/*
    * Copyright (C) 2011-2012, GitHub Inc. and others
    *
    * This program and the accompanying materials are made available under the
    * terms of the Eclipse Distribution License v. 1.0 which is available at
    * https://www.eclipse.org/org/documents/edl-v10.php.
    *
    * SPDX-License-Identifier: BSD-3-Clause
    */
  package org.eclipse.jgit.api;
  
  import static org.junit.Assert.assertEquals;
  import static org.junit.Assert.assertNotEquals;
  import static org.junit.Assert.assertNotNull;
  import static org.junit.Assert.assertNull;
  import static org.junit.Assert.assertSame;
  import static org.junit.Assert.assertTrue;
  import static org.junit.Assert.fail;
  import static org.junit.Assume.assumeTrue;
  
  import java.io.File;
  import java.util.Date;
  import java.util.List;
  import java.util.TimeZone;
  import java.util.concurrent.atomic.AtomicInteger;
  
  import org.eclipse.jgit.api.CherryPickResult.CherryPickStatus;
  import org.eclipse.jgit.api.errors.CanceledException;
  import org.eclipse.jgit.api.errors.EmptyCommitException;
  import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
  import org.eclipse.jgit.diff.DiffEntry;
  import org.eclipse.jgit.dircache.DirCache;
  import org.eclipse.jgit.dircache.DirCacheBuilder;
  import org.eclipse.jgit.dircache.DirCacheEntry;
  import org.eclipse.jgit.junit.RepositoryTestCase;
  import org.eclipse.jgit.junit.time.TimeUtil;
  import org.eclipse.jgit.lib.CommitBuilder;
  import org.eclipse.jgit.lib.ConfigConstants;
  import org.eclipse.jgit.lib.Constants;
  import org.eclipse.jgit.lib.FileMode;
  import org.eclipse.jgit.lib.GpgSigner;
  import org.eclipse.jgit.lib.ObjectId;
  import org.eclipse.jgit.lib.PersonIdent;
  import org.eclipse.jgit.lib.RefUpdate;
  import org.eclipse.jgit.lib.RefUpdate.Result;
  import org.eclipse.jgit.lib.ReflogEntry;
  import org.eclipse.jgit.lib.Repository;
  import org.eclipse.jgit.lib.StoredConfig;
  import org.eclipse.jgit.lib.CommitConfig.CleanupMode;
  import org.eclipse.jgit.revwalk.RevCommit;
  import org.eclipse.jgit.storage.file.FileBasedConfig;
  import org.eclipse.jgit.submodule.SubmoduleWalk;
  import org.eclipse.jgit.transport.CredentialsProvider;
  import org.eclipse.jgit.treewalk.TreeWalk;
  import org.eclipse.jgit.treewalk.filter.TreeFilter;
  import org.eclipse.jgit.util.FS;
  import org.junit.Ignore;
  import org.junit.Test;
  
  /**
   * Unit tests of {@link CommitCommand}.
   */
  public class CommitCommandTest extends RepositoryTestCase {
  
  	@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) {
 				return true;
 			}
 
 			@Override
 			public boolean isCaseSensitive() {
 				return true;
 			}
 		};
 
 		Git git = Git.open(db.getDirectory(), executableFs);
 		String path = "a.txt";
 		writeTrashFile(path, "content");
 		git.add().addFilepattern(path).call();
 		RevCommit commit1 = git.commit().setMessage("commit").call();
 		try (TreeWalk walk = TreeWalk.forPath(db, path, commit1.getTree())) {
 			assertNotNull(walk);
 			assertEquals(FileMode.EXECUTABLE_FILE, walk.getFileMode(0));
 		}
 
 		FS nonExecutableFs = new FS() {
 
 			@Override
 			public boolean supportsExecute() {
 				return false;
 			}
 
 			@Override
 			public boolean setExecute(File f, boolean canExec) {
 				return false;
 			}
 
 			@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) {
 				return false;
 			}
 
 			@Override
 			public boolean isCaseSensitive() {
 				return true;
 			}
 		};
 
 		config = db.getConfig();
 		config.setBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
 				ConfigConstants.CONFIG_KEY_FILEMODE, false);
 		config.save();
 
 		Git git2 = Git.open(db.getDirectory(), nonExecutableFs);
 		writeTrashFile(path, "content2");
 		RevCommit commit2 = git2.commit().setOnly(path).setMessage("commit2")
 				.call();
 		try (TreeWalk walk = TreeWalk.forPath(db, path, commit2.getTree())) {
 			assertNotNull(walk);
 			assertEquals(FileMode.EXECUTABLE_FILE, walk.getFileMode(0));
 		}
 	}
 
