Merge branch 'master' into stable-4.2

Change-Id: Ieec4f51aedadf5734ae0e3f4e8713248a3c4fc52
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

.buckconfig

@@ -0,0 +1,15 @@
+[buildfile]
+  includes = //tools/default.defs
+
+[java]
+  src_roots = src, resources, tst
+
+[project]
+  ignore = .git
+
+[cache]
+  mode = dir
+
+[download]
+  maven_repo = http://repo1.maven.org/maven2
+  in_build = true

.buckversion

@@ -0,0 +1 @@
+1b03b4313b91b634bd604fc3487a05f877e59dee

.gitignore

@@ -1,2 +1,4 @@
 /target
 /.project
+/buck-cache
+/buck-out

BUCK

@@ -0,0 +1,45 @@
+java_library(
+  name = 'jgit',
+  exported_deps = ['//org.eclipse.jgit:jgit'],
+  visibility = ['PUBLIC'],
+)
+
+genrule(
+  name = 'jgit_src',
+  cmd = 'ln -s $(location //org.eclipse.jgit:jgit_src) $OUT',
+  out = 'jgit_src.zip',
+  visibility = ['PUBLIC'],
+)
+
+java_library(
+  name = 'jgit-servlet',
+  exported_deps = [
+    ':jgit',
+    '//org.eclipse.jgit.http.server:jgit-servlet'
+  ],
+  visibility = ['PUBLIC'],
+)
+
+java_library(
+  name = 'jgit-archive',
+  exported_deps = [
+    ':jgit',
+    '//org.eclipse.jgit.archive:jgit-archive'
+  ],
+  visibility = ['PUBLIC'],
+)
+
+java_library(
+  name = 'junit',
+  exported_deps = [
+    ':jgit',
+    '//org.eclipse.jgit.junit:junit'
+  ],
+  visibility = ['PUBLIC'],
+)
+
+genrule(
+  name = 'jgit_bin',
+  cmd = 'ln -s $(location //org.eclipse.jgit.pgm:jgit) $OUT',
+  out = 'jgit_bin',
+)

lib/BUCK

@@ -0,0 +1,125 @@
+maven_jar(
+  name = 'jsch',
+  bin_sha1 = '658b682d5c817b27ae795637dfec047c63d29935',
+  src_sha1 = '791359d94d6edcace686a56d0727ee093a2f7c33',
+  group = 'com.jcraft',
+  artifact = 'jsch',
+  version = '0.1.53',
+)
+
+maven_jar(
+  name = 'javaewah',
+  bin_sha1 = 'eceaf316a8faf0e794296ebe158ae110c7d72a5a',
+  src_sha1 = 'a50d78eb630e05439461f3130b94b3bcd1ea6f03',
+  group = 'com.googlecode.javaewah',
+  artifact = 'JavaEWAH',
+  version = '0.7.9',
+)
+
+maven_jar(
+  name = 'httpcomponents',
+  bin_sha1 = '4c47155e3e6c9a41a28db36680b828ced53b8af4',
+  src_sha1 = 'af4d76be0c46ee26b0d9d1d4a34d244a633cac84',
+  group = 'org.apache.httpcomponents',
+  artifact = 'httpclient',
+  version = '4.3.6',
+)
+
+maven_jar(
+  name = 'httpcore',
+  bin_sha1 = 'f91b7a4aadc5cf486df6e4634748d7dd7a73f06d',
+  src_sha1 = '1b0aa62a6a91e9fa00c16f0a4a2c874804ed3b1e',
+  group = 'org.apache.httpcomponents',
+  artifact = 'httpcore',
+  version = '4.3.3',
+)
+
+maven_jar(
+  name = 'commons-logging',
+  bin_sha1 = 'f6f66e966c70a83ffbdb6f17a0919eaf7c8aca7f',
+  src_sha1 = '28bb0405fddaf04f15058fbfbe01fe2780d7d3b6',
+  group = 'commons-logging',
+  artifact = 'commons-logging',
+  version = '1.1.3',
+)
+
+maven_jar(
+  name = 'slf4j-api',
+  bin_sha1 = '0081d61b7f33ebeab314e07de0cc596f8e858d97',
+  src_sha1 = '58d38f68d4a867d4552ae27960bb348d7eaa1297',
+  group = 'org.slf4j',
+  artifact = 'slf4j-api',
+  version = '1.7.2',
+)
+
+maven_jar(
+  name = 'slf4j-simple',
+  bin_sha1 = '760055906d7353ba4f7ce1b8908bc6b2e91f39fa',
+  src_sha1 = '09474919128b3a7fcf21a5f9c907f5251f234544',
+  group = 'org.slf4j',
+  artifact = 'slf4j-simple',
+  version = '1.7.2',
+)
+
+maven_jar(
+  name = 'servlet-api',
+  bin_sha1 = '3cd63d075497751784b2fa84be59432f4905bf7c',
+  src_sha1 = 'ab3976d4574c48d22dc1abf6a9e8bd0fdf928223',
+  group = 'javax.servlet',
+  artifact = 'javax.servlet-api',
+  version = '3.1.0',
+)
+
+maven_jar(
+  name = 'commons-compress',
+  bin_sha1 = 'c7d9b580aff9e9f1998361f16578e63e5c064699',
+  src_sha1 = '396b81bdfd0fb617178e1707ef64832215307c78',
+  group = 'org.apache.commons',
+  artifact = 'commons-compress',
+  version = '1.6',
+)
+
+maven_jar(
+  name = 'tukaani-xz',
+  bin_sha1 = '66db21c8484120cb6a51b5b3ea47b6f383942bec',
+  src_sha1 = '6396220725701d767c553902c41120d7bf38e9f5',
+  group = 'org.tukaani',
+  artifact = 'xz',
+  version = '1.3',
+)
+
+maven_jar(
+  name = 'args4j',
+  bin_sha1 = '139441471327b9cc6d56436cb2a31e60eb6ed2ba',
+  src_sha1 = '22631b78cc8f60a6918557e8cbdb33e90f63a77f',
+  group = 'args4j',
+  artifact = 'args4j',
+  version = '2.0.15',
+)
+
+maven_jar(
+  name = 'junit',
+  bin_sha1 = '4e031bb61df09069aeb2bffb4019e7a5034a4ee0',
+  src_sha1 = '28e0ad201304e4a4abf999ca0570b7cffc352c3c',
+  group = 'junit',
+  artifact = 'junit',
+  version = '4.11',
+)
+
+maven_jar(
+  name = 'hamcrest-library',
+  bin_sha1 = '4785a3c21320980282f9f33d0d1264a69040538f',
+  src_sha1 = '047a7ee46628ab7133129cd7cef1e92657bc275e',
+  group = 'org.hamcrest',
+  artifact = 'hamcrest-library',
+  version = '1.3',
+)
+
+maven_jar(
+  name = 'hamcrest-core',
+  bin_sha1 = '42a25dc3219429f0e5d060061f71acb49bf010a0',
+  src_sha1 = '1dc37250fbc78e23a65a67fbbaf71d2e9cbc3c0b',
+  group = 'org.hamcrest',
+  artifact = 'hamcrest-core',
+  version = '1.3',
+)

lib/jetty/BUCK

@@ -0,0 +1,56 @@
+VERSION = '9.2.13.v20150730'
+GROUP = 'org.eclipse.jetty'
+
+maven_jar(
+  name = 'servlet',
+  bin_sha1 = '5ad6e38015a97ae9a60b6c2ad744ccfa9cf93a50',
+  src_sha1 = '78fbec19321150552d91f9e079c2f2ca33222b01',
+  group = GROUP,
+  artifact = 'jetty-servlet',
+  version = VERSION,
+)
+
+maven_jar(
+  name = 'security',
+  bin_sha1 = 'cc7c7f27ec4cc279253be1675d9e47e58b995943',
+  src_sha1 = '75632ebdf8bd651faafb97106c92496db59e165d',
+  group = GROUP,
+  artifact = 'jetty-security',
+  version = VERSION,
+)
+
+maven_jar(
+  name = 'server',
+  bin_sha1 = '5be7d1da0a7abffd142de3091d160717c120b6ab',
+  src_sha1 = '203e123f83efe2a5b8a9c74854c7897fe3563302',
+  group = GROUP,
+  artifact = 'jetty-server',
+  version = VERSION,
+)
+
+maven_jar(
+  name = 'http',
+  bin_sha1 = '23a745d9177ef67ef53cc46b9b70c5870082efc2',
+  src_sha1 = '5f87f7ff2057cd4b0995bc4fffe17b2aff64c130',
+  group = GROUP,
+  artifact = 'jetty-http',
+  version = VERSION,
+)
+
+maven_jar(
+  name = 'io',
+  bin_sha1 = '7a351e6a1b63dfd56b6632623f7ca2793ffb67ad',
+  src_sha1 = 'bbd61a84b748fc295456e1c5c3070aaf40a68f62',
+  group = GROUP,
+  artifact = 'jetty-io',
+  version = VERSION,
+)
+
+maven_jar(
+  name = 'util',
+  bin_sha1 = 'c101476360a7cdd0670462de04053507d5e70c97',
+  src_sha1 = '15ceecce141971b4e0facb861b3d10120ad6ce03',
+  group = GROUP,
+  artifact = 'jetty-util',
+  version = VERSION,
+)

org.eclipse.jgit.archive/BUCK

@@ -0,0 +1,13 @@
+java_library(
+  name = 'jgit-archive',
+  srcs = glob(
+    ['src/**'],
+    excludes = ['src/org/eclipse/jgit/archive/FormatActivator.java'],
+  ),
+  resources = glob(['resources/**']),
+  provided_deps = [
+    '//org.eclipse.jgit:jgit',
+    '//lib:commons-compress',
+  ],
+  visibility = ['PUBLIC'],
+)

org.eclipse.jgit.http.apache/BUCK

@@ -0,0 +1,12 @@
+java_library(
+  name = 'http-apache',
+  srcs = glob(['src/**']),
+  resources = glob(['resources/**']),
+  deps = [
+    '//org.eclipse.jgit:jgit',
+    '//lib:commons-logging',
+    '//lib:httpcomponents',
+    '//lib:httpcore',
+  ],
+  visibility = ['PUBLIC'],
+)

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

@@ -7,7 +7,8 @@ Bundle-RequiredExecutionEnvironment: JavaSE-1.7
 Bundle-Localization: plugin
 Bundle-Vendor: %Provider-Name
 Bundle-ActivationPolicy: lazy
-Import-Package: org.apache.http;version="[4.1.0,5.0.0)",
+Import-Package: org.apache.commons.logging;version="[1.1.1,2.0.0)",
+ org.apache.http;version="[4.1.0,5.0.0)",
  org.apache.http.client;version="[4.1.0,5.0.0)",
  org.apache.http.client.methods;version="[4.1.0,5.0.0)",
  org.apache.http.client.params;version="[4.1.0,5.0.0)",

org.eclipse.jgit.http.apache/src/org/eclipse/jgit/transport/http/apache/HttpClientConnection.java

@@ -100,7 +100,7 @@ import org.eclipse.jgit.util.TemporaryBuffer.LocalFile;
 public class HttpClientConnection implements HttpConnection {
 	HttpClient client;
 
-	String urlStr;
+	URL url;
 
 	HttpUriRequest req;
 
@@ -176,16 +176,19 @@ public class HttpClientConnection implements HttpConnection {
 
 	/**
 	 * @param urlStr
+	 * @throws MalformedURLException
 	 */
-	public HttpClientConnection(String urlStr) {
+	public HttpClientConnection(String urlStr) throws MalformedURLException {
 		this(urlStr, null);
 	}
 
 	/**
 	 * @param urlStr
 	 * @param proxy
+	 * @throws MalformedURLException
 	 */
-	public HttpClientConnection(String urlStr, Proxy proxy) {
+	public HttpClientConnection(String urlStr, Proxy proxy)
+			throws MalformedURLException {
 		this(urlStr, proxy, null);
 	}
 
@@ -193,10 +196,12 @@ public class HttpClientConnection implements HttpConnection {
 	 * @param urlStr
 	 * @param proxy
 	 * @param cl
+	 * @throws MalformedURLException
 	 */
-	public HttpClientConnection(String urlStr, Proxy proxy, HttpClient cl) {
+	public HttpClientConnection(String urlStr, Proxy proxy, HttpClient cl)
+			throws MalformedURLException {
 		this.client = cl;
-		this.urlStr = urlStr;
+		this.url = new URL(urlStr);
 		this.proxy = proxy;
 	}
 
@@ -206,11 +211,7 @@ public class HttpClientConnection implements HttpConnection {
 	}
 
 	public URL getURL() {
-		try {
-			return new URL(urlStr);
-		} catch (MalformedURLException e) {
-			return null;
-		}
+		return url;
 	}
 
 	public String getResponseMessage() throws IOException {
@@ -250,11 +251,11 @@ public class HttpClientConnection implements HttpConnection {
 	public void setRequestMethod(String method) throws ProtocolException {
 		this.method = method;
 		if ("GET".equalsIgnoreCase(method)) //$NON-NLS-1$
-			req = new HttpGet(urlStr);
+			req = new HttpGet(url.toString());
 		else if ("PUT".equalsIgnoreCase(method)) //$NON-NLS-1$
-			req = new HttpPut(urlStr);
+			req = new HttpPut(url.toString());
 		else if ("POST".equalsIgnoreCase(method)) //$NON-NLS-1$
-			req = new HttpPost(urlStr);
+			req = new HttpPost(url.toString());
 		else {
 			this.method = null;
 			throw new UnsupportedOperationException();

org.eclipse.jgit.http.server/BUCK

@@ -0,0 +1,10 @@
+java_library(
+  name = 'jgit-servlet',
+  srcs = glob(['src/**']),
+  resources = glob(['resources/**']),
+  provided_deps = [
+    '//org.eclipse.jgit:jgit',
+    '//lib:servlet-api',
+  ],
+  visibility = ['PUBLIC'],
+)

org.eclipse.jgit.http.test/BUCK

@@ -0,0 +1,40 @@
+TESTS = glob(['tst/**/*.java'])
+
+for t in TESTS:
+  n = t[len('tst/'):len(t)-len('.java')].replace('/', '.')
+  java_test(
+    name = n,
+    labels = ['http'],
+    srcs = [t],
+    deps = [
+      ':helpers',
+      '//org.eclipse.jgit:jgit',
+      '//org.eclipse.jgit.http.apache:http-apache',
+      '//org.eclipse.jgit.http.server:jgit-servlet',
+      '//org.eclipse.jgit.junit:junit',
+      '//org.eclipse.jgit.junit.http:junit-http',
+      '//lib:hamcrest-core',
+      '//lib:hamcrest-library',
+      '//lib:junit',
+      '//lib:servlet-api',
+      '//lib/jetty:http',
+      '//lib/jetty:io',
+      '//lib/jetty:server',
+      '//lib/jetty:servlet',
+      '//lib/jetty:security',
+      '//lib/jetty:util',
+    ],
+    source_under_test = ['//org.eclipse.jgit.http.server:jgit-servlet'],
+  )
+
+java_library(
+  name = 'helpers',
+  srcs = glob(['src/**/*.java']),
+  deps = [
+    '//org.eclipse.jgit:jgit',
+    '//org.eclipse.jgit.http.server:jgit-servlet',
+    '//org.eclipse.jgit.junit:junit',
+    '//org.eclipse.jgit.junit.http:junit-http',
+    '//lib:junit',
+  ],
+)

org.eclipse.jgit.http.test/pom.xml

@@ -134,6 +134,10 @@
         <artifactId>maven-surefire-plugin</artifactId>
         <configuration>
           <argLine>-Djava.io.tmpdir=${project.build.directory}  -Xmx300m</argLine>
+          <includes>
+            <include>**/*Test.java</include>
+            <include>**/*Tests.java</include>
+          </includes>
         </configuration>
       </plugin>
     </plugins>

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

@@ -140,8 +140,7 @@ public class DumbClientDumbServerTest extends HttpTestCase {
 		assertEquals("http", remoteURI.getScheme());
 
 		Map<String, Ref> map;
-		Transport t = Transport.open(dst, remoteURI);
-		try {
+		try (Transport t = Transport.open(dst, remoteURI)) {
 			// I didn't make up these public interface names, I just
 			// approved them for inclusion into the code base. Sorry.
 			// --spearce
@@ -149,14 +148,9 @@ public class DumbClientDumbServerTest extends HttpTestCase {
 			assertTrue("isa TransportHttp", t instanceof TransportHttp);
 			assertTrue("isa HttpTransport", t instanceof HttpTransport);
 
-			FetchConnection c = t.openFetch();
-			try {
+			try (FetchConnection c = t.openFetch()) {
 				map = c.getRefsMap();
-			} finally {
-				c.close();
 			}
-		} finally {
-			t.close();
 		}
 
 		assertNotNull("have map of refs", map);
@@ -201,11 +195,8 @@ public class DumbClientDumbServerTest extends HttpTestCase {
 		Repository dst = createBareRepository();
 		assertFalse(dst.hasObject(A_txt));
 
-		Transport t = Transport.open(dst, remoteURI);
-		try {
+		try (Transport t = Transport.open(dst, remoteURI)) {
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
-		} finally {
-			t.close();
 		}
 
 		assertTrue(dst.hasObject(A_txt));
@@ -226,11 +217,8 @@ public class DumbClientDumbServerTest extends HttpTestCase {
 		Repository dst = createBareRepository();
 		assertFalse(dst.hasObject(A_txt));
 
-		Transport t = Transport.open(dst, remoteURI);
-		try {
+		try (Transport t = Transport.open(dst, remoteURI)) {
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
-		} finally {
-			t.close();
 		}
 
 		assertTrue(dst.hasObject(A_txt));
@@ -265,8 +253,7 @@ public class DumbClientDumbServerTest extends HttpTestCase {
 		final RevCommit Q = src.commit().create();
 		final Repository db = src.getRepository();
 
-		Transport t = Transport.open(db, remoteURI);
-		try {
+		try (Transport t = Transport.open(db, remoteURI)) {
 			try {
 				t.push(NullProgressMonitor.INSTANCE, push(src, Q));
 				fail("push incorrectly completed against a dumb server");
@@ -274,8 +261,6 @@ public class DumbClientDumbServerTest extends HttpTestCase {
 				String exp = "remote does not support smart HTTP push";
 				assertEquals(exp, nse.getMessage());
 			}
-		} finally {
-			t.close();
 		}
 	}
 }

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

@@ -60,6 +60,7 @@ import org.eclipse.jgit.http.server.GitServlet;
 import org.eclipse.jgit.http.server.resolver.DefaultReceivePackFactory;
 import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.junit.http.HttpTestCase;
+import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.NullProgressMonitor;
 import org.eclipse.jgit.lib.ObjectChecker;
@@ -221,8 +222,9 @@ public class GitServletResponseTests extends HttpTestCase {
 		preHook = null;
 		oc = new ObjectChecker() {
 			@Override
-			public void checkCommit(byte[] raw) throws CorruptObjectException {
-				throw new IllegalStateException();
+			public void checkCommit(AnyObjectId id, byte[] raw)
+					throws CorruptObjectException {
+				throw new CorruptObjectException("refusing all commits");
 			}
 		};
 

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

@@ -157,8 +157,7 @@ public class HttpClientTests extends HttpTestCase {
 	public void testRepositoryNotFound_Dumb() throws Exception {
 		URIish uri = toURIish("/dumb.none/not-found");
 		Repository dst = createBareRepository();
-		Transport t = Transport.open(dst, uri);
-		try {
+		try (Transport t = Transport.open(dst, uri)) {
 			try {
 				t.openFetch();
 				fail("connection opened to not found repository");
@@ -167,8 +166,6 @@ public class HttpClientTests extends HttpTestCase {
 						+ "/info/refs?service=git-upload-pack not found";
 				assertEquals(exp, err.getMessage());
 			}
-		} finally {
-			t.close();
 		}
 	}
 
@@ -176,8 +173,7 @@ public class HttpClientTests extends HttpTestCase {
 	public void testRepositoryNotFound_Smart() throws Exception {
 		URIish uri = toURIish("/smart.none/not-found");
 		Repository dst = createBareRepository();
-		Transport t = Transport.open(dst, uri);
-		try {
+		try (Transport t = Transport.open(dst, uri)) {
 			try {
 				t.openFetch();
 				fail("connection opened to not found repository");
@@ -186,8 +182,6 @@ public class HttpClientTests extends HttpTestCase {
 						+ "/info/refs?service=git-upload-pack not found";
 				assertEquals(exp, err.getMessage());
 			}
-		} finally {
-			t.close();
 		}
 	}
 
@@ -201,16 +195,9 @@ public class HttpClientTests extends HttpTestCase {
 
 		Repository dst = createBareRepository();
 		Ref head;
-		Transport t = Transport.open(dst, dumbAuthNoneURI);
-		try {
-			FetchConnection c = t.openFetch();
-			try {
-				head = c.getRef(Constants.HEAD);
-			} finally {
-				c.close();
-			}
-		} finally {
-			t.close();
+		try (Transport t = Transport.open(dst, dumbAuthNoneURI);
+				FetchConnection c = t.openFetch()) {
+			head = c.getRef(Constants.HEAD);
 		}
 		assertNotNull("has " + Constants.HEAD, head);
 		assertEquals(Q, head.getObjectId());
@@ -225,16 +212,9 @@ public class HttpClientTests extends HttpTestCase {
 
