Merge "fix PackWriter excluded objects handling"

org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitCloneTask.java

@@ -110,7 +110,7 @@ public class GitCloneTask extends Task {
 		try {
 			clone.setURI(uri).setDirectory(destination).setBranch(branch).setBare(bare);
 			clone.call();
-		} catch (RuntimeException e) {
+		} catch (Exception e) {
 			log("Could not clone repository: " + e, e, Project.MSG_ERR);
 			throw new BuildException("Could not clone repository: " + e.getMessage(), e);
 		}

org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitInitTask.java

@@ -91,7 +91,7 @@ public class GitInitTask extends Task {
 			InitCommand init = Git.init();
 			init.setBare(bare).setDirectory(destination);
 			init.call();
-		} catch (JGitInternalException e) {
+		} catch (Exception e) {
 			throw new BuildException("Could not initialize repository", e);
 		}
 	}

org.eclipse.jgit.http.test/META-INF/MANIFEST.MF

@@ -8,19 +8,20 @@ Bundle-Localization: plugin
 Bundle-RequiredExecutionEnvironment: J2SE-1.5
 Import-Package: javax.servlet;version="[2.5.0,3.0.0)",
  javax.servlet.http;version="[2.5.0,3.0.0)",
- org.eclipse.jetty.continuation;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.http;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.http.security;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.io;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.security;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.security.authentication;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.server;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.server.handler;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.server.nio;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.servlet;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.util.component;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.util.log;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.util.thread;version="[7.1.0,7.6.0)",
+ org.eclipse.jetty.continuation;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.http;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.io;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.security;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.security.authentication;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.server;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.server.handler;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.server.nio;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.servlet;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.util;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.util.component;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.util.log;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.util.security;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.util.thread;version="[7.6.0,8.0.0)",
  org.eclipse.jgit.errors;version="[2.0.0,2.1.0)",
  org.eclipse.jgit.http.server;version="[2.0.0,2.1.0)",
  org.eclipse.jgit.http.server.glue;version="[2.0.0,2.1.0)",

org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/GitServletInitTest.java

@@ -43,7 +43,6 @@
 
 package org.eclipse.jgit.http.test;
 
-import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
@@ -53,6 +52,7 @@ import javax.servlet.ServletException;
 
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
+import org.eclipse.jetty.util.MultiException;
 import org.eclipse.jgit.http.server.GitServlet;
 import org.eclipse.jgit.junit.http.AppServer;
 import org.eclipse.jgit.junit.http.MockServletConfig;
@@ -100,15 +100,28 @@ public class GitServletInitTest {
 		ServletContextHandler app = server.addContext("/");
 		ServletHolder s = app.addServlet(GitServlet.class, "/git");
 		s.setInitOrder(1);
+		s.getServletHandler().setStartWithUnavailable(false);
 
-		server.setUp();
-
-		List<RecordingLogger.Warning> events = RecordingLogger.getWarnings();
-		assertFalse("Servlet started without base-path", events.isEmpty());
-
-		Throwable why = events.get(0).getCause();
-		assertTrue("Caught ServletException", why instanceof ServletException);
-		assertTrue("Wanted base-path", why.getMessage().contains("base-path"));
+		try {
+			server.setUp();
+		} catch (Exception e) {
+			Throwable why = null;
+			if (e instanceof MultiException) {
+				MultiException multi = (MultiException) e;
+				List<Throwable> reasons = multi.getThrowables();
+				why = reasons.get(0);
+				assertTrue("Expected ServletException",
+						why instanceof ServletException);
+			} else if (e instanceof ServletException)
+				why = e;
+
+			if (why != null) {
+				assertTrue("Wanted base-path",
+						why.getMessage().contains("base-path"));
+				return;
+			}
+		}
+		fail("Expected ServletException complaining about unset base-path");
 	}
 
 	@Test

org.eclipse.jgit.junit.http/META-INF/MANIFEST.MF

@@ -9,19 +9,19 @@ Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: J2SE-1.5
 Import-Package: javax.servlet;version="[2.5.0,3.0.0)",
  javax.servlet.http;version="[2.5.0,3.0.0)",
- org.eclipse.jetty.continuation;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.http;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.http.security;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.io;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.security;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.security.authentication;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.server;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.server.handler;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.server.nio;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.servlet;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.util.component;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.util.log;version="[7.1.0,7.6.0)",
- org.eclipse.jetty.util.thread;version="[7.1.0,7.6.0)",
+ org.eclipse.jetty.continuation;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.http;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.io;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.security;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.security.authentication;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.server;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.server.handler;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.server.nio;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.servlet;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.util.component;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.util.log;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.util.security;version="[7.6.0,8.0.0)",
+ org.eclipse.jetty.util.thread;version="[7.6.0,8.0.0)",
  org.eclipse.jgit.errors;version="[2.0.0,2.1.0)",
  org.eclipse.jgit.http.server;version="[2.0.0,2.1.0)",
  org.eclipse.jgit.http.server.resolver;version="[2.0.0,2.1.0)",

org.eclipse.jgit.junit.http/src/org/eclipse/jgit/junit/http/AppServer.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2010, Google Inc.
+ * Copyright (C) 2010, 2012 Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -54,8 +54,6 @@ import java.net.UnknownHostException;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.eclipse.jetty.http.security.Constraint;
-import org.eclipse.jetty.http.security.Password;
 import org.eclipse.jetty.security.Authenticator;
 import org.eclipse.jetty.security.ConstraintMapping;
 import org.eclipse.jetty.security.ConstraintSecurityHandler;
@@ -67,7 +65,8 @@ import org.eclipse.jetty.server.UserIdentity;
 import org.eclipse.jetty.server.handler.ContextHandlerCollection;
 import org.eclipse.jetty.server.nio.SelectChannelConnector;
 import org.eclipse.jetty.servlet.ServletContextHandler;
-import org.eclipse.jetty.util.thread.QueuedThreadPool;
+import org.eclipse.jetty.util.security.Constraint;
+import org.eclipse.jetty.util.security.Password;
 import org.eclipse.jgit.transport.URIish;
 
 /**
@@ -112,17 +111,6 @@ public class AppServer {
 			throw new RuntimeException("Cannot find localhost", e);
 		}
 
-		// We need a handful of threads in the thread pool, otherwise
-		// our tests will deadlock when they can't open enough requests.
-		// In theory we only need 1 concurrent connection at a time, but
-		// I suspect the JRE isn't doing request pipelining on existing
-		// connections like we want it to.
-		//
-		final QueuedThreadPool pool = new QueuedThreadPool();
-		pool.setMinThreads(1);
-		pool.setMaxThreads(4);
-		pool.setMaxQueued(8);
-
 		contexts = new ContextHandlerCollection();
 
 		log = new TestRequestLog();
@@ -130,11 +118,7 @@ public class AppServer {
 
 		server = new Server();
 		server.setConnectors(new Connector[] { connector });
-		server.setThreadPool(pool);
 		server.setHandler(log);
-
-		server.setStopAtShutdown(false);
-		server.setGracefulShutdown(0);
 	}
 
 	/**

org.eclipse.jgit.packaging/org.eclipse.jgit.feature/pom.xml

@@ -63,7 +63,7 @@
     <dependency>
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit</artifactId>
-      <version>2.0.0-SNAPSHOT</version>
+      <version>${project.version}</version>
     </dependency>
   </dependencies>
 

org.eclipse.jgit.packaging/org.eclipse.jgit.junit.feature/pom.xml

@@ -63,17 +63,17 @@
     <dependency>
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit.junit</artifactId>
-      <version>2.0.0-SNAPSHOT</version>
+      <version>${project.version}</version>
     </dependency>
     <dependency>
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit.junit.http</artifactId>
-      <version>2.0.0-SNAPSHOT</version>
+      <version>${project.version}</version>
     </dependency>
     <dependency>
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit.http.server</artifactId>
-      <version>2.0.0-SNAPSHOT</version>
+      <version>${project.version}</version>
     </dependency>
   </dependencies>
 

org.eclipse.jgit.packaging/org.eclipse.jgit.repository/pom.xml

@@ -64,22 +64,22 @@
     <dependency>
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit</artifactId>
-      <version>2.0.0-SNAPSHOT</version>
+      <version>${project.version}</version>
     </dependency>
     <dependency>
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit.junit</artifactId>
-      <version>2.0.0-SNAPSHOT</version>
+      <version>${project.version}</version>
     </dependency>
     <dependency>
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit.junit.http</artifactId>
-      <version>2.0.0-SNAPSHOT</version>
+      <version>${project.version}</version>
     </dependency>
     <dependency>
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit.http.server</artifactId>
-      <version>2.0.0-SNAPSHOT</version>
+      <version>${project.version}</version>
     </dependency>
   </dependencies>
 

org.eclipse.jgit.packaging/pom.xml

@@ -60,6 +60,7 @@
 
   <properties>
     <tycho-version>0.14.1</tycho-version>
+    <jetty-version>7.6.0.v20120127</jetty-version>
     <eclipse-site>http://download.eclipse.org/releases/indigo</eclipse-site>
   </properties>
 
@@ -76,6 +77,11 @@
       <layout>p2</layout>
       <url>${eclipse-site}</url>
     </repository>
+    <repository>
+      <id>jetty</id>
+      <layout>p2</layout>
+      <url>http://download.eclipse.org/jetty/updates/jetty-bundles-7.x/${jetty-version}/</url>
+    </repository>
   </repositories>
 
   <dependencies>
@@ -83,7 +89,7 @@
     <dependency>
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit</artifactId>
-      <version>2.0.0-SNAPSHOT</version>
+      <version>${project.version}</version>
       <classifier>sources</classifier>
     </dependency>
   </dependencies>

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java

@@ -52,6 +52,7 @@ import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.PrintWriter;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.NoFilepatternException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheBuilder;
@@ -72,7 +73,7 @@ import org.junit.Test;
 public class AddCommandTest extends RepositoryTestCase {
 
 	@Test
-	public void testAddNothing() {
+	public void testAddNothing() throws GitAPIException {
 		Git git = new Git(db);
 
 		try {
@@ -85,7 +86,7 @@ public class AddCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testAddNonExistingSingleFile() throws NoFilepatternException {
+	public void testAddNonExistingSingleFile() throws GitAPIException {
 		Git git = new Git(db);
 
 		DirCache dc = git.add().addFilepattern("a.txt").call();
@@ -94,7 +95,7 @@ public class AddCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testAddExistingSingleFile() throws IOException, NoFilepatternException {
+	public void testAddExistingSingleFile() throws IOException, GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
@@ -112,7 +113,7 @@ public class AddCommandTest extends RepositoryTestCase {
 
 	@Test
 	public void testAddExistingSingleSmallFileWithNewLine() throws IOException,
-			NoFilepatternException {
+			GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
@@ -136,7 +137,7 @@ public class AddCommandTest extends RepositoryTestCase {
 
 	@Test
 	public void testAddExistingSingleMediumSizeFileWithNewLine()
-			throws IOException, NoFilepatternException {
+			throws IOException, GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		StringBuilder data = new StringBuilder();
@@ -165,7 +166,7 @@ public class AddCommandTest extends RepositoryTestCase {
 
 	@Test
 	public void testAddExistingSingleBinaryFile() throws IOException,
-			NoFilepatternException {
+			GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
@@ -188,7 +189,8 @@ public class AddCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testAddExistingSingleFileInSubDir() throws IOException, NoFilepatternException {
+	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);
@@ -206,7 +208,8 @@ public class AddCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testAddExistingSingleFileTwice() throws IOException, NoFilepatternException {
+	public void testAddExistingSingleFileTwice() throws IOException,
+			GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/BranchCommandTest.java

@@ -466,9 +466,7 @@ public class BranchCommandTest extends RepositoryTestCase {
 
 	public Ref createBranch(Git actGit, String name, boolean force,
 			String startPoint, SetupUpstreamMode mode)
-			throws JGitInternalException, RefAlreadyExistsException,
-			RefNotFoundException,
-			InvalidRefNameException {
+			throws JGitInternalException, GitAPIException {
 		CreateBranchCommand cmd = actGit.branchCreate();
 		cmd.setName(name);
 		cmd.setForce(force);

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java

@@ -56,11 +56,11 @@ import java.io.FileInputStream;
 import java.io.IOException;
 
 import org.eclipse.jgit.api.CheckoutResult.Status;
-import org.eclipse.jgit.api.errors.CheckoutConflictException;
-import org.eclipse.jgit.api.errors.InvalidRefNameException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
-import org.eclipse.jgit.api.errors.RefAlreadyExistsException;
 import org.eclipse.jgit.api.errors.RefNotFoundException;
+import org.eclipse.jgit.dircache.DirCache;
+import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.RefUpdate;
@@ -127,9 +127,7 @@ public class CheckoutCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testCheckoutToNonExistingBranch() throws JGitInternalException,
-			RefAlreadyExistsException, InvalidRefNameException,
-			CheckoutConflictException {
+	public void testCheckoutToNonExistingBranch() throws GitAPIException {
 		try {
 			git.checkout().setName("badbranch").call();
 			fail("Should have failed");
@@ -223,8 +221,7 @@ public class CheckoutCommandTest extends RepositoryTestCase {
 
 	@Test
 	public void testDetachedHeadOnCheckout() throws JGitInternalException,
-			RefAlreadyExistsException, RefNotFoundException,
-			InvalidRefNameException, IOException, CheckoutConflictException {
+			IOException, GitAPIException {
 		CheckoutCommand co = git.checkout();
 		co.setName("master").call();
 
