTree(), "sub"));
 		File file = new File(db.getWorkTree(), "sub/a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("content");
 		writer.close();
 
 		File file2 = new File(db.getWorkTree(), "sub/b.txt");
 		FileUtils.createNewFile(file2);
 		writer = new PrintWriter(file2);
 		writer.print("content b");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern("sub").call();
 
 			assertEquals(
 					"[sub/a.txt, mode:100644, content:content]" +
 					"[sub/b.txt, mode:100644, content:content b]",
 					indexState(CONTENT));
 
 			git.commit().setMessage("commit").call();
 
 			// new unstaged file sub/c.txt
 			File file3 = new File(db.getWorkTree(), "sub/c.txt");
 			FileUtils.createNewFile(file3);
 			writer = new PrintWriter(file3);
 			writer.print("content c");
 			writer.close();
 
 			// file sub/a.txt is modified
 			writer = new PrintWriter(file);
 			writer.print("modified content");
 			writer.close();
 
 			// file sub/b.txt is deleted
 			FileUtils.delete(file2);
 
 			git.add().addFilepattern("sub").call();
 			// change in sub/a.txt is staged
 			// deletion of sub/b.txt is not staged
 			// sub/c.txt is staged
 			assertEquals(
 					"[sub/a.txt, mode:100644, content:modified content]" +
 					"[sub/b.txt, mode:100644, content:content b]" +
 					"[sub/c.txt, mode:100644, content:content c]",
 					indexState(CONTENT));
 		}
 	}
 
 	// file a exists in workdir and in index -> added
 	// file b exists not in workdir but in index -> deleted
 	// file c exists in workdir but not in index -> unchanged
 	@Test
 	public void testAddWithParameterUpdate() throws Exception {
 		FileUtils.mkdir(new File(db.getWorkTree(), "sub"));
 		File file = new File(db.getWorkTree(), "sub/a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
 		writer.print("content");
 		writer.close();
 
 		File file2 = new File(db.getWorkTree(), "sub/b.txt");
 		FileUtils.createNewFile(file2);
 		writer = new PrintWriter(file2);
 		writer.print("content b");
 		writer.close();
 
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern("sub").call();
 
 			assertEquals(
 					"[sub/a.txt, mode:100644, content:content]" +
 					"[sub/b.txt, mode:100644, content:content b]",
 					indexState(CONTENT));
 
 			git.commit().setMessage("commit").call();
 
 			// new unstaged file sub/c.txt
 			File file3 = new File(db.getWorkTree(), "sub/c.txt");
 			FileUtils.createNewFile(file3);
 			writer = new PrintWriter(file3);
 			writer.print("content c");
 			writer.close();
 
 			// file sub/a.txt is modified
 			writer = new PrintWriter(file);
 			writer.print("modified content");
 			writer.close();
 
 			FileUtils.delete(file2);
 
 			// change in sub/a.txt is staged
 			// deletion of sub/b.txt is staged
 			// sub/c.txt is not staged
 			git.add().addFilepattern("sub").setUpdate(true).call();
 			// change in sub/a.txt is staged
 			assertEquals(
 					"[sub/a.txt, mode:100644, content:modified content]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testAssumeUnchanged() throws Exception {
 		try (Git git = new Git(db)) {
 			String path = "a.txt";
 			writeTrashFile(path, "content");
 			git.add().addFilepattern(path).call();
 			String path2 = "b.txt";
 			writeTrashFile(path2, "content");
 			git.add().addFilepattern(path2).call();
 			git.commit().setMessage("commit").call();
 			assertEquals("[a.txt, mode:100644, content:"
 					+ "content, assume-unchanged:false]"
 					+ "[b.txt, mode:100644, content:content, "
 					+ "assume-unchanged:false]", indexState(CONTENT
 					| ASSUME_UNCHANGED));
 			assumeUnchanged(path2);
 			assertEquals("[a.txt, mode:100644, content:content, "
 					+ "assume-unchanged:false][b.txt, mode:100644, "
 					+ "content:content, assume-unchanged:true]", indexState(CONTENT
 					| ASSUME_UNCHANGED));
 			writeTrashFile(path, "more content");
 			writeTrashFile(path2, "more content");
 
