diff --git a/org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitCloneTask.java b/org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitCloneTask.java
index f40b7b1..8d12ce3 100644
--- a/org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitCloneTask.java
+++ b/org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitCloneTask.java
@@ -110,7 +110,7 @@ public void execute() throws BuildException {
 		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);
 		}
diff --git a/org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitInitTask.java b/org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitInitTask.java
index 7b1610e..efdab42 100644
--- a/org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitInitTask.java
+++ b/org.eclipse.jgit.ant/src/org/eclipse/jgit/ant/tasks/GitInitTask.java
@@ -91,7 +91,7 @@ public void execute() throws BuildException {
 			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);
 		}
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
index 2fb228e..fd74098 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
@@ -52,6 +52,7 @@
 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 @@
 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 void testAddNothing() {
 	}
 
 	@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 void testAddNonExistingSingleFile() throws NoFilepatternException {
 	}
 
 	@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 void testAddExistingSingleFile() throws IOException, NoFilepatternExcepti
 
 	@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 void testAddExistingSingleSmallFileWithNewLine() throws IOException,
 
 	@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 void testAddExistingSingleMediumSizeFileWithNewLine()
 
 	@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 void testAddExistingSingleBinaryFile() throws IOException,
 	}
 
 	@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 void testAddExistingSingleFileInSubDir() throws IOException, NoFilepatter
 	}
 
 	@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);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/BranchCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/BranchCommandTest.java
index 32d2e01..b000fe2 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/BranchCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/BranchCommandTest.java
@@ -466,9 +466,7 @@ public void testCreationImplicitStart() throws JGitInternalException,
 
 	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);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java
index a51a8b4..9060cd5 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java
@@ -56,10 +56,8 @@
 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;
@@ -129,9 +127,7 @@ public void testCreateBranchOnCheckout() throws Exception {
 	}
 
 	@Test
-	public void testCheckoutToNonExistingBranch() throws JGitInternalException,
-			RefAlreadyExistsException, InvalidRefNameException,
-			CheckoutConflictException {
+	public void testCheckoutToNonExistingBranch() throws GitAPIException {
 		try {
 			git.checkout().setName("badbranch").call();
 			fail("Should have failed");
@@ -225,8 +221,7 @@ public void testCheckoutRemoteTrackingWithoutLocalBranch() throws Exception {
 
 	@Test
 	public void testDetachedHeadOnCheckout() throws JGitInternalException,
-			RefAlreadyExistsException, RefNotFoundException,
-			InvalidRefNameException, IOException, CheckoutConflictException {
+			IOException, GitAPIException {
 		CheckoutCommand co = git.checkout();
 		co.setName("master").call();
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CleanCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CleanCommandTest.java
index a660a52..07387e4 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CleanCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CleanCommandTest.java
@@ -44,10 +44,10 @@
 
 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 void setUp() throws Exception {
 	}
 
 	@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 void testClean() throws NoWorkTreeException, IOException {
 	}
 
 	@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 void testCleanWithPaths() throws NoWorkTreeException, IOException {
 	}
 
 	@Test
-	public void testCleanWithDryRun() throws NoWorkTreeException, IOException {
+	public void testCleanWithDryRun() throws NoWorkTreeException,
+			GitAPIException {
 		// create status
 		StatusCommand command = git.status();
 		Status status = command.call();
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
index 906a896..4441ea9 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
@@ -55,6 +55,7 @@
 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 void setUp() throws Exception {
 	}
 
 	@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 void testCloneRepository() throws IOException {
 	}
 
 	@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 void testCloneRepositoryWithBranch() throws IOException {
 	}
 
 	@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 static String allRefNames(List<Ref> refs) {
 
 	@Test
 	public void testCloneRepositoryWhenDestinationDirectoryExistsAndIsNotEmpty()
-			throws IOException {
+			throws IOException, JGitInternalException, GitAPIException {
 		String dirName = "testCloneTargetDirectoryNotEmpty";
 		File directory = createTempDirectory(dirName);
 		CloneCommand command = Git.cloneRepository();
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitAndLogCommandTests.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitAndLogCommandTests.java
index e6b6a09..ed32e27 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitAndLogCommandTests.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitAndLogCommandTests.java
@@ -50,15 +50,12 @@
 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 @@
  */
 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 void testSomeCommits() throws NoHeadException, NoMessageException,
 	}
 