@@ -236,4 +233,41 @@ public class CheckoutCommandTest extends RepositoryTestCase {
 		assertFalse(head.isSymbolic());
 		assertSame(head, head.getTarget());
 	}
+
+	@Test
+	public void testUpdateSmudgedEntries() throws Exception {
+		git.branchCreate().setName("test2").call();
+		RefUpdate rup = db.updateRef(Constants.HEAD);
+		rup.link("refs/heads/test2");
+
+		File file = new File(db.getWorkTree(), "Test.txt");
+		long size = file.length();
+		long mTime = file.lastModified() - 5000L;
+		assertTrue(file.setLastModified(mTime));
+
+		DirCache cache = DirCache.lock(db.getIndexFile(), db.getFS());
+		DirCacheEntry entry = cache.getEntry("Test.txt");
+		assertNotNull(entry);
+		entry.setLength(0);
+		entry.setLastModified(0);
+		cache.write();
+		assertTrue(cache.commit());
+
+		cache = DirCache.read(db.getIndexFile(), db.getFS());
+		entry = cache.getEntry("Test.txt");
+		assertNotNull(entry);
+		assertEquals(0, entry.getLength());
+		assertEquals(0, entry.getLastModified());
+
+		db.getIndexFile().setLastModified(
+				db.getIndexFile().lastModified() - 5000);
+
+		assertNotNull(git.checkout().setName("test").call());
+
+		cache = DirCache.read(db.getIndexFile(), db.getFS());
+		entry = cache.getEntry("Test.txt");
+		assertNotNull(entry);
+		assertEquals(size, entry.getLength());
+		assertEquals(mTime, entry.getLastModified());
+	}
 }

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CleanCommandTest.java

@@ -44,10 +44,10 @@ package org.eclipse.jgit.api;
 
 import static org.junit.Assert.assertTrue;
 
-import java.io.IOException;
 import java.util.Set;
 import java.util.TreeSet;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.errors.NoWorkTreeException;
 import org.eclipse.jgit.lib.RepositoryTestCase;
 import org.junit.Before;
@@ -75,7 +75,7 @@ public class CleanCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testClean() throws NoWorkTreeException, IOException {
+	public void testClean() throws NoWorkTreeException, GitAPIException {
 		// create status
 		StatusCommand command = git.status();
 		Status status = command.call();
@@ -94,7 +94,8 @@ public class CleanCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testCleanWithPaths() throws NoWorkTreeException, IOException {
+	public void testCleanWithPaths() throws NoWorkTreeException,
+			GitAPIException {
 		// create status
 		StatusCommand command = git.status();
 		Status status = command.call();
@@ -114,7 +115,8 @@ public class CleanCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testCleanWithDryRun() throws NoWorkTreeException, IOException {
+	public void testCleanWithDryRun() throws NoWorkTreeException,
+			GitAPIException {
 		// create status
 		StatusCommand command = git.status();
 		Status status = command.call();

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java

@@ -55,6 +55,7 @@ import java.util.List;
 import java.util.Map;
 
 import org.eclipse.jgit.api.ListBranchCommand.ListMode;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.lib.ConfigConstants;
@@ -103,7 +104,8 @@ public class CloneCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testCloneRepository() throws IOException {
+	public void testCloneRepository() throws IOException,
+			JGitInternalException, GitAPIException {
 		File directory = createTempDirectory("testCloneRepository");
 		CloneCommand command = Git.cloneRepository();
 		command.setDirectory(directory);
@@ -131,7 +133,8 @@ public class CloneCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testCloneRepositoryWithBranch() throws IOException {
+	public void testCloneRepositoryWithBranch() throws IOException,
+			JGitInternalException, GitAPIException {
 		File directory = createTempDirectory("testCloneRepositoryWithBranch");
 		CloneCommand command = Git.cloneRepository();
 		command.setBranch("refs/heads/master");
@@ -178,7 +181,8 @@ public class CloneCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testCloneRepositoryOnlyOneBranch() throws IOException {
+	public void testCloneRepositoryOnlyOneBranch() throws IOException,
+			JGitInternalException, GitAPIException {
 		File directory = createTempDirectory("testCloneRepositoryWithBranch");
 		CloneCommand command = Git.cloneRepository();
 		command.setBranch("refs/heads/master");
@@ -222,7 +226,7 @@ public class CloneCommandTest extends RepositoryTestCase {
 
 	@Test
 	public void testCloneRepositoryWhenDestinationDirectoryExistsAndIsNotEmpty()
-			throws IOException {
+			throws IOException, JGitInternalException, GitAPIException {
 		String dirName = "testCloneTargetDirectoryNotEmpty";
 		File directory = createTempDirectory(dirName);
 		CloneCommand command = Git.cloneRepository();

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitAndLogCommandTests.java

@@ -50,15 +50,12 @@ import static org.junit.Assert.fail;
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;
-import org.eclipse.jgit.api.errors.ConcurrentRefUpdateException;
+
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
-import org.eclipse.jgit.api.errors.NoFilepatternException;
-import org.eclipse.jgit.api.errors.NoHeadException;
 import org.eclipse.jgit.api.errors.NoMessageException;
-import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.MissingObjectException;
-import org.eclipse.jgit.errors.UnmergedPathException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.PersonIdent;
@@ -77,9 +74,8 @@ import org.junit.Test;
  */
 public class CommitAndLogCommandTests extends RepositoryTestCase {
 	@Test
-	public void testSomeCommits() throws NoHeadException, NoMessageException,
-			ConcurrentRefUpdateException, JGitInternalException,
-			WrongRepositoryStateException, IOException {
+	public void testSomeCommits() throws JGitInternalException, IOException,
+			GitAPIException {
 
 		// do 4 commits
 		Git git = new Git(db);
@@ -115,9 +111,8 @@ public class CommitAndLogCommandTests extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testLogWithFilter() throws IOException, NoFilepatternException,
-			NoHeadException, NoMessageException, ConcurrentRefUpdateException,
-			JGitInternalException, WrongRepositoryStateException {
+	public void testLogWithFilter() throws IOException, JGitInternalException,
+			GitAPIException {
 
 		Git git = new Git(db);
 
@@ -170,9 +165,7 @@ public class CommitAndLogCommandTests extends RepositoryTestCase {
 
 	// try to do a commit without specifying a message. Should fail!
 	@Test
-	public void testWrongParams() throws UnmergedPathException,
-			NoHeadException, ConcurrentRefUpdateException,
-			JGitInternalException, WrongRepositoryStateException {
+	public void testWrongParams() throws GitAPIException {
 		Git git = new Git(db);
 		try {
 			git.commit().setAuthor(author).call();
@@ -185,10 +178,7 @@ public class CommitAndLogCommandTests extends RepositoryTestCase {
 	// try to work with Commands after command has been invoked. Should throw
 	// exceptions
 	@Test
-	public void testMultipleInvocations() throws NoHeadException,
-			ConcurrentRefUpdateException, NoMessageException,
-			UnmergedPathException, JGitInternalException,
-			WrongRepositoryStateException {
+	public void testMultipleInvocations() throws GitAPIException {
 		Git git = new Git(db);
 		CommitCommand commitCmd = git.commit();
 		commitCmd.setMessage("initial commit").call();
@@ -211,9 +201,8 @@ public class CommitAndLogCommandTests extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testMergeEmptyBranches() throws IOException, NoHeadException,
-			NoMessageException, ConcurrentRefUpdateException,
-			JGitInternalException, WrongRepositoryStateException {
+	public void testMergeEmptyBranches() throws IOException,
+			JGitInternalException, GitAPIException {
 		Git git = new Git(db);
 		git.commit().setMessage("initial commit").call();
 		RefUpdate r = db.updateRef("refs/heads/side");
@@ -235,10 +224,8 @@ public class CommitAndLogCommandTests extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testAddUnstagedChanges() throws IOException, NoHeadException,
-			NoMessageException, ConcurrentRefUpdateException,
-			JGitInternalException, WrongRepositoryStateException,
-			NoFilepatternException {
+	public void testAddUnstagedChanges() throws IOException,
+			JGitInternalException, GitAPIException {
 		File file = new File(db.getWorkTree(), "a.txt");
 		FileUtils.createNewFile(file);
 		PrintWriter writer = new PrintWriter(file);
@@ -268,9 +255,7 @@ public class CommitAndLogCommandTests extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testModeChange() throws IOException, NoFilepatternException,
-			NoHeadException, NoMessageException, ConcurrentRefUpdateException,
-			JGitInternalException, WrongRepositoryStateException {
+	public void testModeChange() throws IOException, GitAPIException {
 		Git git = new Git(db);
 
 		// create file
@@ -298,10 +283,9 @@ public class CommitAndLogCommandTests extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testCommitRange() throws NoHeadException, NoMessageException,
-			UnmergedPathException, ConcurrentRefUpdateException,
-			JGitInternalException, WrongRepositoryStateException,
-			IncorrectObjectTypeException, MissingObjectException {
+	public void testCommitRange() throws GitAPIException,
+			JGitInternalException, MissingObjectException,
+			IncorrectObjectTypeException {
 		// do 4 commits and set the range to the second and fourth one
 		Git git = new Git(db);
 		git.commit().setMessage("first commit").call();
@@ -334,9 +318,8 @@ public class CommitAndLogCommandTests extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testCommitAmend() throws NoHeadException, NoMessageException,
-			ConcurrentRefUpdateException, JGitInternalException,
-			WrongRepositoryStateException, IOException {
+	public void testCommitAmend() throws JGitInternalException, IOException,
+			GitAPIException {
 		Git git = new Git(db);
 		git.commit().setMessage("first comit").call(); // typo
 		git.commit().setAmend(true).setMessage("first commit").call();
@@ -357,10 +340,8 @@ public class CommitAndLogCommandTests extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testInsertChangeId() throws NoHeadException,
-			NoMessageException,
-			UnmergedPathException, ConcurrentRefUpdateException,
-			JGitInternalException, WrongRepositoryStateException {
+	public void testInsertChangeId() throws JGitInternalException,
+			GitAPIException {
 		Git git = new Git(db);
 		String messageHeader = "Some header line\n\nSome detail explanation\n";
 		String changeIdTemplate = "\nChange-Id: I"

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitCommandTest.java

@@ -50,6 +50,7 @@ import java.io.File;
 import java.util.List;
 
 import org.eclipse.jgit.diff.DiffEntry;
+import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
@@ -258,4 +259,110 @@ public class CommitCommandTest extends RepositoryTestCase {
 		assertEquals(path, subDiff.getNewPath());
 		assertEquals(path, subDiff.getOldPath());
 	}
+
+	@Test
+	public void commitUpdatesSmudgedEntries() throws Exception {
+		Git git = new Git(db);
+
+		File file1 = writeTrashFile("file1.txt", "content1");
+		assertTrue(file1.setLastModified(file1.lastModified() - 5000));
+		File file2 = writeTrashFile("file2.txt", "content2");
+		assertTrue(file2.setLastModified(file2.lastModified() - 5000));
+		File file3 = writeTrashFile("file3.txt", "content3");
+		assertTrue(file3.setLastModified(file3.lastModified() - 5000));
+
+		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());
+
+		long indexTime = db.getIndexFile().lastModified();
+		db.getIndexFile().setLastModified(indexTime - 5000);
+
+		write(file1, "content4");
+		assertTrue(file1.setLastModified(file1.lastModified() + 1000));
+		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());
+	}
+
+	@Test
+	public void commitIgnoresSmudgedEntryWithDifferentId() throws Exception {
+		Git git = new Git(db);
+
+		File file1 = writeTrashFile("file1.txt", "content1");
+		assertTrue(file1.setLastModified(file1.lastModified() - 5000));
+		File file2 = writeTrashFile("file2.txt", "content2");
+		assertTrue(file2.setLastModified(file2.lastModified() - 5000));
+
+		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());
+
+		long indexTime = db.getIndexFile().lastModified();
+		db.getIndexFile().setLastModified(indexTime - 5000);
+
+		write(file1, "content5");
+		assertTrue(file1.setLastModified(file1.lastModified() + 1000));
+
+		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());
+	}
 }

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/GitConstructionTest.java

@@ -48,6 +48,8 @@ import static org.junit.Assert.fail;
 import java.io.IOException;
 
 import org.eclipse.jgit.api.ListBranchCommand.ListMode;
+import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.errors.RepositoryNotFoundException;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.RepositoryTestCase;
@@ -84,7 +86,7 @@ public class GitConstructionTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testWrap() {
+	public void testWrap() throws JGitInternalException, GitAPIException {
 		Git git = Git.wrap(db);
 		assertEquals(1, git.branchList().call().size());
 
@@ -101,7 +103,8 @@ public class GitConstructionTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testOpen() throws IOException {
+	public void testOpen() throws IOException, JGitInternalException,
+			GitAPIException {
 		Git git = Git.open(db.getDirectory());
 		assertEquals(1, git.branchList().call().size());
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/InitCommandTest.java

@@ -48,6 +48,8 @@ import static org.junit.Assert.assertTrue;
 import java.io.File;
 import java.io.IOException;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.RepositoryTestCase;
 import org.junit.Before;
@@ -62,7 +64,8 @@ public class InitCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testInitRepository() throws IOException {
+	public void testInitRepository() throws IOException, JGitInternalException,
+			GitAPIException {
 		File directory = createTempDirectory("testInitRepository");
 		InitCommand command = new InitCommand();
 		command.setDirectory(directory);
@@ -72,7 +75,8 @@ public class InitCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testInitNonEmptyRepository() throws IOException {
+	public void testInitNonEmptyRepository() throws IOException,
+			JGitInternalException, GitAPIException {
 		File directory = createTempDirectory("testInitRepository2");
 		File someFile = new File(directory, "someFile");
 		someFile.createNewFile();
@@ -86,7 +90,8 @@ public class InitCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testInitBareRepository() throws IOException {
+	public void testInitBareRepository() throws IOException,
+			JGitInternalException, GitAPIException {
 		File directory = createTempDirectory("testInitBareRepository");
 		InitCommand command = new InitCommand();
 		command.setDirectory(directory);