 	@Test
 	public void commitNewSubmodule() throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("file.txt", "content");
 			git.add().addFilepattern("file.txt").call();
 			RevCommit commit = git.commit().setMessage("create file").call();
 
 			SubmoduleAddCommand command = new SubmoduleAddCommand(db);
 			String path = "sub";
 			command.setPath(path);
 			String uri = db.getDirectory().toURI().toString();
 			command.setURI(uri);
 			Repository repo = command.call();
 			assertNotNull(repo);
 			addRepoToClose(repo);
 
 			try (SubmoduleWalk generator = SubmoduleWalk.forIndex(db)) {
 				assertTrue(generator.next());
 				assertEquals(path, generator.getPath());
 				assertEquals(commit, generator.getObjectId());
 				assertEquals(uri, generator.getModulesUrl());
 				assertEquals(path, generator.getModulesPath());
 				assertEquals(uri, generator.getConfigUrl());
 				try (Repository subModRepo = generator.getRepository()) {
 					assertNotNull(subModRepo);
 				}
 			}
 			assertEquals(commit, repo.resolve(Constants.HEAD));
 
 			RevCommit submoduleCommit = git.commit().setMessage("submodule add")
 					.setOnly(path).call();
 			assertNotNull(submoduleCommit);
 			try (TreeWalk walk = new TreeWalk(db)) {
 				walk.addTree(commit.getTree());
 				walk.addTree(submoduleCommit.getTree());
 				walk.setFilter(TreeFilter.ANY_DIFF);
 				List<DiffEntry> diffs = DiffEntry.scan(walk);
 				assertEquals(1, diffs.size());
 				DiffEntry subDiff = diffs.get(0);
 				assertEquals(FileMode.MISSING, subDiff.getOldMode());
 				assertEquals(FileMode.GITLINK, subDiff.getNewMode());
 				assertEquals(ObjectId.zeroId(), subDiff.getOldId().toObjectId());
 				assertEquals(commit, subDiff.getNewId().toObjectId());
 				assertEquals(path, subDiff.getNewPath());
 			}
 		}
 	}
 
 	@Test
 	public void commitSubmoduleUpdate() throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("file.txt", "content");
 			git.add().addFilepattern("file.txt").call();
 			RevCommit commit = git.commit().setMessage("create file").call();
 			writeTrashFile("file.txt", "content2");
 			git.add().addFilepattern("file.txt").call();
 			RevCommit commit2 = git.commit().setMessage("edit file").call();
 
 			SubmoduleAddCommand command = new SubmoduleAddCommand(db);
 			String path = "sub";
 			command.setPath(path);
 			String uri = db.getDirectory().toURI().toString();
 			command.setURI(uri);
 			Repository repo = command.call();
 			assertNotNull(repo);
 			addRepoToClose(repo);
 
 			try (SubmoduleWalk generator = SubmoduleWalk.forIndex(db)) {
 				assertTrue(generator.next());
 				assertEquals(path, generator.getPath());
 				assertEquals(commit2, generator.getObjectId());
 				assertEquals(uri, generator.getModulesUrl());
 				assertEquals(path, generator.getModulesPath());
 				assertEquals(uri, generator.getConfigUrl());
 				try (Repository subModRepo = generator.getRepository()) {
 					assertNotNull(subModRepo);
 				}
 			}
 			assertEquals(commit2, repo.resolve(Constants.HEAD));
 
 			RevCommit submoduleAddCommit = git.commit().setMessage("submodule add")
 					.setOnly(path).call();
 			assertNotNull(submoduleAddCommit);
 
 			RefUpdate update = repo.updateRef(Constants.HEAD);
 			update.setNewObjectId(commit);
 			assertEquals(Result.FORCED, update.forceUpdate());
 
 			RevCommit submoduleEditCommit = git.commit()
 					.setMessage("submodule add").setOnly(path).call();
 			assertNotNull(submoduleEditCommit);
 			try (TreeWalk walk = new TreeWalk(db)) {
 				walk.addTree(submoduleAddCommit.getTree());
 				walk.addTree(submoduleEditCommit.getTree());
 				walk.setFilter(TreeFilter.ANY_DIFF);
 				List<DiffEntry> diffs = DiffEntry.scan(walk);
 				assertEquals(1, diffs.size());
 				DiffEntry subDiff = diffs.get(0);
 				assertEquals(FileMode.GITLINK, subDiff.getOldMode());
 				assertEquals(FileMode.GITLINK, subDiff.getNewMode());
 				assertEquals(commit2, subDiff.getOldId().toObjectId());
 				assertEquals(commit, subDiff.getNewId().toObjectId());
 				assertEquals(path, subDiff.getNewPath());
 				assertEquals(path, subDiff.getOldPath());
 			}
 		}
 	}
 