 		Repository dst = createBareRepository();
 		Ref head;
-		Transport t = Transport.open(dst, dumbAuthNoneURI);
-		try {
-			FetchConnection c = t.openFetch();
-			try {
-				head = c.getRef(Constants.HEAD);
-			} finally {
-				c.close();
-			}
-		} finally {
-			t.close();
+		try (Transport t = Transport.open(dst, dumbAuthNoneURI);
+				FetchConnection c = t.openFetch()) {
+			head = c.getRef(Constants.HEAD);
 		}
 		assertNull("has no " + Constants.HEAD, head);
 	}
@@ -249,16 +229,9 @@ public class HttpClientTests extends HttpTestCase {
 
 		Repository dst = createBareRepository();
 		Ref head;
-		Transport t = Transport.open(dst, smartAuthNoneURI);
-		try {
-			FetchConnection c = t.openFetch();
-			try {
-				head = c.getRef(Constants.HEAD);
-			} finally {
-				c.close();
-			}
-		} finally {
-			t.close();
+		try (Transport t = Transport.open(dst, smartAuthNoneURI);
+				FetchConnection c = t.openFetch()) {
+			head = c.getRef(Constants.HEAD);
 		}
 		assertNotNull("has " + Constants.HEAD, head);
 		assertEquals(Q, head.getObjectId());
@@ -268,16 +241,13 @@ public class HttpClientTests extends HttpTestCase {
 	public void testListRemote_Smart_WithQueryParameters() throws Exception {
 		URIish myURI = toURIish("/snone/do?r=1&p=test.git");
 		Repository dst = createBareRepository();
-		Transport t = Transport.open(dst, myURI);
-		try {
+		try (Transport t = Transport.open(dst, myURI)) {
 			try {
 				t.openFetch();
 				fail("test did not fail to find repository as expected");
 			} catch (NoRemoteRepositoryException err) {
 				// expected
 			}
-		} finally {
-			t.close();
 		}
 
 		List<AccessEvent> requests = getRequests();
@@ -296,62 +266,52 @@ public class HttpClientTests extends HttpTestCase {
 	@Test
 	public void testListRemote_Dumb_NeedsAuth() throws Exception {
 		Repository dst = createBareRepository();
-		Transport t = Transport.open(dst, dumbAuthBasicURI);
-		try {
+		try (Transport t = Transport.open(dst, dumbAuthBasicURI)) {
 			try {
 				t.openFetch();
 				fail("connection opened even info/refs needs auth basic");
 			} catch (TransportException err) {
 				String exp = dumbAuthBasicURI + ": "
-						+ JGitText.get().notAuthorized;
+						+ JGitText.get().noCredentialsProvider;
 				assertEquals(exp, err.getMessage());
 			}
-		} finally {
-			t.close();
 		}
 	}
 
 	@Test
 	public void testListRemote_Dumb_Auth() throws Exception {
 		Repository dst = createBareRepository();
-		Transport t = Transport.open(dst, dumbAuthBasicURI);
-		t.setCredentialsProvider(new UsernamePasswordCredentialsProvider(
-				AppServer.username, AppServer.password));
-		try {
-			t.openFetch();
-		} finally {
-			t.close();
+		try (Transport t = Transport.open(dst, dumbAuthBasicURI)) {
+			t.setCredentialsProvider(new UsernamePasswordCredentialsProvider(
+					AppServer.username, AppServer.password));
+			t.openFetch().close();
 		}
-		t = Transport.open(dst, dumbAuthBasicURI);
-		t.setCredentialsProvider(new UsernamePasswordCredentialsProvider(
-				AppServer.username, ""));
-		try {
-			t.openFetch();
-			fail("connection opened even info/refs needs auth basic and we provide wrong password");
-		} catch (TransportException err) {
-			String exp = dumbAuthBasicURI + ": "
-					+ JGitText.get().notAuthorized;
-			assertEquals(exp, err.getMessage());
-		} finally {
-			t.close();
+		try (Transport t = Transport.open(dst, dumbAuthBasicURI)) {
+			t.setCredentialsProvider(new UsernamePasswordCredentialsProvider(
+					AppServer.username, ""));
+			try {
+				t.openFetch();
+				fail("connection opened even info/refs needs auth basic and we provide wrong password");
+			} catch (TransportException err) {
+				String exp = dumbAuthBasicURI + ": "
+						+ JGitText.get().notAuthorized;
+				assertEquals(exp, err.getMessage());
+			}
 		}
 	}
 
 	@Test
 	public void testListRemote_Smart_UploadPackNeedsAuth() throws Exception {
 		Repository dst = createBareRepository();
-		Transport t = Transport.open(dst, smartAuthBasicURI);
-		try {
+		try (Transport t = Transport.open(dst, smartAuthBasicURI)) {
 			try {
 				t.openFetch();
 				fail("connection opened even though service disabled");
 			} catch (TransportException err) {
 				String exp = smartAuthBasicURI + ": "
-						+ JGitText.get().notAuthorized;
+						+ JGitText.get().noCredentialsProvider;
 				assertEquals(exp, err.getMessage());
 			}
-		} finally {
-			t.close();
 		}
 	}
 
@@ -363,33 +323,24 @@ public class HttpClientTests extends HttpTestCase {
 		cfg.save();
 
 		Repository dst = createBareRepository();
-		Transport t = Transport.open(dst, smartAuthNoneURI);
-		try {
+		try (Transport t = Transport.open(dst, smartAuthNoneURI)) {
 			try {
 				t.openFetch();
 				fail("connection opened even though service disabled");
 			} catch (TransportException err) {
-				String exp = smartAuthNoneURI + ": Git access forbidden";
+				String exp = smartAuthNoneURI + ": "
+						+ JGitText.get().serviceNotEnabledNoName;
 				assertEquals(exp, err.getMessage());
 			}
-		} finally {
-			t.close();
 		}
 	}
 
 	@Test
 	public void testListRemoteWithoutLocalRepository() throws Exception {
-		Transport t = Transport.open(smartAuthNoneURI);
-		try {
-			FetchConnection c = t.openFetch();
-			try {
-				Ref head = c.getRef(Constants.HEAD);
-				assertNotNull(head);
-			} finally {
-				c.close();
-			}
-		} finally {
-			t.close();
+		try (Transport t = Transport.open(smartAuthNoneURI);
+				FetchConnection c = t.openFetch()) {
+			Ref head = c.getRef(Constants.HEAD);
+			assertNotNull(head);
 		}
 	}
 }

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

@@ -211,8 +211,7 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 		assertEquals("http", remoteURI.getScheme());
 
 		Map<String, Ref> map;
-		Transport t = Transport.open(dst, remoteURI);
-		try {
+		try (Transport t = Transport.open(dst, remoteURI)) {
 			// I didn't make up these public interface names, I just
 			// approved them for inclusion into the code base. Sorry.
 			// --spearce
@@ -226,8 +225,6 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 			} finally {
 				c.close();
 			}
-		} finally {
-			t.close();
 		}
 
 		assertNotNull("have map of refs", map);
@@ -257,8 +254,7 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 	public void testListRemote_BadName() throws IOException, URISyntaxException {
 		Repository dst = createBareRepository();
 		URIish uri = new URIish(this.remoteURI.toString() + ".invalid");
-		Transport t = Transport.open(dst, uri);
-		try {
+		try (Transport t = Transport.open(dst, uri)) {
 			try {
 				t.openFetch();
 				fail("fetch connection opened");
@@ -266,8 +262,6 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 				assertEquals(uri + ": Git repository not found",
 						notFound.getMessage());
 			}
-		} finally {
-			t.close();
 		}
 
 		List<AccessEvent> requests = getRequests();
@@ -288,11 +282,8 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 		Repository dst = createBareRepository();
 		assertFalse(dst.hasObject(A_txt));
 
-		Transport t = Transport.open(dst, remoteURI);
-		try {
+		try (Transport t = Transport.open(dst, remoteURI)) {
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
-		} finally {
-			t.close();
 		}
 
 		assertTrue(dst.hasObject(A_txt));
@@ -331,11 +322,8 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 		// Bootstrap by doing the clone.
 		//
 		TestRepository dst = createTestRepository();
-		Transport t = Transport.open(dst.getRepository(), remoteURI);
-		try {
+		try (Transport t = Transport.open(dst.getRepository(), remoteURI)) {
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
-		} finally {
-			t.close();
 		}
 		assertEquals(B, dst.getRepository().exactRef(master).getObjectId());
 		List<AccessEvent> cloneRequests = getRequests();
@@ -352,11 +340,8 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 
 		// Now incrementally update.
 		//
-		t = Transport.open(dst.getRepository(), remoteURI);
-		try {
+		try (Transport t = Transport.open(dst.getRepository(), remoteURI)) {
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
-		} finally {
-			t.close();
 		}
 		assertEquals(Z, dst.getRepository().exactRef(master).getObjectId());
 
@@ -394,11 +379,8 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 		// Bootstrap by doing the clone.
 		//
 		TestRepository dst = createTestRepository();
-		Transport t = Transport.open(dst.getRepository(), remoteURI);
-		try {
+		try (Transport t = Transport.open(dst.getRepository(), remoteURI)) {
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
-		} finally {
-			t.close();
 		}
 		assertEquals(B, dst.getRepository().exactRef(master).getObjectId());
 		List<AccessEvent> cloneRequests = getRequests();
@@ -418,11 +400,8 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 
 		// Now incrementally update.
 		//
-		t = Transport.open(dst.getRepository(), remoteURI);
-		try {
+		try (Transport t = Transport.open(dst.getRepository(), remoteURI)) {
 			t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
-		} finally {
-			t.close();
 		}
 		assertEquals(Z, dst.getRepository().exactRef(master).getObjectId());
 
@@ -474,8 +453,7 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 		Repository dst = createBareRepository();
 		assertFalse(dst.hasObject(A_txt));
 
-		Transport t = Transport.open(dst, brokenURI);
-		try {
+		try (Transport t = Transport.open(dst, brokenURI)) {
 			try {
 				t.fetch(NullProgressMonitor.INSTANCE, mirror(master));
 				fail("fetch completed despite upload-pack being broken");
@@ -485,8 +463,6 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 						+ " received Content-Type text/plain; charset=UTF-8";
 				assertEquals(exp, err.getMessage());
 			}
-		} finally {
-			t.close();
 		}
 
 		List<AccessEvent> requests = getRequests();
@@ -517,12 +493,10 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 		final RevCommit Q = src.commit().add("Q", Q_txt).create();
 		final Repository db = src.getRepository();
 		final String dstName = Constants.R_HEADS + "new.branch";
-		Transport t;
 
 		// push anonymous shouldn't be allowed.
 		//
-		t = Transport.open(db, remoteURI);
-		try {
+		try (Transport t = Transport.open(db, remoteURI)) {
 			final String srcExpr = Q.name();
 			final boolean forceUpdate = false;
 			final String localName = null;
@@ -538,8 +512,6 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 						+ JGitText.get().authenticationNotSupported;
 				assertEquals(exp, e.getMessage());
 			}
-		} finally {
-			t.close();
 		}
 
 		List<AccessEvent> requests = getRequests();
@@ -560,12 +532,10 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 		final RevCommit Q = src.commit().add("Q", Q_txt).create();
 		final Repository db = src.getRepository();
 		final String dstName = Constants.R_HEADS + "new.branch";
-		Transport t;
 
 		enableReceivePack();
 
-		t = Transport.open(db, remoteURI);
-		try {
+		try (Transport t = Transport.open(db, remoteURI)) {
 			final String srcExpr = Q.name();
 			final boolean forceUpdate = false;
 			final String localName = null;
@@ -574,8 +544,6 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 			RemoteRefUpdate u = new RemoteRefUpdate(src.getRepository(),
 					srcExpr, dstName, forceUpdate, localName, oldId);
 			t.push(NullProgressMonitor.INSTANCE, Collections.singleton(u));
-		} finally {
-			t.close();
 		}
 
 		assertTrue(remoteRepository.hasObject(Q_txt));
@@ -633,7 +601,6 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 		final RevCommit Q = src.commit().add("Q", Q_bin).create();
 		final Repository db = src.getRepository();
 		final String dstName = Constants.R_HEADS + "new.branch";
-		Transport t;
 
 		enableReceivePack();
 
@@ -642,8 +609,7 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 		cfg.setInt("http", null, "postbuffer", 8 * 1024);
 		cfg.save();
 
-		t = Transport.open(db, remoteURI);
-		try {
+		try (Transport t = Transport.open(db, remoteURI)) {
 			final String srcExpr = Q.name();
 			final boolean forceUpdate = false;
 			final String localName = null;
@@ -652,8 +618,6 @@ public class SmartClientSmartServerTest extends HttpTestCase {
 			RemoteRefUpdate u = new RemoteRefUpdate(src.getRepository(),
 					srcExpr, dstName, forceUpdate, localName, oldId);
 			t.push(NullProgressMonitor.INSTANCE, Collections.singleton(u));
-		} finally {
-			t.close();
 		}
 
 		assertTrue(remoteRepository.hasObject(Q_bin));

org.eclipse.jgit.junit.http/BUCK

@@ -0,0 +1,18 @@
+java_library(
+  name = 'junit-http',
+  srcs = glob(['src/**']),
+  resources = glob(['resources/**']),
+  provided_deps = [
+    '//org.eclipse.jgit:jgit',
+    '//org.eclipse.jgit.http.server:jgit-servlet',
+    '//org.eclipse.jgit.junit:junit',
+    '//lib:junit',
+    '//lib:servlet-api',
+    '//lib/jetty:http',
+    '//lib/jetty:server',
+    '//lib/jetty:servlet',
+    '//lib/jetty:security',
+    '//lib/jetty:util',
+  ],
+  visibility = ['PUBLIC'],
+)

org.eclipse.jgit.junit/BUCK

@@ -0,0 +1,10 @@
+java_library(
+  name = 'junit',
+  srcs = glob(['src/**']),
+  resources = glob(['resources/**']),
+  provided_deps = [
+    '//org.eclipse.jgit:jgit',
+    '//lib:junit',
+  ],
+  visibility = ['PUBLIC'],
+)

org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java

@@ -822,7 +822,7 @@ public class TestRepository<R extends Repository> {
 					break;
 
 				final byte[] bin = db.open(o, o.getType()).getCachedBytes();
-				oc.checkCommit(bin);
+				oc.checkCommit(o, bin);
 				assertHash(o, bin);
 			}
 
@@ -832,7 +832,7 @@ public class TestRepository<R extends Repository> {
 					break;
 
 				final byte[] bin = db.open(o, o.getType()).getCachedBytes();
-				oc.check(o.getType(), bin);
+				oc.check(o, o.getType(), bin);
 				assertHash(o, bin);
 			}
 		}
@@ -866,7 +866,7 @@ public class TestRepository<R extends Repository> {
 				Set<ObjectId> all = new HashSet<ObjectId>();
 				for (Ref r : db.getAllRefs().values())
 					all.add(r.getObjectId());
-				pw.preparePack(m, all, Collections.<ObjectId> emptySet());
+				pw.preparePack(m, all, PackWriter.NONE);
 
 				final ObjectId name = pw.computeName();
 
@@ -1155,8 +1155,7 @@ public class TestRepository<R extends Repository> {
 			return self;
 		}
 
-		private void insertChangeId(org.eclipse.jgit.lib.CommitBuilder c)
-				throws IOException {
+		private void insertChangeId(org.eclipse.jgit.lib.CommitBuilder c) {
 			if (changeId == null)
 				return;
 			int idx = ChangeIdUtil.indexOfChangeId(message, "\n");

org.eclipse.jgit.pgm.test/BUCK

@@ -0,0 +1,38 @@
+TESTS = glob(['tst/**/*.java'])
+
+for t in TESTS:
+  n = t[len('tst/'):len(t)-len('.java')].replace('/', '.')
+  java_test(
+    name = n,
+    labels = ['pgm'],
+    srcs = [t],
+    deps = [
+      ':helpers',
+      '//org.eclipse.jgit:jgit',
+      '//org.eclipse.jgit.archive:jgit-archive',
+      '//org.eclipse.jgit.junit:junit',
+      '//org.eclipse.jgit.pgm:pgm',
+      '//lib:hamcrest-core',
+      '//lib:hamcrest-library',
+      '//lib:javaewah',
+      '//lib:junit',
+      '//lib:slf4j-api',
+      '//lib:slf4j-simple',
+      '//lib:commons-compress',
+      '//lib:tukaani-xz',
+    ],
+    source_under_test = ['//org.eclipse.jgit.pgm:pgm'],
+    vm_args = ['-Xmx256m', '-Dfile.encoding=UTF-8'],
+  )
+
+java_library(
+  name = 'helpers',
+  srcs = glob(['src/**/*.java']),
+  deps = [
+    '//org.eclipse.jgit:jgit',
+    '//org.eclipse.jgit.pgm:pgm',
+    '//org.eclipse.jgit.junit:junit',
+    '//lib:args4j',
+    '//lib:junit',
+  ],
+)

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

@@ -11,6 +11,7 @@ Import-Package: org.eclipse.jgit.api;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.api.errors;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.diff;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.dircache;version="[4.2.0,4.3.0)",
+ org.eclipse.jgit.internal.storage.file;version="4.2.0",
  org.eclipse.jgit.junit;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.lib;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.merge;version="[4.2.0,4.3.0)",

org.eclipse.jgit.pgm.test/org.eclipse.jgit.pgm--All-Tests (Java8) (de).launch

@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.junit.launchconfig">
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/org.eclipse.jgit.pgm.test/tst"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="2"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
+<mapAttribute key="org.eclipse.debug.core.environmentVariables">
+<mapEntry key="LANG" value="de_DE.UTF-8"/>
+</mapAttribute>
+<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
+<listEntry value="org.eclipse.debug.ui.launchGroup.debug"/>
+<listEntry value="org.eclipse.debug.ui.launchGroup.run"/>
+</listAttribute>
+<stringAttribute key="org.eclipse.jdt.junit.CONTAINER" value="=org.eclipse.jgit.pgm.test/tst"/>
+<booleanAttribute key="org.eclipse.jdt.junit.KEEPRUNNING_ATTR" value="false"/>
+<stringAttribute key="org.eclipse.jdt.junit.TESTNAME" value=""/>
+<stringAttribute key="org.eclipse.jdt.junit.TEST_KIND" value="org.eclipse.jdt.junit.loader.junit4"/>
+<booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_START_ON_FIRST_THREAD" value="true"/>
+<listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#10;&lt;runtimeClasspathEntry containerPath=&quot;org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7&quot; path=&quot;1&quot; type=&quot;4&quot;/&gt;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#10;&lt;runtimeClasspathEntry id=&quot;org.eclipse.jdt.launching.classpathentry.defaultClasspath&quot;&gt;&#10;&lt;memento exportedEntriesOnly=&quot;false&quot; project=&quot;org.eclipse.jgit.pgm.test&quot;/&gt;&#10;&lt;/runtimeClasspathEntry&gt;&#10;"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
+<stringAttribute key="org.eclipse.jdt.launching.JRE_CONTAINER" value="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value=""/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="org.eclipse.jgit.pgm.test"/>
+</launchConfiguration>

org.eclipse.jgit.pgm.test/src/org/eclipse/jgit/lib/CLIRepositoryTestCase.java

@@ -46,12 +46,16 @@ import static org.junit.Assert.assertEquals;
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Path;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 import org.eclipse.jgit.junit.JGitTestUtil;
 import org.eclipse.jgit.junit.LocalDiskRepositoryTestCase;
 import org.eclipse.jgit.pgm.CLIGitCommand;
+import org.eclipse.jgit.pgm.CLIGitCommand.Result;
+import org.eclipse.jgit.pgm.TextBuiltin.TerminatedByHelpException;
 import org.junit.Before;
 
 public class CLIRepositoryTestCase extends LocalDiskRepositoryTestCase {
@@ -69,13 +73,59 @@ public class CLIRepositoryTestCase extends LocalDiskRepositoryTestCase {
 		trash = db.getWorkTree();
 	}
 
+	/**
+	 * Executes specified git commands (with arguments)
+	 *
+	 * @param cmds
+	 *            each string argument must be a valid git command line, e.g.
+	 *            "git branch -h"
+	 * @return command output
+	 * @throws Exception
+	 */
+	protected String[] executeUnchecked(String... cmds) throws Exception {
+		List<String> result = new ArrayList<String>(cmds.length);
+		for (String cmd : cmds) {
+			result.addAll(CLIGitCommand.executeUnchecked(cmd, db));
+		}
+		return result.toArray(new String[0]);
+	}
+
+	/**
+	 * Executes specified git commands (with arguments), throws exception and
+	 * stops execution on first command which output contains a 'fatal:' error
+	 *
+	 * @param cmds
+	 *            each string argument must be a valid git command line, e.g.
+	 *            "git branch -h"
+	 * @return command output
+	 * @throws Exception
+	 */
 	protected String[] execute(String... cmds) throws Exception {
 		List<String> result = new ArrayList<String>(cmds.length);
-		for (String cmd : cmds)
-			result.addAll(CLIGitCommand.execute(cmd, db));
+		for (String cmd : cmds) {
+			Result r = CLIGitCommand.executeRaw(cmd, db);
+			if (r.ex instanceof TerminatedByHelpException) {
+				result.addAll(r.errLines());
+			} else if (r.ex != null) {
+				throw r.ex;
+			}
+			result.addAll(r.outLines());
+		}
 		return result.toArray(new String[0]);
 	}
 