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RebaseCommandTest.java

@@ -293,7 +293,8 @@ public class RebaseCommandTest extends RepositoryTestCase {
 		// change third line in topic branch
 		writeTrashFile(FILE1, "1\n2\n3\ntopic\n");
 		git.add().addFilepattern(FILE1).call();
-		git.commit().setMessage("change file1 in topic").call();
+		RevCommit origHead = git.commit().setMessage("change file1 in topic")
+				.call();
 
 		RebaseResult res = git.rebase().setUpstream("refs/heads/master").call();
 		assertEquals(Status.OK, res.getStatus());
@@ -302,6 +303,7 @@ public class RebaseCommandTest extends RepositoryTestCase {
 		assertEquals("refs/heads/topic", db.getFullBranch());
 		assertEquals(lastMasterChange, new RevWalk(db).parseCommit(
 				db.resolve(Constants.HEAD)).getParent(0));
+		assertEquals(origHead, db.readOrigHead());
 	}
 
 	@Test

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java

@@ -54,12 +54,8 @@ import java.io.IOException;
 import java.io.PrintWriter;
 
 import org.eclipse.jgit.api.ResetCommand.ResetType;
-import org.eclipse.jgit.api.errors.ConcurrentRefUpdateException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
-import org.eclipse.jgit.api.errors.NoFilepatternException;
-import org.eclipse.jgit.api.errors.NoHeadException;
-import org.eclipse.jgit.api.errors.NoMessageException;
-import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.errors.AmbiguousObjectException;
@@ -87,9 +83,8 @@ public class ResetCommandTest extends RepositoryTestCase {
 
 	private DirCacheEntry prestage;
 
-	public void setupRepository() throws IOException, NoFilepatternException,
-			NoHeadException, NoMessageException, ConcurrentRefUpdateException,
-			JGitInternalException, WrongRepositoryStateException {
+	public void setupRepository() throws IOException, JGitInternalException,
+			GitAPIException {
 
 		// create initial commit
 		git = new Git(db);
@@ -138,9 +133,7 @@ public class ResetCommandTest extends RepositoryTestCase {
 
 	@Test
 	public void testHardReset() throws JGitInternalException,
-			AmbiguousObjectException, IOException, NoFilepatternException,
-			NoHeadException, NoMessageException, ConcurrentRefUpdateException,
-			WrongRepositoryStateException {
+			AmbiguousObjectException, IOException, GitAPIException {
 		setupRepository();
 		ObjectId prevHead = db.resolve(Constants.HEAD);
 		git.reset().setMode(ResetType.HARD).setRef(initialCommit.getName())
@@ -156,11 +149,12 @@ public class ResetCommandTest extends RepositoryTestCase {
 		assertFalse(inHead(fileInIndexPath));
 		assertFalse(inIndex(indexFile.getName()));
 		assertReflog(prevHead, head);
+		assertEquals(prevHead, db.readOrigHead());
 	}
 
 	@Test
 	public void testResetToNonexistingHEAD() throws JGitInternalException,
-			AmbiguousObjectException, IOException {
+			AmbiguousObjectException, IOException, GitAPIException {
 
 		// create a file in the working tree of a fresh repo
 		git = new Git(db);
@@ -176,9 +170,7 @@ public class ResetCommandTest extends RepositoryTestCase {
 
 	@Test
 	public void testSoftReset() throws JGitInternalException,
-			AmbiguousObjectException, IOException, NoFilepatternException,
-			NoHeadException, NoMessageException, ConcurrentRefUpdateException,
-			WrongRepositoryStateException {
+			AmbiguousObjectException, IOException, GitAPIException {
 		setupRepository();
 		ObjectId prevHead = db.resolve(Constants.HEAD);
 		git.reset().setMode(ResetType.SOFT).setRef(initialCommit.getName())
@@ -194,13 +186,12 @@ public class ResetCommandTest extends RepositoryTestCase {
 		assertFalse(inHead(fileInIndexPath));
 		assertTrue(inIndex(indexFile.getName()));
 		assertReflog(prevHead, head);
+		assertEquals(prevHead, db.readOrigHead());
 	}
 
 	@Test
 	public void testMixedReset() throws JGitInternalException,
-			AmbiguousObjectException, IOException, NoFilepatternException,
-			NoHeadException, NoMessageException, ConcurrentRefUpdateException,
-			WrongRepositoryStateException {
+			AmbiguousObjectException, IOException, GitAPIException {
 		setupRepository();
 		ObjectId prevHead = db.resolve(Constants.HEAD);
 		git.reset().setMode(ResetType.MIXED).setRef(initialCommit.getName())
@@ -217,6 +208,49 @@ public class ResetCommandTest extends RepositoryTestCase {
 		assertFalse(inIndex(indexFile.getName()));
 
 		assertReflog(prevHead, head);
+		assertEquals(prevHead, db.readOrigHead());
+	}
+
+	@Test
+	public void testMixedResetRetainsSizeAndModifiedTime() throws Exception {
+		git = new Git(db);
+
+		writeTrashFile("a.txt", "a").setLastModified(
+				System.currentTimeMillis() - 60 * 1000);
+		assertNotNull(git.add().addFilepattern("a.txt").call());
+		assertNotNull(git.commit().setMessage("a commit").call());
+
+		writeTrashFile("b.txt", "b").setLastModified(
+				System.currentTimeMillis() - 60 * 1000);
+		assertNotNull(git.add().addFilepattern("b.txt").call());
+		RevCommit commit2 = git.commit().setMessage("b commit").call();
+		assertNotNull(commit2);
+
+		DirCache cache = db.readDirCache();
+
+		DirCacheEntry aEntry = cache.getEntry("a.txt");
+		assertNotNull(aEntry);
+		assertTrue(aEntry.getLength() > 0);
+		assertTrue(aEntry.getLastModified() > 0);
+
+		DirCacheEntry bEntry = cache.getEntry("b.txt");
+		assertNotNull(bEntry);
+		assertTrue(bEntry.getLength() > 0);
+		assertTrue(bEntry.getLastModified() > 0);
+
+		git.reset().setMode(ResetType.MIXED).setRef(commit2.getName()).call();
+
+		cache = db.readDirCache();
+
+		DirCacheEntry mixedAEntry = cache.getEntry("a.txt");
+		assertNotNull(mixedAEntry);
+		assertEquals(aEntry.getLastModified(), mixedAEntry.getLastModified());
+		assertEquals(aEntry.getLastModified(), mixedAEntry.getLastModified());
+
+		DirCacheEntry mixedBEntry = cache.getEntry("b.txt");
+		assertNotNull(mixedBEntry);
+		assertEquals(bEntry.getLastModified(), mixedBEntry.getLastModified());
+		assertEquals(bEntry.getLastModified(), mixedBEntry.getLastModified());
 	}
 
 	@Test

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RmCommandTest.java

@@ -46,8 +46,8 @@ import static org.junit.Assert.assertEquals;
 
 import java.io.IOException;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
-import org.eclipse.jgit.api.errors.NoFilepatternException;
 import org.eclipse.jgit.lib.RepositoryTestCase;
 import org.junit.Before;
 import org.junit.Test;
@@ -71,7 +71,7 @@ public class RmCommandTest extends RepositoryTestCase {
 
 	@Test
 	public void testRemove() throws JGitInternalException,
-			NoFilepatternException, IllegalStateException, IOException {
+			IllegalStateException, IOException, GitAPIException {
 		assertEquals("[test.txt, mode:100644, content:Hello world]",
 				indexState(CONTENT));
 		RmCommand command = git.rm();

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/StatusCommandTest.java

@@ -52,13 +52,15 @@ import java.util.Set;
 
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.NoFilepatternException;
+import org.eclipse.jgit.errors.NoWorkTreeException;
 import org.eclipse.jgit.lib.RepositoryTestCase;
 import org.junit.Test;
 
 public class StatusCommandTest extends RepositoryTestCase {
 
 	@Test
-	public void testEmptyStatus() throws IOException {
+	public void testEmptyStatus() throws NoWorkTreeException,
+			GitAPIException {
 		Git git = new Git(db);
 
 		Status stat = git.status().call();

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/TagCommandTest.java

@@ -48,15 +48,9 @@ import static org.junit.Assert.fail;
 import java.io.IOException;
 import java.util.List;
 
-import org.eclipse.jgit.api.errors.ConcurrentRefUpdateException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidTagNameException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
-import org.eclipse.jgit.api.errors.NoHeadException;
-import org.eclipse.jgit.api.errors.NoMessageException;
-import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
-import org.eclipse.jgit.errors.IncorrectObjectTypeException;
-import org.eclipse.jgit.errors.MissingObjectException;
-import org.eclipse.jgit.errors.UnmergedPathException;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.RepositoryTestCase;
@@ -67,10 +61,7 @@ import org.junit.Test;
 public class TagCommandTest extends RepositoryTestCase {
 
 	@Test
-	public void testTaggingOnHead() throws NoHeadException, NoMessageException,
-			ConcurrentRefUpdateException, JGitInternalException,
-			WrongRepositoryStateException, InvalidTagNameException,
-			MissingObjectException, IncorrectObjectTypeException, IOException {
+	public void testTaggingOnHead() throws GitAPIException, IOException {
 		Git git = new Git(db);
 		RevCommit commit = git.commit().setMessage("initial commit").call();
 		Ref tagRef = git.tag().setName("tag").call();
@@ -80,10 +71,7 @@ public class TagCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testTagging() throws NoHeadException, NoMessageException,
-			UnmergedPathException, ConcurrentRefUpdateException,
-			JGitInternalException, WrongRepositoryStateException,
-			InvalidTagNameException {
+	public void testTagging() throws GitAPIException, JGitInternalException {
 		Git git = new Git(db);
 		git.commit().setMessage("initial commit").call();
 		RevCommit commit = git.commit().setMessage("second commit").call();
@@ -93,9 +81,7 @@ public class TagCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testEmptyTagName() throws NoHeadException, NoMessageException,
-			UnmergedPathException, ConcurrentRefUpdateException,
-			JGitInternalException, WrongRepositoryStateException {
+	public void testEmptyTagName() throws GitAPIException {
 		Git git = new Git(db);
 		git.commit().setMessage("initial commit").call();
 		try {
@@ -108,10 +94,7 @@ public class TagCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testInvalidTagName() throws NoHeadException,
-			NoMessageException, UnmergedPathException,
-			ConcurrentRefUpdateException, JGitInternalException,
-			WrongRepositoryStateException {
+	public void testInvalidTagName() throws GitAPIException {
 		Git git = new Git(db);
 		git.commit().setMessage("initial commit").call();
 		try {
@@ -123,10 +106,7 @@ public class TagCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testFailureOnSignedTags() throws NoHeadException,
-			NoMessageException, UnmergedPathException,
-			ConcurrentRefUpdateException, JGitInternalException,
-			WrongRepositoryStateException, InvalidTagNameException {
+	public void testFailureOnSignedTags() throws GitAPIException {
 		Git git = new Git(db);
 		git.commit().setMessage("initial commit").call();
 		try {

org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutMaliciousPathTest.java

@@ -46,14 +46,8 @@ import java.io.IOException;
 import java.util.Arrays;
 
 import org.eclipse.jgit.api.Git;
-import org.eclipse.jgit.api.errors.CheckoutConflictException;
-import org.eclipse.jgit.api.errors.InvalidRefNameException;
-import org.eclipse.jgit.api.errors.JGitInternalException;
-import org.eclipse.jgit.api.errors.RefAlreadyExistsException;
-import org.eclipse.jgit.api.errors.RefNotFoundException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.dircache.InvalidPathException;
-import org.eclipse.jgit.errors.IncorrectObjectTypeException;
-import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.junit.MockSystemReader;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.util.SystemReader;
@@ -338,20 +332,11 @@ public class DirCacheCheckoutMaliciousPathTest extends RepositoryTestCase {
 	 *            perform the actual test on the second checkout
 	 * @param path
 	 *            to the blob, one or more levels
+	 * @throws GitAPIException
 	 * @throws IOException
-	 * @throws RefAlreadyExistsException
-	 * @throws RefNotFoundException
-	 * @throws InvalidRefNameException
-	 * @throws MissingObjectException
-	 * @throws IncorrectObjectTypeException
-	 * @throws CheckoutConflictException
-	 * @throws JGitInternalException
 	 */
-	private void testMaliciousPath(boolean good, boolean secondCheckout, String... path)
-			throws IOException, RefAlreadyExistsException,
-			RefNotFoundException, InvalidRefNameException,
-			MissingObjectException, IncorrectObjectTypeException,
-			JGitInternalException, CheckoutConflictException {
+	private void testMaliciousPath(boolean good, boolean secondCheckout,
+			String... path) throws GitAPIException, IOException {
 		Git git = new Git(db);
 		ObjectInserter newObjectInserter;
 		newObjectInserter = git.getRepository().newObjectInserter();

org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffTest.java

@@ -59,7 +59,7 @@ import java.util.TreeSet;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.MergeResult;
 import org.eclipse.jgit.api.MergeResult.MergeStatus;
-import org.eclipse.jgit.api.errors.NoFilepatternException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEditor;
 import org.eclipse.jgit.dircache.DirCacheEditor.PathEdit;
@@ -139,7 +139,7 @@ public class IndexDiffTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testModified() throws IOException, NoFilepatternException {
+	public void testModified() throws IOException, GitAPIException {
 
 		writeTrashFile("file2", "file2");
 		writeTrashFile("dir/file3", "dir/file3");
@@ -291,8 +291,7 @@ public class IndexDiffTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testUnchangedSimple() throws IOException,
-			NoFilepatternException {
+	public void testUnchangedSimple() throws IOException, GitAPIException {
 		writeTrashFile("a.b", "a.b");
 		writeTrashFile("a.c", "a.c");
 		writeTrashFile("a=c", "a=c");
@@ -328,11 +327,10 @@ public class IndexDiffTest extends RepositoryTestCase {
 	 * used by Git.
 	 *
 	 * @throws IOException
-	 * @throws NoFilepatternException
+	 * @throws GitAPIException
 	 */
 	@Test
-	public void testUnchangedComplex() throws IOException,
-			NoFilepatternException {
+	public void testUnchangedComplex() throws IOException, GitAPIException {
 		Git git = new Git(db);
 		writeTrashFile("a.b", "a.b");
 		writeTrashFile("a.c", "a.c");

org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/PackWriterTest.java

@@ -63,10 +63,14 @@ import java.util.Set;
 
 import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.junit.JGitTestUtil;
+import org.eclipse.jgit.junit.TestRepository;
+import org.eclipse.jgit.junit.TestRepository.BranchBuilder;
 import org.eclipse.jgit.lib.NullProgressMonitor;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectInserter;
 import org.eclipse.jgit.lib.SampleDataRepositoryTestCase;
+import org.eclipse.jgit.revwalk.RevBlob;
+import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevObject;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.storage.file.PackIndex.MutableEntry;
@@ -447,6 +451,68 @@ public class PackWriterTest extends SampleDataRepositoryTestCase {
 		}
 	}
 