 			git.add().addFilepattern(".").call();
 
 			assertEquals("[a.txt, mode:100644, content:more content,"
 					+ " assume-unchanged:false][b.txt, mode:100644,"
 					+ " content:content, assume-unchanged:true]",
 					indexState(CONTENT
 					| ASSUME_UNCHANGED));
 		}
 	}
 
 	@Test
 	public void testReplaceFileWithDirectory()
 			throws IOException, NoFilepatternException, GitAPIException {
 		try (Git git = new Git(db)) {
 			writeTrashFile("df", "before replacement");
 			git.add().addFilepattern("df").call();
 			assertEquals("[df, mode:100644, content:before replacement]",
 					indexState(CONTENT));
 			FileUtils.delete(new File(db.getWorkTree(), "df"));
 			writeTrashFile("df/f", "after replacement");
 			git.add().addFilepattern("df").call();
 			assertEquals("[df/f, mode:100644, content:after replacement]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testReplaceDirectoryWithFile()
 			throws IOException, NoFilepatternException, GitAPIException {
 		try (Git git = new Git(db)) {
 			writeTrashFile("df/f", "before replacement");
 			git.add().addFilepattern("df").call();
 			assertEquals("[df/f, mode:100644, content:before replacement]",
 					indexState(CONTENT));
 			FileUtils.delete(new File(db.getWorkTree(), "df"), RECURSIVE);
 			writeTrashFile("df", "after replacement");
 			git.add().addFilepattern("df").call();
 			assertEquals("[df, mode:100644, content:after replacement]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testReplaceFileByPartOfDirectory()
 			throws IOException, NoFilepatternException, GitAPIException {
 		try (Git git = new Git(db)) {
 			writeTrashFile("src/main", "df", "before replacement");
 			writeTrashFile("src/main", "z", "z");
 			writeTrashFile("z", "z2");
 			git.add().addFilepattern("src/main/df")
 				.addFilepattern("src/main/z")
 				.addFilepattern("z")
 				.call();
 			assertEquals(
 					"[src/main/df, mode:100644, content:before replacement]" +
 					"[src/main/z, mode:100644, content:z]" +
 					"[z, mode:100644, content:z2]",
 					indexState(CONTENT));
 			FileUtils.delete(new File(db.getWorkTree(), "src/main/df"));
 			writeTrashFile("src/main/df", "a", "after replacement");
 			writeTrashFile("src/main/df", "b", "unrelated file");
 			git.add().addFilepattern("src/main/df/a").call();
 			assertEquals(
 					"[src/main/df/a, mode:100644, content:after replacement]" +
 					"[src/main/z, mode:100644, content:z]" +
 					"[z, mode:100644, content:z2]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testReplaceDirectoryConflictsWithFile()
 			throws IOException, NoFilepatternException, GitAPIException {
 		DirCache dc = db.lockDirCache();
 		try (ObjectInserter oi = db.newObjectInserter()) {
 			DirCacheBuilder builder = dc.builder();
 			File f = writeTrashFile("a", "df", "content");
 			addEntryToBuilder("a", f, oi, builder, 1);
 
 			f = writeTrashFile("a", "df", "other content");
 			addEntryToBuilder("a/df", f, oi, builder, 3);
 
 			f = writeTrashFile("a", "df", "our content");
 			addEntryToBuilder("a/df", f, oi, builder, 2);
 