 	@Ignore("very flaky when run with Hudson")
 	@Test
 	public void commitUpdatesSmudgedEntries() throws Exception {
 		try (Git git = new Git(db)) {
 			File file1 = writeTrashFile("file1.txt", "content1");
 			TimeUtil.setLastModifiedWithOffset(file1.toPath(), -5000L);
 			File file2 = writeTrashFile("file2.txt", "content2");
 			TimeUtil.setLastModifiedWithOffset(file2.toPath(), -5000L);
 			File file3 = writeTrashFile("file3.txt", "content3");
 			TimeUtil.setLastModifiedWithOffset(file3.toPath(), -5000L);
 
 			assertNotNull(git.add().addFilepattern("file1.txt")
 					.addFilepattern("file2.txt").addFilepattern("file3.txt").call());
 			RevCommit commit = git.commit().setMessage("add files").call();
 			assertNotNull(commit);
 
 			DirCache cache = DirCache.read(db.getIndexFile(), db.getFS());
 			int file1Size = cache.getEntry("file1.txt").getLength();
 			int file2Size = cache.getEntry("file2.txt").getLength();
 			int file3Size = cache.getEntry("file3.txt").getLength();
 			ObjectId file2Id = cache.getEntry("file2.txt").getObjectId();
 			ObjectId file3Id = cache.getEntry("file3.txt").getObjectId();
 			assertTrue(file1Size > 0);
 			assertTrue(file2Size > 0);
 			assertTrue(file3Size > 0);
 
 			// Smudge entries
 			cache = DirCache.lock(db.getIndexFile(), db.getFS());
 			cache.getEntry("file1.txt").setLength(0);
 			cache.getEntry("file2.txt").setLength(0);
 			cache.getEntry("file3.txt").setLength(0);
 			cache.write();
 			assertTrue(cache.commit());
 
 			// Verify entries smudged
 			cache = DirCache.read(db.getIndexFile(), db.getFS());
 			assertEquals(0, cache.getEntry("file1.txt").getLength());
 			assertEquals(0, cache.getEntry("file2.txt").getLength());
 			assertEquals(0, cache.getEntry("file3.txt").getLength());
 
 			TimeUtil.setLastModifiedWithOffset(db.getIndexFile().toPath(),
 					-5000L);
 
 			write(file1, "content4");
 
 			TimeUtil.setLastModifiedWithOffset(file1.toPath(), 2500L);
 			assertNotNull(git.commit().setMessage("edit file").setOnly("file1.txt")
 					.call());
 
 			cache = db.readDirCache();
 			assertEquals(file1Size, cache.getEntry("file1.txt").getLength());
 			assertEquals(file2Size, cache.getEntry("file2.txt").getLength());
 			assertEquals(file3Size, cache.getEntry("file3.txt").getLength());
 			assertEquals(file2Id, cache.getEntry("file2.txt").getObjectId());
 			assertEquals(file3Id, cache.getEntry("file3.txt").getObjectId());
 		}
 	}
 
 	@Ignore("very flaky when run with Hudson")
 	@Test
 	public void commitIgnoresSmudgedEntryWithDifferentId() throws Exception {
 		try (Git git = new Git(db)) {
 			File file1 = writeTrashFile("file1.txt", "content1");
 			TimeUtil.setLastModifiedWithOffset(file1.toPath(), -5000L);
 			File file2 = writeTrashFile("file2.txt", "content2");
 			TimeUtil.setLastModifiedWithOffset(file2.toPath(), -5000L);
 
 			assertNotNull(git.add().addFilepattern("file1.txt")
 					.addFilepattern("file2.txt").call());
 			RevCommit commit = git.commit().setMessage("add files").call();
 			assertNotNull(commit);
 
 			DirCache cache = DirCache.read(db.getIndexFile(), db.getFS());
 			int file1Size = cache.getEntry("file1.txt").getLength();
 			int file2Size = cache.getEntry("file2.txt").getLength();
 			assertTrue(file1Size > 0);
 			assertTrue(file2Size > 0);
 
 			writeTrashFile("file2.txt", "content3");
 			assertNotNull(git.add().addFilepattern("file2.txt").call());
 			writeTrashFile("file2.txt", "content4");
 