+	@Test
+	public void testExclude() throws Exception {
+		FileRepository repo = createBareRepository();
+
+		TestRepository<FileRepository> testRepo = new TestRepository<FileRepository>(
+				repo);
+		BranchBuilder bb = testRepo.branch("refs/heads/master");
+		RevBlob contentA = testRepo.blob("A");
+		RevCommit c1 = bb.commit().add("f", contentA).create();
+		testRepo.getRevWalk().parseHeaders(c1);
+		PackIndex pf1 = writePack(repo, Collections.singleton(c1),
+				Collections.<PackIndex> emptySet());
+		assertContent(
+				pf1,
+				Arrays.asList(c1.getId(), c1.getTree().getId(),
+						contentA.getId()));
+		RevBlob contentB = testRepo.blob("B");
+		RevCommit c2 = bb.commit().add("f", contentB).create();
+		testRepo.getRevWalk().parseHeaders(c2);
+		PackIndex pf2 = writePack(repo, Collections.singleton(c2),
+				Collections.singleton(pf1));
+		assertContent(
+				pf2,
+				Arrays.asList(c2.getId(), c2.getTree().getId(),
+						contentB.getId()));
+	}
+
+	private void assertContent(PackIndex pi, List<ObjectId> expected) {
+		assertEquals("Pack index has wrong size.", expected.size(),
+				pi.getObjectCount());
+		for (int i = 0; i < pi.getObjectCount(); i++)
+			assertTrue(
+					"Pack index didn't contain the expected id "
+							+ pi.getObjectId(i),
+					expected.contains(pi.getObjectId(i)));
+	}
+
+	private PackIndex writePack(FileRepository repo,
+			Set<? extends ObjectId> want, Set<PackIndex> excludeObjects)
+			throws IOException {
+		PackWriter pw = new PackWriter(repo);
+		pw.setDeltaBaseAsOffset(true);
+		pw.setReuseDeltaCommits(false);
+		for (PackIndex idx : excludeObjects)
+			pw.excludeObjects(idx);
+		pw.preparePack(NullProgressMonitor.INSTANCE, want,
+				Collections.<ObjectId> emptySet());
+		String id = pw.computeName().getName();
+		File packdir = new File(repo.getObjectsDirectory(), "pack");
+		File packFile = new File(packdir, "pack-" + id + ".pack");
+		FileOutputStream packOS = new FileOutputStream(packFile);
+		pw.writePack(NullProgressMonitor.INSTANCE,
+				NullProgressMonitor.INSTANCE, packOS);
+		packOS.close();
+		File idxFile = new File(packdir, "pack-" + id + ".idx");
+		FileOutputStream idxOS = new FileOutputStream(idxFile);
+		pw.writeIndex(idxOS);
+		idxOS.close();
+		pw.release();
+		return PackIndex.open(idxFile);
+	}
+
 	// TODO: testWritePackDeltasCycle()
 	// TODO: testWritePackDeltasDepth()
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/RefDirectoryTest.java

@@ -60,6 +60,8 @@ import static org.junit.Assert.fail;
 import java.io.File;
 import java.io.IOException;
 import java.util.Map;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.concurrent.atomic.AtomicReference;
 
 import org.eclipse.jgit.events.ListenerHandle;
 import org.eclipse.jgit.events.RefsChangedEvent;
@@ -1077,6 +1079,36 @@ public class RefDirectoryTest extends LocalDiskRepositoryTestCase {
 		assertSame(master_p2, refdir.peel(master_p2));
 	}
 
+	@Test
+	public void testRefsChangedStackOverflow() throws Exception {
+		final FileRepository newRepo = createBareRepository();
+		final RefDatabase refDb = newRepo.getRefDatabase();
+		File packedRefs = new File(newRepo.getDirectory(), "packed-refs");
+		assertTrue(packedRefs.createNewFile());
+		final AtomicReference<StackOverflowError> error = new AtomicReference<StackOverflowError>();
+		final AtomicReference<IOException> exception = new AtomicReference<IOException>();
+		final AtomicInteger changeCount = new AtomicInteger();
+		newRepo.getListenerList().addRefsChangedListener(
+				new RefsChangedListener() {
+
+					public void onRefsChanged(RefsChangedEvent event) {
+						try {
+							refDb.getRefs("ref");
+							changeCount.incrementAndGet();
+						} catch (StackOverflowError soe) {
+							error.set(soe);
+						} catch (IOException ioe) {
+							exception.set(ioe);
+						}
+					}
+				});
+		refDb.getRefs("ref");
+		refDb.getRefs("ref");
+		assertNull(error.get());
+		assertNull(exception.get());
+		assertEquals(1, changeCount.get());
+	}
+
 	private void writeLooseRef(String name, AnyObjectId id) throws IOException {
 		writeLooseRef(name, id.name() + "\n");
 	}

org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleAddTest.java

@@ -53,6 +53,7 @@ import java.text.MessageFormat;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.Status;
 import org.eclipse.jgit.api.SubmoduleAddCommand;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEditor;
@@ -75,7 +76,7 @@ import org.junit.Test;
 public class SubmoduleAddTest extends RepositoryTestCase {
 
 	@Test
-	public void commandWithNullPath() {
+	public void commandWithNullPath() throws GitAPIException {
 		try {
 			new SubmoduleAddCommand(db).setURI("uri").call();
 			fail("Exception not thrown");
@@ -85,7 +86,7 @@ public class SubmoduleAddTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void commandWithEmptyPath() {
+	public void commandWithEmptyPath() throws GitAPIException {
 		try {
 			new SubmoduleAddCommand(db).setPath("").setURI("uri").call();
 			fail("Exception not thrown");
@@ -95,7 +96,7 @@ public class SubmoduleAddTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void commandWithNullUri() {
+	public void commandWithNullUri() throws GitAPIException {
 		try {
 			new SubmoduleAddCommand(db).setPath("sub").call();
 			fail("Exception not thrown");
@@ -105,7 +106,7 @@ public class SubmoduleAddTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void commandWithEmptyUri() {
+	public void commandWithEmptyUri() throws GitAPIException {
 		try {
 			new SubmoduleAddCommand(db).setPath("sub").setURI("").call();
 			fail("Exception not thrown");

org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleInitTest.java

@@ -53,6 +53,7 @@ import java.io.IOException;
 import java.util.Collection;
 
 import org.eclipse.jgit.api.SubmoduleInitCommand;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEditor;
@@ -73,7 +74,7 @@ import org.junit.Test;
 public class SubmoduleInitTest extends RepositoryTestCase {
 
 	@Test
-	public void repositoryWithNoSubmodules() {
+	public void repositoryWithNoSubmodules() throws GitAPIException {
 		SubmoduleInitCommand command = new SubmoduleInitCommand(db);
 		Collection<String> modules = command.call();
 		assertNotNull(modules);
@@ -82,7 +83,7 @@ public class SubmoduleInitTest extends RepositoryTestCase {
 
 	@Test
 	public void repositoryWithUninitializedModule() throws IOException,
-			ConfigInvalidException {
+			ConfigInvalidException, GitAPIException {
 		final String path = addSubmoduleToIndex();
 
 		SubmoduleWalk generator = SubmoduleWalk.forIndex(db);
@@ -156,7 +157,7 @@ public class SubmoduleInitTest extends RepositoryTestCase {
 
 	@Test
 	public void resolveOneLevelHigherRelativeUrl() throws IOException,
-			ConfigInvalidException {
+			ConfigInvalidException, GitAPIException {
 		final String path = addSubmoduleToIndex();
 
 		String base = "git://server/repo.git";
@@ -197,7 +198,7 @@ public class SubmoduleInitTest extends RepositoryTestCase {
 
 	@Test
 	public void resolveTwoLevelHigherRelativeUrl() throws IOException,
-			ConfigInvalidException {
+			ConfigInvalidException, GitAPIException {
 		final String path = addSubmoduleToIndex();
 
 		String base = "git://server/repo.git";
@@ -238,7 +239,7 @@ public class SubmoduleInitTest extends RepositoryTestCase {
 
 	@Test
 	public void resolveWorkingDirectoryRelativeUrl() throws IOException,
-			ConfigInvalidException {
+			GitAPIException, ConfigInvalidException {
 		final String path = addSubmoduleToIndex();
 
 		String base = db.getWorkTree().getAbsolutePath();
@@ -281,7 +282,7 @@ public class SubmoduleInitTest extends RepositoryTestCase {
 
 	@Test
 	public void resolveInvalidParentUrl() throws IOException,
-			ConfigInvalidException {
+			ConfigInvalidException, GitAPIException {
 		final String path = addSubmoduleToIndex();
 
 		String base = "no_slash";

org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleStatusTest.java

@@ -53,6 +53,7 @@ import java.util.Map.Entry;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.SubmoduleStatusCommand;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEditor;
 import org.eclipse.jgit.dircache.DirCacheEditor.PathEdit;
@@ -74,7 +75,7 @@ import org.junit.Test;
 public class SubmoduleStatusTest extends RepositoryTestCase {
 
 	@Test
-	public void repositoryWithNoSubmodules() {
+	public void repositoryWithNoSubmodules() throws GitAPIException {
 		SubmoduleStatusCommand command = new SubmoduleStatusCommand(db);
 		Map<String, SubmoduleStatus> statuses = command.call();
 		assertNotNull(statuses);
@@ -82,7 +83,8 @@ public class SubmoduleStatusTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void repositoryWithMissingSubmodule() throws IOException {
+	public void repositoryWithMissingSubmodule() throws IOException,
+			GitAPIException {
 		final ObjectId id = ObjectId
 				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
 		final String path = "sub";
@@ -113,7 +115,8 @@ public class SubmoduleStatusTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void repositoryWithUninitializedSubmodule() throws IOException {
+	public void repositoryWithUninitializedSubmodule() throws IOException,
+			GitAPIException {
 		final ObjectId id = ObjectId
 				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
 		final String path = "sub";
@@ -152,7 +155,8 @@ public class SubmoduleStatusTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void repositoryWithNoHeadInSubmodule() throws IOException {
+	public void repositoryWithNoHeadInSubmodule() throws IOException,
+			GitAPIException {
 		final ObjectId id = ObjectId
 				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
 		final String path = "sub";
@@ -202,7 +206,8 @@ public class SubmoduleStatusTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void repositoryWithNoSubmoduleRepository() throws IOException {
+	public void repositoryWithNoSubmoduleRepository() throws IOException,
+			GitAPIException {
 		final ObjectId id = ObjectId
 				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
 		final String path = "sub";
@@ -247,7 +252,8 @@ public class SubmoduleStatusTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void repositoryWithInitializedSubmodule() throws IOException {
+	public void repositoryWithInitializedSubmodule() throws IOException,
+			GitAPIException {
 		final ObjectId id = ObjectId
 				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
 		final String path = "sub";
@@ -302,7 +308,7 @@ public class SubmoduleStatusTest extends RepositoryTestCase {
 
 	@Test
 	public void repositoryWithDifferentRevCheckedOutSubmodule()
-			throws IOException {
+			throws IOException, GitAPIException {
 		final ObjectId id = ObjectId
 				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
 		final String path = "sub";

org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleSyncTest.java

@@ -53,6 +53,7 @@ import java.util.Map.Entry;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.SubmoduleSyncCommand;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEditor;
 import org.eclipse.jgit.dircache.DirCacheEditor.PathEdit;
@@ -73,7 +74,7 @@ import org.junit.Test;
 public class SubmoduleSyncTest extends RepositoryTestCase {
 