 	@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 void testLogWithFilter() throws IOException, NoFilepatternException,
 
 	// 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 void testWrongParams() throws UnmergedPathException,
 	// 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 void testMultipleInvocations() throws NoHeadException,
 	}
 
 	@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 void testMergeEmptyBranches() throws IOException, NoHeadException,
 	}
 
 	@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 void testAddUnstagedChanges() throws IOException, NoHeadException,
 	}
 
 	@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 void testModeChange() throws IOException, NoFilepatternException,
 	}
 
 	@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 void testCommitRange() throws NoHeadException, NoMessageException,
 	}
 
 	@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 void testCommitAmend() throws NoHeadException, NoMessageException,
 	}
 
 	@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"
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/GitConstructionTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/GitConstructionTest.java
index 8031769..d8e1a05 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/GitConstructionTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/GitConstructionTest.java
@@ -48,6 +48,8 @@
 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 void tearDown() throws Exception {
 	}
 
 	@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 void testWrap() {
 	}
 
 	@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());
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/InitCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/InitCommandTest.java
index 2823636..7db9ce7 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/InitCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/InitCommandTest.java
@@ -48,6 +48,8 @@
 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 void setUp() throws Exception {
 	}
 
 	@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 void testInitRepository() throws IOException {
 	}
 
 	@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 void testInitNonEmptyRepository() throws IOException {
 	}
 
 	@Test
-	public void testInitBareRepository() throws IOException {
+	public void testInitBareRepository() throws IOException,
+			JGitInternalException, GitAPIException {
 		File directory = createTempDirectory("testInitBareRepository");
 		InitCommand command = new InitCommand();
 		command.setDirectory(directory);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java
index 3087ca8..f16d436 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java
@@ -54,12 +54,8 @@
 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 void setupRepository() throws IOException, NoFilepatternException,
 
 	@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())
@@ -160,7 +153,7 @@ public void testHardReset() throws JGitInternalException,
 
 	@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 +169,7 @@ public void testResetToNonexistingHEAD() throws JGitInternalException,
 
 	@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())
@@ -198,9 +189,7 @@ public void testSoftReset() throws JGitInternalException,
 
 	@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())
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RmCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RmCommandTest.java
index d826b4c..2eb4f22 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RmCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RmCommandTest.java
@@ -46,8 +46,8 @@
 
 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 void setUp() throws Exception {
 
 	@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();
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/StatusCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/StatusCommandTest.java
index faca7ea..c9a6048 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/StatusCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/StatusCommandTest.java
@@ -52,13 +52,15 @@
 
 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();
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/TagCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/TagCommandTest.java
index 7f381e3..b417b44 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/TagCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/TagCommandTest.java
@@ -48,15 +48,9 @@
 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 @@
 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 void testTaggingOnHead() throws NoHeadException, NoMessageException,
 	}
 
 	@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 void testTagging() throws NoHeadException, NoMessageException,
 	}
 
 	@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 void testEmptyTagName() throws NoHeadException, NoMessageException,
 	}
 
 	@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 void testInvalidTagName() throws NoHeadException,
 	}
 
 	@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 {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutMaliciousPathTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutMaliciousPathTest.java
index 65d0418..fb9cc2c 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutMaliciousPathTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/DirCacheCheckoutMaliciousPathTest.java
@@ -46,14 +46,8 @@
 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 @@ private void testMaliciousPathGoodSecondCheckout(String... paths) throws Excepti
 	 *            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();
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffTest.java
index b7caecc..dde32d7 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffTest.java
@@ -59,7 +59,7 @@
 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 void testRemoved() throws IOException {
 	}
 
 	@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 void testConflictingFromMultipleCreations() throws Exception {
 	}
 
 	@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 void testUnchangedSimple() throws IOException,
 	 * 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");
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleAddTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleAddTest.java
index 568cd9e..940a78a 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleAddTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleAddTest.java
@@ -53,6 +53,7 @@
 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 @@
 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 void commandWithNullPath() {
 	}
 
 	@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 void commandWithEmptyPath() {
 	}
 
 	@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 void commandWithNullUri() {
 	}
 