 			// Smudge entries
 			cache = DirCache.lock(db.getIndexFile(), db.getFS());
 			cache.getEntry("file1.txt").setLength(0);
 			cache.getEntry("file2.txt").setLength(0);
 			cache.write();
 			assertTrue(cache.commit());
 
 			// Verify entries smudged
 			cache = db.readDirCache();
 			assertEquals(0, cache.getEntry("file1.txt").getLength());
 			assertEquals(0, cache.getEntry("file2.txt").getLength());
 
 			TimeUtil.setLastModifiedWithOffset(db.getIndexFile().toPath(),
 					-5000L);
 
 			write(file1, "content5");
 			TimeUtil.setLastModifiedWithOffset(file1.toPath(), 1000L);
 
 			assertNotNull(git.commit().setMessage("edit file").setOnly("file1.txt")
 					.call());
 
 			cache = db.readDirCache();
 			assertEquals(file1Size, cache.getEntry("file1.txt").getLength());
 			assertEquals(0, cache.getEntry("file2.txt").getLength());
 		}
 	}
 
 	@Test
 	public void commitAfterSquashMerge() throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("file1", "file1");
 			git.add().addFilepattern("file1").call();
 			RevCommit first = git.commit().setMessage("initial commit").call();
 
 			assertTrue(new File(db.getWorkTree(), "file1").exists());
 			createBranch(first, "refs/heads/branch1");
 			checkoutBranch("refs/heads/branch1");
 
 			writeTrashFile("file2", "file2");
 			git.add().addFilepattern("file2").call();
 			git.commit().setMessage("second commit").call();
 			assertTrue(new File(db.getWorkTree(), "file2").exists());
 
 			checkoutBranch("refs/heads/master");
 
 			MergeResult result = git.merge()
 					.include(db.exactRef("refs/heads/branch1"))
 					.setSquash(true)
 					.call();
 
 			assertTrue(new File(db.getWorkTree(), "file1").exists());
 			assertTrue(new File(db.getWorkTree(), "file2").exists());
 			assertEquals(MergeResult.MergeStatus.FAST_FORWARD_SQUASHED,
 					result.getMergeStatus());
 
 			// comment not set, should be inferred from SQUASH_MSG
 			RevCommit squashedCommit = git.commit().call();
 
 			assertEquals(1, squashedCommit.getParentCount());
 			assertNull(db.readSquashCommitMsg());
 			assertEquals("commit: Squashed commit of the following:", db
 					.getReflogReader(Constants.HEAD).getLastEntry().getComment());
 			assertEquals("commit: Squashed commit of the following:", db
 					.getReflogReader(db.getBranch()).getLastEntry().getComment());
 		}
 	}
 
 	@Test
 	public void testReflogs() throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("f", "1");
 			git.add().addFilepattern("f").call();
 			git.commit().setMessage("c1").call();
 			writeTrashFile("f", "2");
 			git.commit().setMessage("c2").setAll(true).setReflogComment(null)
 					.call();
 			writeTrashFile("f", "3");
 			git.commit().setMessage("c3").setAll(true)
 					.setReflogComment("testRl").call();
 
 			db.getReflogReader(Constants.HEAD).getReverseEntries();
 
 			assertEquals("testRl;commit (initial): c1;", reflogComments(
 					db.getReflogReader(Constants.HEAD).getReverseEntries()));
 			assertEquals("testRl;commit (initial): c1;", reflogComments(
 					db.getReflogReader(db.getBranch()).getReverseEntries()));
 		}
 	}
 
 	private static String reflogComments(List<ReflogEntry> entries) {
 		StringBuilder b = new StringBuilder();
 		for (ReflogEntry e : entries) {
 			b.append(e.getComment()).append(";");
 		}
 		return b.toString();
 	}
 
 	@Test(expected = WrongRepositoryStateException.class)
 	public void commitAmendOnInitialShouldFail() throws Exception {
 		try (Git git = new Git(db)) {
 			git.commit().setAmend(true).setMessage("initial commit").call();
 		}
 	}
 
 	@Test
 	public void commitAmendWithoutAuthorShouldSetOriginalAuthorAndAuthorTime()
 			throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("file1", "file1");
 			git.add().addFilepattern("file1").call();
 
 			final String authorName = "First Author";
 			final String authorEmail = "author@example.org";
 			final Date authorDate = new Date(1349621117000L);
 			PersonIdent firstAuthor = new PersonIdent(authorName, authorEmail,
 					authorDate, TimeZone.getTimeZone("UTC"));
 			git.commit().setMessage("initial commit").setAuthor(firstAuthor).call();
 
 			RevCommit amended = git.commit().setAmend(true)
 					.setMessage("amend commit").call();
 