 	@Test
-	public void repositoryWithNoSubmodules() {
+	public void repositoryWithNoSubmodules() throws GitAPIException {
 		SubmoduleSyncCommand command = new SubmoduleSyncCommand(db);
 		Map<String, String> modules = command.call();
 		assertNotNull(modules);

org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleUpdateTest.java

@@ -52,6 +52,7 @@ import java.util.Collection;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.SubmoduleUpdateCommand;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEditor;
 import org.eclipse.jgit.dircache.DirCacheEditor.PathEdit;
@@ -73,7 +74,7 @@ import org.junit.Test;
 public class SubmoduleUpdateTest extends RepositoryTestCase {
 
 	@Test
-	public void repositoryWithNoSubmodules() {
+	public void repositoryWithNoSubmodules() throws GitAPIException {
 		SubmoduleUpdateCommand command = new SubmoduleUpdateCommand(db);
 		Collection<String> modules = command.call();
 		assertNotNull(modules);
@@ -125,7 +126,8 @@ public class SubmoduleUpdateTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void repositoryWithUnconfiguredSubmodule() throws IOException {
+	public void repositoryWithUnconfiguredSubmodule() throws IOException,
+			GitAPIException {
 		final ObjectId id = ObjectId
 				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
 		final String path = "sub";
@@ -159,7 +161,8 @@ public class SubmoduleUpdateTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void repositoryWithInitializedSubmodule() throws IOException {
+	public void repositoryWithInitializedSubmodule() throws IOException,
+			GitAPIException {
 		final ObjectId id = ObjectId
 				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
 		final String path = "sub";

org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java

@@ -48,6 +48,7 @@ import java.io.InputStream;
 import java.util.Collection;
 import java.util.LinkedList;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.NoFilepatternException;
 import org.eclipse.jgit.dircache.DirCache;
@@ -122,7 +123,7 @@ public class AddCommand extends GitCommand<DirCache> {
 	 *
 	 * @return the DirCache after Add
 	 */
-	public DirCache call() throws NoFilepatternException {
+	public DirCache call() throws GitAPIException, NoFilepatternException {
 
 		if (filepatterns.isEmpty())
 			throw new NoFilepatternException(JGitText.get().atLeastOnePatternIsRequired);

org.eclipse.jgit/src/org/eclipse/jgit/api/AddNoteCommand.java

@@ -44,6 +44,7 @@ package org.eclipse.jgit.api;
 
 import java.io.IOException;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.lib.CommitBuilder;
 import org.eclipse.jgit.lib.Constants;
@@ -80,11 +81,7 @@ public class AddNoteCommand extends GitCommand<Note> {
 		super(repo);
 	}
 
-	/**
-	 * @throws JGitInternalException
-	 *             upon internal failure
-	 */
-	public Note call() throws JGitInternalException {
+	public Note call() throws GitAPIException {
 		checkCallable();
 		RevWalk walk = new RevWalk(repo);
 		ObjectInserter inserter = repo.newObjectInserter();

org.eclipse.jgit/src/org/eclipse/jgit/api/BlameCommand.java

@@ -48,6 +48,7 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.blame.BlameGenerator;
 import org.eclipse.jgit.blame.BlameResult;
@@ -189,7 +190,7 @@ public class BlameCommand extends GitCommand<BlameResult> {
 	 *
 	 * @return list of lines
 	 */
-	public BlameResult call() throws JGitInternalException {
+	public BlameResult call() throws GitAPIException {
 		checkCallable();
 		BlameGenerator gen = new BlameGenerator(repo, path);
 		try {

org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java

@@ -51,6 +51,7 @@ import java.util.List;
 
 import org.eclipse.jgit.api.CheckoutResult.Status;
 import org.eclipse.jgit.api.errors.CheckoutConflictException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRefNameException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.RefAlreadyExistsException;
@@ -121,9 +122,11 @@ public class CheckoutCommand extends GitCommand<Ref> {
 	 * @throws InvalidRefNameException
 	 *             if the provided name is <code>null</code> or otherwise
 	 *             invalid
+	 * @throws CheckoutConflictException
+	 *             if the checkout results in a conflict
 	 * @return the newly created branch
 	 */
-	public Ref call() throws JGitInternalException, RefAlreadyExistsException,
+	public Ref call() throws GitAPIException, RefAlreadyExistsException,
 			RefNotFoundException, InvalidRefNameException,
 			CheckoutConflictException {
 		checkCallable();

org.eclipse.jgit/src/org/eclipse/jgit/api/CleanCommand.java

@@ -49,6 +49,7 @@ import java.util.Collections;
 import java.util.Set;
 import java.util.TreeSet;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.util.FileUtils;
@@ -81,7 +82,7 @@ public class CleanCommand extends GitCommand<Set<String>> {
 	 *
 	 * @return a set of strings representing each file cleaned.
 	 */
-	public Set<String> call() {
+	public Set<String> call() throws GitAPIException {
 		Set<String> files = new TreeSet<String>();
 		try {
 			StatusCommand command = new StatusCommand(repo);
@@ -113,7 +114,7 @@ public class CleanCommand extends GitCommand<Set<String>> {
 
 	/**
 	 * If dryRun is set, the paths in question will not actually be deleted.
-	 * 
+	 *
 	 * @param dryRun
 	 *            whether to do a dry run or not
 	 * @return {@code this}

org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java

@@ -50,6 +50,7 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRemoteException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.dircache.DirCache;
@@ -111,11 +112,9 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	/**
 	 * Executes the {@code Clone} command.
 	 *
-	 * @throws JGitInternalException
-	 *             if the repository can't be created
 	 * @return the newly created {@code Git} object with associated repository
 	 */
-	public Git call() throws JGitInternalException {
+	public Git call() throws GitAPIException {
 		try {
 			URIish u = new URIish(uri);
 			Repository repository = init(u);
@@ -132,7 +131,7 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 		}
 	}
 
-	private Repository init(URIish u) {
+	private Repository init(URIish u) throws GitAPIException {
 		InitCommand command = Git.init();
 		command.setBare(bare);
 		if (directory == null)
@@ -145,9 +144,7 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	}
 
 	private FetchResult fetch(Repository clonedRepo, URIish u)
-			throws URISyntaxException,
-			JGitInternalException,
-			InvalidRemoteException, IOException {
+			throws URISyntaxException, IOException, GitAPIException {
 		// create the remote config and save it
 		RemoteConfig config = new RemoteConfig(clonedRepo.getConfig(), remote);
 		config.addURI(u);
@@ -193,8 +190,8 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 	}
 
 	private void checkout(Repository clonedRepo, FetchResult result)
-			throws JGitInternalException,
-			MissingObjectException, IncorrectObjectTypeException, IOException {
+			throws MissingObjectException, IncorrectObjectTypeException,
+			IOException, GitAPIException {
 
 		Ref head = result.getAdvertisedRef(branch);
 		if (branch.equals(Constants.HEAD)) {
@@ -230,7 +227,8 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 		}
 	}
 
-	private void cloneSubmodules(Repository clonedRepo) throws IOException {
+	private void cloneSubmodules(Repository clonedRepo) throws IOException,
+			GitAPIException {
 		SubmoduleInitCommand init = new SubmoduleInitCommand(clonedRepo);
 		if (init.call().isEmpty())
 			return;

org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java

@@ -50,10 +50,12 @@ import java.util.LinkedList;
 import java.util.List;
 
 import org.eclipse.jgit.api.errors.ConcurrentRefUpdateException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.NoFilepatternException;
 import org.eclipse.jgit.api.errors.NoHeadException;
 import org.eclipse.jgit.api.errors.NoMessageException;
+import org.eclipse.jgit.api.errors.UnmergedPathsException;
 import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheBuilder;
@@ -134,21 +136,18 @@ public class CommitCommand extends GitCommand<RevCommit> {
 	 *             when called on a git repo without a HEAD reference
 	 * @throws NoMessageException
 	 *             when called without specifying a commit message
-	 * @throws UnmergedPathException
+	 * @throws UnmergedPathsException
 	 *             when the current index contained unmerged paths (conflicts)
+	 * @throws ConcurrentRefUpdateException
+	 *             when HEAD or branch ref is updated concurrently by someone
+	 *             else
 	 * @throws WrongRepositoryStateException
 	 *             when repository is not in the right state for committing
-	 * @throws JGitInternalException
-	 *             a low-level exception of JGit has occurred. The original
-	 *             exception can be retrieved by calling
-	 *             {@link Exception#getCause()}. Expect only
-	 *             {@code IOException's} to be wrapped. Subclasses of
-	 *             {@link IOException} (e.g. {@link UnmergedPathException}) are
-	 *             typically not wrapped here but thrown as original exception
 	 */
-	public RevCommit call() throws NoHeadException, NoMessageException,
-			UnmergedPathException, ConcurrentRefUpdateException,
-			JGitInternalException, WrongRepositoryStateException {
+	public RevCommit call() throws GitAPIException, NoHeadException,
+			NoMessageException, UnmergedPathsException,
+			ConcurrentRefUpdateException,
+			WrongRepositoryStateException {
 		checkCallable();
 
 		RepositoryState state = repo.getRepositoryState();
@@ -269,10 +268,7 @@ public class CommitCommand extends GitCommand<RevCommit> {
 				index.unlock();
 			}
 		} catch (UnmergedPathException e) {
-			// since UnmergedPathException is a subclass of IOException
-			// which should not be wrapped by a JGitInternalException we
-			// have to catch and re-throw it here
-			throw e;
+			throw new UnmergedPathsException(e);
 		} catch (IOException e) {
 			throw new JGitInternalException(
 					JGitText.get().exceptionCaughtDuringExecutionOfCommitCommand, e);

org.eclipse.jgit/src/org/eclipse/jgit/api/CreateBranchCommand.java

@@ -46,6 +46,7 @@ package org.eclipse.jgit.api;
 import java.io.IOException;
 import java.text.MessageFormat;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRefNameException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.RefAlreadyExistsException;
@@ -57,9 +58,9 @@ import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.RefUpdate;
+import org.eclipse.jgit.lib.RefUpdate.Result;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.StoredConfig;
-import org.eclipse.jgit.lib.RefUpdate.Result;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevWalk;
 
@@ -119,7 +120,7 @@ public class CreateBranchCommand extends GitCommand<Ref> {
 	 *             invalid
 	 * @return the newly created branch
 	 */
-	public Ref call() throws JGitInternalException, RefAlreadyExistsException,
+	public Ref call() throws GitAPIException, RefAlreadyExistsException,
 			RefNotFoundException, InvalidRefNameException {
 		checkCallable();
 		processOptions();

org.eclipse.jgit/src/org/eclipse/jgit/api/DeleteBranchCommand.java

@@ -51,6 +51,7 @@ import java.util.List;
 import java.util.Set;
 
 import org.eclipse.jgit.api.errors.CannotDeleteCurrentBranchException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.NotMergedException;
 import org.eclipse.jgit.internal.JGitText;
@@ -58,9 +59,9 @@ import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.RefUpdate;
+import org.eclipse.jgit.lib.RefUpdate.Result;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.StoredConfig;
-import org.eclipse.jgit.lib.RefUpdate.Result;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevWalk;
 
@@ -93,9 +94,10 @@ public class DeleteBranchCommand extends GitCommand<List<String>> {
 	 * @throws NotMergedException
 	 *             when trying to delete a branch which has not been merged into
 	 *             the currently checked out branch without force
+	 * @throws CannotDeleteCurrentBranchException
 	 * @return the list with the (full) names of the deleted branches
 	 */
-	public List<String> call() throws JGitInternalException,
+	public List<String> call() throws GitAPIException,
 			NotMergedException, CannotDeleteCurrentBranchException {
 		checkCallable();
 		List<String> result = new ArrayList<String>();

org.eclipse.jgit/src/org/eclipse/jgit/api/DeleteTagCommand.java

@@ -49,6 +49,7 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Ref;
@@ -77,12 +78,9 @@ public class DeleteTagCommand extends GitCommand<List<String>> {
 	}
 
 	/**
-	 * @throws JGitInternalException
-	 *             when trying to delete a tag that doesn't exist
-	 *
 	 * @return the list with the full names of the deleted tags
 	 */
-	public List<String> call() throws JGitInternalException {
+	public List<String> call() throws GitAPIException {
 		checkCallable();
 		List<String> result = new ArrayList<String>();
 		if (tags.isEmpty())

org.eclipse.jgit/src/org/eclipse/jgit/api/DiffCommand.java

@@ -50,6 +50,7 @@ import java.io.OutputStream;
 import java.util.List;
 
 import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.NoHeadException;
 import org.eclipse.jgit.diff.DiffEntry;
 import org.eclipse.jgit.diff.DiffFormatter;
@@ -108,7 +109,7 @@ public class DiffCommand extends GitCommand<List<DiffEntry>> {
 	 *
 	 * @return a DiffEntry for each path which is different
 	 */
-	public List<DiffEntry> call() throws GitAPIException, IOException {
+	public List<DiffEntry> call() throws GitAPIException {
 		final DiffFormatter diffFmt;
 		if (out != null && !showNameAndStatusOnly)
 			diffFmt = new DiffFormatter(new BufferedOutputStream(out));
@@ -155,6 +156,8 @@ public class DiffCommand extends GitCommand<List<DiffEntry>> {
 				diffFmt.flush();
 				return result;
 			}
+		} catch (IOException e) {
+			throw new JGitInternalException(e.getMessage(), e);
 		} finally {
 			diffFmt.release();
 		}

org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java

@@ -47,6 +47,7 @@ import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRemoteException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.errors.NoRemoteRepositoryException;
@@ -106,13 +107,11 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 	 *         result
 	 * @throws InvalidRemoteException
 	 *             when called with an invalid remote uri
-	 * @throws JGitInternalException
-	 *             a low-level exception of JGit has occurred. The original
-	 *             exception can be retrieved by calling
-	 *             {@link Exception#getCause()}.
+	 * @throws org.eclipse.jgit.api.errors.TransportException
+	 *             when an error occurs during transport
 	 */
-	public FetchResult call() throws JGitInternalException,
-			InvalidRemoteException {
+	public FetchResult call() throws GitAPIException, InvalidRemoteException,
+			org.eclipse.jgit.api.errors.TransportException {
 		checkCallable();
 
 		try {
@@ -135,7 +134,7 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 			throw new InvalidRemoteException(MessageFormat.format(
 					JGitText.get().invalidRemote, remote), e);
 		} catch (TransportException e) {
-			throw new JGitInternalException(
+			throw new org.eclipse.jgit.api.errors.TransportException(
 					JGitText.get().exceptionCaughtDuringExecutionOfFetchCommand,
 					e);
 		} catch (URISyntaxException e) {

org.eclipse.jgit/src/org/eclipse/jgit/api/GitCommand.java

@@ -40,6 +40,7 @@ package org.eclipse.jgit.api;
 import java.text.MessageFormat;
 import java.util.concurrent.Callable;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Repository;
 