 			f = writeTrashFile("z", "z");
 			addEntryToBuilder("z", f, oi, builder, 0);
 			builder.commit();
 		}
 		assertEquals(
 				"[a, mode:100644, stage:1, content:content]" +
 				"[a/df, mode:100644, stage:2, content:our content]" +
 				"[a/df, mode:100644, stage:3, content:other content]" +
 				"[z, mode:100644, content:z]",
 				indexState(CONTENT));
 
 		try (Git git = new Git(db)) {
 			FileUtils.delete(new File(db.getWorkTree(), "a"), RECURSIVE);
 			writeTrashFile("a", "merged");
 			git.add().addFilepattern("a").call();
 			assertEquals("[a, mode:100644, content:merged]" +
 					"[z, mode:100644, content:z]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void testExecutableRetention() throws Exception {
 		StoredConfig config = db.getConfig();
 		config.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
 				ConfigConstants.CONFIG_KEY_FILEMODE, true);
 		config.save();
 
 		FS executableFs = new FS() {
 
 			@Override
 			public boolean supportsExecute() {
 				return true;
 			}
 
 			@Override
 			public boolean setExecute(File f, boolean canExec) {
 				return true;
 			}
 
 			@Override
 			public ProcessBuilder runInShell(String cmd, String[] args) {
 				return null;
 			}
 
 			@Override
 			public boolean retryFailedLockFileCommit() {
 				return false;
 			}
 
 			@Override
 			public FS newInstance() {
 				return this;
 			}
 
 			@Override
 			protected File discoverGitExe() {
 				return null;
 			}
 
 			@Override
 			public boolean canExecute(File f) {
 				try {
 					return read(f).startsWith("binary:");
 				} catch (IOException e) {
 					return false;
 				}
 			}
 
 			@Override
 			public boolean isCaseSensitive() {
 				return false;
 			}
 		};
 
 		Git git = Git.open(db.getDirectory(), executableFs);
 		String path = "a.txt";
 		String path2 = "a.sh";
 		writeTrashFile(path, "content");
 		writeTrashFile(path2, "binary: content");
 		git.add().addFilepattern(path).addFilepattern(path2).call();
 		RevCommit commit1 = git.commit().setMessage("commit").call();
 		try (TreeWalk walk = new TreeWalk(db)) {
 			walk.addTree(commit1.getTree());
 			walk.next();
 			assertEquals(path2, walk.getPathString());
 			assertEquals(FileMode.EXECUTABLE_FILE, walk.getFileMode(0));
 			walk.next();
 			assertEquals(path, walk.getPathString());
 			assertEquals(FileMode.REGULAR_FILE, walk.getFileMode(0));
 		}
 
 		config = db.getConfig();
 		config.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
 				ConfigConstants.CONFIG_KEY_FILEMODE, false);
 		config.save();
 
 		Git git2 = Git.open(db.getDirectory(), executableFs);
 		writeTrashFile(path2, "content2");
 		writeTrashFile(path, "binary: content2");
 		git2.add().addFilepattern(path).addFilepattern(path2).call();
 		RevCommit commit2 = git2.commit().setMessage("commit2").call();
 		try (TreeWalk walk = new TreeWalk(db)) {
 			walk.addTree(commit2.getTree());
 			walk.next();
 			assertEquals(path2, walk.getPathString());
 			assertEquals(FileMode.EXECUTABLE_FILE, walk.getFileMode(0));
 			walk.next();
 			assertEquals(path, walk.getPathString());
 			assertEquals(FileMode.REGULAR_FILE, walk.getFileMode(0));
 		}
 	}
 
 	@Test
 	public void testAddGitlink() throws Exception {
 		createNestedRepo("git-link-dir");
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern("git-link-dir").call();
 
 			assertEquals(
 					"[git-link-dir, mode:160000]",
 					indexState(0));
 			Set<String> untrackedFiles = git.status().call().getUntracked();
 			assert (untrackedFiles.isEmpty());
 		}
 
 	}
 
 	@Test
 	public void testAddSubrepoWithDirNoGitlinks() throws Exception {
 		createNestedRepo("nested-repo");
 