 			PersonIdent amendedAuthor = amended.getAuthorIdent();
 			assertEquals(authorName, amendedAuthor.getName());
 			assertEquals(authorEmail, amendedAuthor.getEmailAddress());
 			assertEquals(authorDate.getTime(), amendedAuthor.getWhen().getTime());
 		}
 	}
 
 	@Test
 	public void commitAmendWithAuthorShouldUseIt() throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("file1", "file1");
 			git.add().addFilepattern("file1").call();
 			git.commit().setMessage("initial commit").call();
 
 			RevCommit amended = git.commit().setAmend(true)
 					.setAuthor("New Author", "newauthor@example.org")
 					.setMessage("amend commit").call();
 
 			PersonIdent amendedAuthor = amended.getAuthorIdent();
 			assertEquals("New Author", amendedAuthor.getName());
 			assertEquals("newauthor@example.org", amendedAuthor.getEmailAddress());
 		}
 	}
 
 	@Test
 	public void commitMessageVerbatim() throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("file1", "file1");
 			git.add().addFilepattern("file1").call();
 			RevCommit committed = git.commit().setMessage("#initial commit")
 					.call();
 
 			assertEquals("#initial commit", committed.getFullMessage());
 		}
 	}
 
 	@Test
 	public void commitMessageStrip() throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("file1", "file1");
 			git.add().addFilepattern("file1").call();
 			RevCommit committed = git.commit().setMessage(
 					"#Comment\ninitial commit\t\n\n commit body \n \t#another comment")
 					.setCleanupMode(CleanupMode.STRIP).call();
 
 			assertEquals("initial commit\n\n commit body",
 					committed.getFullMessage());
 		}
 	}
 
 	@Test
 	public void commitMessageDefault() throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("file1", "file1");
 			git.add().addFilepattern("file1").call();
 			RevCommit committed = git.commit().setMessage(
 					"#Comment\ninitial commit\t\n\n commit body \n\n\n \t#another comment  ")
 					.setCleanupMode(CleanupMode.DEFAULT).call();
 
 			assertEquals("initial commit\n\n commit body",
 					committed.getFullMessage());
 		}
 	}
 
 	@Test
 	public void commitMessageDefaultWhitespace() throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("file1", "file1");
 			git.add().addFilepattern("file1").call();
 			RevCommit committed = git.commit().setMessage(
 					"#Comment\ninitial commit\t\n\n commit body \n\n\n \t#another comment  ")
 					.setCleanupMode(CleanupMode.DEFAULT).setDefaultClean(false)
 					.call();
 
 			assertEquals(
 					"#Comment\ninitial commit\n\n commit body\n\n \t#another comment",
 					committed.getFullMessage());
 		}
 	}
 
 	@Test
 	public void commitEmptyCommits() throws Exception {
 		try (Git git = new Git(db)) {
 
 			writeTrashFile("file1", "file1");
 			git.add().addFilepattern("file1").call();
 			RevCommit initial = git.commit().setMessage("initial commit")
 					.call();
 
 			RevCommit emptyFollowUp = git.commit()
 					.setAuthor("New Author", "newauthor@example.org")
 					.setMessage("no change").call();
 
 			assertNotEquals(initial.getId(), emptyFollowUp.getId());
 			assertEquals(initial.getTree().getId(),
 					emptyFollowUp.getTree().getId());
 
 			try {
 				git.commit().setAuthor("New Author", "newauthor@example.org")
 						.setMessage("again no change").setAllowEmpty(false)
 						.call();
 				fail("Didn't get the expected EmptyCommitException");
 			} catch (EmptyCommitException e) {
 				// expect this exception
 			}
 
 			// Allow empty commits also when setOnly was set
 			git.commit().setAuthor("New Author", "newauthor@example.org")
 					.setMessage("again no change").setOnly("file1")
 					.setAllowEmpty(true).call();
 		}
 	}
 
 	@Test
 	public void commitOnlyShouldCommitUnmergedPathAndNotAffectOthers()
 			throws Exception {
 		DirCache index = db.lockDirCache();
 		DirCacheBuilder builder = index.builder();
 		addUnmergedEntry("unmerged1", builder);
 		addUnmergedEntry("unmerged2", builder);
 		DirCacheEntry other = new DirCacheEntry("other");
 		other.setFileMode(FileMode.REGULAR_FILE);
 		builder.add(other);
 		builder.commit();
 
 		writeTrashFile("unmerged1", "unmerged1 data");
 		writeTrashFile("unmerged2", "unmerged2 data");
 		writeTrashFile("other", "other data");
 