@@ -116,4 +117,13 @@ public abstract class GitCommand<T> implements Callable<T> {
 					JGitText.get().commandWasCalledInTheWrongState
 					, this.getClass().getName()));
 	}
+
+	/**
+	 * Executes the command
+	 *
+	 * @return T a result. Each command has its own return type
+	 * @throws GitAPIException
+	 *             or subclass thereof when an error occurs
+	 */
+	public abstract T call() throws GitAPIException;
 }

org.eclipse.jgit/src/org/eclipse/jgit/api/InitCommand.java

@@ -46,6 +46,7 @@ import java.io.File;
 import java.io.IOException;
 import java.util.concurrent.Callable;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Repository;
@@ -65,11 +66,9 @@ public class InitCommand implements Callable<Git> {
 	/**
 	 * Executes the {@code Init} command.
 	 *
-	 * @throws JGitInternalException
-	 *             if the repository can't be created
 	 * @return the newly created {@code Git} object with associated repository
 	 */
-	public Git call() throws JGitInternalException {
+	public Git call() throws GitAPIException {
 		try {
 			RepositoryBuilder builder = new RepositoryBuilder();
 			if (bare)

org.eclipse.jgit/src/org/eclipse/jgit/api/ListBranchCommand.java

@@ -47,10 +47,11 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.HashMap;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Ref;
@@ -88,11 +89,7 @@ public class ListBranchCommand extends GitCommand<List<Ref>> {
 		super(repo);
 	}
 
-	/**
-	 * @throws JGitInternalException
-	 *             upon internal failure
-	 */
-	public List<Ref> call() throws JGitInternalException {
+	public List<Ref> call() throws GitAPIException {
 		checkCallable();
 		Map<String, Ref> refList;
 		try {

org.eclipse.jgit/src/org/eclipse/jgit/api/ListNotesCommand.java

@@ -47,6 +47,7 @@ import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Ref;
@@ -74,10 +75,9 @@ public class ListNotesCommand extends GitCommand<List<Note>> {
 	}
 
 	/**
-	 * @throws JGitInternalException
-	 *             upon internal failure
+	 * @return the requested notes
 	 */
-	public List<Note> call() throws JGitInternalException {
+	public List<Note> call() throws GitAPIException {
 		checkCallable();
 		List<Note> notes = new ArrayList<Note>();
 		RevWalk walk = new RevWalk(repo);

org.eclipse.jgit/src/org/eclipse/jgit/api/ListTagCommand.java

@@ -49,6 +49,7 @@ import java.util.Comparator;
 import java.util.List;
 import java.util.Map;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Ref;
@@ -71,11 +72,9 @@ public class ListTagCommand extends GitCommand<List<Ref>> {
 	}
 
 	/**
-	 * @throws JGitInternalException
-	 *             upon internal failure
 	 * @return the tags available
 	 */
-	public List<Ref> call() throws JGitInternalException {
+	public List<Ref> call() throws GitAPIException {
 		checkCallable();
 		Map<String, Ref> refList;
 		List<Ref> tags = new ArrayList<Ref>();

org.eclipse.jgit/src/org/eclipse/jgit/api/LogCommand.java

@@ -47,6 +47,7 @@ import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.NoHeadException;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
@@ -108,9 +109,10 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 	 * method twice on an instance.
 	 *
 	 * @return an iteration over RevCommits
+	 * @throws NoHeadException
+	 *             of the references ref cannot be resolved
 	 */
-	public Iterable<RevCommit> call() throws NoHeadException,
-			JGitInternalException {
+	public Iterable<RevCommit> call() throws GitAPIException, NoHeadException {
 		checkCallable();
 		if (pathFilters.size() > 0)
 			walk.setTreeFilter(AndTreeFilter.create(
@@ -166,7 +168,7 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 	 *             typically not wrapped here but thrown as original exception
 	 */
 	public LogCommand add(AnyObjectId start) throws MissingObjectException,
-			IncorrectObjectTypeException, JGitInternalException {
+			IncorrectObjectTypeException {
 		return add(true, start);
 	}
 
@@ -194,7 +196,7 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 	 *             typically not wrapped here but thrown as original exception
 	 */
 	public LogCommand not(AnyObjectId start) throws MissingObjectException,
-			IncorrectObjectTypeException, JGitInternalException {
+			IncorrectObjectTypeException {
 		return add(false, start);
 	}
 
@@ -223,8 +225,7 @@ public class LogCommand extends GitCommand<Iterable<RevCommit>> {
 	 *             typically not wrapped here but thrown as original exception
 	 */
 	public LogCommand addRange(AnyObjectId since, AnyObjectId until)
-			throws MissingObjectException, IncorrectObjectTypeException,
-			JGitInternalException {
+			throws MissingObjectException, IncorrectObjectTypeException {
 		return not(since).add(until);
 	}
 

org.eclipse.jgit/src/org/eclipse/jgit/api/LsRemoteCommand.java

@@ -144,13 +144,11 @@ public class LsRemoteCommand extends
 	 * @return a collection of references in the remote repository
 	 * @throws InvalidRemoteException
 	 *             when called with an invalid remote uri
-	 * @throws JGitInternalException
-	 *             a low-level exception of JGit has occurred. The original
-	 *             exception can be retrieved by calling
-	 *             {@link Exception#getCause()}.
+	 * @throws org.eclipse.jgit.api.errors.TransportException
+	 *             for errors that occurs during transport
 	 */
 	public Collection<Ref> call() throws GitAPIException,
-			JGitInternalException {
+			org.eclipse.jgit.api.errors.TransportException {
 		checkCallable();
 
 		Transport transport = null;

org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java

@@ -54,6 +54,7 @@ import java.util.Map;
 import org.eclipse.jgit.api.MergeResult.MergeStatus;
 import org.eclipse.jgit.api.errors.CheckoutConflictException;
 import org.eclipse.jgit.api.errors.ConcurrentRefUpdateException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidMergeHeadsException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.NoHeadException;
@@ -109,7 +110,7 @@ public class MergeCommand extends GitCommand<MergeResult> {
 	 *
 	 * @return the result of the merge
 	 */
-	public MergeResult call() throws NoHeadException,
+	public MergeResult call() throws GitAPIException, NoHeadException,
 			ConcurrentRefUpdateException, CheckoutConflictException,
 			InvalidMergeHeadsException, WrongRepositoryStateException, NoMessageException {
 		checkCallable();

org.eclipse.jgit/src/org/eclipse/jgit/api/PullCommand.java

@@ -110,7 +110,7 @@ public class PullCommand extends TransportCommand<PullCommand, PullResult> {
 	 *
 	 * @return the result of the pull
 	 */
-	public PullResult call() throws WrongRepositoryStateException,
+	public PullResult call() throws GitAPIException, WrongRepositoryStateException,
 			InvalidConfigurationException, DetachedHeadException,
 			InvalidRemoteException, CanceledException, RefNotFoundException,
 			NoHeadException {

org.eclipse.jgit/src/org/eclipse/jgit/api/PushCommand.java

@@ -50,6 +50,7 @@ import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRemoteException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.errors.NotSupportedException;
@@ -108,12 +109,8 @@ public class PushCommand extends
 	 * @return an iteration over {@link PushResult} objects
 	 * @throws InvalidRemoteException
 	 *             when called with an invalid remote uri
-	 * @throws JGitInternalException
-	 *             a low-level exception of JGit has occurred. The original
-	 *             exception can be retrieved by calling
-	 *             {@link Exception#getCause()}.
 	 */
-	public Iterable<PushResult> call() throws JGitInternalException,
+	public Iterable<PushResult> call() throws GitAPIException,
 			InvalidRemoteException {
 		checkCallable();
 
@@ -325,7 +322,7 @@ public class PushCommand extends
 	 * @throws JGitInternalException
 	 *             the reference name cannot be resolved.
 	 */
-	public PushCommand add(String nameOrSpec) throws JGitInternalException {
+	public PushCommand add(String nameOrSpec) {
 		if (0 <= nameOrSpec.indexOf(':')) {
 			refSpecs.add(new RefSpec(nameOrSpec));
 		} else {

org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java

@@ -190,8 +190,8 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	 *
 	 * @return an object describing the result of this command
 	 */
-	public RebaseResult call() throws NoHeadException, RefNotFoundException,
-			JGitInternalException, GitAPIException {
+	public RebaseResult call() throws GitAPIException, NoHeadException,
+			RefNotFoundException {
 		RevCommit newHead = null;
 		boolean lastStepWasForward = false;
 		checkCallable();
@@ -325,8 +325,7 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 		}
 	}
 
-	private RevCommit checkoutCurrentHead() throws IOException,
-			NoHeadException, JGitInternalException {
+	private RevCommit checkoutCurrentHead() throws IOException, NoHeadException {
 		ObjectId headTree = repo.resolve(Constants.HEAD + "^{tree}");
 		if (headTree == null)
 			throw new NoHeadException(
@@ -517,8 +516,8 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 		}
 	}
 
-	private RebaseResult initFilesAndRewind() throws RefNotFoundException,
-			IOException, NoHeadException, JGitInternalException {
+	private RebaseResult initFilesAndRewind() throws IOException,
+			GitAPIException {
 		// we need to store everything into files so that we can implement
 		// --skip, --continue, and --abort
 
@@ -576,7 +575,7 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 		// create the folder for the meta information
 		FileUtils.mkdir(rebaseDir);
 
-		createFile(repo.getDirectory(), Constants.ORIG_HEAD, headId.name());
+		repo.writeOrigHead(headId);
 		createFile(rebaseDir, REBASE_HEAD, headId.name());
 		createFile(rebaseDir, HEAD_NAME, headName);
 		createFile(rebaseDir, ONTO, upstreamCommit.name());
@@ -626,11 +625,11 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	 *
 	 * @param newCommit
 	 * @return the new head, or null
-	 * @throws RefNotFoundException
 	 * @throws IOException
+	 * @throws GitAPIException
 	 */
-	public RevCommit tryFastForward(RevCommit newCommit)
-			throws RefNotFoundException, IOException {
+	public RevCommit tryFastForward(RevCommit newCommit) throws IOException,
+			GitAPIException {
 		Ref head = repo.getRef(Constants.HEAD);
 		if (head == null || head.getObjectId() == null)
 			throw new RefNotFoundException(MessageFormat.format(
@@ -653,7 +652,7 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 	}
 
 	private RevCommit tryFastForward(String headName, RevCommit oldCommit,
-			RevCommit newCommit) throws IOException, JGitInternalException {
+			RevCommit newCommit) throws IOException, GitAPIException {
 		boolean tryRebase = false;
 		for (RevCommit parentCommit : newCommit.getParents())
 			if (parentCommit.equals(oldCommit))
@@ -733,7 +732,8 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 
 	private RebaseResult abort(RebaseResult result) throws IOException {
 		try {
-			String commitId = readFile(repo.getDirectory(), Constants.ORIG_HEAD);
+			ObjectId origHead = repo.readOrigHead();
+			String commitId = origHead != null ? origHead.name() : null;
 			monitor.beginTask(MessageFormat.format(
 					JGitText.get().abortingRebase, commitId),
 					ProgressMonitor.UNKNOWN);

org.eclipse.jgit/src/org/eclipse/jgit/api/ReflogCommand.java

@@ -46,6 +46,7 @@ import java.io.IOException;
 import java.text.MessageFormat;
 import java.util.Collection;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRefNameException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
@@ -84,7 +85,7 @@ public class ReflogCommand extends GitCommand<Collection<ReflogEntry>> {
 		return this;
 	}
 
-	public Collection<ReflogEntry> call() throws Exception {
+	public Collection<ReflogEntry> call() throws GitAPIException {
 		checkCallable();
 
 		try {

org.eclipse.jgit/src/org/eclipse/jgit/api/RemoveNoteCommand.java

@@ -44,6 +44,7 @@ package org.eclipse.jgit.api;
 
 import java.io.IOException;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.lib.CommitBuilder;
 import org.eclipse.jgit.lib.Constants;
@@ -78,11 +79,7 @@ public class RemoveNoteCommand extends GitCommand<Note> {
 		super(repo);
 	}
 