+	/**
+	 * @param link
+	 *            the path of the symbolic link to create
+	 * @param target
+	 *            the target of the symbolic link
+	 * @return the path to the symbolic link
+	 * @throws Exception
+	 */
+	protected Path writeLink(String link, String target) throws Exception {
+		return JGitTestUtil.writeLink(db, link, target);
+	}
+
 	protected File writeTrashFile(final String name, final String data)
 			throws IOException {
 		return JGitTestUtil.writeTrashFile(db, name, data);
@@ -173,15 +223,36 @@ public class CLIRepositoryTestCase extends LocalDiskRepositoryTestCase {
 	}
 
 	protected void assertArrayOfLinesEquals(String[] expected, String[] actual) {
-		assertEquals(toText(expected), toText(actual));
+		assertEquals(toString(expected), toString(actual));
+	}
+
+	public static String toString(String... lines) {
+		return toString(Arrays.asList(lines));
 	}
 
-	private static String toText(String[] lines) {
+	public static String toString(List<String> lines) {
 		StringBuilder b = new StringBuilder();
 		for (String s : lines) {
-			b.append(s);
-			b.append('\n');
+			// trim indentation, to simplify tests
+			s = s.trim();
+			if (s != null && !s.isEmpty()) {
+				b.append(s);
+				b.append('\n');
+			}
+		}
+		// delete last line break to allow simpler tests with one line compare
+		if (b.length() > 0 && b.charAt(b.length() - 1) == '\n') {
+			b.deleteCharAt(b.length() - 1);
 		}
 		return b.toString();
 	}
+
+	public static boolean contains(List<String> lines, String str) {
+		for (String s : lines) {
+			if (s.contains(str)) {
+				return true;
+			}
+		}
+		return false;
+	}
 }

org.eclipse.jgit.pgm.test/src/org/eclipse/jgit/pgm/CLIGitCommand.java

@@ -42,71 +42,140 @@
  */
 package org.eclipse.jgit.pgm;
 
+import static org.junit.Assert.assertNull;
+
 import java.io.ByteArrayOutputStream;
-import java.text.MessageFormat;
+import java.io.File;
+
+import java.io.IOException;
+import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.eclipse.jgit.internal.storage.file.FileRepository;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.pgm.internal.CLIText;
-import org.eclipse.jgit.pgm.opt.CmdLineParser;
-import org.eclipse.jgit.pgm.opt.SubcommandHandler;
+import org.eclipse.jgit.pgm.TextBuiltin.TerminatedByHelpException;
 import org.eclipse.jgit.util.IO;
-import org.kohsuke.args4j.Argument;
 
-public class CLIGitCommand {
-	@Argument(index = 0, metaVar = "metaVar_command", required = true, handler = SubcommandHandler.class)
-	private TextBuiltin subcommand;
+public class CLIGitCommand extends Main {
 
-	@Argument(index = 1, metaVar = "metaVar_arg")
-	private List<String> arguments = new ArrayList<String>();
+	private final Result result;
 
-	public TextBuiltin getSubcommand() {
-		return subcommand;
+	private final Repository db;
+
+	public CLIGitCommand(Repository db) {
+		super();
+		this.db = db;
+		result = new Result();
 	}
 
-	public List<String> getArguments() {
-		return arguments;
+	/**
+	 * Executes git commands (with arguments) specified on the command line. The
+	 * git repository (same for all commands) can be specified via system
+	 * property "-Dgit_work_tree=path_to_work_tree". If the property is not set,
+	 * current directory is used.
+	 *
+	 * @param args
+	 *            each element in the array must be a valid git command line,
+	 *            e.g. "git branch -h"
+	 * @throws Exception
+	 */
+	public static void main(String[] args) throws Exception {
+		String workDir = System.getProperty("git_work_tree");
+		if (workDir == null) {
+			workDir = ".";
+			System.out.println(
+					"System property 'git_work_tree' not specified, using current directory: "
+							+ new File(workDir).getAbsolutePath());
+		}
+		try (Repository db = new FileRepository(workDir + "/.git")) {
+			for (String cmd : args) {
+				List<String> result = execute(cmd, db);
+				for (String line : result) {
+					System.out.println(line);
+				}
+			}
+		}
 	}
 
 	public static List<String> execute(String str, Repository db)
 			throws Exception {
+		Result result = executeRaw(str, db);
+		return getOutput(result);
+	}
+
+	public static Result executeRaw(String str, Repository db)
+			throws Exception {
+		CLIGitCommand cmd = new CLIGitCommand(db);
+		cmd.run(str);
+		return cmd.result;
+	}
+
+	public static List<String> executeUnchecked(String str, Repository db)
+			throws Exception {
+		CLIGitCommand cmd = new CLIGitCommand(db);
+		try {
+			cmd.run(str);
+			return getOutput(cmd.result);
+		} catch (Throwable e) {
+			return cmd.result.errLines();
+		}
+	}
+
+	private static List<String> getOutput(Result result) {
+		if (result.ex instanceof TerminatedByHelpException) {
+			return result.errLines();
+		}
+		return result.outLines();
+	}
+
+	private void run(String commandLine) throws Exception {
+		String[] argv = convertToMainArgs(commandLine);
 		try {
-			return IO.readLines(new String(rawExecute(str, db)));
-		} catch (Die e) {
-			return IO.readLines(MessageFormat.format(CLIText.get().fatalError,
-					e.getMessage()));
+			super.run(argv);
+		} catch (TerminatedByHelpException e) {
+			// this is not a failure, super called exit() on help
+		} finally {
+			writer.flush();
 		}
 	}
 
-	public static byte[] rawExecute(String str, Repository db)
+	private static String[] convertToMainArgs(String str)
 			throws Exception {
 		String[] args = split(str);
-		if (!args[0].equalsIgnoreCase("git") || args.length < 2)
+		if (!args[0].equalsIgnoreCase("git") || args.length < 2) {
 			throw new IllegalArgumentException(
 					"Expected 'git <command> [<args>]', was:" + str);
+		}
 		String[] argv = new String[args.length - 1];
 		System.arraycopy(args, 1, argv, 0, args.length - 1);
+		return argv;
+	}
 
-		CLIGitCommand bean = new CLIGitCommand();
-		final CmdLineParser clp = new CmdLineParser(bean);
-		clp.parseArgument(argv);
-
-		final TextBuiltin cmd = bean.getSubcommand();
-		ByteArrayOutputStream baos = new ByteArrayOutputStream();
-		cmd.outs = baos;
-		if (cmd.requiresRepository())
-			cmd.init(db, null);
-		else
-			cmd.init(null, null);
-		try {
-			cmd.execute(bean.getArguments().toArray(
-					new String[bean.getArguments().size()]));
-		} finally {
-			if (cmd.outw != null)
-				cmd.outw.flush();
+	@Override
+	PrintWriter createErrorWriter() {
+		return new PrintWriter(result.err);
+	}
+
+	void init(final TextBuiltin cmd) throws IOException {
+		cmd.outs = result.out;
+		cmd.errs = result.err;
+		super.init(cmd);
+	}
+
+	@Override
+	protected Repository openGitDir(String aGitdir) throws IOException {
+		assertNull(aGitdir);
+		return db;
+	}
+
+	@Override
+	void exit(int status, Exception t) throws Exception {
+		if (t == null) {
+			t = new IllegalStateException(Integer.toString(status));
 		}
-		return baos.toByteArray();
+		result.ex = t;
+		throw t;
 	}
 
 	/**
@@ -164,4 +233,36 @@ public class CLIGitCommand {
 		return list.toArray(new String[list.size()]);
 	}
 
+	public static class Result {
+		public final ByteArrayOutputStream out = new ByteArrayOutputStream();
+
+		public final ByteArrayOutputStream err = new ByteArrayOutputStream();
+
+		public Exception ex;
+
+		public byte[] outBytes() {
+			return out.toByteArray();
+		}
+
+		public byte[] errBytes() {
+			return err.toByteArray();
+		}
+
+		public String outString() {
+			return out.toString();
+		}
+
+		public List<String> outLines() {
+			return IO.readLines(out.toString());
+		}
+
+		public String errString() {
+			return err.toString();
+		}
+
+		public List<String> errLines() {
+			return IO.readLines(err.toString());
+		}
+	}
+
 }

org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/AddTest.java

@@ -45,15 +45,12 @@ package org.eclipse.jgit.pgm;
 import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
-
-import java.lang.Exception;
-import java.lang.String;
+import static org.junit.Assert.fail;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.lib.CLIRepositoryTestCase;
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
 
 public class AddTest extends CLIRepositoryTestCase {
@@ -66,14 +63,16 @@ public class AddTest extends CLIRepositoryTestCase {
 		git = new Git(db);
 	}
 
-	@Ignore("args4j exit()s on error instead of throwing, JVM goes down")
 	@Test
 	public void testAddNothing() throws Exception {
-		assertEquals("fatal: Argument \"filepattern\" is required", //
-				execute("git add")[0]);
+		try {
+			execute("git add");
+			fail("Must die");
+		} catch (Die e) {
+			// expected, requires argument
+		}
 	}
 
-	@Ignore("args4j exit()s for --help, too")
 	@Test
 	public void testAddUsage() throws Exception {
 		execute("git add --help");

org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ArchiveTest.java

@@ -52,17 +52,15 @@ import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
-import java.io.InputStreamReader;
 import java.io.IOException;
+import java.io.InputStreamReader;
 import java.io.OutputStream;
-import java.lang.Object;
-import java.lang.String;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.concurrent.Callable;
-import java.util.concurrent.Executors;
 import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
@@ -71,9 +69,7 @@ import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.lib.CLIRepositoryTestCase;
 import org.eclipse.jgit.lib.FileMode;
-import org.eclipse.jgit.pgm.CLIGitCommand;
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
 
 public class ArchiveTest extends CLIRepositoryTestCase {
@@ -89,25 +85,26 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		emptyTree = db.resolve("HEAD^{tree}").abbreviate(12).name();
 	}
 
-	@Ignore("Some versions of java.util.zip refuse to write an empty ZIP")
 	@Test
 	public void testEmptyArchive() throws Exception {
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --format=zip " + emptyTree, db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --format=zip " + emptyTree, db).outBytes();
 		assertArrayEquals(new String[0], listZipEntries(result));
 	}
 
 	@Test
 	public void testEmptyTar() throws Exception {
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --format=tar " + emptyTree, db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --format=tar " + emptyTree, db).outBytes();
 		assertArrayEquals(new String[0], listTarEntries(result));
 	}
 
 	@Test
 	public void testUnrecognizedFormat() throws Exception {
-		String[] expect = new String[] { "fatal: Unknown archive format 'nonsense'" };
-		String[] actual = execute("git archive --format=nonsense " + emptyTree);
+		String[] expect = new String[] {
+				"fatal: Unknown archive format 'nonsense'", "" };
+		String[] actual = executeUnchecked(
+				"git archive --format=nonsense " + emptyTree);
 		assertArrayEquals(expect, actual);
 	}
 
@@ -120,8 +117,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern("c").call();
 		git.commit().setMessage("populate toplevel").call();
 
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --format=zip HEAD", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --format=zip HEAD", db).outBytes();
 		assertArrayEquals(new String[] { "a", "c" },
 				listZipEntries(result));
 	}
@@ -135,8 +132,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	@Test
 	public void testDefaultFormatIsTar() throws Exception {
 		commitGreeting();
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive HEAD", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive HEAD", db).outBytes();
 		assertArrayEquals(new String[] { "greeting" },
 				listTarEntries(result));
 	}
@@ -302,8 +299,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern("b").call();
 		git.commit().setMessage("add subdir").call();
 
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --format=zip master", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --format=zip master", db).outBytes();
 		String[] expect = { "a", "b.c", "b0c", "b/", "b/a", "b/b", "c" };
 		String[] actual = listZipEntries(result);
 
@@ -328,8 +325,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern("b").call();
 		git.commit().setMessage("add subdir").call();
 
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --format=tar master", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --format=tar master", db).outBytes();
 		String[] expect = { "a", "b.c", "b0c", "b/", "b/a", "b/b", "c" };
 		String[] actual = listTarEntries(result);
 
@@ -349,8 +346,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	@Test
 	public void testArchivePrefixOption() throws Exception {
 		commitBazAndFooSlashBar();
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --prefix=x/ --format=zip master", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --prefix=x/ --format=zip master", db).outBytes();
 		String[] expect = { "x/baz", "x/foo/", "x/foo/bar" };
 		String[] actual = listZipEntries(result);
 
@@ -362,8 +359,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	@Test
 	public void testTarPrefixOption() throws Exception {
 		commitBazAndFooSlashBar();
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --prefix=x/ --format=tar master", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --prefix=x/ --format=tar master", db).outBytes();
 		String[] expect = { "x/baz", "x/foo/", "x/foo/bar" };
 		String[] actual = listTarEntries(result);
 
@@ -381,8 +378,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	@Test
 	public void testPrefixDoesNotNormalizeDoubleSlash() throws Exception {
 		commitFoo();
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --prefix=x// --format=zip master", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --prefix=x// --format=zip master", db).outBytes();
 		String[] expect = { "x//foo" };
 		assertArrayEquals(expect, listZipEntries(result));
 	}
@@ -390,8 +387,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	@Test
 	public void testPrefixDoesNotNormalizeDoubleSlashInTar() throws Exception {
 		commitFoo();
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --prefix=x// --format=tar master", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --prefix=x// --format=tar master", db).outBytes();
 		String[] expect = { "x//foo" };
 		assertArrayEquals(expect, listTarEntries(result));
 	}
@@ -408,8 +405,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	@Test
 	public void testPrefixWithoutTrailingSlash() throws Exception {
 		commitBazAndFooSlashBar();
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --prefix=my- --format=zip master", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --prefix=my- --format=zip master", db).outBytes();
 		String[] expect = { "my-baz", "my-foo/", "my-foo/bar" };
 		String[] actual = listZipEntries(result);
 
@@ -421,8 +418,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 	@Test
 	public void testTarPrefixWithoutTrailingSlash() throws Exception {
 		commitBazAndFooSlashBar();
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --prefix=my- --format=tar master", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --prefix=my- --format=tar master", db).outBytes();
 		String[] expect = { "my-baz", "my-foo/", "my-foo/bar" };
 		String[] actual = listTarEntries(result);
 
@@ -441,8 +438,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.submoduleAdd().setURI("./.").setPath("b").call().close();
 		git.commit().setMessage("add submodule").call();
 
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --format=zip master", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --format=zip master", db).outBytes();
 		String[] expect = { ".gitmodules", "a", "b/", "c" };
 		String[] actual = listZipEntries(result);
 
@@ -461,8 +458,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.submoduleAdd().setURI("./.").setPath("b").call().close();
 		git.commit().setMessage("add submodule").call();
 
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --format=tar master", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --format=tar master", db).outBytes();
 		String[] expect = { ".gitmodules", "a", "b/", "c" };
 		String[] actual = listTarEntries(result);
 
@@ -491,8 +488,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 
 		git.commit().setMessage("three files with different modes").call();
 
-		byte[] zipData = CLIGitCommand.rawExecute(
-				"git archive --format=zip master", db);
+		byte[] zipData = CLIGitCommand.executeRaw(
+				"git archive --format=zip master", db).outBytes();
 		writeRaw("zip-with-modes.zip", zipData);
 		assertContainsEntryWithMode("zip-with-modes.zip", "-rw-", "plain");
 		assertContainsEntryWithMode("zip-with-modes.zip", "-rwx", "executable");
@@ -520,8 +517,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 
 		git.commit().setMessage("three files with different modes").call();
 
-		byte[] archive = CLIGitCommand.rawExecute(
-				"git archive --format=tar master", db);
+		byte[] archive = CLIGitCommand.executeRaw(
+				"git archive --format=tar master", db).outBytes();
 		writeRaw("with-modes.tar", archive);
 		assertTarContainsEntry("with-modes.tar", "-rw-r--r--", "plain");
 		assertTarContainsEntry("with-modes.tar", "-rwxr-xr-x", "executable");
@@ -543,8 +540,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern("1234567890").call();
 		git.commit().setMessage("file with long name").call();
 
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --format=zip HEAD", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --format=zip HEAD", db).outBytes();
 		assertArrayEquals(l.toArray(new String[l.size()]),
 				listZipEntries(result));
 	}
@@ -563,8 +560,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern("1234567890").call();
 		git.commit().setMessage("file with long name").call();
 
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --format=tar HEAD", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --format=tar HEAD", db).outBytes();
 		assertArrayEquals(l.toArray(new String[l.size()]),
 				listTarEntries(result));
 	}
@@ -576,8 +573,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern("xyzzy").call();
 		git.commit().setMessage("add file with content").call();
 
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --format=zip HEAD", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --format=zip HEAD", db).outBytes();
 		assertArrayEquals(new String[] { payload },
 				zipEntryContent(result, "xyzzy"));
 	}
@@ -589,8 +586,8 @@ public class ArchiveTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern("xyzzy").call();
 		git.commit().setMessage("add file with content").call();
 
-		byte[] result = CLIGitCommand.rawExecute(
-				"git archive --format=tar HEAD", db);
+		byte[] result = CLIGitCommand.executeRaw(
+				"git archive --format=tar HEAD", db).outBytes();
 		assertArrayEquals(new String[] { payload },
 				tarEntryContent(result, "xyzzy"));
 	}

org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/BranchTest.java

@@ -43,11 +43,17 @@
 package org.eclipse.jgit.pgm;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.File;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.lib.CLIRepositoryTestCase;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.RefUpdate;
+import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.junit.Before;
 import org.junit.Test;
@@ -62,10 +68,20 @@ public class BranchTest extends CLIRepositoryTestCase {
 		}
 	}
 
+	@Test
+	public void testHelpAfterDelete() throws Exception {
+		String err = toString(executeUnchecked("git branch -d"));
+		String help = toString(executeUnchecked("git branch -h"));
+		String errAndHelp = toString(executeUnchecked("git branch -d -h"));
+		assertEquals(CLIText.fatalError(CLIText.get().branchNameRequired), err);
+		assertEquals(toString(err, help), errAndHelp);
+	}
+
 	@Test
 	public void testList() throws Exception {
+		assertEquals("* master", toString(execute("git branch")));
 		assertEquals("* master 6fd41be initial commit",
-				execute("git branch -v")[0]);
+				toString(execute("git branch -v")));
 	}
 
 	@Test
@@ -73,26 +89,188 @@ public class BranchTest extends CLIRepositoryTestCase {
 		RefUpdate updateRef = db.updateRef(Constants.HEAD, true);
 		updateRef.setNewObjectId(db.resolve("6fd41be"));
 		updateRef.update();
-		assertEquals("* (no branch) 6fd41be initial commit",
-				execute("git branch -v")[0]);
+		assertEquals(
+				toString("* (no branch) 6fd41be initial commit",
+						"master      6fd41be initial commit"),
+				toString(execute("git branch -v")));
 	}
 
 	@Test
 	public void testListContains() throws Exception {
 		try (Git git = new Git(db)) {
-				git.branchCreate().setName("initial").call();
+			git.branchCreate().setName("initial").call();
 			RevCommit second = git.commit().setMessage("second commit")
 					.call();
-			assertArrayOfLinesEquals(new String[] { "  initial", "* master", "" },
-					execute("git branch --contains 6fd41be"));
-			assertArrayOfLinesEquals(new String[] { "* master", "" },
-					execute("git branch --contains " + second.name()));
+			assertEquals(toString("  initial", "* master"),
+					toString(execute("git branch --contains 6fd41be")));
+			assertEquals("* master",
+					toString(execute("git branch --contains " + second.name())));
 		}
 	}
 