 	@Test
-	public void commandWithEmptyUri() {
+	public void commandWithEmptyUri() throws GitAPIException {
 		try {
 			new SubmoduleAddCommand(db).setPath("sub").setURI("").call();
 			fail("Exception not thrown");
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleInitTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleInitTest.java
index f0a0750..424ad01 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleInitTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleInitTest.java
@@ -53,6 +53,7 @@
 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 @@
 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 void repositoryWithNoSubmodules() {
 
 	@Test
 	public void repositoryWithUninitializedModule() throws IOException,
-			ConfigInvalidException {
+			ConfigInvalidException, GitAPIException {
 		final String path = addSubmoduleToIndex();
 
 		SubmoduleWalk generator = SubmoduleWalk.forIndex(db);
@@ -156,7 +157,7 @@ public void resolveSameLevelRelativeUrl() throws Exception {
 
 	@Test
 	public void resolveOneLevelHigherRelativeUrl() throws IOException,
-			ConfigInvalidException {
+			ConfigInvalidException, GitAPIException {
 		final String path = addSubmoduleToIndex();
 
 		String base = "git://server/repo.git";
@@ -197,7 +198,7 @@ public void resolveOneLevelHigherRelativeUrl() throws IOException,
 
 	@Test
 	public void resolveTwoLevelHigherRelativeUrl() throws IOException,
-			ConfigInvalidException {
+			ConfigInvalidException, GitAPIException {
 		final String path = addSubmoduleToIndex();
 
 		String base = "git://server/repo.git";
@@ -238,7 +239,7 @@ public void resolveTwoLevelHigherRelativeUrl() throws IOException,
 
 	@Test
 	public void resolveWorkingDirectoryRelativeUrl() throws IOException,
-			ConfigInvalidException {
+			GitAPIException, ConfigInvalidException {
 		final String path = addSubmoduleToIndex();
 
 		String base = db.getWorkTree().getAbsolutePath();
@@ -281,7 +282,7 @@ public void resolveWorkingDirectoryRelativeUrl() throws IOException,
 
 	@Test
 	public void resolveInvalidParentUrl() throws IOException,
-			ConfigInvalidException {
+			ConfigInvalidException, GitAPIException {
 		final String path = addSubmoduleToIndex();
 
 		String base = "no_slash";
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleStatusTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleStatusTest.java
index dc79d84..6feefdb 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleStatusTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleStatusTest.java
@@ -53,6 +53,7 @@
 
 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 @@
 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 void repositoryWithNoSubmodules() {
 	}
 
 	@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 void apply(DirCacheEntry ent) {
 	}
 
 	@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 void apply(DirCacheEntry ent) {
 	}
 
 	@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 void apply(DirCacheEntry ent) {
 	}
 
 	@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 void apply(DirCacheEntry ent) {
 	}
 
 	@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 void apply(DirCacheEntry ent) {
 
 	@Test
 	public void repositoryWithDifferentRevCheckedOutSubmodule()
-			throws IOException {
+			throws IOException, GitAPIException {
 		final ObjectId id = ObjectId
 				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
 		final String path = "sub";
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleSyncTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleSyncTest.java
index 4df9077..3f9ad11 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleSyncTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleSyncTest.java
@@ -53,6 +53,7 @@
 
 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 @@
 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);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleUpdateTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleUpdateTest.java
index 9bb4a63..eb0cf2b 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleUpdateTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/submodule/SubmoduleUpdateTest.java
@@ -52,6 +52,7 @@
 
 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 @@
 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 void apply(DirCacheEntry ent) {
 	}
 
 	@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 void apply(DirCacheEntry ent) {
 	}
 
 	@Test
-	public void repositoryWithInitializedSubmodule() throws IOException {
+	public void repositoryWithInitializedSubmodule() throws IOException,
+			GitAPIException {
 		final ObjectId id = ObjectId
 				.fromString("abcd1234abcd1234abcd1234abcd1234abcd1234");
 		final String path = "sub";
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
index 3da9640..f89f3e4 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
@@ -48,6 +48,7 @@
 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 AddCommand setWorkingTreeIterator(WorkingTreeIterator f) {
 	 *
 	 * @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);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/AddNoteCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/AddNoteCommand.java
index d1c75e2..3af8695 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/AddNoteCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/AddNoteCommand.java
@@ -44,6 +44,7 @@
 