 		assertEquals("[other, mode:100644]"
 				+ "[unmerged1, mode:100644, stage:1]"
 				+ "[unmerged1, mode:100644, stage:2]"
 				+ "[unmerged1, mode:100644, stage:3]"
 				+ "[unmerged2, mode:100644, stage:1]"
 				+ "[unmerged2, mode:100644, stage:2]"
 				+ "[unmerged2, mode:100644, stage:3]",
 				indexState(0));
 
 		try (Git git = new Git(db)) {
 			RevCommit commit = git.commit().setOnly("unmerged1")
 					.setMessage("Only one file").call();
 
 			assertEquals("[other, mode:100644]" + "[unmerged1, mode:100644]"
 					+ "[unmerged2, mode:100644, stage:1]"
 					+ "[unmerged2, mode:100644, stage:2]"
 					+ "[unmerged2, mode:100644, stage:3]",
 					indexState(0));
 
 			try (TreeWalk walk = TreeWalk.forPath(db, "unmerged1", commit.getTree())) {
 				assertEquals(FileMode.REGULAR_FILE, walk.getFileMode(0));
 			}
 		}
 	}
 
 	@Test
 	public void commitOnlyShouldHandleIgnored() throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("subdir/foo", "Hello World");
 			writeTrashFile("subdir/bar", "Hello World");
 			writeTrashFile(".gitignore", "bar");
 			git.add().addFilepattern("subdir").call();
 			git.commit().setOnly("subdir").setMessage("first commit").call();
 			assertEquals("[subdir/foo, mode:100644, content:Hello World]",
 					indexState(CONTENT));
 		}
 	}
 
 	private void nonNormalizedIndexTest(boolean executable) throws Exception {
 		String mode = executable ? "100755" : "100644";
 		try (Git git = new Git(db)) {
 			// Commit a file with CR/LF into the index
 			FileBasedConfig config = db.getConfig();
 			config.setString("core", null, "autocrlf", "false");
 			config.save();
 			File testFile = writeTrashFile("file.txt", "line 1\r\nline 2\r\n");
 			if (executable) {
 				FS.DETECTED.setExecute(testFile, true);
 			}
 			git.add().addFilepattern("file.txt").call();
 			git.commit().setMessage("Initial").call();
 			assertEquals(
 					"[file.txt, mode:" + mode
 							+ ", content:line 1\r\nline 2\r\n]",
 					indexState(CONTENT));
 			config.setString("core", null, "autocrlf", "true");
 			config.save();
 			writeTrashFile("file.txt", "line 1\r\nline 1.5\r\nline 2\r\n");
 			testFile = writeTrashFile("file2.txt", "new\r\nfile\r\n");
 			if (executable) {
 				FS.DETECTED.setExecute(testFile, true);
 			}
 			git.add().addFilepattern("file.txt").addFilepattern("file2.txt")
 					.call();
 			git.commit().setMessage("Second").call();
 			assertEquals(
 					"[file.txt, mode:" + mode
 							+ ", content:line 1\r\nline 1.5\r\nline 2\r\n]"
 							+ "[file2.txt, mode:" + mode
 							+ ", content:new\nfile\n]",
 					indexState(CONTENT));
 			writeTrashFile("file2.txt", "new\r\nfile\r\ncontent\r\n");
 			git.add().addFilepattern("file2.txt").call();
 			git.commit().setMessage("Third").call();
 			assertEquals(
 					"[file.txt, mode:" + mode
 							+ ", content:line 1\r\nline 1.5\r\nline 2\r\n]"
 							+ "[file2.txt, mode:" + mode
 							+ ", content:new\nfile\ncontent\n]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void commitWithAutoCrlfAndNonNormalizedIndex() throws Exception {
 		nonNormalizedIndexTest(false);
 	}
 
 	@Test
 	public void commitExecutableWithAutoCrlfAndNonNormalizedIndex()
 			throws Exception {
 		assumeTrue(FS.DETECTED.supportsExecute());
 		nonNormalizedIndexTest(true);
 	}
 