 	@Test
 	public void testExistingBranch() throws Exception {
 		assertEquals("fatal: A branch named 'master' already exists.",
-				execute("git branch master")[0]);
+				toString(executeUnchecked("git branch master")));
+	}
+
+	@Test
+	public void testRenameSingleArg() throws Exception {
+		try {
+			toString(execute("git branch -m"));
+			fail("Must die");
+		} catch (Die e) {
+			// expected, requires argument
+		}
+		String result = toString(execute("git branch -m slave"));
+		assertEquals("", result);
+		result = toString(execute("git branch -a"));
+		assertEquals("* slave", result);
+	}
+
+	@Test
+	public void testRenameTwoArgs() throws Exception {
+		String result = toString(execute("git branch -m master slave"));
+		assertEquals("", result);
+		result = toString(execute("git branch -a"));
+		assertEquals("* slave", result);
+	}
+
+	@Test
+	public void testCreate() throws Exception {
+		try {
+			toString(execute("git branch a b"));
+			fail("Must die");
+		} catch (Die e) {
+			// expected, too many arguments
+		}
+		String result = toString(execute("git branch second"));
+		assertEquals("", result);
+		result = toString(execute("git branch"));
+		assertEquals(toString("* master", "second"), result);
+		result = toString(execute("git branch -v"));
+		assertEquals(toString("* master 6fd41be initial commit",
+				"second 6fd41be initial commit"), result);
+	}
+
+	@Test
+	public void testDelete() throws Exception {
+		try {
+			toString(execute("git branch -d"));
+			fail("Must die");
+		} catch (Die e) {
+			// expected, requires argument
+		}
+		String result = toString(execute("git branch second"));
+		assertEquals("", result);
+		result = toString(execute("git branch -d second"));
+		assertEquals("", result);
+		result = toString(execute("git branch"));
+		assertEquals("* master", result);
+	}
+
+	@Test
+	public void testDeleteMultiple() throws Exception {
+		String result = toString(execute("git branch second",
+				"git branch third", "git branch fourth"));
+		assertEquals("", result);
+		result = toString(execute("git branch -d second third fourth"));
+		assertEquals("", result);
+		result = toString(execute("git branch"));
+		assertEquals("* master", result);
+	}
+
+	@Test
+	public void testDeleteForce() throws Exception {
+		try {
+			toString(execute("git branch -D"));
+			fail("Must die");
+		} catch (Die e) {
+			// expected, requires argument
+		}
+		String result = toString(execute("git branch second"));
+		assertEquals("", result);
+		result = toString(execute("git checkout second"));
+		assertEquals("Switched to branch 'second'", result);
+
+		File a = writeTrashFile("a", "a");
+		assertTrue(a.exists());
+		execute("git add a", "git commit -m 'added a'");
+
+		result = toString(execute("git checkout master"));
+		assertEquals("Switched to branch 'master'", result);
+
+		result = toString(execute("git branch"));
+		assertEquals(toString("* master", "second"), result);
+
+		try {
+			toString(execute("git branch -d second"));
+			fail("Must die");
+		} catch (Die e) {
+			// expected, the current HEAD is on second and not merged to master
+		}
+		result = toString(execute("git branch -D second"));
+		assertEquals("", result);
+
+		result = toString(execute("git branch"));
+		assertEquals("* master", result);
+	}
+
+	@Test
+	public void testDeleteForceMultiple() throws Exception {
+		String result = toString(execute("git branch second",
+				"git branch third", "git branch fourth"));
+
+		assertEquals("", result);
+		result = toString(execute("git checkout second"));
+		assertEquals("Switched to branch 'second'", result);
+
+		File a = writeTrashFile("a", "a");
+		assertTrue(a.exists());
+		execute("git add a", "git commit -m 'added a'");
+
+		result = toString(execute("git checkout master"));
+		assertEquals("Switched to branch 'master'", result);
+
+		result = toString(execute("git branch"));
+		assertEquals(toString("fourth", "* master", "second", "third"), result);
+
+		try {
+			toString(execute("git branch -d second third fourth"));
+			fail("Must die");
+		} catch (Die e) {
+			// expected, the current HEAD is on second and not merged to master
+		}
+		result = toString(execute("git branch"));
+		assertEquals(toString("fourth", "* master", "second", "third"), result);
+
+		result = toString(execute("git branch -D second third fourth"));
+		assertEquals("", result);
+
+		result = toString(execute("git branch"));
+		assertEquals("* master", result);
+	}
+
+	@Test
+	public void testCreateFromOldCommit() throws Exception {
+		File a = writeTrashFile("a", "a");
+		assertTrue(a.exists());
+		execute("git add a", "git commit -m 'added a'");
+		File b = writeTrashFile("b", "b");
+		assertTrue(b.exists());
+		execute("git add b", "git commit -m 'added b'");
+		String result = toString(execute("git log -n 1 --reverse"));
+		String firstCommitId = result.substring("commit ".length(),
+				result.indexOf('\n'));
+
+		result = toString(execute("git branch -f second " + firstCommitId));
+		assertEquals("", result);
+
+		result = toString(execute("git branch"));
+		assertEquals(toString("* master", "second"), result);
+
+		result = toString(execute("git checkout second"));
+		assertEquals("Switched to branch 'second'", result);
+		assertFalse(b.exists());
 	}
 }

org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/CheckoutTest.java

@@ -44,9 +44,14 @@ package org.eclipse.jgit.pgm;
 
 import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
 
 import java.io.File;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Arrays;
 import java.util.List;
 
 import org.eclipse.jgit.api.Git;
@@ -59,7 +64,9 @@ import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.treewalk.FileTreeIterator;
 import org.eclipse.jgit.treewalk.FileTreeIterator.FileEntry;
 import org.eclipse.jgit.treewalk.TreeWalk;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
+import org.junit.Assume;
 import org.junit.Test;
 
 public class CheckoutTest extends CLIRepositoryTestCase {
@@ -109,14 +116,14 @@ public class CheckoutTest extends CLIRepositoryTestCase {
 
 			assertStringArrayEquals(
 					"fatal: A branch named 'master' already exists.",
-					execute("git checkout -b master"));
+				executeUnchecked("git checkout -b master"));
 		}
 	}
 
 	@Test
 	public void testCheckoutNewBranchOnBranchToBeBorn() throws Exception {
 		assertStringArrayEquals("fatal: You are on a branch yet to be born",
-				execute("git checkout -b side"));
+				executeUnchecked("git checkout -b side"));
 	}
 
 	@Test
@@ -599,4 +606,34 @@ public class CheckoutTest extends CLIRepositoryTestCase {
 			assertEquals("Hello world b", read(b));
 		}
 	}
+
+	@Test
+	public void testCheckouSingleFile() throws Exception {
+		try (Git git = new Git(db)) {
+			File a = writeTrashFile("a", "file a");
+			git.add().addFilepattern(".").call();
+			git.commit().setMessage("commit file a").call();
+			writeTrashFile("a", "b");
+			assertEquals("b", read(a));
+			assertEquals("[]", Arrays.toString(execute("git checkout -- a")));
+			assertEquals("file a", read(a));
+		}
+	}
+
+	@Test
+	public void testCheckoutLink() throws Exception {
+		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
+		try (Git git = new Git(db)) {
+			Path path = writeLink("a", "link_a");
+			assertTrue(Files.isSymbolicLink(path));
+			git.add().addFilepattern(".").call();
+			git.commit().setMessage("commit link a").call();
+			deleteTrashFile("a");
+			writeTrashFile("a", "Hello world a");
+			assertFalse(Files.isSymbolicLink(path));
+			assertEquals("[]", Arrays.toString(execute("git checkout -- a")));
+			assertEquals("link_a", FileUtils.readSymLink(path.toFile()));
+			assertTrue(Files.isSymbolicLink(path));
+		}
+	}
 }

org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/CommitTest.java

@@ -0,0 +1,100 @@
+/*
+ * Copyright (C) 2015, Andrey Loskutov <loskutov@gmx.de>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.pgm;
+
+import static org.junit.Assert.assertEquals;
+
+import org.eclipse.jgit.lib.CLIRepositoryTestCase;
+import org.junit.Test;
+
+public class CommitTest extends CLIRepositoryTestCase {
+
+	@Test
+	public void testCommitPath() throws Exception {
+		writeTrashFile("a", "a");
+		writeTrashFile("b", "a");
+		String result = toString(execute("git add a"));
+		assertEquals("", result);
+
+		result = toString(execute("git status -- a"));
+		assertEquals(toString("On branch master", "Changes to be committed:",
+				"new file:   a"), result);
+
+		result = toString(execute("git status -- b"));
+		assertEquals(toString("On branch master", "Untracked files:", "b"),
+				result);
+
+		result = toString(execute("git commit a -m 'added a'"));
+		assertEquals(
+				"[master 8cb3ef7e5171aaee1792df6302a5a0cd30425f7a] added a",
+				result);
+
+		result = toString(execute("git status -- a"));
+		assertEquals("On branch master", result);
+
+		result = toString(execute("git status -- b"));
+		assertEquals(toString("On branch master", "Untracked files:", "b"),
+				result);
+	}
+
+	@Test
+	public void testCommitAll() throws Exception {
+		writeTrashFile("a", "a");
+		writeTrashFile("b", "a");
+		String result = toString(execute("git add a b"));
+		assertEquals("", result);
+
+		result = toString(execute("git status -- a b"));
+		assertEquals(toString("On branch master", "Changes to be committed:",
+				"new file:   a", "new file:   b"), result);
+
+		result = toString(execute("git commit -m 'added a b'"));
+		assertEquals(
+				"[master 3c93fa8e3a28ee26690498be78016edcb3a38c73] added a b",
+				result);
+
+		result = toString(execute("git status -- a b"));
+		assertEquals("On branch master", result);
+	}
+
+}

org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/DescribeTest.java

@@ -43,9 +43,15 @@
 package org.eclipse.jgit.pgm;
 
 import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.util.Arrays;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.lib.CLIRepositoryTestCase;
+import org.eclipse.jgit.pgm.internal.CLIText;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -67,17 +73,15 @@ public class DescribeTest extends CLIRepositoryTestCase {
 
 	@Test
 	public void testNoHead() throws Exception {
-		assertArrayEquals(
-				new String[] { "fatal: No names found, cannot describe anything." },
-				execute("git describe"));
+		assertEquals(CLIText.fatalError(CLIText.get().noNamesFound),
+				toString(executeUnchecked("git describe")));
 	}
 
 	@Test
 	public void testHeadNoTag() throws Exception {
 		git.commit().setMessage("initial commit").call();
-		assertArrayEquals(
-				new String[] { "fatal: No names found, cannot describe anything." },
-				execute("git describe"));
+		assertEquals(CLIText.fatalError(CLIText.get().noNamesFound),
+				toString(executeUnchecked("git describe")));
 	}
 
 	@Test
@@ -103,4 +107,22 @@ public class DescribeTest extends CLIRepositoryTestCase {
 		assertArrayEquals(new String[] { "v1.0-0-g6fd41be", "" },
 				execute("git describe --long HEAD"));
 	}
+
+	@Test
+	public void testHelpArgumentBeforeUnknown() throws Exception {
+		String[] output = execute("git describe -h -XYZ");
+		String all = Arrays.toString(output);
+		assertTrue("Unexpected help output: " + all,
+				all.contains("jgit describe"));
+		assertFalse("Unexpected help output: " + all, all.contains("fatal"));
+	}
+
+	@Test
+	public void testHelpArgumentAfterUnknown() throws Exception {
+		String[] output = executeUnchecked("git describe -XYZ -h");
+		String all = Arrays.toString(output);
+		assertTrue("Unexpected help output: " + all,
+				all.contains("jgit describe"));
+		assertTrue("Unexpected help output: " + all, all.contains("fatal"));
+	}
 }

org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/MergeTest.java

@@ -50,6 +50,7 @@ import java.util.Iterator;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.lib.CLIRepositoryTestCase;
 import org.eclipse.jgit.merge.MergeStrategy;
+import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.junit.Before;
 import org.junit.Test;
@@ -194,8 +195,9 @@ public class MergeTest extends CLIRepositoryTestCase {
 
 	@Test
 	public void testNoFastForwardAndSquash() throws Exception {
-		assertEquals("fatal: You cannot combine --squash with --no-ff.",
-				execute("git merge master --no-ff --squash")[0]);
+		assertEquals(
+				CLIText.fatalError(CLIText.get().cannotCombineSquashWithNoff),
+				executeUnchecked("git merge master --no-ff --squash")[0]);
 	}
 
 	@Test
@@ -209,8 +211,8 @@ public class MergeTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern("file").call();
 		git.commit().setMessage("commit#2").call();
 
-		assertEquals("fatal: Not possible to fast-forward, aborting.",
-				execute("git merge master --ff-only")[0]);
+		assertEquals(CLIText.fatalError(CLIText.get().ffNotPossibleAborting),
+				executeUnchecked("git merge master --ff-only")[0]);
 	}
 
 	@Test

org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/RepoTest.java

@@ -44,8 +44,11 @@ package org.eclipse.jgit.pgm;
 
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
 
 import java.io.File;
+import java.util.Arrays;
+
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.junit.JGitTestUtil;
 import org.eclipse.jgit.lib.CLIRepositoryTestCase;
@@ -97,6 +100,31 @@ public class RepoTest extends CLIRepositoryTestCase {
 		resolveRelativeUris();
 	}
 
+	@Test
+	public void testMissingPath() throws Exception {
+		try {
+			execute("git repo");
+			fail("Must die");
+		} catch (Die e) {
+			// expected, requires argument
+		}
+	}
+
+	/**
+	 * See bug 484951: "git repo -h" should not print unexpected values
+	 *
+	 * @throws Exception
+	 */
+	@Test
+	public void testZombieHelpArgument() throws Exception {
+		String[] output = execute("git repo -h");
+		String all = Arrays.toString(output);
+		assertTrue("Unexpected help output: " + all,
+				all.contains("jgit repo"));
+		assertFalse("Unexpected help output: " + all,
+				all.contains("jgit repo VAL"));
+	}
+
 	@Test
 	public void testAddRepoManifest() throws Exception {
 		StringBuilder xmlContent = new StringBuilder();

org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/ResetTest.java

@@ -48,6 +48,7 @@ import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.lib.CLIRepositoryTestCase;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Test;
 
 public class ResetTest extends CLIRepositoryTestCase {
@@ -61,6 +62,20 @@ public class ResetTest extends CLIRepositoryTestCase {
 		git = new Git(db);
 	}
 
+	@Test
+	public void testPathOptionHelp() throws Exception {
+		String[] result = execute("git reset -h");
+		assertTrue("Unexpected argument: " + result[1],
+				result[1].endsWith("[-- path ... ...]"));
+	}
+
+	@Test
+	public void testZombieArgument_Bug484951() throws Exception {
+		String[] result = execute("git reset -h");
+		assertFalse("Unexpected argument: " + result[0],
+				result[0].contains("[VAL ...]"));
+	}
+
 	@Test
 	public void testResetSelf() throws Exception {
 		RevCommit commit = git.commit().setMessage("initial commit").call();
@@ -91,15 +106,28 @@ public class ResetTest extends CLIRepositoryTestCase {
 
 	@Test
 	public void testResetPathDoubleDash() throws Exception {
-		resetPath(true);
+		resetPath(true, true);
 	}
 
 	@Test
 	public void testResetPathNoDoubleDash() throws Exception {
-		resetPath(false);
+		resetPath(false, true);
+	}
+
+	@Test
+	public void testResetPathDoubleDashNoRef() throws Exception {
+		resetPath(true, false);
+	}
+
+	@Ignore("Currently we cannote recognize if a name is a commit-ish or a path, "
+			+ "so 'git reset a' will not work if 'a' is not a branch name but a file path")
+	@Test
+	public void testResetPathNoDoubleDashNoRef() throws Exception {
+		resetPath(false, false);
 	}
 
-	private void resetPath(boolean useDoubleDash) throws Exception {
+	private void resetPath(boolean useDoubleDash, boolean supplyCommit)
+			throws Exception {
 		// create files a and b
 		writeTrashFile("a", "Hello world a");
 		writeTrashFile("b", "Hello world b");
@@ -115,8 +143,9 @@ public class ResetTest extends CLIRepositoryTestCase {
 		git.add().addFilepattern(".").call();
 
 		// reset only file a
-		String cmd = String.format("git reset %s%s a", commit.getId().name(),
-				(useDoubleDash) ? " --" : "");
+		String cmd = String.format("git reset %s%s a",
+				supplyCommit ? commit.getId().name() : "",
+				useDoubleDash ? " --" : "");
 		assertStringArrayEquals("", execute(cmd));
 		assertEquals(commit.getId(),
 				git.getRepository().exactRef("HEAD").getObjectId());

org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/StatusTest.java

@@ -44,6 +44,7 @@ package org.eclipse.jgit.pgm;
 
 import static org.eclipse.jgit.lib.Constants.MASTER;
 import static org.eclipse.jgit.lib.Constants.R_HEADS;
+import static org.junit.Assert.assertTrue;
 
 import java.io.IOException;
 
@@ -55,6 +56,13 @@ import org.junit.Test;
 
 public class StatusTest extends CLIRepositoryTestCase {
 
+	@Test
+	public void testPathOptionHelp() throws Exception {
+		String[] result = execute("git status -h");
+		assertTrue("Unexpected argument: " + result[1],
+				result[1].endsWith("[-- path ... ...]"));
+	}
+
 	@Test
 	public void testStatusDefault() throws Exception {
 		executeTest("git status", false, true);

org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/TagTest.java

@@ -68,6 +68,6 @@ public class TagTest extends CLIRepositoryTestCase {
 		git.commit().setMessage("commit").call();
 
 		assertEquals("fatal: tag 'test' already exists",
-				execute("git tag test")[0]);
+				executeUnchecked("git tag test")[0]);
 	}
 }

org.eclipse.jgit.pgm/BUCK

@@ -0,0 +1,70 @@
+include_defs('//tools/git.defs')
+
+java_library(
+  name = 'pgm',
+  srcs = glob(['src/**']),
+  resources = glob(['resources/**']),
+  deps = [
+    ':services',
+    '//org.eclipse.jgit:jgit',
+    '//org.eclipse.jgit.archive:jgit-archive',
+    '//org.eclipse.jgit.http.apache:http-apache',
+    '//org.eclipse.jgit.ui:ui',
+    '//lib:args4j',
+  ],
+  visibility = ['PUBLIC'],
+)
+
+prebuilt_jar(
+  name = 'services',
+  binary_jar = ':services__jar',
+)
+
+genrule(
+  name = 'services__jar',
+  cmd = 'cd $SRCDIR ; zip -qr $OUT .',
+  srcs = glob(['META-INF/services/*']),
+  out = 'services.jar',
+)
+
+genrule(
+  name = 'jgit',
+  cmd = ''.join([
+    'mkdir $TMP/META-INF &&',
+    'cp $(location :binary_manifest) $TMP/META-INF/MANIFEST.MF &&',
+    'cp $(location :jgit_jar) $TMP/jgit.jar &&',
+    'cd $TMP && zip $TMP/jgit.jar META-INF/MANIFEST.MF &&',
+    'cat $SRCDIR/jgit.sh $TMP/jgit.jar >$OUT &&',
+    'chmod a+x $OUT',
+  ]),
+  srcs = ['jgit.sh'],
+  out = 'jgit',
+  visibility = ['PUBLIC'],
+)
+
+java_binary(
+  name = 'jgit_jar',
+  deps = [
+    ':pgm',
+    '//lib:slf4j-simple',
+    '//lib:tukaani-xz',
+  ],
+  blacklist = [
+    'META-INF/DEPENDENCIES',
+    'META-INF/maven/.*',
+  ],
+)
+
+genrule(
+  name = 'binary_manifest',
+  cmd = ';'.join(['echo "%s: %s" >>$OUT' % e for e in [
+    ('Manifest-Version', '1.0'),
+    ('Main-Class', 'org.eclipse.jgit.pgm.Main'),
+    ('Bundle-Version', git_version()),
+    ('Implementation-Title', 'JGit Command Line Interface'),
+    ('Implementation-Vendor', 'Eclipse.org - JGit'),
+    ('Implementation-Vendor-URL', 'http://www.eclipse.org/jgit/'),
+    ('Implementation-Vendor-Id', 'org.eclipse.jgit'),
+  ]] + ['echo >>$OUT']),
+  out = 'MANIFEST.MF',
+)

org.eclipse.jgit.pgm/META-INF/MANIFEST.MF

@@ -21,6 +21,7 @@ Import-Package: org.apache.commons.compress.archivers;version="[1.3,2.0)",
  org.eclipse.jgit.gitrepo;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.internal.storage.file;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.internal.storage.pack;version="[4.2.0,4.3.0)",
+ org.eclipse.jgit.internal.storage.reftree;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.lib;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.merge;version="4.2.0",
  org.eclipse.jgit.nls;version="[4.2.0,4.3.0)",
@@ -31,6 +32,7 @@ Import-Package: org.apache.commons.compress.archivers;version="[1.3,2.0)",
  org.eclipse.jgit.storage.file;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.storage.pack;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.transport;version="[4.2.0,4.3.0)",
+ org.eclipse.jgit.transport.http.apache;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.transport.resolver;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.treewalk;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.treewalk.filter;version="[4.2.0,4.3.0)",

org.eclipse.jgit.pgm/META-INF/services/org.eclipse.jgit.pgm.TextBuiltin

@@ -41,6 +41,7 @@ org.eclipse.jgit.pgm.debug.DiffAlgorithms
 org.eclipse.jgit.pgm.debug.MakeCacheTree
 org.eclipse.jgit.pgm.debug.ReadDirCache
 org.eclipse.jgit.pgm.debug.RebuildCommitGraph
+org.eclipse.jgit.pgm.debug.RebuildRefTree
 org.eclipse.jgit.pgm.debug.ShowCacheTree
 org.eclipse.jgit.pgm.debug.ShowCommands
 org.eclipse.jgit.pgm.debug.ShowDirCache

org.eclipse.jgit.pgm/pom.xml

@@ -94,6 +94,17 @@
       <version>${project.version}</version>
     </dependency>
 