 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 @@ protected AddNoteCommand(Repository repo) {
 		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();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/BlameCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/BlameCommand.java
index 400d94b..12be64b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/BlameCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/BlameCommand.java
@@ -48,6 +48,7 @@
 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 BlameCommand reverse(AnyObjectId start, Collection<ObjectId> end)
 	 *
 	 * @return list of lines
 	 */
-	public BlameResult call() throws JGitInternalException {
+	public BlameResult call() throws GitAPIException {
 		checkCallable();
 		BlameGenerator gen = new BlameGenerator(repo, path);
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
index e6d56c8..03df65d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
@@ -51,6 +51,7 @@
 
 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 @@ protected CheckoutCommand(Repository repo) {
 	 * @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();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CleanCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CleanCommand.java
index e31f119..341be91 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CleanCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CleanCommand.java
@@ -49,6 +49,7 @@
 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 @@ protected CleanCommand(Repository repo) {
 	 *
 	 * @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 CleanCommand setPaths(Set<String> paths) {
 
 	/**
 	 * 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}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
index f354de1..23bbc2a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java
@@ -50,6 +50,7 @@
 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 CloneCommand() {
 	/**
 	 * 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 Git call() throws JGitInternalException {
 		}
 	}
 
-	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 @@ private Repository init(URIish u) {
 	}
 
 	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 @@ else if (branchesToClone != null
 	}
 
 	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 @@ private void checkout(Repository clonedRepo, FetchResult result)
 		}
 	}
 
-	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;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
index 242d11e..eac6fe6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
@@ -50,10 +50,12 @@
 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 @@ protected CommitCommand(Repository repo) {
 	 *             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 RevCommit call() throws NoHeadException, NoMessageException,
 				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);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CreateBranchCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CreateBranchCommand.java
index 7ef1f2e..4fb3c17 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CreateBranchCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CreateBranchCommand.java
@@ -46,6 +46,7 @@
 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.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 @@ protected CreateBranchCommand(Repository repo) {
 	 *             invalid
 	 * @return the newly created branch
 	 */
-	public Ref call() throws JGitInternalException, RefAlreadyExistsException,
+	public Ref call() throws GitAPIException, RefAlreadyExistsException,
 			RefNotFoundException, InvalidRefNameException {
 		checkCallable();
 		processOptions();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/DeleteBranchCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/DeleteBranchCommand.java
index fe629f3..0d03162 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/DeleteBranchCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/DeleteBranchCommand.java
@@ -51,6 +51,7 @@
 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.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 @@ protected DeleteBranchCommand(Repository repo) {
 	 * @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>();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/DeleteTagCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/DeleteTagCommand.java
index bd4c8ec..ae511c6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/DeleteTagCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/DeleteTagCommand.java
@@ -49,6 +49,7 @@
 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 @@ protected DeleteTagCommand(Repository repo) {
 	}
 
 	/**
-	 * @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())
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/DiffCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/DiffCommand.java
index e82b048..9b4476d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/DiffCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/DiffCommand.java
@@ -50,6 +50,7 @@
 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 @@ protected DiffCommand(Repository repo) {
 	 *
 	 * @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 List<DiffEntry> call() throws GitAPIException, IOException {
 				diffFmt.flush();
 				return result;
 			}
+		} catch (IOException e) {
+			throw new JGitInternalException(e.getMessage(), e);
 		} finally {
 			diffFmt.release();
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
index 181c4c4..6df244b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
@@ -47,6 +47,7 @@
 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 @@ protected FetchCommand(Repository repo) {
 	 *         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 FetchResult call() throws JGitInternalException,
 			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) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/GitCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/GitCommand.java
index 83e7cfd..329b1b5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/GitCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/GitCommand.java
@@ -40,6 +40,7 @@
 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 @@ protected void checkCallable() {
 					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;
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/InitCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/InitCommand.java
index 77fc304..8777be5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/InitCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/InitCommand.java
@@ -46,6 +46,7 @@
 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)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/ListBranchCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/ListBranchCommand.java
index 846c538..ea6f34b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ListBranchCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ListBranchCommand.java
@@ -47,10 +47,11 @@
 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 @@ protected ListBranchCommand(Repository repo) {
 		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 {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/ListNotesCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/ListNotesCommand.java
index 92f883a0..84fa355 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ListNotesCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ListNotesCommand.java
@@ -47,6 +47,7 @@
 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 @@ protected ListNotesCommand(Repository repo) {
 	}
 