 	@Test
 	public void testDeletionConflictWithAutoCrlf() throws Exception {
 		try (Git git = new Git(db)) {
 			// Commit a file with CR/LF into the index
 			FileBasedConfig config = db.getConfig();
 			config.setString("core", null, "autocrlf", "false");
 			config.save();
 			File file = writeTrashFile("file.txt", "foo\r\n");
 			git.add().addFilepattern("file.txt").call();
 			git.commit().setMessage("Initial").call();
 			// Switch to side branch
 			git.checkout().setCreateBranch(true).setName("side").call();
 			assertTrue(file.delete());
 			git.rm().addFilepattern("file.txt").call();
 			git.commit().setMessage("Side").call();
 			// Switch on autocrlf=true
 			config.setString("core", null, "autocrlf", "true");
 			config.save();
 			// Switch back to master and commit a conflict
 			git.checkout().setName("master").call();
 			writeTrashFile("file.txt", "foob\r\n");
 			git.add().addFilepattern("file.txt").call();
 			assertEquals("[file.txt, mode:100644, content:foob\r\n]",
 					indexState(CONTENT));
 			writeTrashFile("g", "file2.txt", "anything");
 			git.add().addFilepattern("g/file2.txt");
 			RevCommit master = git.commit().setMessage("Second").call();
 			// Switch to side branch again so that the deletion is "ours"
 			git.checkout().setName("side").call();
 			// Cherry pick master: produces a delete-modify conflict.
 			CherryPickResult pick = git.cherryPick().include(master).call();
 			assertEquals("Expected a cherry-pick conflict",
 					CherryPickStatus.CONFLICTING, pick.getStatus());
 			// XXX: g/file2.txt should actually be staged already, but isn't.
 			git.add().addFilepattern("g/file2.txt").call();
 			// Resolve the conflict by taking the master version
 			writeTrashFile("file.txt", "foob\r\n");
 			git.add().addFilepattern("file.txt").call();
 			git.commit().setMessage("Cherry").call();
 			// We expect this to be committed with a single LF since there is no
 			// "ours" stage.
 			assertEquals(
 					"[file.txt, mode:100644, content:foob\n]"
 							+ "[g/file2.txt, mode:100644, content:anything]",
 					indexState(CONTENT));
 		}
 	}
 
 	private void testConflictWithAutoCrlf(String baseLf, String lf)
 			throws Exception {
 		try (Git git = new Git(db)) {
 			// Commit a file with CR/LF into the index
 			FileBasedConfig config = db.getConfig();
 			config.setString("core", null, "autocrlf", "false");
 			config.save();
 			writeTrashFile("file.txt", "foo" + baseLf);
 			git.add().addFilepattern("file.txt").call();
 			git.commit().setMessage("Initial").call();
 			// Switch to side branch
 			git.checkout().setCreateBranch(true).setName("side").call();
 			writeTrashFile("file.txt", "bar\r\n");
 			git.add().addFilepattern("file.txt").call();
 			RevCommit side = git.commit().setMessage("Side").call();
 			// Switch back to master and commit a conflict with the given lf
 			git.checkout().setName("master");
 			writeTrashFile("file.txt", "foob" + lf);
 			git.add().addFilepattern("file.txt").call();
 			git.commit().setMessage("Second").call();
 			// Switch on autocrlf=true
 			config.setString("core", null, "autocrlf", "true");
 			config.save();
 			// Cherry pick side: conflict. Resolve with CR-LF and commit.
 			CherryPickResult pick = git.cherryPick().include(side).call();
 			assertEquals("Expected a cherry-pick conflict",
 					CherryPickStatus.CONFLICTING, pick.getStatus());
 			writeTrashFile("file.txt", "foobar\r\n");
 			git.add().addFilepattern("file.txt").call();
 			git.commit().setMessage("Second").call();
 			assertEquals("[file.txt, mode:100644, content:foobar" + lf + "]",
 					indexState(CONTENT));
 		}
 	}
 
 	@Test
 	public void commitConflictWithAutoCrlfBaseCrLfOursLf() throws Exception {
 		testConflictWithAutoCrlf("\r\n", "\n");
 	}
 
 	@Test
 	public void commitConflictWithAutoCrlfBaseLfOursLf() throws Exception {
 		testConflictWithAutoCrlf("\n", "\n");
 	}
 
 	@Test
 	public void commitConflictWithAutoCrlfBasCrLfOursCrLf() throws Exception {
 		testConflictWithAutoCrlf("\r\n", "\r\n");
 	}
 
 	@Test
 	public void commitConflictWithAutoCrlfBaseLfOursCrLf() throws Exception {
 		testConflictWithAutoCrlf("\n", "\r\n");
 	}
 
 	private static void addUnmergedEntry(String file, DirCacheBuilder builder) {
 		DirCacheEntry stage1 = new DirCacheEntry(file, DirCacheEntry.STAGE_1);
 		DirCacheEntry stage2 = new DirCacheEntry(file, DirCacheEntry.STAGE_2);
 		DirCacheEntry stage3 = new DirCacheEntry(file, DirCacheEntry.STAGE_3);
 		stage1.setFileMode(FileMode.REGULAR_FILE);
 		stage2.setFileMode(FileMode.REGULAR_FILE);
 		stage3.setFileMode(FileMode.REGULAR_FILE);
 		builder.add(stage1);
 		builder.add(stage2);
 		builder.add(stage3);
 	}
 