-	/**
-	 * @throws JGitInternalException
-	 *             upon internal failure
-	 */
-	public Note call() throws JGitInternalException {
+	public Note call() throws GitAPIException {
 		checkCallable();
 		RevWalk walk = new RevWalk(repo);
 		ObjectInserter inserter = repo.newObjectInserter();

org.eclipse.jgit/src/org/eclipse/jgit/api/RenameBranchCommand.java

@@ -48,6 +48,7 @@ import java.text.MessageFormat;
 import java.util.Arrays;
 
 import org.eclipse.jgit.api.errors.DetachedHeadException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRefNameException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.RefAlreadyExistsException;
@@ -58,9 +59,9 @@ import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.RefRename;
+import org.eclipse.jgit.lib.RefUpdate.Result;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.StoredConfig;
-import org.eclipse.jgit.lib.RefUpdate.Result;
 
 /**
  * Used to rename branches.
@@ -94,7 +95,7 @@ public class RenameBranchCommand extends GitCommand<Ref> {
 	 *             if rename is tried without specifying the old name and HEAD
 	 *             is detached
 	 */
-	public Ref call() throws RefNotFoundException, InvalidRefNameException,
+	public Ref call() throws GitAPIException, RefNotFoundException, InvalidRefNameException,
 			RefAlreadyExistsException, DetachedHeadException {
 		checkCallable();
 

org.eclipse.jgit/src/org/eclipse/jgit/api/ResetCommand.java

@@ -47,11 +47,13 @@ import java.text.MessageFormat;
 import java.util.Collection;
 import java.util.LinkedList;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.dircache.DirCache;
-import org.eclipse.jgit.dircache.DirCacheBuilder;
 import org.eclipse.jgit.dircache.DirCacheCheckout;
 import org.eclipse.jgit.dircache.DirCacheEditor;
+import org.eclipse.jgit.dircache.DirCacheEditor.DeletePath;
+import org.eclipse.jgit.dircache.DirCacheEditor.PathEdit;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.dircache.DirCacheIterator;
 import org.eclipse.jgit.internal.JGitText;
@@ -64,6 +66,7 @@ import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.RepositoryState;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevWalk;
+import org.eclipse.jgit.treewalk.AbstractTreeIterator;
 import org.eclipse.jgit.treewalk.CanonicalTreeParser;
 import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
@@ -133,7 +136,7 @@ public class ResetCommand extends GitCommand<Ref> {
 	 *
 	 * @return the Ref after reset
 	 */
-	public Ref call() throws IOException {
+	public Ref call() throws GitAPIException {
 		checkCallable();
 
 		Ref r;
@@ -192,6 +195,10 @@ public class ResetCommand extends GitCommand<Ref> {
 				throw new JGitInternalException(MessageFormat.format(
 						JGitText.get().cannotLock, ru.getName()));
 
+			ObjectId origHead = ru.getOldObjectId();
+			if (origHead != null)
+				repo.writeOrigHead(origHead);
+
 			switch (mode) {
 				case HARD:
 					checkoutIndex(commit);
@@ -313,14 +320,49 @@ public class ResetCommand extends GitCommand<Ref> {
 
 	private void resetIndex(RevCommit commit) throws IOException {
 		DirCache dc = repo.lockDirCache();
+		TreeWalk walk = null;
 		try {
-			dc.clear();
-			DirCacheBuilder dcb = dc.builder();
-			dcb.addTree(new byte[0], 0, repo.newObjectReader(),
-					commit.getTree());
-			dcb.commit();
+			DirCacheEditor editor = dc.editor();
+
+			walk = new TreeWalk(repo);
+			walk.addTree(commit.getTree());
+			walk.addTree(new DirCacheIterator(dc));
+			walk.setRecursive(true);
+
+			while (walk.next()) {
+				AbstractTreeIterator cIter = walk.getTree(0,
+						AbstractTreeIterator.class);
+				if (cIter == null) {
+					editor.add(new DeletePath(walk.getPathString()));
+					continue;
+				}
+
+				final DirCacheEntry entry = new DirCacheEntry(walk.getRawPath());
+				entry.setFileMode(cIter.getEntryFileMode());
+				entry.setObjectIdFromRaw(cIter.idBuffer(), cIter.idOffset());
+
+				DirCacheIterator dcIter = walk.getTree(1,
+						DirCacheIterator.class);
+				if (dcIter != null && dcIter.idEqual(cIter)) {
+					DirCacheEntry indexEntry = dcIter.getDirCacheEntry();
+					entry.setLastModified(indexEntry.getLastModified());
+					entry.setLength(indexEntry.getLength());
+				}
+
+				editor.add(new PathEdit(entry) {
+
+					@Override
+					public void apply(DirCacheEntry ent) {
+						ent.copyMetaData(entry);
+					}
+				});
+			}
+
+			editor.commit();
 		} finally {
 			dc.unlock();
+			if (walk != null)
+				walk.release();
 		}
 	}
 

org.eclipse.jgit/src/org/eclipse/jgit/api/RevertCommand.java

@@ -50,8 +50,8 @@ import java.util.Map;
 
 import org.eclipse.jgit.api.MergeResult.MergeStatus;
 import org.eclipse.jgit.api.errors.GitAPIException;
-import org.eclipse.jgit.api.errors.MultipleParentsNotAllowedException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
+import org.eclipse.jgit.api.errors.MultipleParentsNotAllowedException;
 import org.eclipse.jgit.api.errors.NoHeadException;
 import org.eclipse.jgit.dircache.DirCacheCheckout;
 import org.eclipse.jgit.internal.JGitText;

org.eclipse.jgit/src/org/eclipse/jgit/api/RmCommand.java

@@ -47,6 +47,7 @@ import java.io.IOException;
 import java.util.Collection;
 import java.util.LinkedList;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.NoFilepatternException;
 import org.eclipse.jgit.dircache.DirCache;
@@ -99,7 +100,8 @@ public class RmCommand extends GitCommand<DirCache> {
 	 *
 	 * @return the DirCache after Rm
 	 */
-	public DirCache call() throws NoFilepatternException {
+	public DirCache call() throws GitAPIException,
+			NoFilepatternException {
 
 		if (filepatterns.isEmpty())
 			throw new NoFilepatternException(JGitText.get().atLeastOnePatternIsRequired);

org.eclipse.jgit/src/org/eclipse/jgit/api/ShowNoteCommand.java

@@ -44,6 +44,7 @@ package org.eclipse.jgit.api;
 
 import java.io.IOException;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Ref;
@@ -73,11 +74,7 @@ public class ShowNoteCommand extends GitCommand<Note> {
 		super(repo);
 	}
 
-	/**
-	 * @throws JGitInternalException
-	 *             upon internal failure
-	 */
-	public Note call() throws JGitInternalException {
+	public Note call() throws GitAPIException {
 		checkCallable();
 		RevWalk walk = new RevWalk(repo);
 		NoteMap map = NoteMap.newEmptyMap();

org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java

@@ -189,8 +189,7 @@ public class StashApplyCommand extends GitCommand<ObjectId> {
 		return false;
 	}
 
-	private ObjectId getHeadTree() throws JGitInternalException,
-			GitAPIException {
+	private ObjectId getHeadTree() throws GitAPIException {
 		final ObjectId headTree;
 		try {
 			headTree = repo.resolve(Constants.HEAD + "^{tree}");
@@ -202,7 +201,7 @@ public class StashApplyCommand extends GitCommand<ObjectId> {
 		return headTree;
 	}
 
-	private ObjectId getStashId() throws JGitInternalException, GitAPIException {
+	private ObjectId getStashId() throws GitAPIException {
 		final String revision = stashRef != null ? stashRef : DEFAULT_REF;
 		final ObjectId stashId;
 		try {
@@ -298,7 +297,7 @@ public class StashApplyCommand extends GitCommand<ObjectId> {
 	 *
 	 * @return id of stashed commit that was applied
 	 */
-	public ObjectId call() throws GitAPIException, JGitInternalException {
+	public ObjectId call() throws GitAPIException {
 		checkCallable();
 
 		if (repo.getRepositoryState() != RepositoryState.SAFE)

org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java

@@ -212,7 +212,7 @@ public class StashCreateCommand extends GitCommand<RevCommit> {
 	 *
 	 * @return stashed commit or null if no changes to stash
 	 */
-	public RevCommit call() throws GitAPIException, JGitInternalException {
+	public RevCommit call() throws GitAPIException {
 		checkCallable();
 
 		Ref head = getHead();

org.eclipse.jgit/src/org/eclipse/jgit/api/StashDropCommand.java

@@ -168,7 +168,7 @@ public class StashDropCommand extends GitCommand<ObjectId> {
 	 *
 	 * @return commit id of stash reference or null if no more stashed changes
 	 */
-	public ObjectId call() throws GitAPIException, JGitInternalException {
+	public ObjectId call() throws GitAPIException {
 		checkCallable();
 
 		Ref stashRef = getRef();

org.eclipse.jgit/src/org/eclipse/jgit/api/StashListCommand.java

@@ -49,6 +49,7 @@ import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidRefNameException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.internal.JGitText;
@@ -75,7 +76,7 @@ public class StashListCommand extends GitCommand<Collection<RevCommit>> {
 		super(repo);
 	}
 
-	public Collection<RevCommit> call() throws Exception {
+	public Collection<RevCommit> call() throws GitAPIException {
 		checkCallable();
 
 		try {

org.eclipse.jgit/src/org/eclipse/jgit/api/StatusCommand.java

@@ -44,6 +44,8 @@ package org.eclipse.jgit.api;
 
 import java.io.IOException;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.errors.NoWorkTreeException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.IndexDiff;
@@ -80,14 +82,17 @@ public class StatusCommand extends GitCommand<Status> {
 	 * @return a {@link Status} object telling about each path where working
 	 *         tree, index or HEAD differ from each other.
 	 */
-	public Status call() throws IOException, NoWorkTreeException {
+	public Status call() throws GitAPIException, NoWorkTreeException {
 		if (workingTreeIt == null)
 			workingTreeIt = new FileTreeIterator(repo);
 
-		IndexDiff diff = new IndexDiff(repo, Constants.HEAD, workingTreeIt);
-		diff.diff();
-
-		return new Status(diff);
+		try {
+			IndexDiff diff = new IndexDiff(repo, Constants.HEAD, workingTreeIt);
+			diff.diff();
+			return new Status(diff);
+		} catch (IOException e) {
+			throw new JGitInternalException(e.getMessage(), e);
+		}
 	}
 
 	/**

org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleAddCommand.java

@@ -46,6 +46,7 @@ import java.io.File;
 import java.io.IOException;
 import java.text.MessageFormat;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.NoFilepatternException;
 import org.eclipse.jgit.errors.ConfigInvalidException;
@@ -134,7 +135,7 @@ public class SubmoduleAddCommand extends
 		return SubmoduleWalk.forIndex(repo).setFilter(filter).next();
 	}
 
-	public Repository call() throws JGitInternalException {
+	public Repository call() throws GitAPIException {
 		checkCallable();
 		if (path == null || path.length() == 0)
 			throw new IllegalArgumentException(JGitText.get().pathNotConfigured);

org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleInitCommand.java

@@ -47,6 +47,7 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.lib.ConfigConstants;
@@ -89,7 +90,7 @@ public class SubmoduleInitCommand extends GitCommand<Collection<String>> {
 		return this;
 	}
 
-	public Collection<String> call() throws JGitInternalException {
+	public Collection<String> call() throws GitAPIException {
 		checkCallable();
 
 		try {

org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleStatusCommand.java

@@ -48,6 +48,7 @@ import java.util.Collection;
 import java.util.HashMap;
 import java.util.Map;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.lib.Constants;
@@ -89,7 +90,7 @@ public class SubmoduleStatusCommand extends
 		return this;
 	}
 
-	public Map<String, SubmoduleStatus> call() throws JGitInternalException {
+	public Map<String, SubmoduleStatus> call() throws GitAPIException {
 		checkCallable();
 
 		try {

org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleSyncCommand.java

@@ -48,6 +48,7 @@ import java.util.Collection;
 import java.util.HashMap;
 import java.util.Map;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.lib.ConfigConstants;
@@ -106,7 +107,7 @@ public class SubmoduleSyncCommand extends GitCommand<Map<String, String>> {
 			return null;
 	}
 
-	public Map<String, String> call() throws JGitInternalException {
+	public Map<String, String> call() throws GitAPIException {
 		checkCallable();
 
 		try {

org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleUpdateCommand.java

@@ -109,7 +109,7 @@ public class SubmoduleUpdateCommand extends
 		return this;
 	}
 
-	public Collection<String> call() throws JGitInternalException {
+	public Collection<String> call() throws GitAPIException {
 		checkCallable();
 
 		try {

org.eclipse.jgit/src/org/eclipse/jgit/api/TagCommand.java

@@ -46,6 +46,7 @@ import java.io.IOException;
 import java.text.MessageFormat;
 
 import org.eclipse.jgit.api.errors.ConcurrentRefUpdateException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.InvalidTagNameException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.NoHeadException;
@@ -100,15 +101,10 @@ public class TagCommand extends GitCommand<Ref> {
 	 * @return a {@link Ref} a ref pointing to a tag
 	 * @throws NoHeadException
 	 *             when called on a git repo without a HEAD reference
-	 * @throws JGitInternalException
-	 *             a low-level exception of JGit has occurred. The original
-	 *             exception can be retrieved by calling
-	 *             {@link Exception#getCause()}. Expect only
-	 *             {@code IOException's} to be wrapped.
 	 * @since 2.0
 	 */
-	public Ref call() throws JGitInternalException,
-			ConcurrentRefUpdateException, InvalidTagNameException, NoHeadException {
+	public Ref call() throws GitAPIException, ConcurrentRefUpdateException,
+			InvalidTagNameException, NoHeadException {
 		checkCallable();
 