 	/**
-	 * @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);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/ListTagCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/ListTagCommand.java
index c1ae887..a0a5d95 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ListTagCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ListTagCommand.java
@@ -49,6 +49,7 @@
 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 @@ protected ListTagCommand(Repository repo) {
 	}
 
 	/**
-	 * @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>();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/LogCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/LogCommand.java
index 04a87b0..6d4b347 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/LogCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/LogCommand.java
@@ -47,6 +47,7 @@
 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 @@ protected LogCommand(Repository repo) {
 	 * 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 @@ else if (maxCount > -1)
 	 *             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 LogCommand add(AnyObjectId start) throws MissingObjectException,
 	 *             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 LogCommand not(AnyObjectId start) throws MissingObjectException,
 	 *             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);
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/LsRemoteCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/LsRemoteCommand.java
index 947b3f5..b041f33 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/LsRemoteCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/LsRemoteCommand.java
@@ -144,13 +144,11 @@ public LsRemoteCommand setUploadPack(String uploadPack) {
 	 * @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;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java
index 05743e6..c5a9552 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/MergeCommand.java
@@ -54,6 +54,7 @@
 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 @@ protected MergeCommand(Repository repo) {
 	 *
 	 * @return the result of the merge
 	 */
-	public MergeResult call() throws NoHeadException,
+	public MergeResult call() throws GitAPIException, NoHeadException,
 			ConcurrentRefUpdateException, CheckoutConflictException,
 			InvalidMergeHeadsException, WrongRepositoryStateException, NoMessageException {
 		checkCallable();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/PullCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/PullCommand.java
index 3a85f10..86d38fb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/PullCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/PullCommand.java
@@ -110,7 +110,7 @@ public PullCommand setProgressMonitor(ProgressMonitor monitor) {
 	 *
 	 * @return the result of the pull
 	 */
-	public PullResult call() throws WrongRepositoryStateException,
+	public PullResult call() throws GitAPIException, WrongRepositoryStateException,
 			InvalidConfigurationException, DetachedHeadException,
 			InvalidRemoteException, CanceledException, RefNotFoundException,
 			NoHeadException {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/PushCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/PushCommand.java
index e7f0b06..edfb2f7 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/PushCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/PushCommand.java
@@ -50,6 +50,7 @@
 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 @@ protected PushCommand(Repository repo) {
 	 * @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 PushCommand add(Ref ref) {
 	 * @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 {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
index aa65726..5b73657 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
@@ -190,8 +190,8 @@ protected RebaseCommand(Repository repo) {
 	 *
 	 * @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 @@ private void updateHead(String headName, RevCommit newHead)
 		}
 	}
 
-	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 @@ private void popSteps(int numSteps) throws IOException {
 		}
 	}
 
-	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
 
@@ -626,11 +625,11 @@ else if (walk.isMergedInto(headCommit, upstream)) {
 	 *
 	 * @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 RevCommit tryFastForward(RevCommit newCommit)
 	}
 
 	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))
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/ReflogCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/ReflogCommand.java
index 10757a8..c4d112a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ReflogCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ReflogCommand.java
@@ -46,6 +46,7 @@
 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 ReflogCommand setRef(String ref) {
 		return this;
 	}
 
-	public Collection<ReflogEntry> call() throws Exception {
+	public Collection<ReflogEntry> call() throws GitAPIException {
 		checkCallable();
 
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RemoveNoteCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RemoveNoteCommand.java
index 5b9075e4..d1e2770 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RemoveNoteCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RemoveNoteCommand.java
@@ -44,6 +44,7 @@
 
 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 @@ protected RemoveNoteCommand(Repository repo) {
 		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();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RenameBranchCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RenameBranchCommand.java
index f5dfa2b..f9cb828 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RenameBranchCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RenameBranchCommand.java
@@ -48,6 +48,7 @@
 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.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 @@ protected RenameBranchCommand(Repository repo) {
 	 *             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();
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/ResetCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/ResetCommand.java
index 0af684e..2f46b7f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ResetCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ResetCommand.java
@@ -47,6 +47,7 @@
 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.DirCacheCheckout;
@@ -135,7 +136,7 @@ public ResetCommand(Repository repo) {
 	 *
 	 * @return the Ref after reset
 	 */
-	public Ref call() throws IOException {
+	public Ref call() throws GitAPIException {
 		checkCallable();
 