+    <dependency>
+      <groupId>org.eclipse.jgit</groupId>
+      <artifactId>org.eclipse.jgit.http.apache</artifactId>
+      <version>${project.version}</version>
+    </dependency>
+
+    <dependency>
+      <groupId>org.apache.httpcomponents</groupId>
+      <artifactId>httpclient</artifactId>
+    </dependency>
+
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>slf4j-api</artifactId>

org.eclipse.jgit.pgm/resources/org/eclipse/jgit/pgm/internal/CLIText.properties

@@ -20,6 +20,7 @@ branchAlreadyExists=A branch named ''{0}'' already exists.
 branchCreatedFrom=branch: Created from {0}
 branchDetachedHEAD=detached HEAD
 branchIsNotAnAncestorOfYourCurrentHEAD=The branch ''{0}'' is not an ancestor of your current HEAD.\nIf you are sure you want to delete it, run ''jgit branch -D {0}''.
+branchNameRequired=branch name required
 branchNotFound=branch ''{0}'' not found.
 cacheTreePathInfo="{0}": {1} entries, {2} children
 cannotBeRenamed={0} cannot be renamed
@@ -89,7 +90,9 @@ metaVar_author=AUTHOR
 metaVar_base=base
 metaVar_blameL=START,END
 metaVar_blameReverse=START..END
+metaVar_branchAndStartPoint=branch [start-name]
 metaVar_branchName=branch
+metaVar_branchNames=branch ...
 metaVar_bucket=BUCKET
 metaVar_command=command
 metaVar_commandDetail=DETAIL
@@ -109,6 +112,7 @@ metaVar_message=message
 metaVar_n=n
 metaVar_name=name
 metaVar_object=object
+metaVar_oldNewBranchNames=[oldbranch] newbranch
 metaVar_op=OP
 metaVar_pass=PASS
 metaVar_path=path
@@ -125,6 +129,7 @@ metaVar_treeish=tree-ish
 metaVar_uriish=uri-ish
 metaVar_url=URL
 metaVar_user=USER
+metaVar_values=value ...
 metaVar_version=VERSION
 mostCommonlyUsedCommandsAre=The most commonly used commands are:
 needApprovalToDestroyCurrentRepository=Need approval to destroy current repository
@@ -223,6 +228,7 @@ usage_MergeBase=Find as good common ancestors as possible for a merge
 usage_MergesTwoDevelopmentHistories=Merges two development histories
 usage_ReadDirCache= Read the DirCache 100 times
 usage_RebuildCommitGraph=Recreate a repository from another one's commit graph
+usage_RebuildRefTree=Copy references into a RefTree
 usage_Remote=Manage set of tracked repositories
 usage_RepositoryToReadFrom=Repository to read from
 usage_RepositoryToReceiveInto=Repository to receive into
@@ -337,6 +343,7 @@ usage_recordChangesToRepository=Record changes to the repository
 usage_recurseIntoSubtrees=recurse into subtrees
 usage_renameLimit=limit size of rename matrix
 usage_reset=Reset current HEAD to the specified state
+usage_resetReference=Reset to given reference name
 usage_resetHard=Resets the index and working tree
 usage_resetSoft=Resets without touching the index file nor the working tree
 usage_resetMixed=Resets the index but not the working tree
@@ -353,6 +360,7 @@ usage_tags=fetch all tags
 usage_notags=do not fetch tags
 usage_tagMessage=tag message
 usage_untrackedFilesMode=show untracked files
+usage_updateRef=reference to update
 usage_updateRemoteRefsFromAnotherRepository=Update remote refs from another repository
 usage_useNameInsteadOfOriginToTrackUpstream=use <name> instead of 'origin' to track upstream
 usage_checkoutBranchAfterClone=checkout named branch instead of remotes's HEAD

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java

@@ -45,7 +45,6 @@ package org.eclipse.jgit.pgm;
 
 import java.io.IOException;
 import java.text.MessageFormat;
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -65,15 +64,18 @@ import org.eclipse.jgit.lib.RefUpdate;
 import org.eclipse.jgit.lib.RefUpdate.Result;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.pgm.internal.CLIText;
-import org.eclipse.jgit.pgm.opt.CmdLineParser;
+import org.eclipse.jgit.pgm.opt.OptionWithValuesListHandler;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.kohsuke.args4j.Argument;
-import org.kohsuke.args4j.ExampleMode;
 import org.kohsuke.args4j.Option;
 
 @Command(common = true, usage = "usage_listCreateOrDeleteBranches")
 class Branch extends TextBuiltin {
 
+	private String otherBranch;
+	private boolean createForce;
+	private boolean rename;
+
 	@Option(name = "--remote", aliases = { "-r" }, usage = "usage_actOnRemoteTrackingBranches")
 	private boolean remote = false;
 
@@ -83,23 +85,69 @@ class Branch extends TextBuiltin {
 	@Option(name = "--contains", metaVar = "metaVar_commitish", usage = "usage_printOnlyBranchesThatContainTheCommit")
 	private String containsCommitish;
 
-	@Option(name = "--delete", aliases = { "-d" }, usage = "usage_deleteFullyMergedBranch")
-	private boolean delete = false;
+	private List<String> delete;
 
-	@Option(name = "--delete-force", aliases = { "-D" }, usage = "usage_deleteBranchEvenIfNotMerged")
-	private boolean deleteForce = false;
+	@Option(name = "--delete", aliases = {
+			"-d" }, metaVar = "metaVar_branchNames", usage = "usage_deleteFullyMergedBranch", handler = OptionWithValuesListHandler.class)
+	public void delete(List<String> names) {
+		if (names.isEmpty()) {
+			throw die(CLIText.get().branchNameRequired);
+		}
+		delete = names;
+	}
 
-	@Option(name = "--create-force", aliases = { "-f" }, usage = "usage_forceCreateBranchEvenExists")
-	private boolean createForce = false;
+	private List<String> deleteForce;
 
-	@Option(name = "-m", usage = "usage_moveRenameABranch")
-	private boolean rename = false;
+	@Option(name = "--delete-force", aliases = {
+			"-D" }, metaVar = "metaVar_branchNames", usage = "usage_deleteBranchEvenIfNotMerged", handler = OptionWithValuesListHandler.class)
+	public void deleteForce(List<String> names) {
+		if (names.isEmpty()) {
+			throw die(CLIText.get().branchNameRequired);
+		}
+		deleteForce = names;
+	}
+
+	@Option(name = "--create-force", aliases = {
+			"-f" }, metaVar = "metaVar_branchAndStartPoint", usage = "usage_forceCreateBranchEvenExists", handler = OptionWithValuesListHandler.class)
+	public void createForce(List<String> branchAndStartPoint) {
+		createForce = true;
+		if (branchAndStartPoint.isEmpty()) {
+			throw die(CLIText.get().branchNameRequired);
+		}
+		if (branchAndStartPoint.size() > 2) {
+			throw die(CLIText.get().tooManyRefsGiven);
+		}
+		if (branchAndStartPoint.size() == 1) {
+			branch = branchAndStartPoint.get(0);
+		} else {
+			branch = branchAndStartPoint.get(0);
+			otherBranch = branchAndStartPoint.get(1);
+		}
+	}
+
+	@Option(name = "--move", aliases = {
+			"-m" }, metaVar = "metaVar_oldNewBranchNames", usage = "usage_moveRenameABranch", handler = OptionWithValuesListHandler.class)
+	public void moveRename(List<String> currentAndNew) {
+		rename = true;
+		if (currentAndNew.isEmpty()) {
+			throw die(CLIText.get().branchNameRequired);
+		}
+		if (currentAndNew.size() > 2) {
+			throw die(CLIText.get().tooManyRefsGiven);
+		}
+		if (currentAndNew.size() == 1) {
+			branch = currentAndNew.get(0);
+		} else {
+			branch = currentAndNew.get(0);
+			otherBranch = currentAndNew.get(1);
+		}
+	}
 
 	@Option(name = "--verbose", aliases = { "-v" }, usage = "usage_beVerbose")
 	private boolean verbose = false;
 
-	@Argument
-	private List<String> branches = new ArrayList<String>();
+	@Argument(metaVar = "metaVar_name")
+	private String branch;
 
 	private final Map<String, Ref> printRefs = new LinkedHashMap<String, Ref>();
 
@@ -110,30 +158,33 @@ class Branch extends TextBuiltin {
 
 	@Override
 	protected void run() throws Exception {
-		if (delete || deleteForce)
-			delete(deleteForce);
-		else {
-			if (branches.size() > 2)
-				throw die(CLIText.get().tooManyRefsGiven + new CmdLineParser(this).printExample(ExampleMode.ALL));
-
+		if (delete != null || deleteForce != null) {
+			if (delete != null) {
+				delete(delete, false);
+			}
+			if (deleteForce != null) {
+				delete(deleteForce, true);
+			}
+		} else {
 			if (rename) {
 				String src, dst;
-				if (branches.size() == 1) {
+				if (otherBranch == null) {
 					final Ref head = db.getRef(Constants.HEAD);
-					if (head != null && head.isSymbolic())
+					if (head != null && head.isSymbolic()) {
 						src = head.getLeaf().getName();
-					else
+					} else {
 						throw die(CLIText.get().cannotRenameDetachedHEAD);
-					dst = branches.get(0);
+					}
+					dst = branch;
 				} else {
-					src = branches.get(0);
+					src = branch;
 					final Ref old = db.getRef(src);
 					if (old == null)
 						throw die(MessageFormat.format(CLIText.get().doesNotExist, src));
 					if (!old.getName().startsWith(Constants.R_HEADS))
 						throw die(MessageFormat.format(CLIText.get().notABranch, src));
 					src = old.getName();
-					dst = branches.get(1);
+					dst = otherBranch;
 				}
 
 				if (!dst.startsWith(Constants.R_HEADS))
@@ -145,13 +196,14 @@ class Branch extends TextBuiltin {
 				if (r.rename() != Result.RENAMED)
 					throw die(MessageFormat.format(CLIText.get().cannotBeRenamed, src));
 
-			} else if (branches.size() > 0) {
-				String newHead = branches.get(0);
+			} else if (createForce || branch != null) {
+				String newHead = branch;
 				String startBranch;
-				if (branches.size() == 2)
-					startBranch = branches.get(1);
-				else
+				if (createForce) {
+					startBranch = otherBranch;
+				} else {
 					startBranch = Constants.HEAD;
+				}
 				Ref startRef = db.getRef(startBranch);
 				ObjectId startAt = db.resolve(startBranch + "^0"); //$NON-NLS-1$
 				if (startRef != null) {
@@ -164,22 +216,27 @@ class Branch extends TextBuiltin {
 				}
 				startBranch = Repository.shortenRefName(startBranch);
 				String newRefName = newHead;
-				if (!newRefName.startsWith(Constants.R_HEADS))
+				if (!newRefName.startsWith(Constants.R_HEADS)) {
 					newRefName = Constants.R_HEADS + newRefName;
-				if (!Repository.isValidRefName(newRefName))
+				}
+				if (!Repository.isValidRefName(newRefName)) {
 					throw die(MessageFormat.format(CLIText.get().notAValidRefName, newRefName));
-				if (!createForce && db.resolve(newRefName) != null)
+				}
+				if (!createForce && db.resolve(newRefName) != null) {
 					throw die(MessageFormat.format(CLIText.get().branchAlreadyExists, newHead));
+				}
 				RefUpdate updateRef = db.updateRef(newRefName);
 				updateRef.setNewObjectId(startAt);
 				updateRef.setForceUpdate(createForce);
 				updateRef.setRefLogMessage(MessageFormat.format(CLIText.get().branchCreatedFrom, startBranch), false);
 				Result update = updateRef.update();
-				if (update == Result.REJECTED)
+				if (update == Result.REJECTED) {
 					throw die(MessageFormat.format(CLIText.get().couldNotCreateBranch, newHead, update.toString()));
+				}
 			} else {
-				if (verbose)
+				if (verbose) {
 					rw = new RevWalk(db);
+				}
 				list();
 			}
 		}
@@ -249,7 +306,8 @@ class Branch extends TextBuiltin {
 		outw.println();
 	}
 
-	private void delete(boolean force) throws IOException {
+	private void delete(List<String> branches, boolean force)
+			throws IOException {
 		String current = db.getBranch();
 		ObjectId head = db.resolve(Constants.HEAD);
 		for (String branch : branches) {

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Checkout.java

@@ -60,7 +60,7 @@ import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.Option;
-import org.kohsuke.args4j.spi.StopOptionHandler;
+import org.kohsuke.args4j.spi.RestOfArgumentsHandler;
 
 @Command(common = true, usage = "usage_checkout")
 class Checkout extends TextBuiltin {
@@ -74,11 +74,10 @@ class Checkout extends TextBuiltin {
 	@Option(name = "--orphan", usage = "usage_orphan")
 	private boolean orphan = false;
 
-	@Argument(required = true, index = 0, metaVar = "metaVar_name", usage = "usage_checkout")
+	@Argument(required = false, index = 0, metaVar = "metaVar_name", usage = "usage_checkout")
 	private String name;
 
-	@Argument(index = 1)
-	@Option(name = "--", metaVar = "metaVar_paths", multiValued = true, handler = StopOptionHandler.class)
+	@Option(name = "--", metaVar = "metaVar_paths", multiValued = true, handler = RestOfArgumentsHandler.class)
 	private List<String> paths = new ArrayList<String>();
 
 	@Override

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Clone.java

@@ -50,6 +50,7 @@ import org.eclipse.jgit.api.CloneCommand;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.InvalidRemoteException;
 import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.TextProgressMonitor;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.transport.URIish;
 import org.eclipse.jgit.util.SystemReader;
@@ -70,6 +71,9 @@ class Clone extends AbstractFetchCommand {
 	@Option(name = "--bare", usage = "usage_bareClone")
 	private boolean isBare;
 
+	@Option(name = "--quiet", usage = "usage_quiet")
+	private Boolean quiet;
+
 	@Argument(index = 0, required = true, metaVar = "metaVar_uriish")
 	private String sourceUri;
 
@@ -109,10 +113,16 @@ class Clone extends AbstractFetchCommand {
 
 		command.setGitDir(gitdir == null ? null : new File(gitdir));
 		command.setDirectory(localNameF);
-		outw.println(MessageFormat.format(CLIText.get().cloningInto, localName));
+		boolean msgs = quiet == null || !quiet.booleanValue();
+		if (msgs) {
+			command.setProgressMonitor(new TextProgressMonitor(errw));
+			outw.println(MessageFormat.format(
+					CLIText.get().cloningInto, localName));
+			outw.flush();
+		}
 		try {
 			db = command.call().getRepository();
-			if (db.resolve(Constants.HEAD) == null)
+			if (msgs && db.resolve(Constants.HEAD) == null)
 				outw.println(CLIText.get().clonedEmptyRepository);
 		} catch (InvalidRemoteException e) {
 			throw die(MessageFormat.format(CLIText.get().doesNotExist,
@@ -121,8 +131,9 @@ class Clone extends AbstractFetchCommand {
 			if (db != null)
 				db.close();
 		}
-
-		outw.println();
-		outw.flush();
+		if (msgs) {
+			outw.println();
+			outw.flush();
+		}
 	}
 }

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Die.java

@@ -86,6 +86,21 @@ public class Die extends RuntimeException {
 	 * @since 3.4
 	 */
 	public Die(boolean aborted) {
+		this(aborted, null);
+	}
+
+	/**
+	 * Construct a new exception reflecting the fact that the command execution
+	 * has been aborted before running.
+	 *
+	 * @param aborted
+	 *            boolean indicating the fact the execution has been aborted
+	 * @param cause
+	 *            can be null
+	 * @since 4.2
+	 */
+	public Die(boolean aborted, final Throwable cause) {
+		super(cause != null ? cause.getMessage() : null, cause);
 		this.aborted = aborted;
 	}
 

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java

@@ -62,6 +62,8 @@ import org.eclipse.jgit.lib.RepositoryBuilder;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.pgm.opt.CmdLineParser;
 import org.eclipse.jgit.pgm.opt.SubcommandHandler;
+import org.eclipse.jgit.transport.HttpTransport;
+import org.eclipse.jgit.transport.http.apache.HttpClientConnectionFactory;
 import org.eclipse.jgit.util.CachedAuthenticator;
 import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.CmdLineException;
@@ -88,13 +90,23 @@ public class Main {
 	@Argument(index = 1, metaVar = "metaVar_arg")
 	private List<String> arguments = new ArrayList<String>();
 
+	PrintWriter writer;
+
+	/**
+	 *
+	 */
+	public Main() {
+		HttpTransport.setConnectionFactory(new HttpClientConnectionFactory());
+	}
+
 	/**
 	 * Execute the command line.
 	 *
 	 * @param argv
 	 *            arguments.
+	 * @throws Exception
 	 */
-	public static void main(final String[] argv) {
+	public static void main(final String[] argv) throws Exception {
 		new Main().run(argv);
 	}
 
@@ -113,8 +125,10 @@ public class Main {
 	 *
 	 * @param argv
 	 *            arguments.
+	 * @throws Exception
 	 */
-	protected void run(final String[] argv) {
+	protected void run(final String[] argv) throws Exception {
+		writer = createErrorWriter();
 		try {
 			if (!installConsole()) {
 				AwtAuthenticator.install();
@@ -123,12 +137,14 @@ public class Main {
 			configureHttpProxy();
 			execute(argv);
 		} catch (Die err) {
-			if (err.isAborted())
-				System.exit(1);
-			System.err.println(MessageFormat.format(CLIText.get().fatalError, err.getMessage()));
-			if (showStackTrace)
-				err.printStackTrace();
-			System.exit(128);
+			if (err.isAborted()) {
+				exit(1, err);
+			}
+			writer.println(CLIText.fatalError(err.getMessage()));
+			if (showStackTrace) {
+				err.printStackTrace(writer);
+			}
+			exit(128, err);
 		} catch (Exception err) {
 			// Try to detect errno == EPIPE and exit normally if that happens
 			// There may be issues with operating system versions and locale,
@@ -136,46 +152,54 @@ public class Main {
 			// under other circumstances.
 			if (err.getClass() == IOException.class) {
 				// Linux, OS X
-				if (err.getMessage().equals("Broken pipe")) //$NON-NLS-1$
-					System.exit(0);
+				if (err.getMessage().equals("Broken pipe")) { //$NON-NLS-1$
+					exit(0, err);
+				}
 				// Windows
-				if (err.getMessage().equals("The pipe is being closed")) //$NON-NLS-1$
-					System.exit(0);
+				if (err.getMessage().equals("The pipe is being closed")) { //$NON-NLS-1$
+					exit(0, err);
+				}
 			}
 			if (!showStackTrace && err.getCause() != null
-					&& err instanceof TransportException)
-				System.err.println(MessageFormat.format(CLIText.get().fatalError, err.getCause().getMessage()));
+					&& err instanceof TransportException) {
+				writer.println(CLIText.fatalError(err.getCause().getMessage()));
+			}
 
 			if (err.getClass().getName().startsWith("org.eclipse.jgit.errors.")) { //$NON-NLS-1$
-				System.err.println(MessageFormat.format(CLIText.get().fatalError, err.getMessage()));
-				if (showStackTrace)
+				writer.println(CLIText.fatalError(err.getMessage()));
+				if (showStackTrace) {
 					err.printStackTrace();
-				System.exit(128);
+				}
+				exit(128, err);
 			}
 			err.printStackTrace();
-			System.exit(1);
+			exit(1, err);
 		}
 		if (System.out.checkError()) {
-			System.err.println(CLIText.get().unknownIoErrorStdout);
-			System.exit(1);
+			writer.println(CLIText.get().unknownIoErrorStdout);
+			exit(1, null);
 		}
-		if (System.err.checkError()) {
+		if (writer.checkError()) {
 			// No idea how to present an error here, most likely disk full or
 			// broken pipe
-			System.exit(1);
+			exit(1, null);
 		}
 	}
 
+	PrintWriter createErrorWriter() {
+		return new PrintWriter(System.err);
+	}
+
 	private void execute(final String[] argv) throws Exception {
-		final CmdLineParser clp = new CmdLineParser(this);
-		PrintWriter writer = new PrintWriter(System.err);
+		final CmdLineParser clp = new SubcommandLineParser(this);
+
 		try {
 			clp.parseArgument(argv);
 		} catch (CmdLineException err) {
 			if (argv.length > 0 && !help && !version) {
-				writer.println(MessageFormat.format(CLIText.get().fatalError, err.getMessage()));
+				writer.println(CLIText.fatalError(err.getMessage()));
 				writer.flush();
-				System.exit(1);
+				exit(1, err);
 			}
 		}
 
@@ -191,22 +215,24 @@ public class Main {
 				writer.println(CLIText.get().mostCommonlyUsedCommandsAre);
 				final CommandRef[] common = CommandCatalog.common();
 				int width = 0;
-				for (final CommandRef c : common)
+				for (final CommandRef c : common) {
 					width = Math.max(width, c.getName().length());
+				}
 				width += 2;
 
 				for (final CommandRef c : common) {
 					writer.print(' ');
 					writer.print(c.getName());
-					for (int i = c.getName().length(); i < width; i++)
+					for (int i = c.getName().length(); i < width; i++) {
 						writer.print(' ');
+					}
 					writer.print(CLIText.get().resourceBundle().getString(c.getUsage()));
 					writer.println();
 				}
 				writer.println();
 			}
 			writer.flush();
-			System.exit(1);
+			exit(1, null);
 		}
 
 		if (version) {
@@ -215,20 +241,38 @@ public class Main {
 		}
 
 		final TextBuiltin cmd = subcommand;
-		if (cmd.requiresRepository())
-			cmd.init(openGitDir(gitdir), null);
-		else
-			cmd.init(null, gitdir);
+		init(cmd);
 		try {
 			cmd.execute(arguments.toArray(new String[arguments.size()]));
 		} finally {
-			if (cmd.outw != null)
+			if (cmd.outw != null) {
 				cmd.outw.flush();
-			if (cmd.errw != null)
+			}
+			if (cmd.errw != null) {
 				cmd.errw.flush();
+			}
+		}
+	}
+
+	void init(final TextBuiltin cmd) throws IOException {
+		if (cmd.requiresRepository()) {
+			cmd.init(openGitDir(gitdir), null);
+		} else {
+			cmd.init(null, gitdir);
 		}
 	}
 
+	/**
+	 * @param status
+	 * @param t
+	 *            can be {@code null}
+	 * @throws Exception
+	 */
+	void exit(int status, Exception t) throws Exception {
+		writer.flush();
+		System.exit(status);
+	}
+
 	/**
 	 * Evaluate the {@code --git-dir} option and open the repository.
 	 *
@@ -278,7 +322,7 @@ public class Main {
 			throws IllegalAccessException, InvocationTargetException,
 			NoSuchMethodException, ClassNotFoundException {
 		try {
-		Class.forName(name).getMethod("install").invoke(null); //$NON-NLS-1$
+			Class.forName(name).getMethod("install").invoke(null); //$NON-NLS-1$
 		} catch (InvocationTargetException e) {
 			if (e.getCause() instanceof RuntimeException)
 				throw (RuntimeException) e.getCause();
@@ -332,4 +376,19 @@ public class Main {
 			}
 		}
 	}
+
+	/**
+	 * Parser for subcommands which doesn't stop parsing on help options and so
+	 * proceeds all specified options
+	 */
+	static class SubcommandLineParser extends CmdLineParser {
+		public SubcommandLineParser(Object bean) {
+			super(bean);
+		}
+
+		@Override
+		protected boolean containsHelp(String... args) {
+			return false;
+		}
+	}
 }