 	@Test
 	public void callSignerWithProperSigningKey() throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("file1", "file1");
 			git.add().addFilepattern("file1").call();
 
 			String[] signingKey = new String[1];
 			PersonIdent[] signingCommitters = new PersonIdent[1];
 			AtomicInteger callCount = new AtomicInteger();
 			GpgSigner.setDefault(new GpgSigner() {
 				@Override
 				public void sign(CommitBuilder commit, String gpgSigningKey,
 						PersonIdent signingCommitter, CredentialsProvider credentialsProvider) {
 					signingKey[0] = gpgSigningKey;
 					signingCommitters[0] = signingCommitter;
 					callCount.incrementAndGet();
 				}
 
 				@Override
 				public boolean canLocateSigningKey(String gpgSigningKey,
 						PersonIdent signingCommitter,
 						CredentialsProvider credentialsProvider)
 						throws CanceledException {
 					return false;
 				}
 			});
 
 			// first call should use config, which is expected to be null at
 			// this time
 			git.commit().setCommitter(committer).setSign(Boolean.TRUE)
 					.setMessage("initial commit")
 					.call();
 			assertNull(signingKey[0]);
 			assertEquals(1, callCount.get());
 			assertSame(committer, signingCommitters[0]);
 
 			writeTrashFile("file2", "file2");
 			git.add().addFilepattern("file2").call();
 
 			// second commit applies config value
 			String expectedConfigSigningKey = "config-" + System.nanoTime();
 			StoredConfig config = git.getRepository().getConfig();
 			config.setString("user", null, "signingKey",
 					expectedConfigSigningKey);
 			config.save();
 
 			git.commit().setCommitter(committer).setSign(Boolean.TRUE)
 					.setMessage("initial commit")
 					.call();
 			assertEquals(expectedConfigSigningKey, signingKey[0]);
 			assertEquals(2, callCount.get());
 			assertSame(committer, signingCommitters[0]);
 
 			writeTrashFile("file3", "file3");
 			git.add().addFilepattern("file3").call();
 
 			// now use specific on api
 			String expectedSigningKey = "my-" + System.nanoTime();
 			git.commit().setCommitter(committer).setSign(Boolean.TRUE)
 					.setSigningKey(expectedSigningKey)
 					.setMessage("initial commit").call();
 			assertEquals(expectedSigningKey, signingKey[0]);
 			assertEquals(3, callCount.get());
 			assertSame(committer, signingCommitters[0]);
 		}
 	}
 
 	@Test
 	public void callSignerOnlyWhenSigning() throws Exception {
 		try (Git git = new Git(db)) {
 			writeTrashFile("file1", "file1");
 			git.add().addFilepattern("file1").call();
 
 			AtomicInteger callCount = new AtomicInteger();
 			GpgSigner.setDefault(new GpgSigner() {
 				@Override
 				public void sign(CommitBuilder commit, String gpgSigningKey,
 						PersonIdent signingCommitter, CredentialsProvider credentialsProvider) {
 					callCount.incrementAndGet();
 				}
 
 				@Override
 				public boolean canLocateSigningKey(String gpgSigningKey,
 						PersonIdent signingCommitter,
 						CredentialsProvider credentialsProvider)
 						throws CanceledException {
 					return false;
 				}
 			});
 
 			// first call should use config, which is expected to be null at
 			// this time
 			git.commit().setMessage("initial commit").call();
 			assertEquals(0, callCount.get());
 
 			writeTrashFile("file2", "file2");
 			git.add().addFilepattern("file2").call();
 
 			// now force signing
 			git.commit().setSign(Boolean.TRUE).setMessage("commit").call();
 			assertEquals(1, callCount.get());
 
 			writeTrashFile("file3", "file3");
 			git.add().addFilepattern("file3").call();
 
 			// now rely on config
 			StoredConfig config = git.getRepository().getConfig();
 			config.setBoolean("commit", null, "gpgSign", true);
 			config.save();
 
 			git.commit().setMessage("commit").call();
 			assertEquals(2, callCount.get());
 
 			writeTrashFile("file4", "file4");
 			git.add().addFilepattern("file4").call();
 
 			// now force "no-sign" (even though config is true)
 			git.commit().setSign(Boolean.FALSE).setMessage("commit").call();
 			assertEquals(2, callCount.get());
 		}
 	}
 }