 		Ref r;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RevertCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RevertCommand.java
index b6757d8..416677c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RevertCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RevertCommand.java
@@ -50,8 +50,8 @@
 
 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;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RmCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RmCommand.java
index 2b8cafc..d29d547 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RmCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RmCommand.java
@@ -47,6 +47,7 @@
 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 RmCommand addFilepattern(String filepattern) {
 	 *
 	 * @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);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/ShowNoteCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/ShowNoteCommand.java
index 45f53e7..7d411c3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ShowNoteCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ShowNoteCommand.java
@@ -44,6 +44,7 @@
 
 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 @@ protected ShowNoteCommand(Repository repo) {
 		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();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
index 3876e48..4992d3c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
@@ -189,8 +189,7 @@ private boolean isConflict(AbstractTreeIterator stashIndexIter,
 		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 @@ private ObjectId getHeadTree() throws JGitInternalException,
 		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 void apply(DirCacheEntry ent) {
 	 *
 	 * @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)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java
index 5ba6162..4056894 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java
@@ -212,7 +212,7 @@ private Ref getHead() throws GitAPIException {
 	 *
 	 * @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();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashDropCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashDropCommand.java
index e718417..eb61298 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashDropCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashDropCommand.java
@@ -168,7 +168,7 @@ private void updateRef(Ref stashRef, ObjectId newId) {
 	 *
 	 * @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();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashListCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashListCommand.java
index 8f7bf2e..407b5ab 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashListCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashListCommand.java
@@ -49,6 +49,7 @@
 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 StashListCommand(final Repository repo) {
 		super(repo);
 	}
 
-	public Collection<RevCommit> call() throws Exception {
+	public Collection<RevCommit> call() throws GitAPIException {
 		checkCallable();
 
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/StatusCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/StatusCommand.java
index 7d7eb18..b3e112f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/StatusCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/StatusCommand.java
@@ -44,6 +44,8 @@
 
 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 @@ protected StatusCommand(Repository repo) {
 	 * @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);
+		}
 	}
 
 	/**
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleAddCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleAddCommand.java
index 454fc23..bfef053 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleAddCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleAddCommand.java
@@ -46,6 +46,7 @@
 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 @@ protected boolean submoduleExists() throws IOException {
 		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);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleInitCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleInitCommand.java
index fef1370..e799bfb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleInitCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleInitCommand.java
@@ -47,6 +47,7 @@
 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 SubmoduleInitCommand addPath(final String path) {
 		return this;
 	}
 
-	public Collection<String> call() throws JGitInternalException {
+	public Collection<String> call() throws GitAPIException {
 		checkCallable();
 
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleStatusCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleStatusCommand.java
index 0542583..d27f90c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleStatusCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleStatusCommand.java
@@ -48,6 +48,7 @@
 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 SubmoduleStatusCommand addPath(final String path) {
 		return this;
 	}
 
-	public Map<String, SubmoduleStatus> call() throws JGitInternalException {
+	public Map<String, SubmoduleStatus> call() throws GitAPIException {
 		checkCallable();
 
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleSyncCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleSyncCommand.java
index fd8ddc9..edc54ff 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleSyncCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleSyncCommand.java
@@ -48,6 +48,7 @@
 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 @@ protected String getHeadBranch(final Repository subRepo) throws IOException {
 			return null;
 	}
 
-	public Map<String, String> call() throws JGitInternalException {
+	public Map<String, String> call() throws GitAPIException {
 		checkCallable();
 
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleUpdateCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleUpdateCommand.java
index f94b209..be705ee 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleUpdateCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/SubmoduleUpdateCommand.java
@@ -109,7 +109,7 @@ public SubmoduleUpdateCommand addPath(final String path) {
 		return this;
 	}
 
-	public Collection<String> call() throws JGitInternalException {
+	public Collection<String> call() throws GitAPIException {
 		checkCallable();
 
 		try {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/TagCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/TagCommand.java
index c867b53..cef9e18 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/TagCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/TagCommand.java
@@ -46,6 +46,7 @@
 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 @@ protected TagCommand(Repository repo) {
 	 * @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();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/UnmergedPathsException.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/UnmergedPathsException.java
index 19101db..0990040 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/errors/UnmergedPathsException.java
+++ b/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);
 	}
 }