 		RepositoryState state = repo.getRepositoryState();

org.eclipse.jgit/src/org/eclipse/jgit/api/errors/UnmergedPathsException.java

@@ -49,6 +49,16 @@ public class UnmergedPathsException extends GitAPIException {
 	 * The default constructor with a default message
 	 */
 	public UnmergedPathsException() {
-		super(JGitText.get().unmergedPaths);
+		this(null);
+	}
+
+	/**
+	 * The default constructor with a default message
+	 *
+	 * @param cause
+	 *            original exception
+	 */
+	public UnmergedPathsException(Throwable cause) {
+		super(JGitText.get().unmergedPaths, cause);
 	}
 }

org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCache.java

@@ -69,8 +69,11 @@ import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectInserter;
+import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.storage.file.FileSnapshot;
 import org.eclipse.jgit.storage.file.LockFile;
+import org.eclipse.jgit.treewalk.FileTreeIterator;
+import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.IO;
 import org.eclipse.jgit.util.MutableInteger;
@@ -138,6 +141,30 @@ public class DirCache {
 		return new DirCache(null, null);
 	}
 
+	/**
+	 * Create a new in-core index representation and read an index from disk.
+	 * <p>
+	 * The new index will be read before it is returned to the caller. Read
+	 * failures are reported as exceptions and therefore prevent the method from
+	 * returning a partially populated index.
+	 *
+	 * @param repository
+	 *            repository containing the index to read
+	 * @return a cache representing the contents of the specified index file (if
+	 *         it exists) or an empty cache if the file does not exist.
+	 * @throws IOException
+	 *             the index file is present but could not be read.
+	 * @throws CorruptObjectException
+	 *             the index file is using a format or extension that this
+	 *             library does not support.
+	 */
+	public static DirCache read(final Repository repository)
+			throws CorruptObjectException, IOException {
+		final DirCache c = read(repository.getIndexFile(), repository.getFS());
+		c.repository = repository;
+		return c;
+	}
+
 	/**
 	 * Create a new in-core index representation and read an index from disk.
 	 * <p>
@@ -209,6 +236,37 @@ public class DirCache {
 		return c;
 	}
 
+	/**
+	 * Create a new in-core index representation, lock it, and read from disk.
+	 * <p>
+	 * The new index will be locked and then read before it is returned to the
+	 * caller. Read failures are reported as exceptions and therefore prevent
+	 * the method from returning a partially populated index. On read failure,
+	 * the lock is released.
+	 *
+	 * @param repository
+	 *            repository containing the index to lock and read
+	 * @param indexChangedListener
+	 *            listener to be informed when DirCache is committed
+	 * @return a cache representing the contents of the specified index file (if
+	 *         it exists) or an empty cache if the file does not exist.
+	 * @throws IOException
+	 *             the index file is present but could not be read, or the lock
+	 *             could not be obtained.
+	 * @throws CorruptObjectException
+	 *             the index file is using a format or extension that this
+	 *             library does not support.
+	 * @since 2.0
+	 */
+	public static DirCache lock(final Repository repository,
+			final IndexChangedListener indexChangedListener)
+			throws CorruptObjectException, IOException {
+		DirCache c = lock(repository.getIndexFile(), repository.getFS(),
+				indexChangedListener);
+		c.repository = repository;
+		return c;
+	}
+
 	/**
 	 * Create a new in-core index representation, lock it, and read from disk.
 	 * <p>
@@ -272,6 +330,9 @@ public class DirCache {
 	/** listener to be informed on commit */
 	private IndexChangedListener indexChangedListener;
 
+	/** Repository containing this index */
+	private Repository repository;
+
 	/**
 	 * Create a new in-core index representation.
 	 * <p>
@@ -591,6 +652,13 @@ public class DirCache {
 			smudge_s = 0;
 		}
 
+		// Check if tree is non-null here since calling updateSmudgedEntries
+		// will automatically build it via creating a DirCacheIterator
+		final boolean writeTree = tree != null;
+
+		if (repository != null && entryCnt > 0)
+			updateSmudgedEntries();
+
 		for (int i = 0; i < entryCnt; i++) {
 			final DirCacheEntry e = sortedEntries[i];
 			if (e.mightBeRacilyClean(smudge_s, smudge_ns))
@@ -598,7 +666,7 @@ public class DirCache {
 			e.write(dos);
 		}
 
-		if (tree != null) {
+		if (writeTree) {
 			final TemporaryBuffer bb = new TemporaryBuffer.LocalFile();
 			tree.write(tmp, bb);
 			bb.close();
@@ -865,4 +933,35 @@ public class DirCache {
 	private void registerIndexChangedListener(IndexChangedListener listener) {
 		this.indexChangedListener = listener;
 	}
+
+	/**
+	 * Update any smudged entries with information from the working tree.
+	 *
+	 * @throws IOException
+	 */
+	private void updateSmudgedEntries() throws IOException {
+		TreeWalk walk = new TreeWalk(repository);
+		try {
+			DirCacheIterator iIter = new DirCacheIterator(this);
+			FileTreeIterator fIter = new FileTreeIterator(repository);
+			walk.addTree(iIter);
+			walk.addTree(fIter);
+			walk.setRecursive(true);
+			while (walk.next()) {
+				iIter = walk.getTree(0, DirCacheIterator.class);
+				if (iIter == null)
+					continue;
+				fIter = walk.getTree(1, FileTreeIterator.class);
+				if (fIter == null)
+					continue;
+				DirCacheEntry entry = iIter.getDirCacheEntry();
+				if (entry.isSmudged() && iIter.idEqual(fIter)) {
+					entry.setLength(fIter.getEntryLength());
+					entry.setLastModified(fIter.getEntryLastModified());
+				}
+			}
+		} finally {
+			walk.release();
+		}
+	}
 }

org.eclipse.jgit/src/org/eclipse/jgit/errors/GitlinksNotSupportedException.java

@@ -1,65 +0,0 @@
-/*
- * Copyright (C) 2009, Jonas Fonseca <fonseca@diku.dk>
- * Copyright (C) 2007, Robin Rosenberg <robin.rosenberg@dewire.com>
- * Copyright (C) 2007, 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.errors;
-
-import java.io.IOException;
-
-/**
- * An exception thrown when a gitlink entry is found and cannot be
- * handled.
- */
-public class GitlinksNotSupportedException extends IOException {
-	private static final long serialVersionUID = 1L;
-
-	/**
-	 * Construct a GitlinksNotSupportedException for the specified link
-	 *
-	 * @param s name of link in tree or workdir
-	 */
-	public GitlinksNotSupportedException(final String s) {
-		super(s);
-	}
-}

org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java

@@ -871,7 +871,7 @@ public abstract class Repository {
 	 */
 	public DirCache readDirCache() throws NoWorkTreeException,
 			CorruptObjectException, IOException {
-		return DirCache.read(getIndexFile(), getFS());
+		return DirCache.read(this);
 	}
 
 	/**
@@ -903,7 +903,7 @@ public abstract class Repository {
 				notifyIndexChanged();
 			}
 		};
-		return DirCache.lock(getIndexFile(), getFS(), l);
+		return DirCache.lock(this, l);
 	}
 
 	static byte[] gitInternalSlash(byte[] bytes) {
@@ -1247,6 +1247,39 @@ public abstract class Repository {
 		writeHeadsFile(heads, Constants.CHERRY_PICK_HEAD);
 	}
 
+	/**
+	 * Write original HEAD commit into $GIT_DIR/ORIG_HEAD.
+	 *
+	 * @param head
+	 *            an object id of the original HEAD commit or <code>null</code>
+	 *            to delete the file
+	 * @throws IOException
+	 */
+	public void writeOrigHead(ObjectId head) throws IOException {
+		List<ObjectId> heads = head != null ? Collections.singletonList(head)
+				: null;
+		writeHeadsFile(heads, Constants.ORIG_HEAD);
+	}
+
+	/**
+	 * Return the information stored in the file $GIT_DIR/ORIG_HEAD.
+	 *
+	 * @return object id from ORIG_HEAD file or {@code null} if this file
+	 *         doesn't exist. Also if the file exists but is empty {@code null}
+	 *         will be returned
+	 * @throws IOException
+	 * @throws NoWorkTreeException
+	 *             if this is bare, which implies it has no working directory.
+	 *             See {@link #isBare()}.
+	 */
+	public ObjectId readOrigHead() throws IOException, NoWorkTreeException {
+		if (isBare() || getDirectory() == null)
+			throw new NoWorkTreeException();
+
+		byte[] raw = readGitDirectoryFile(Constants.ORIG_HEAD);
+		return raw != null ? ObjectId.fromString(raw, 0) : null;
+	}
+
 	/**
 	 * Read a file from the git directory.
 	 *

org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotWalk.java

@@ -172,6 +172,11 @@ public class PlotWalk extends RevWalk {
 				return ((RevCommit) o).getCommitTime();
 			if (o instanceof RevTag) {
 				RevTag tag = (RevTag) o;
+				try {
+					parseBody(tag);
+				} catch (IOException e) {
+					return 0;
+				}
 				PersonIdent who = tag.getTaggerIdent();
 				return who != null ? who.getWhen().getTime() : 0;
 			}

org.eclipse.jgit/src/org/eclipse/jgit/storage/file/RefDirectory.java

@@ -63,6 +63,8 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.security.DigestInputStream;
+import java.security.MessageDigest;
 import java.text.MessageFormat;
 import java.util.Arrays;
 import java.util.LinkedList;
@@ -626,24 +628,27 @@ public class RefDirectory extends RefDatabase {
 			return curList;
 
 		final PackedRefList newList = readPackedRefs();
-		if (packedRefs.compareAndSet(curList, newList))
+		if (packedRefs.compareAndSet(curList, newList)
+				&& !curList.id.equals(newList.id))
 			modCnt.incrementAndGet();
 		return newList;
 	}
 
-	private PackedRefList readPackedRefs()
-			throws IOException {
+	private PackedRefList readPackedRefs() throws IOException {
 		final FileSnapshot snapshot = FileSnapshot.save(packedRefsFile);
 		final BufferedReader br;
+		final MessageDigest digest = Constants.newMessageDigest();
 		try {
-			br = new BufferedReader(new InputStreamReader(new FileInputStream(
-					packedRefsFile), CHARSET));
+			br = new BufferedReader(new InputStreamReader(
+					new DigestInputStream(new FileInputStream(packedRefsFile),
+							digest), CHARSET));
 		} catch (FileNotFoundException noPackedRefs) {
 			// Ignore it and leave the new list empty.
 			return PackedRefList.NO_PACKED_REFS;
 		}
 		try {
-			return new PackedRefList(parsePackedRefs(br), snapshot);
+			return new PackedRefList(parsePackedRefs(br), snapshot,
+					ObjectId.fromRaw(digest.digest()));
 		} finally {
 			br.close();
 		}
@@ -724,8 +729,9 @@ public class RefDirectory extends RefDatabase {
 				if (!lck.commit())
 					throw new ObjectWritingException(MessageFormat.format(JGitText.get().unableToWrite, name));
 
-				packedRefs.compareAndSet(oldPackedList, new PackedRefList(
-						refs, lck.getCommitSnapshot()));
+				byte[] digest = Constants.newMessageDigest().digest(content);
+				packedRefs.compareAndSet(oldPackedList, new PackedRefList(refs,
+						lck.getCommitSnapshot(), ObjectId.fromRaw(digest)));
 			}
 		}.writePackedRefs();
 	}
@@ -899,13 +905,17 @@ public class RefDirectory extends RefDatabase {
 
 	private static class PackedRefList extends RefList<Ref> {
 		static final PackedRefList NO_PACKED_REFS = new PackedRefList(
-				RefList.emptyList(), FileSnapshot.MISSING_FILE);
+				RefList.emptyList(), FileSnapshot.MISSING_FILE,
+				ObjectId.zeroId());
 
 		final FileSnapshot snapshot;
 
-		PackedRefList(RefList<Ref> src, FileSnapshot s) {
+		final ObjectId id;
+
+		PackedRefList(RefList<Ref> src, FileSnapshot s, ObjectId i) {
 			super(src);
 			snapshot = s;
+			id = i;
 		}
 	}
 

org.eclipse.jgit/src/org/eclipse/jgit/storage/pack/PackWriter.java

@@ -1660,7 +1660,8 @@ public class PackWriter {
 
 				for (int i = 0; i < cmit.getParentCount(); i++) {
 					RevCommit p = cmit.getParent(i);
-					if (!p.has(added) && !p.has(RevFlag.UNINTERESTING)) {
+					if (!p.has(added) && !p.has(RevFlag.UNINTERESTING)
+							&& !exclude(p)) {
 						p.add(added);
 						addObject(p, 0);
 						commitCnt++;

pom.xml

@@ -173,7 +173,7 @@
     <junit-version>4.5</junit-version>
     <args4j-version>2.0.12</args4j-version>
     <servlet-api-version>2.5</servlet-api-version>
-    <jetty-version>7.1.6.v20100715</jetty-version>
+    <jetty-version>7.6.0.v20120127</jetty-version>
     <protobuf-version>2.4.0a</protobuf-version>
     <clirr-version>2.3</clirr-version>
   </properties>
@@ -183,6 +183,11 @@
       <id>jgit-repository</id>
       <url>http://download.eclipse.org/jgit/maven</url>
     </repository>
+    <repository>
+      <id>jetty</id>
+      <layout>p2</layout>
+      <url>http://download.eclipse.org/jetty/updates/jetty-bundles-7.x/${jetty-version}/</url>
+    </repository>
   </repositories>
 
   <build>