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Merge.java

@@ -148,9 +148,12 @@ class Merge extends TextBuiltin {
 			break;
 		case FAST_FORWARD:
 			ObjectId oldHeadId = oldHead.getObjectId();
-			outw.println(MessageFormat.format(CLIText.get().updating, oldHeadId
-					.abbreviate(7).name(), result.getNewHead().abbreviate(7)
-					.name()));
+			if (oldHeadId != null) {
+				String oldId = oldHeadId.abbreviate(7).name();
+				String newId = result.getNewHead().abbreviate(7).name();
+				outw.println(MessageFormat.format(CLIText.get().updating, oldId,
+						newId));
+			}
 			outw.println(result.getMergeStatus().toString());
 			break;
 		case CHECKOUT_CONFLICT:

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Remote.java

@@ -144,7 +144,7 @@ class Remote extends TextBuiltin {
 	}
 
 	@Override
-	public void printUsageAndExit(final String message, final CmdLineParser clp)
+	public void printUsage(final String message, final CmdLineParser clp)
 			throws IOException {
 		errw.println(message);
 		errw.println("jgit remote [--verbose (-v)] [--help (-h)]"); //$NON-NLS-1$
@@ -160,7 +160,6 @@ class Remote extends TextBuiltin {
 		errw.println();
 
 		errw.flush();
-		throw die(true);
 	}
 
 	private void print(List<RemoteConfig> remotes) throws IOException {

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Repo.java

@@ -55,7 +55,7 @@ class Repo extends TextBuiltin {
 	@Option(name = "--groups", aliases = { "-g" }, usage = "usage_groups")
 	private String groups = "default"; //$NON-NLS-1$
 
-	@Argument(required = true, usage = "usage_pathToXml")
+	@Argument(required = true, metaVar = "metaVar_path", usage = "usage_pathToXml")
 	private String path;
 
 	@Option(name = "--record-remote-branch", usage = "usage_branches")

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Reset.java

@@ -51,7 +51,7 @@ import org.eclipse.jgit.api.ResetCommand;
 import org.eclipse.jgit.api.ResetCommand.ResetType;
 import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.Option;
-import org.kohsuke.args4j.spi.StopOptionHandler;
+import org.kohsuke.args4j.spi.RestOfArgumentsHandler;
 
 @Command(common = true, usage = "usage_reset")
 class Reset extends TextBuiltin {
@@ -65,12 +65,12 @@ class Reset extends TextBuiltin {
 	@Option(name = "--hard", usage = "usage_resetHard")
 	private boolean hard = false;
 
-	@Argument(required = true, index = 0, metaVar = "metaVar_name", usage = "usage_reset")
+	@Argument(required = false, index = 0, metaVar = "metaVar_commitish", usage = "usage_resetReference")
 	private String commit;
 
-	@Argument(index = 1)
-	@Option(name = "--", metaVar = "metaVar_paths", multiValued = true, handler = StopOptionHandler.class)
-	private List<String> paths = new ArrayList<String>();
+	@Argument(required = false, index = 1, metaVar = "metaVar_paths")
+	@Option(name = "--", metaVar = "metaVar_paths", multiValued = true, handler = RestOfArgumentsHandler.class)
+	private List<String> paths = new ArrayList<>();
 
 	@Override
 	protected void run() throws Exception {

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevParse.java

@@ -75,7 +75,13 @@ class RevParse extends TextBuiltin {
 		if (all) {
 			Map<String, Ref> allRefs = db.getRefDatabase().getRefs(ALL);
 			for (final Ref r : allRefs.values()) {
-				outw.println(r.getObjectId().name());
+				ObjectId objectId = r.getObjectId();
+				// getRefs skips dangling symrefs, so objectId should never be
+				// null.
+				if (objectId == null) {
+					throw new NullPointerException();
+				}
+				outw.println(objectId.name());
 			}
 		} else {
 			if (verify && commits.size() > 1) {

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Status.java

@@ -59,8 +59,9 @@ import org.eclipse.jgit.lib.IndexDiff.StageState;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.pgm.internal.CLIText;
+import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.Option;
-
+import org.kohsuke.args4j.spi.RestOfArgumentsHandler;
 import org.eclipse.jgit.pgm.opt.UntrackedFilesHandler;
 
 /**
@@ -83,7 +84,8 @@ class Status extends TextBuiltin {
 	@Option(name = "--untracked-files", aliases = { "-u", "-uno", "-uall" }, usage = "usage_untrackedFilesMode", handler = UntrackedFilesHandler.class)
 	protected String untrackedFilesMode = "all"; // default value //$NON-NLS-1$
 
-	@Option(name = "--", metaVar = "metaVar_path", multiValued = true)
+	@Argument(required = false, index = 0, metaVar = "metaVar_paths")
+	@Option(name = "--", metaVar = "metaVar_paths", multiValued = true, handler = RestOfArgumentsHandler.class)
 	protected List<String> filterPaths;
 
 	@Override

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java

@@ -212,17 +212,20 @@ public abstract class TextBuiltin {
 	 */
 	protected void parseArguments(final String[] args) throws IOException {
 		final CmdLineParser clp = new CmdLineParser(this);
+		help = containsHelp(args);
 		try {
 			clp.parseArgument(args);
 		} catch (CmdLineException err) {
-			if (!help) {
-				this.errw.println(MessageFormat.format(CLIText.get().fatalError, err.getMessage()));
-				throw die(true);
+			this.errw.println(CLIText.fatalError(err.getMessage()));
+			if (help) {
+				printUsage("", clp); //$NON-NLS-1$
 			}
+			throw die(true, err);
 		}
 
 		if (help) {
-			printUsageAndExit(clp);
+			printUsage("", clp); //$NON-NLS-1$
+			throw new TerminatedByHelpException();
 		}
 
 		argWalk = clp.getRevWalkGently();
@@ -246,6 +249,20 @@ public abstract class TextBuiltin {
 	 * @throws IOException
 	 */
 	public void printUsageAndExit(final String message, final CmdLineParser clp) throws IOException {
+		printUsage(message, clp);
+		throw die(true);
+	}
+
+	/**
+	 * @param message
+	 *            non null
+	 * @param clp
+	 *            parser used to print options
+	 * @throws IOException
+	 * @since 4.2
+	 */
+	protected void printUsage(final String message, final CmdLineParser clp)
+			throws IOException {
 		errw.println(message);
 		errw.print("jgit "); //$NON-NLS-1$
 		errw.print(commandName);
@@ -257,12 +274,19 @@ public abstract class TextBuiltin {
 		errw.println();
 
 		errw.flush();
-		throw die(true);
 	}
 
 	/**
-	 * @return the resource bundle that will be passed to args4j for purpose
-	 *         of string localization
+	 * @return error writer, typically this is standard error.
+	 * @since 4.2
+	 */
+	public ThrowingPrintWriter getErrorWriter() {
+		return errw;
+	}
+
+	/**
+	 * @return the resource bundle that will be passed to args4j for purpose of
+	 *         string localization
 	 */
 	protected ResourceBundle getResourceBundle() {
 		return CLIText.get().resourceBundle();
@@ -324,6 +348,19 @@ public abstract class TextBuiltin {
 		return new Die(aborted);
 	}
 
+	/**
+	 * @param aborted
+	 *            boolean indicating that the execution has been aborted before
+	 *            running
+	 * @param cause
+	 *            why the command has failed.
+	 * @return a runtime exception the caller is expected to throw
+	 * @since 4.2
+	 */
+	protected static Die die(boolean aborted, final Throwable cause) {
+		return new Die(aborted, cause);
+	}
+
 	String abbreviateRef(String dst, boolean abbreviateRemote) {
 		if (dst.startsWith(R_HEADS))
 			dst = dst.substring(R_HEADS.length());
@@ -333,4 +370,36 @@ public abstract class TextBuiltin {
 			dst = dst.substring(R_REMOTES.length());
 		return dst;
 	}
+
+	/**
+	 * @param args
+	 *            non null
+	 * @return true if the given array contains help option
+	 * @since 4.2
+	 */
+	public static boolean containsHelp(String[] args) {
+		for (String str : args) {
+			if (str.equals("-h") || str.equals("--help")) { //$NON-NLS-1$ //$NON-NLS-2$
+				return true;
+			}
+		}
+		return false;
+	}
+
+	/**
+	 * Exception thrown by {@link TextBuiltin} if it proceeds 'help' option
+	 *
+	 * @since 4.2
+	 */
+	public static class TerminatedByHelpException extends Die {
+		private static final long serialVersionUID = 1L;
+
+		/**
+		 * Default constructor
+		 */
+		public TerminatedByHelpException() {
+			super(true);
+		}
+
+	}
 }

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildRefTree.java

@@ -0,0 +1,145 @@
+/*
+ * Copyright (C) 2015, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.pgm.debug;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import org.eclipse.jgit.internal.storage.reftree.RefTree;
+import org.eclipse.jgit.internal.storage.reftree.RefTreeDatabase;
+import org.eclipse.jgit.lib.CommitBuilder;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectInserter;
+import org.eclipse.jgit.lib.ObjectReader;
+import org.eclipse.jgit.lib.PersonIdent;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.RefDatabase;
+import org.eclipse.jgit.lib.RefUpdate;
+import org.eclipse.jgit.pgm.Command;
+import org.eclipse.jgit.pgm.TextBuiltin;
+import org.eclipse.jgit.revwalk.RevWalk;
+
+@Command(usage = "usage_RebuildRefTree")
+class RebuildRefTree extends TextBuiltin {
+	private String txnNamespace;
+	private String txnCommitted;
+
+	@Override
+	protected void run() throws Exception {
+		try (ObjectReader reader = db.newObjectReader();
+				RevWalk rw = new RevWalk(reader);
+				ObjectInserter inserter = db.newObjectInserter()) {
+			RefDatabase refDb = db.getRefDatabase();
+			if (refDb instanceof RefTreeDatabase) {
+				RefTreeDatabase d = (RefTreeDatabase) refDb;
+				refDb = d.getBootstrap();
+				txnNamespace = d.getTxnNamespace();
+				txnCommitted = d.getTxnCommitted();
+			} else {
+				RefTreeDatabase d = new RefTreeDatabase(db, refDb);
+				txnNamespace = d.getTxnNamespace();
+				txnCommitted = d.getTxnCommitted();
+			}
+
+			errw.format("Rebuilding %s from %s", //$NON-NLS-1$
+					txnCommitted, refDb.getClass().getSimpleName());
+			errw.println();
+			errw.flush();
+
+			CommitBuilder b = new CommitBuilder();
+			Ref ref = refDb.exactRef(txnCommitted);
+			RefUpdate update = refDb.newUpdate(txnCommitted, true);
+			ObjectId oldTreeId;
+
+			if (ref != null && ref.getObjectId() != null) {
+				ObjectId oldId = ref.getObjectId();
+				update.setExpectedOldObjectId(oldId);
+				b.setParentId(oldId);
+				oldTreeId = rw.parseCommit(oldId).getTree();
+			} else {
+				update.setExpectedOldObjectId(ObjectId.zeroId());
+				oldTreeId = ObjectId.zeroId();
+			}
+
+			RefTree tree = rebuild(refDb.getRefs(RefDatabase.ALL));
+			b.setTreeId(tree.writeTree(inserter));
+			b.setAuthor(new PersonIdent(db));
+			b.setCommitter(b.getAuthor());
+			if (b.getTreeId().equals(oldTreeId)) {
+				return;
+			}
+
+			update.setNewObjectId(inserter.insert(b));
+			inserter.flush();
+
+			RefUpdate.Result result = update.update(rw);
+			switch (result) {
+			case NEW:
+			case FAST_FORWARD:
+				break;
+			default:
+				throw die(String.format("%s: %s", update.getName(), result)); //$NON-NLS-1$
+			}
+		}
+	}
+
+	private RefTree rebuild(Map<String, Ref> refMap) {
+		RefTree tree = RefTree.newEmptyTree();
+		List<org.eclipse.jgit.internal.storage.reftree.Command> cmds
+			= new ArrayList<>();
+
+		for (Ref r : refMap.values()) {
+			if (r.getName().equals(txnCommitted)
+					|| r.getName().startsWith(txnNamespace)) {
+				continue;
+			}
+			cmds.add(new org.eclipse.jgit.internal.storage.reftree.Command(
+					null,
+					db.peel(r)));
+		}
+		tree.apply(cmds);
+		return tree;
+	}
+}

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/CLIText.java

@@ -74,6 +74,19 @@ public class CLIText extends TranslationBundle {
 		return MessageFormat.format(get().lineFormat, line);
 	}
 
+	/**
+	 * Format the given argument as fatal error using the format defined by
+	 * {@link #fatalError} ("fatal: " by default).
+	 *
+	 * @param message
+	 *            the message to format
+	 * @return the formatted line
+	 * @since 4.2
+	 */
+	public static String fatalError(String message) {
+		return MessageFormat.format(get().fatalError, message);
+	}
+
 	// @formatter:off
 	/***/ public String alreadyOnBranch;
 	/***/ public String alreadyUpToDate;
@@ -85,6 +98,7 @@ public class CLIText extends TranslationBundle {
 	/***/ public String branchCreatedFrom;
 	/***/ public String branchDetachedHEAD;
 	/***/ public String branchIsNotAnAncestorOfYourCurrentHEAD;
+	/***/ public String branchNameRequired;
 	/***/ public String branchNotFound;
 	/***/ public String cacheTreePathInfo;
 	/***/ public String configFileNotFound;
@@ -184,6 +198,7 @@ public class CLIText extends TranslationBundle {
 	/***/ public String metaVar_uriish;
 	/***/ public String metaVar_url;
 	/***/ public String metaVar_user;
+	/***/ public String metaVar_values;
 	/***/ public String metaVar_version;
 	/***/ public String mostCommonlyUsedCommandsAre;
 	/***/ public String needApprovalToDestroyCurrentRepository;

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/CmdLineParser.java

@@ -43,19 +43,18 @@
 
 package org.eclipse.jgit.pgm.opt;
 
+import java.io.IOException;
+import java.io.Writer;
 import java.lang.reflect.Field;
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.ResourceBundle;
 
-import org.kohsuke.args4j.Argument;
-import org.kohsuke.args4j.CmdLineException;
-import org.kohsuke.args4j.IllegalAnnotationError;
-import org.kohsuke.args4j.NamedOptionDef;
-import org.kohsuke.args4j.Option;
-import org.kohsuke.args4j.OptionDef;
-import org.kohsuke.args4j.spi.OptionHandler;
-import org.kohsuke.args4j.spi.Setter;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.pgm.Die;
 import org.eclipse.jgit.pgm.TextBuiltin;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.revwalk.RevCommit;
@@ -63,6 +62,15 @@ import org.eclipse.jgit.revwalk.RevTree;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.treewalk.AbstractTreeIterator;
+import org.kohsuke.args4j.Argument;
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.IllegalAnnotationError;
+import org.kohsuke.args4j.NamedOptionDef;
+import org.kohsuke.args4j.Option;
+import org.kohsuke.args4j.OptionDef;
+import org.kohsuke.args4j.spi.OptionHandler;
+import org.kohsuke.args4j.spi.RestOfArgumentsHandler;
+import org.kohsuke.args4j.spi.Setter;
 
 /**
  * Extended command line parser which handles --foo=value arguments.
@@ -80,12 +88,17 @@ public class CmdLineParser extends org.kohsuke.args4j.CmdLineParser {
 		registerHandler(RefSpec.class, RefSpecHandler.class);
 		registerHandler(RevCommit.class, RevCommitHandler.class);
 		registerHandler(RevTree.class, RevTreeHandler.class);
+		registerHandler(List.class, OptionWithValuesListHandler.class);
 	}
 
 	private final Repository db;
 
 	private RevWalk walk;
 
+	private boolean seenHelp;
+
+	private TextBuiltin cmd;
+
 	/**
 	 * Creates a new command line owner that parses arguments/options and set
 	 * them into the given object.
@@ -117,8 +130,12 @@ public class CmdLineParser extends org.kohsuke.args4j.CmdLineParser {
 	 */
 	public CmdLineParser(final Object bean, Repository repo) {
 		super(bean);
-		if (repo == null && bean instanceof TextBuiltin)
-			repo = ((TextBuiltin) bean).getRepository();
+		if (bean instanceof TextBuiltin) {
+			cmd = (TextBuiltin) bean;
+		}
+		if (repo == null && cmd != null) {
+			repo = cmd.getRepository();
+		}
 		this.db = repo;
 	}
 
@@ -143,9 +160,75 @@ public class CmdLineParser extends org.kohsuke.args4j.CmdLineParser {
 			}
 
 			tmp.add(str);
+
+			if (containsHelp(args)) {
+				// suppress exceptions on required parameters if help is present
+				seenHelp = true;
+				// stop argument parsing here
+				break;
+			}
+		}
+		List<OptionHandler> backup = null;
+		if (seenHelp) {
+			backup = unsetRequiredOptions();
 		}
 
-		super.parseArgument(tmp.toArray(new String[tmp.size()]));
+		try {
+			super.parseArgument(tmp.toArray(new String[tmp.size()]));
+		} catch (Die e) {
+			if (!seenHelp) {
+				throw e;
+			}
+			printToErrorWriter(CLIText.fatalError(e.getMessage()));
+		} finally {
+			// reset "required" options to defaults for correct command printout
+			if (backup != null && !backup.isEmpty()) {
+				restoreRequiredOptions(backup);
+			}
+			seenHelp = false;
+		}
+	}
+
+	private void printToErrorWriter(String error) {
+		if (cmd == null) {
+			System.err.println(error);
+		} else {
+			try {
+				cmd.getErrorWriter().println(error);
+			} catch (IOException e1) {
+				System.err.println(error);
+			}
+		}
+	}
+
+	private List<OptionHandler> unsetRequiredOptions() {
+		List<OptionHandler> options = getOptions();
+		List<OptionHandler> backup = new ArrayList<>(options);
+		for (Iterator<OptionHandler> iterator = options.iterator(); iterator
+				.hasNext();) {
+			OptionHandler handler = iterator.next();
+			if (handler.option instanceof NamedOptionDef
+					&& handler.option.required()) {
+				iterator.remove();
+			}
+		}
+		return backup;
+	}
+
+	private void restoreRequiredOptions(List<OptionHandler> backup) {
+		List<OptionHandler> options = getOptions();
+		options.clear();
+		options.addAll(backup);
+	}
+
+	/**
+	 * @param args
+	 *            non null
+	 * @return true if the given array contains help option
+	 * @since 4.2
+	 */
+	protected boolean containsHelp(final String... args) {
+		return TextBuiltin.containsHelp(args);
 	}
 
 	/**
@@ -181,7 +264,7 @@ public class CmdLineParser extends org.kohsuke.args4j.CmdLineParser {
 		return walk;
 	}
 
-	static class MyOptionDef extends OptionDef {
+	class MyOptionDef extends OptionDef {
 
 		public MyOptionDef(OptionDef o) {
 			super(o.usage(), o.metaVar(), o.required(), o.handler(), o
@@ -201,6 +284,11 @@ public class CmdLineParser extends org.kohsuke.args4j.CmdLineParser {
 				return metaVar();
 			}
 		}
+
+		@Override
+		public boolean required() {
+			return seenHelp ? false : super.required();
+		}
 	}
 
 	@Override
@@ -211,4 +299,55 @@ public class CmdLineParser extends org.kohsuke.args4j.CmdLineParser {
 			return super.createOptionHandler(new MyOptionDef(o), setter);
 
 	}
+
+	@SuppressWarnings("unchecked")
+	private List<OptionHandler> getOptions() {
+		List<OptionHandler> options = null;
+		try {
+			Field field = org.kohsuke.args4j.CmdLineParser.class
+					.getDeclaredField("options"); //$NON-NLS-1$
+			field.setAccessible(true);
+			options = (List<OptionHandler>) field.get(this);
+		} catch (NoSuchFieldException | SecurityException
+				| IllegalArgumentException | IllegalAccessException e) {
+			// ignore
+		}
+		if (options == null) {
+			return Collections.emptyList();
+		}
+		return options;
+	}
+
+	@Override
+	public void printSingleLineUsage(Writer w, ResourceBundle rb) {
+		List<OptionHandler> options = getOptions();
+		if (options.isEmpty()) {
+			super.printSingleLineUsage(w, rb);
+			return;
+		}
+		List<OptionHandler> backup = new ArrayList<>(options);
+		boolean changed = sortRestOfArgumentsHandlerToTheEnd(options);
+		try {
+			super.printSingleLineUsage(w, rb);
+		} finally {
+			if (changed) {
+				options.clear();
+				options.addAll(backup);
+			}
+		}
+	}
+
+	private boolean sortRestOfArgumentsHandlerToTheEnd(
+			List<OptionHandler> options) {
+		for (int i = 0; i < options.size(); i++) {
+			OptionHandler handler = options.get(i);
+			if (handler instanceof RestOfArgumentsHandler
+					|| handler instanceof PathTreeFilterHandler) {
+				options.remove(i);
+				options.add(handler);
+				return true;
+			}
+		}
+		return false;
+	}
 }

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/opt/OptionWithValuesListHandler.java