 		// Set DIR_NO_GITLINKS
 		StoredConfig config = db.getConfig();
 		config.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
 				ConfigConstants.CONFIG_KEY_DIRNOGITLINKS, true);
 		config.save();
 
 		assert (db.getConfig().get(WorkingTreeOptions.KEY).isDirNoGitLinks());
 
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern("nested-repo").call();
 
 			assertEquals(
 					"[nested-repo/README1.md, mode:100644]" +
 							"[nested-repo/README2.md, mode:100644]",
 					indexState(0));
 		}
 
 		// Turn off DIR_NO_GITLINKS, ensure nested-repo is still treated as
 		// a normal directory
 		// Set DIR_NO_GITLINKS
 		config.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
 				ConfigConstants.CONFIG_KEY_DIRNOGITLINKS, false);
 		config.save();
 
 		writeTrashFile("nested-repo", "README3.md", "content");
 
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern("nested-repo").call();
 
 			assertEquals(
 					"[nested-repo/README1.md, mode:100644]" +
 							"[nested-repo/README2.md, mode:100644]" +
 							"[nested-repo/README3.md, mode:100644]",
 					indexState(0));
 		}
 	}
 
 	@Test
 	public void testAddGitlinkDoesNotChange() throws Exception {
 		createNestedRepo("nested-repo");
 
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern("nested-repo").call();
 
 			assertEquals(
 					"[nested-repo, mode:160000]",
 					indexState(0));
 		}
 
 		// Set DIR_NO_GITLINKS
 		StoredConfig config = db.getConfig();
 		config.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
 				ConfigConstants.CONFIG_KEY_DIRNOGITLINKS, true);
 		config.save();
 
 		assert (db.getConfig().get(WorkingTreeOptions.KEY).isDirNoGitLinks());
 
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern("nested-repo").call();
 
 			assertEquals(
 					"[nested-repo, mode:160000]",
 					indexState(0));
 		}
 	}
 
 	private static DirCacheEntry addEntryToBuilder(String path, File file,
 			ObjectInserter newObjectInserter, DirCacheBuilder builder, int stage)
 			throws IOException {
 		FileInputStream inputStream = new FileInputStream(file);
 		ObjectId id = newObjectInserter.insert(
 				Constants.OBJ_BLOB, file.length(), inputStream);
 		inputStream.close();
 		DirCacheEntry entry = new DirCacheEntry(path, stage);
 		entry.setObjectId(id);
 		entry.setFileMode(FileMode.REGULAR_FILE);
 		entry.setLastModified(file.lastModified());
 		entry.setLength((int) file.length());
 
 		builder.add(entry);
 		return entry;
 	}
 
 	private void assumeUnchanged(String path) throws IOException {
 		final DirCache dirc = db.lockDirCache();
 		final DirCacheEntry ent = dirc.getEntry(path);
 		if (ent != null)
 			ent.setAssumeValid(true);
 		dirc.write();
 		if (!dirc.commit())
 			throw new IOException("could not commit");
 	}
 
 	private void createNestedRepo(String path) throws IOException {
 		File gitLinkDir = new File(db.getWorkTree(), path);
 		FileUtils.mkdir(gitLinkDir);
 
 		FileRepositoryBuilder nestedBuilder = new FileRepositoryBuilder();
 		nestedBuilder.setWorkTree(gitLinkDir);
 
 		Repository nestedRepo = nestedBuilder.build();
 		nestedRepo.create();
 
 		writeTrashFile(path, "README1.md", "content");
 		writeTrashFile(path, "README2.md", "content");
 
 		// Commit these changes in the subrepo
 		try (Git git = new Git(nestedRepo)) {
 			git.add().addFilepattern(".").call();
 			git.commit().setMessage("subrepo commit").call();
 		} catch (GitAPIException e) {
 			throw new RuntimeException(e);
 		}
 	}
 }