@@ -0,0 +1,52 @@
+package org.eclipse.jgit.pgm.opt;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.eclipse.jgit.pgm.internal.CLIText;
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.OptionDef;
+import org.kohsuke.args4j.spi.OptionHandler;
+import org.kohsuke.args4j.spi.Parameters;
+import org.kohsuke.args4j.spi.Setter;
+
+/**
+ * Handler which allows to parse option with few values
+ *
+ * @since 4.2
+ */
+public class OptionWithValuesListHandler extends OptionHandler<List<?>> {
+
+	/**
+	 * @param parser
+	 * @param option
+	 * @param setter
+	 */
+	public OptionWithValuesListHandler(CmdLineParser parser,
+			OptionDef option, Setter<List<?>> setter) {
+		super(parser, option, setter);
+	}
+
+	@Override
+	public int parseArguments(Parameters params) throws CmdLineException {
+		final List<String> list = new ArrayList<>();
+		for (int idx = 0; idx < params.size(); idx++) {
+			final String p;
+			try {
+				p = params.getParameter(idx);
+			} catch (CmdLineException cle) {
+				break;
+			}
+			list.add(p);
+		}
+		setter.addValue(list);
+		return list.size();
+	}
+
+	@Override
+	public String getDefaultMetaVariable() {
+		return CLIText.get().metaVar_values;
+	}
+
+}

org.eclipse.jgit.test/BUCK

@@ -0,0 +1,95 @@
+PKG = 'tst/org/eclipse/jgit/'
+HELPERS = glob(['src/**/*.java']) + [PKG + c for c in [
+  'api/AbstractRemoteCommandTest.java',
+  'diff/AbstractDiffTestCase.java',
+  'internal/storage/file/GcTestCase.java',
+  'internal/storage/file/PackIndexTestCase.java',
+  'internal/storage/file/XInputStream.java',
+  'nls/GermanTranslatedBundle.java',
+  'nls/MissingPropertyBundle.java',
+  'nls/NoPropertiesBundle.java',
+  'nls/NonTranslatedBundle.java',
+  'revwalk/RevQueueTestCase.java',
+  'revwalk/RevWalkTestCase.java',
+  'transport/SpiTransport.java',
+  'treewalk/FileTreeIteratorWithTimeControl.java',
+  'treewalk/filter/AlwaysCloneTreeFilter.java',
+  'test/resources/SampleDataRepositoryTestCase.java',
+  'util/CPUTimeStopWatch.java',
+  'util/io/Strings.java',
+]]
+
+DATA = [
+  PKG + 'lib/empty.gitindex.dat',
+  PKG + 'lib/sorttest.gitindex.dat',
+]
+
+TESTS = glob(
+  ['tst/**/*.java'],
+  excludes = HELPERS + DATA,
+)
+
+DEPS = {
+  PKG + 'nls/RootLocaleTest.java': [
+    '//org.eclipse.jgit.pgm:pgm',
+    '//org.eclipse.jgit.ui:ui',
+  ],
+}
+
+for src in TESTS:
+  name = src[len('tst/'):len(src)-len('.java')].replace('/', '.')
+  labels = []
+  if name.startswith('org.eclipse.jgit.'):
+    l = name[len('org.eclipse.jgit.'):]
+    if l.startswith('internal.storage.'):
+      l = l[len('internal.storage.'):]
+    i = l.find('.')
+    if i > 0:
+      labels.append(l[:i])
+    else:
+      labels.append(i)
+  if 'lib' not in labels:
+    labels.append('lib')
+
+  java_test(
+    name = name,
+    labels = labels,
+    srcs = [src],
+    deps = [
+      ':helpers',
+      ':tst_rsrc',
+      '//org.eclipse.jgit:jgit',
+      '//org.eclipse.jgit.junit:junit',
+      '//lib:hamcrest-core',
+      '//lib:hamcrest-library',
+      '//lib:javaewah',
+      '//lib:junit',
+      '//lib:slf4j-api',
+      '//lib:slf4j-simple',
+    ] + DEPS.get(src, []),
+    source_under_test = ['//org.eclipse.jgit:jgit'],
+    vm_args = ['-Xmx256m', '-Dfile.encoding=UTF-8'],
+  )
+
+java_library(
+  name = 'helpers',
+  srcs = HELPERS,
+  resources = DATA,
+  deps = [
+    '//org.eclipse.jgit:jgit',
+    '//org.eclipse.jgit.junit:junit',
+    '//lib:junit',
+  ],
+)
+
+prebuilt_jar(
+  name = 'tst_rsrc',
+  binary_jar = ':tst_rsrc_jar',
+)
+
+genrule(
+  name = 'tst_rsrc_jar',
+  cmd = 'cd $SRCDIR/tst-rsrc ; zip -qr $OUT .',
+  srcs = glob(['tst-rsrc/**']),
+  out = 'tst_rsrc.jar',
+)

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

@@ -26,6 +26,7 @@ Import-Package: com.googlecode.javaewah;version="[0.7.9,0.8.0)",
  org.eclipse.jgit.internal.storage.dfs;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.internal.storage.file;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.internal.storage.pack;version="[4.2.0,4.3.0)",
+ org.eclipse.jgit.internal.storage.reftree;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.junit;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.lib;version="[4.2.0,4.3.0)",
  org.eclipse.jgit.merge;version="[4.2.0,4.3.0)",

org.eclipse.jgit.test/org.eclipse.jgit.core--All-Tests (Java 8) (de).launch

@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.junit.launchconfig">
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/org.eclipse.jgit.test/tst"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="2"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
+<mapAttribute key="org.eclipse.debug.core.environmentVariables">
+<mapEntry key="LANG" value="de_DE.UTF-8"/>
+</mapAttribute>
+<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
+<listEntry value="org.eclipse.debug.ui.launchGroup.debug"/>
+<listEntry value="org.eclipse.debug.ui.launchGroup.run"/>
+</listAttribute>
+<stringAttribute key="org.eclipse.jdt.junit.CONTAINER" value="=org.eclipse.jgit.test/tst"/>
+<booleanAttribute key="org.eclipse.jdt.junit.KEEPRUNNING_ATTR" value="false"/>
+<stringAttribute key="org.eclipse.jdt.junit.TESTNAME" value=""/>
+<stringAttribute key="org.eclipse.jdt.junit.TEST_KIND" value="org.eclipse.jdt.junit.loader.junit4"/>
+<booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_START_ON_FIRST_THREAD" value="true"/>
+<listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#10;&lt;runtimeClasspathEntry containerPath=&quot;org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6&quot; path=&quot;1&quot; type=&quot;4&quot;/&gt;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#10;&lt;runtimeClasspathEntry id=&quot;org.eclipse.jdt.launching.classpathentry.defaultClasspath&quot;&gt;&#10;&lt;memento exportedEntriesOnly=&quot;false&quot; project=&quot;org.eclipse.jgit.test&quot;/&gt;&#10;&lt;/runtimeClasspathEntry&gt;&#10;"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
+<stringAttribute key="org.eclipse.jdt.launching.JRE_CONTAINER" value="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value=""/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="org.eclipse.jgit.test"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xmx256m"/>
+</launchConfiguration>

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

@@ -43,6 +43,7 @@
  */
 package org.eclipse.jgit.api;
 
+import static org.eclipse.jgit.util.FileUtils.RECURSIVE;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
@@ -797,13 +798,108 @@ public class AddCommandTest extends RepositoryTestCase {
 
 			assertEquals("[a.txt, mode:100644, content:more content,"
 					+ " assume-unchanged:false][b.txt, mode:100644,"
-					+ "" + ""
 					+ " content:content, assume-unchanged:true]",
 					indexState(CONTENT
 					| ASSUME_UNCHANGED));
 		}
 	}
 
+	@Test
+	public void testReplaceFileWithDirectory()
+			throws IOException, NoFilepatternException, GitAPIException {
+		try (Git git = new Git(db)) {
+			writeTrashFile("df", "before replacement");
+			git.add().addFilepattern("df").call();
+			assertEquals("[df, mode:100644, content:before replacement]",
+					indexState(CONTENT));
+			FileUtils.delete(new File(db.getWorkTree(), "df"));
+			writeTrashFile("df/f", "after replacement");
+			git.add().addFilepattern("df").call();
+			assertEquals("[df/f, mode:100644, content:after replacement]",
+					indexState(CONTENT));
+		}
+	}
+
+	@Test
+	public void testReplaceDirectoryWithFile()
+			throws IOException, NoFilepatternException, GitAPIException {
+		try (Git git = new Git(db)) {
+			writeTrashFile("df/f", "before replacement");
+			git.add().addFilepattern("df").call();
+			assertEquals("[df/f, mode:100644, content:before replacement]",
+					indexState(CONTENT));
+			FileUtils.delete(new File(db.getWorkTree(), "df"), RECURSIVE);
+			writeTrashFile("df", "after replacement");
+			git.add().addFilepattern("df").call();
+			assertEquals("[df, mode:100644, content:after replacement]",
+					indexState(CONTENT));
+		}
+	}
+
+	@Test
+	public void testReplaceFileByPartOfDirectory()
+			throws IOException, NoFilepatternException, GitAPIException {
+		try (Git git = new Git(db)) {
+			writeTrashFile("src/main", "df", "before replacement");
+			writeTrashFile("src/main", "z", "z");
+			writeTrashFile("z", "z2");
+			git.add().addFilepattern("src/main/df")
+				.addFilepattern("src/main/z")
+				.addFilepattern("z")
+				.call();
+			assertEquals(
+					"[src/main/df, mode:100644, content:before replacement]" +
+					"[src/main/z, mode:100644, content:z]" +
+					"[z, mode:100644, content:z2]",
+					indexState(CONTENT));
+			FileUtils.delete(new File(db.getWorkTree(), "src/main/df"));
+			writeTrashFile("src/main/df", "a", "after replacement");
+			writeTrashFile("src/main/df", "b", "unrelated file");
+			git.add().addFilepattern("src/main/df/a").call();
+			assertEquals(
+					"[src/main/df/a, mode:100644, content:after replacement]" +
+					"[src/main/z, mode:100644, content:z]" +
+					"[z, mode:100644, content:z2]",
+					indexState(CONTENT));
+		}
+	}
+
+	@Test
+	public void testReplaceDirectoryConflictsWithFile()
+			throws IOException, NoFilepatternException, GitAPIException {
+		DirCache dc = db.lockDirCache();
+		try (ObjectInserter oi = db.newObjectInserter()) {
+			DirCacheBuilder builder = dc.builder();
+			File f = writeTrashFile("a", "df", "content");
+			addEntryToBuilder("a", f, oi, builder, 1);
+
+			f = writeTrashFile("a", "df", "other content");
+			addEntryToBuilder("a/df", f, oi, builder, 3);
+
+			f = writeTrashFile("a", "df", "our content");
+			addEntryToBuilder("a/df", f, oi, builder, 2);
+
+			f = writeTrashFile("z", "z");
+			addEntryToBuilder("z", f, oi, builder, 0);
+			builder.commit();
+		}
+		assertEquals(
+				"[a, mode:100644, stage:1, content:content]" +
+				"[a/df, mode:100644, stage:2, content:our content]" +
+				"[a/df, mode:100644, stage:3, content:other content]" +
+				"[z, mode:100644, content:z]",
+				indexState(CONTENT));
+
+		try (Git git = new Git(db)) {
+			FileUtils.delete(new File(db.getWorkTree(), "a"), RECURSIVE);
+			writeTrashFile("a", "merged");
+			git.add().addFilepattern("a").call();
+			assertEquals("[a, mode:100644, content:merged]" +
+					"[z, mode:100644, content:z]",
+					indexState(CONTENT));
+		}
+	}
+
 	@Test
 	public void testExecutableRetention() throws Exception {
 		StoredConfig config = db.getConfig();

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

@@ -46,12 +46,15 @@ import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.fail;
 
 import java.io.File;
 import java.util.Date;
 import java.util.List;
 import java.util.TimeZone;
 
+import org.eclipse.jgit.api.errors.EmtpyCommitException;
 import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
 import org.eclipse.jgit.diff.DiffEntry;
 import org.eclipse.jgit.dircache.DirCache;
@@ -476,6 +479,34 @@ public class CommitCommandTest extends RepositoryTestCase {
 		assertEquals("newauthor@example.org", amendedAuthor.getEmailAddress());
 	}
 
+	@Test
+	public void commitEmptyCommits() throws Exception {
+		try (Git git = new Git(db)) {
+
+			writeTrashFile("file1", "file1");
+			git.add().addFilepattern("file1").call();
+			RevCommit initial = git.commit().setMessage("initial commit")
+					.call();
+
+			RevCommit emptyFollowUp = git.commit()
+					.setAuthor("New Author", "newauthor@example.org")
+					.setMessage("no change").call();
+
+			assertNotEquals(initial.getId(), emptyFollowUp.getId());
+			assertEquals(initial.getTree().getId(),
+					emptyFollowUp.getTree().getId());
+
+			try {
+				git.commit().setAuthor("New Author", "newauthor@example.org")
+						.setMessage("again no change").setAllowEmpty(false)
+						.call();
+				fail("Didn't get the expected EmtpyCommitException");
+			} catch (EmtpyCommitException e) {
+				// expect this exception
+			}
+		}
+	}
+
 	@Test
 	public void commitOnlyShouldCommitUnmergedPathAndNotAffectOthers()
 			throws Exception {

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

@@ -43,10 +43,12 @@
 package org.eclipse.jgit.api;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Path;
 
 import org.eclipse.jgit.api.CheckoutCommand.Stage;
 import org.eclipse.jgit.api.errors.JGitInternalException;
@@ -59,6 +61,9 @@ import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.RepositoryState;
 import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.util.FileUtils;
+import org.junit.Assume;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -73,6 +78,8 @@ public class PathCheckoutCommandTest extends RepositoryTestCase {
 
 	private static final String FILE3 = "Test3.txt";
 
+	private static final String LINK = "link";
+
 	Git git;
 
 	RevCommit initialCommit;
@@ -98,6 +105,64 @@ public class PathCheckoutCommandTest extends RepositoryTestCase {
 		git.commit().setMessage("Third commit").call();
 	}
 
+	@Test
+	public void testUpdateSymLink() throws Exception {
+		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
+
+		Path path = writeLink(LINK, FILE1);
+		git.add().addFilepattern(LINK).call();
+		git.commit().setMessage("Added link").call();
+		assertEquals("3", read(path.toFile()));
+
+		writeLink(LINK, FILE2);
+		assertEquals("c", read(path.toFile()));
+
+		CheckoutCommand co = git.checkout();
+		co.addPath(LINK).call();
+
+		assertEquals("3", read(path.toFile()));
+	}
+
+	@Test
+	public void testUpdateBrokenSymLinkToDirectory() throws Exception {
+		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
+
+		Path path = writeLink(LINK, "f");
+		git.add().addFilepattern(LINK).call();
+		git.commit().setMessage("Added link").call();
+		assertEquals("f", FileUtils.readSymLink(path.toFile()));
+		assertTrue(path.toFile().exists());
+
+		writeLink(LINK, "link_to_nowhere");
+		assertFalse(path.toFile().exists());
+		assertEquals("link_to_nowhere", FileUtils.readSymLink(path.toFile()));
+
+		CheckoutCommand co = git.checkout();
+		co.addPath(LINK).call();
+
+		assertEquals("f", FileUtils.readSymLink(path.toFile()));
+	}
+
+	@Test
+	public void testUpdateBrokenSymLink() throws Exception {
+		Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
+
+		Path path = writeLink(LINK, FILE1);
+		git.add().addFilepattern(LINK).call();
+		git.commit().setMessage("Added link").call();
+		assertEquals("3", read(path.toFile()));
+		assertEquals(FILE1, FileUtils.readSymLink(path.toFile()));
+
+		writeLink(LINK, "link_to_nowhere");
+		assertFalse(path.toFile().exists());
+		assertEquals("link_to_nowhere", FileUtils.readSymLink(path.toFile()));
+
+		CheckoutCommand co = git.checkout();
+		co.addPath(LINK).call();
+
+		assertEquals("3", read(path.toFile()));
+	}
+
 	@Test
 	public void testUpdateWorkingDirectory() throws Exception {
 		CheckoutCommand co = git.checkout();

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

@@ -65,6 +65,7 @@ import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.treewalk.TreeWalk;
@@ -139,8 +140,8 @@ public class ResetCommandTest extends RepositoryTestCase {
 			AmbiguousObjectException, IOException, GitAPIException {
 		setupRepository();
 		ObjectId prevHead = db.resolve(Constants.HEAD);
-		git.reset().setMode(ResetType.HARD).setRef(initialCommit.getName())
-				.call();
+		assertSameAsHead(git.reset().setMode(ResetType.HARD)
+				.setRef(initialCommit.getName()).call());
 		// check if HEAD points to initial commit now
 		ObjectId head = db.resolve(Constants.HEAD);
 		assertEquals(initialCommit, head);
@@ -176,8 +177,8 @@ public class ResetCommandTest extends RepositoryTestCase {
 			AmbiguousObjectException, IOException, GitAPIException {
 		setupRepository();
 		ObjectId prevHead = db.resolve(Constants.HEAD);
-		git.reset().setMode(ResetType.SOFT).setRef(initialCommit.getName())
-				.call();
+		assertSameAsHead(git.reset().setMode(ResetType.SOFT)
+				.setRef(initialCommit.getName()).call());
 		// check if HEAD points to initial commit now
 		ObjectId head = db.resolve(Constants.HEAD);
 		assertEquals(initialCommit, head);
@@ -197,8 +198,8 @@ public class ResetCommandTest extends RepositoryTestCase {
 			AmbiguousObjectException, IOException, GitAPIException {
 		setupRepository();
 		ObjectId prevHead = db.resolve(Constants.HEAD);
-		git.reset().setMode(ResetType.MIXED).setRef(initialCommit.getName())
-				.call();
+		assertSameAsHead(git.reset().setMode(ResetType.MIXED)
+				.setRef(initialCommit.getName()).call());
 		// check if HEAD points to initial commit now
 		ObjectId head = db.resolve(Constants.HEAD);
 		assertEquals(initialCommit, head);
@@ -241,7 +242,8 @@ public class ResetCommandTest extends RepositoryTestCase {
 		assertTrue(bEntry.getLength() > 0);
 		assertTrue(bEntry.getLastModified() > 0);
 
-		git.reset().setMode(ResetType.MIXED).setRef(commit2.getName()).call();
+		assertSameAsHead(git.reset().setMode(ResetType.MIXED)
+				.setRef(commit2.getName()).call());
 
 		cache = db.readDirCache();
 
@@ -280,7 +282,7 @@ public class ResetCommandTest extends RepositoryTestCase {
 				+ "[a.txt, mode:100644, stage:3]",
 				indexState(0));
 
-		git.reset().setMode(ResetType.MIXED).call();
+		assertSameAsHead(git.reset().setMode(ResetType.MIXED).call());
 
 		assertEquals("[a.txt, mode:100644]" + "[b.txt, mode:100644]",
 				indexState(0));
@@ -298,8 +300,8 @@ public class ResetCommandTest extends RepositoryTestCase {
 
 		// 'a.txt' has already been modified in setupRepository
 		// 'notAddedToIndex.txt' has been added to repository
-		git.reset().addPath(indexFile.getName())
-				.addPath(untrackedFile.getName()).call();
+		assertSameAsHead(git.reset().addPath(indexFile.getName())
+				.addPath(untrackedFile.getName()).call());
 
 		DirCacheEntry postReset = DirCache.read(db.getIndexFile(), db.getFS())
 				.getEntry(indexFile.getName());
@@ -329,7 +331,7 @@ public class ResetCommandTest extends RepositoryTestCase {
 		git.add().addFilepattern(untrackedFile.getName()).call();
 
 		// 'dir/b.txt' has already been modified in setupRepository
-		git.reset().addPath("dir").call();
+		assertSameAsHead(git.reset().addPath("dir").call());
 
 		DirCacheEntry postReset = DirCache.read(db.getIndexFile(), db.getFS())
 				.getEntry("dir/b.txt");
@@ -358,9 +360,9 @@ public class ResetCommandTest extends RepositoryTestCase {
 		// 'a.txt' has already been modified in setupRepository
 		// 'notAddedToIndex.txt' has been added to repository
 		// reset to the inital commit
-		git.reset().setRef(initialCommit.getName())
-				.addPath(indexFile.getName())
-				.addPath(untrackedFile.getName()).call();
+		assertSameAsHead(git.reset().setRef(initialCommit.getName())
+				.addPath(indexFile.getName()).addPath(untrackedFile.getName())
+				.call());
 
 		// check that HEAD hasn't moved
 		ObjectId head = db.resolve(Constants.HEAD);
@@ -397,7 +399,7 @@ public class ResetCommandTest extends RepositoryTestCase {
 				+ "[b.txt, mode:100644]",
 				indexState(0));
 
-		git.reset().addPath(file).call();
+		assertSameAsHead(git.reset().addPath(file).call());
 
 		assertEquals("[a.txt, mode:100644]" + "[b.txt, mode:100644]",
 				indexState(0));
@@ -409,7 +411,7 @@ public class ResetCommandTest extends RepositoryTestCase {
 		writeTrashFile("a.txt", "content");
 		git.add().addFilepattern("a.txt").call();
 		// Should assume an empty tree, like in C Git 1.8.2
-		git.reset().addPath("a.txt").call();
+		assertSameAsHead(git.reset().addPath("a.txt").call());
 
 		DirCache cache = db.readDirCache();
 		DirCacheEntry aEntry = cache.getEntry("a.txt");
@@ -421,7 +423,8 @@ public class ResetCommandTest extends RepositoryTestCase {
 		git = new Git(db);
 		writeTrashFile("a.txt", "content");
 		git.add().addFilepattern("a.txt").call();
-		git.reset().setRef("doesnotexist").addPath("a.txt").call();
+		assertSameAsHead(
+				git.reset().setRef("doesnotexist").addPath("a.txt").call());
 	}
 
 	@Test
@@ -431,7 +434,7 @@ public class ResetCommandTest extends RepositoryTestCase {
 		git.add().addFilepattern("a.txt").call();
 		writeTrashFile("a.txt", "modified");
 		// should use default mode MIXED
-		git.reset().call();
+		assertSameAsHead(git.reset().call());
 
 		DirCache cache = db.readDirCache();
 		DirCacheEntry aEntry = cache.getEntry("a.txt");
@@ -452,7 +455,7 @@ public class ResetCommandTest extends RepositoryTestCase {
 
 		git.add().addFilepattern(untrackedFile.getName()).call();
 
-		git.reset().setRef(tagName).setMode(HARD).call();
+		assertSameAsHead(git.reset().setRef(tagName).setMode(HARD).call());
 
 		ObjectId head = db.resolve(Constants.HEAD);
 		assertEquals(secondCommit, head);
@@ -486,7 +489,8 @@ public class ResetCommandTest extends RepositoryTestCase {
 				result.getMergeStatus());
 		assertNotNull(db.readSquashCommitMsg());
 
-		g.reset().setMode(ResetType.HARD).setRef(first.getName()).call();
+		assertSameAsHead(g.reset().setMode(ResetType.HARD)
+				.setRef(first.getName()).call());
 
 		assertNull(db.readSquashCommitMsg());
 	}
@@ -497,7 +501,7 @@ public class ResetCommandTest extends RepositoryTestCase {
 		File fileA = writeTrashFile("a.txt", "content");
 		git.add().addFilepattern("a.txt").call();
 		// Should assume an empty tree, like in C Git 1.8.2
-		git.reset().setMode(ResetType.HARD).call();
+		assertSameAsHead(git.reset().setMode(ResetType.HARD).call());
 
 		DirCache cache = db.readDirCache();
 		DirCacheEntry aEntry = cache.getEntry("a.txt");
@@ -558,4 +562,14 @@ public class ResetCommandTest extends RepositoryTestCase {
 		return dc.getEntry(path) != null;
 	}
 
+	/**
+	 * Asserts that a certain ref is similar to repos HEAD.
+	 * @param ref
+	 * @throws IOException
+	 */
+	private void assertSameAsHead(Ref ref) throws IOException {
+		Ref headRef = db.getRef(Constants.HEAD);
+		assertEquals(headRef.getName(), ref.getName());
+		assertEquals(headRef.getObjectId(), ref.getObjectId());
+	}
 }

org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCachePathEditTest.java

@@ -43,11 +43,13 @@
 package org.eclipse.jgit.dircache;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
 
 import java.util.ArrayList;
 import java.util.List;
 
 import org.eclipse.jgit.dircache.DirCacheEditor.PathEdit;
+import org.eclipse.jgit.errors.DirCacheNameConflictException;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
 import org.junit.Test;
@@ -154,6 +156,125 @@ public class DirCachePathEditTest {
 		assertEquals(DirCacheEntry.STAGE_3, entries.get(2).getStage());
 	}
 
+	@Test
+	public void testFileReplacesTree() throws Exception {
+		DirCache dc = DirCache.newInCore();
+		DirCacheEditor editor = dc.editor();
+		editor.add(new AddEdit("a"));
+		editor.add(new AddEdit("b/c"));
+		editor.add(new AddEdit("b/d"));
+		editor.add(new AddEdit("e"));
+		editor.finish();
+
+		editor = dc.editor();
+		editor.add(new AddEdit("b"));
+		editor.finish();
+
+		assertEquals(3, dc.getEntryCount());
+		assertEquals("a", dc.getEntry(0).getPathString());
+		assertEquals("b", dc.getEntry(1).getPathString());
+		assertEquals("e", dc.getEntry(2).getPathString());
+
+		dc.clear();
+		editor = dc.editor();
+		editor.add(new AddEdit("A.c"));
+		editor.add(new AddEdit("A/c"));
+		editor.add(new AddEdit("A0c"));
+		editor.finish();
+
+		editor = dc.editor();
+		editor.add(new AddEdit("A"));
+		editor.finish();
+		assertEquals(3, dc.getEntryCount());
+		assertEquals("A", dc.getEntry(0).getPathString());
+		assertEquals("A.c", dc.getEntry(1).getPathString());
+		assertEquals("A0c", dc.getEntry(2).getPathString());
+	}
+
+	@Test
+	public void testTreeReplacesFile() throws Exception {
+		DirCache dc = DirCache.newInCore();
+		DirCacheEditor editor = dc.editor();
+		editor.add(new AddEdit("a"));
+		editor.add(new AddEdit("ab"));
+		editor.add(new AddEdit("b"));
+		editor.add(new AddEdit("e"));
+		editor.finish();
+
+		editor = dc.editor();
+		editor.add(new AddEdit("b/c/d/f"));
+		editor.add(new AddEdit("b/g/h/i"));
+		editor.finish();
+
+		assertEquals(5, dc.getEntryCount());
+		assertEquals("a", dc.getEntry(0).getPathString());
+		assertEquals("ab", dc.getEntry(1).getPathString());
+		assertEquals("b/c/d/f", dc.getEntry(2).getPathString());
+		assertEquals("b/g/h/i", dc.getEntry(3).getPathString());
+		assertEquals("e", dc.getEntry(4).getPathString());
+	}
+
+	@Test
+	public void testDuplicateFiles() throws Exception {
+		DirCache dc = DirCache.newInCore();
+		DirCacheEditor editor = dc.editor();
+		editor.add(new AddEdit("a"));
+		editor.add(new AddEdit("a"));
+
+		try {
+			editor.finish();
+			fail("Expected DirCacheNameConflictException to be thrown");
+		} catch (DirCacheNameConflictException e) {
+			assertEquals("a a", e.getMessage());
+			assertEquals("a", e.getPath1());
+			assertEquals("a", e.getPath2());
+		}
+	}
+
+	@Test
+	public void testFileOverlapsTree() throws Exception {
+		DirCache dc = DirCache.newInCore();
+		DirCacheEditor editor = dc.editor();
+		editor.add(new AddEdit("a"));
+		editor.add(new AddEdit("a/b").setReplace(false));
+		try {
+			editor.finish();
+			fail("Expected DirCacheNameConflictException to be thrown");
+		} catch (DirCacheNameConflictException e) {
+			assertEquals("a a/b", e.getMessage());
+			assertEquals("a", e.getPath1());
+			assertEquals("a/b", e.getPath2());
+		}
+
+		editor = dc.editor();
+		editor.add(new AddEdit("A.c"));
+		editor.add(new AddEdit("A/c").setReplace(false));
+		editor.add(new AddEdit("A0c"));
+		editor.add(new AddEdit("A"));
+		try {
+			editor.finish();
+			fail("Expected DirCacheNameConflictException to be thrown");
+		} catch (DirCacheNameConflictException e) {
+			assertEquals("A A/c", e.getMessage());
+			assertEquals("A", e.getPath1());
+			assertEquals("A/c", e.getPath2());
+		}
+
+		editor = dc.editor();
+		editor.add(new AddEdit("A.c"));
+		editor.add(new AddEdit("A/b/c/d").setReplace(false));
+		editor.add(new AddEdit("A/b/c"));
+		editor.add(new AddEdit("A0c"));
+		try {
+			editor.finish();
+			fail("Expected DirCacheNameConflictException to be thrown");
+		} catch (DirCacheNameConflictException e) {
+			assertEquals("A/b/c A/b/c/d", e.getMessage());
+			assertEquals("A/b/c", e.getPath1());
+			assertEquals("A/b/c/d", e.getPath2());
+		}
+	}
+
 	private static DirCacheEntry createEntry(String path, int stage) {
 		DirCacheEntry entry = new DirCacheEntry(path, stage);
 		entry.setFileMode(FileMode.REGULAR_FILE);

org.eclipse.jgit.test/tst/org/eclipse/jgit/gitrepo/RepoCommandTest.java

@@ -409,6 +409,7 @@ public class RepoCommandTest extends RepositoryTestCase {
 					.append("<project path=\"foo\" name=\"").append(defaultUri)
 					.append("\" revision=\"").append(BRANCH).append("\" >")
 					.append("<copyfile src=\"hello.txt\" dest=\"Hello\" />")
+					.append("<copyfile src=\"hello.txt\" dest=\"foo/Hello\" />")
 					.append("</project>").append("</manifest>");
 			JGitTestUtil.writeTrashFile(tempDb, "manifest.xml",
 					xmlContent.toString());
@@ -423,8 +424,12 @@ public class RepoCommandTest extends RepositoryTestCase {
 					.getRepository();
 			// The Hello file should exist
 			File hello = new File(localDb.getWorkTree(), "Hello");
-			localDb.close();
 			assertTrue("The Hello file should exist", hello.exists());
+			// The foo/Hello file should be skipped.
+			File foohello = new File(localDb.getWorkTree(), "foo/Hello");
+			assertFalse(
+					"The foo/Hello file should be skipped", foohello.exists());
+			localDb.close();
 			// The content of Hello file should be expected
 			BufferedReader reader = new BufferedReader(new FileReader(hello));
 			String content = reader.readLine();

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileRepositoryBuilderTest.java

@@ -107,7 +107,7 @@ public class FileRepositoryBuilderTest extends LocalDiskRepositoryTestCase {
 		Repository r = createWorkRepository();
 		StoredConfig config = r.getConfig();
 		config.setLong(ConfigConstants.CONFIG_CORE_SECTION, null,
-				ConfigConstants.CONFIG_KEY_REPO_FORMAT_VERSION, 1);
+				ConfigConstants.CONFIG_KEY_REPO_FORMAT_VERSION, 999999);
 		config.save();
 
 		try {

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

@@ -43,11 +43,13 @@
 
 package org.eclipse.jgit.internal.storage.file;
 
+import static org.eclipse.jgit.lib.Constants.OBJ_BLOB;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
+import static org.eclipse.jgit.internal.storage.pack.PackWriter.NONE;
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
@@ -66,19 +68,19 @@ import java.util.Set;
 import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.internal.storage.file.PackIndex.MutableEntry;
 import org.eclipse.jgit.internal.storage.pack.PackWriter;
-import org.eclipse.jgit.internal.storage.pack.PackWriter.ObjectIdSet;
 import org.eclipse.jgit.junit.JGitTestUtil;
 import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.junit.TestRepository.BranchBuilder;
-import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.NullProgressMonitor;
 import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectIdSet;
 import org.eclipse.jgit.lib.ObjectInserter;
 import org.eclipse.jgit.revwalk.RevBlob;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevObject;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.storage.pack.PackConfig;
+import org.eclipse.jgit.storage.pack.PackStatistics;
 import org.eclipse.jgit.test.resources.SampleDataRepositoryTestCase;
 import org.eclipse.jgit.transport.PackParser;
 import org.junit.After;
@@ -87,9 +89,6 @@ import org.junit.Test;
 
 public class PackWriterTest extends SampleDataRepositoryTestCase {
 
-	private static final Set<ObjectId> EMPTY_SET_OBJECT = Collections
-			.<ObjectId> emptySet();
-
 	private static final List<RevObject> EMPTY_LIST_REVS = Collections
 			.<RevObject> emptyList();
 
@@ -170,7 +169,7 @@ public class PackWriterTest extends SampleDataRepositoryTestCase {
 	 */
 	@Test
 	public void testWriteEmptyPack1() throws IOException {
-		createVerifyOpenPack(EMPTY_SET_OBJECT, EMPTY_SET_OBJECT, false, false);
+		createVerifyOpenPack(NONE, NONE, false, false);
 
 		assertEquals(0, writer.getObjectCount());
 		assertEquals(0, pack.getObjectCount());
@@ -203,8 +202,8 @@ public class PackWriterTest extends SampleDataRepositoryTestCase {
 		final ObjectId nonExisting = ObjectId
 				.fromString("0000000000000000000000000000000000000001");
 		try {
-			createVerifyOpenPack(EMPTY_SET_OBJECT, Collections.singleton(
-					nonExisting), false, false);
+			createVerifyOpenPack(NONE, Collections.singleton(nonExisting),
+					false, false);
 			fail("Should have thrown MissingObjectException");
 		} catch (MissingObjectException x) {
 			// expected
@@ -220,8 +219,8 @@ public class PackWriterTest extends SampleDataRepositoryTestCase {
 	public void testIgnoreNonExistingObjects() throws IOException {
 		final ObjectId nonExisting = ObjectId
 				.fromString("0000000000000000000000000000000000000001");
-		createVerifyOpenPack(EMPTY_SET_OBJECT, Collections.singleton(
-				nonExisting), false, true);
+		createVerifyOpenPack(NONE, Collections.singleton(nonExisting),
+				false, true);
 		// shouldn't throw anything
 	}
 
@@ -239,8 +238,8 @@ public class PackWriterTest extends SampleDataRepositoryTestCase {
 		final ObjectId nonExisting = ObjectId
 				.fromString("0000000000000000000000000000000000000001");
 		new GC(db).gc();
-		createVerifyOpenPack(EMPTY_SET_OBJECT,
-				Collections.singleton(nonExisting), false, true, true);
+		createVerifyOpenPack(NONE, Collections.singleton(nonExisting), false,
+				true, true);
 		// shouldn't throw anything
 	}
 
@@ -437,6 +436,38 @@ public class PackWriterTest extends SampleDataRepositoryTestCase {
 		assertTrue(sizePack4 > sizePack4Thin);
 	}
 
+	@Test
+	public void testDeltaStatistics() throws Exception {
+		config.setDeltaCompress(true);
+		FileRepository repo = createBareRepository();
+		TestRepository<FileRepository> testRepo = new TestRepository<FileRepository>(repo);
+		ArrayList<RevObject> blobs = new ArrayList<>();
+		blobs.add(testRepo.blob(genDeltableData(1000)));
+		blobs.add(testRepo.blob(genDeltableData(1005)));
+
+		try (PackWriter pw = new PackWriter(repo)) {
+			NullProgressMonitor m = NullProgressMonitor.INSTANCE;
+			pw.preparePack(blobs.iterator());
+			pw.writePack(m, m, os);
+			PackStatistics stats = pw.getStatistics();
+			assertEquals(1, stats.getTotalDeltas());
+			assertTrue("Delta bytes not set.",
+					stats.byObjectType(OBJ_BLOB).getDeltaBytes() > 0);
+		}
+	}
+
+	// Generate consistent junk data for building files that delta well
+	private String genDeltableData(int length) {
+		assertTrue("Generated data must have a length > 0", length > 0);
+		char[] data = {'a', 'b', 'c', '\n'};
+		StringBuilder builder = new StringBuilder(length);
+		for (int i = 0; i < length; i++) {
+			builder.append(data[i % 4]);
+		}
+		return builder.toString();
+	}
+
+
 	@Test
 	public void testWriteIndex() throws Exception {
 		config.setIndexVersion(2);
@@ -494,7 +525,7 @@ public class PackWriterTest extends SampleDataRepositoryTestCase {
 		RevCommit c2 = bb.commit().add("f", contentB).create();
 		testRepo.getRevWalk().parseHeaders(c2);
 		PackIndex pf2 = writePack(repo, Collections.singleton(c2),
-				Collections.singleton(objectIdSet(pf1)));
+				Collections.<ObjectIdSet> singleton(pf1));
 		assertContent(
 				pf2,
 				Arrays.asList(c2.getId(), c2.getTree().getId(),
@@ -519,8 +550,7 @@ public class PackWriterTest extends SampleDataRepositoryTestCase {
 			pw.setReuseDeltaCommits(false);
 			for (ObjectIdSet idx : excludeObjects)
 				pw.excludeObjects(idx);
-			pw.preparePack(NullProgressMonitor.INSTANCE, want,
-					Collections.<ObjectId> emptySet());
+			pw.preparePack(NullProgressMonitor.INSTANCE, want, NONE);
 			String id = pw.computeName().getName();
 			File packdir = new File(repo.getObjectsDirectory(), "pack");
 			File packFile = new File(packdir, "pack-" + id + ".pack");
@@ -543,7 +573,7 @@ public class PackWriterTest extends SampleDataRepositoryTestCase {
 		final HashSet<ObjectId> interestings = new HashSet<ObjectId>();
 		interestings.add(ObjectId
 				.fromString("82c6b885ff600be425b4ea96dee75dca255b69e7"));
-		createVerifyOpenPack(interestings, EMPTY_SET_OBJECT, false, false);
+		createVerifyOpenPack(interestings, NONE, false, false);
 
 		final ObjectId expectedOrder[] = new ObjectId[] {
 				ObjectId.fromString("82c6b885ff600be425b4ea96dee75dca255b69e7"),
@@ -699,12 +729,4 @@ public class PackWriterTest extends SampleDataRepositoryTestCase {
 			assertEquals(objectsOrder[i++].toObjectId(), me.toObjectId());
 		}
 	}
-
-	private static ObjectIdSet objectIdSet(final PackIndex idx) {
-		return new ObjectIdSet() {
-			public boolean contains(AnyObjectId objectId) {
-				return idx.hasObject(objectId);
-			}
-		};
-	}
 }

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/T0003_BasicTest.java

@@ -67,7 +67,6 @@ import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.CommitBuilder;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
-import org.eclipse.jgit.lib.FileTreeEntry;
 import org.eclipse.jgit.lib.ObjectDatabase;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectInserter;
@@ -75,7 +74,6 @@ import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.RefUpdate;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.TagBuilder;
-import org.eclipse.jgit.lib.Tree;
 import org.eclipse.jgit.lib.TreeFormatter;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevTag;
@@ -419,29 +417,6 @@ public class T0003_BasicTest extends SampleDataRepositoryTestCase {
 		assertEquals(c.getCommitter(), c2.getCommitterIdent());
 	}
 
-	@Test
-	public void test012_SubtreeExternalSorting() throws IOException {
-		final ObjectId emptyBlob = insertEmptyBlob();
-		final Tree t = new Tree(db);
-		final FileTreeEntry e0 = t.addFile("a-");
-		final FileTreeEntry e1 = t.addFile("a-b");
-		final FileTreeEntry e2 = t.addFile("a/b");
-		final FileTreeEntry e3 = t.addFile("a=");
-		final FileTreeEntry e4 = t.addFile("a=b");
-
-		e0.setId(emptyBlob);
-		e1.setId(emptyBlob);
-		e2.setId(emptyBlob);
-		e3.setId(emptyBlob);
-		e4.setId(emptyBlob);
-
-		final Tree a = (Tree) t.findTreeMember("a");
-		a.setId(insertTree(a));
-		assertEquals(ObjectId
-				.fromString("b47a8f0a4190f7572e11212769090523e23eb1ea"),
-				insertTree(t));
-	}
-
 	@Test
 	public void test020_createBlobTag() throws IOException {
 		final ObjectId emptyId = insertEmptyBlob();
@@ -465,9 +440,8 @@ public class T0003_BasicTest extends SampleDataRepositoryTestCase {
 	@Test
 	public void test021_createTreeTag() throws IOException {
 		final ObjectId emptyId = insertEmptyBlob();
-		final Tree almostEmptyTree = new Tree(db);
-		almostEmptyTree.addEntry(new FileTreeEntry(almostEmptyTree, emptyId,
-				"empty".getBytes(), false));
+		TreeFormatter almostEmptyTree = new TreeFormatter();
+		almostEmptyTree.append("empty", FileMode.REGULAR_FILE, emptyId);
 		final ObjectId almostEmptyTreeId = insertTree(almostEmptyTree);
 		final TagBuilder t = new TagBuilder();
 		t.setObjectId(almostEmptyTreeId, Constants.OBJ_TREE);
@@ -489,9 +463,8 @@ public class T0003_BasicTest extends SampleDataRepositoryTestCase {
 	@Test
 	public void test022_createCommitTag() throws IOException {
 		final ObjectId emptyId = insertEmptyBlob();
-		final Tree almostEmptyTree = new Tree(db);
-		almostEmptyTree.addEntry(new FileTreeEntry(almostEmptyTree, emptyId,
-				"empty".getBytes(), false));
+		TreeFormatter almostEmptyTree = new TreeFormatter();
+		almostEmptyTree.append("empty", FileMode.REGULAR_FILE, emptyId);
 		final ObjectId almostEmptyTreeId = insertTree(almostEmptyTree);
 		final CommitBuilder almostEmptyCommit = new CommitBuilder();
 		almostEmptyCommit.setAuthor(new PersonIdent(author, 1154236443000L,
@@ -521,9 +494,8 @@ public class T0003_BasicTest extends SampleDataRepositoryTestCase {
 	@Test
 	public void test023_createCommitNonAnullii() throws IOException {
 		final ObjectId emptyId = insertEmptyBlob();
-		final Tree almostEmptyTree = new Tree(db);
-		almostEmptyTree.addEntry(new FileTreeEntry(almostEmptyTree, emptyId,
-				"empty".getBytes(), false));
+		TreeFormatter almostEmptyTree = new TreeFormatter();
+		almostEmptyTree.append("empty", FileMode.REGULAR_FILE, emptyId);
 		final ObjectId almostEmptyTreeId = insertTree(almostEmptyTree);
 		CommitBuilder commit = new CommitBuilder();
 		commit.setTreeId(almostEmptyTreeId);
@@ -543,9 +515,8 @@ public class T0003_BasicTest extends SampleDataRepositoryTestCase {
 	@Test
 	public void test024_createCommitNonAscii() throws IOException {
 		final ObjectId emptyId = insertEmptyBlob();
-		final Tree almostEmptyTree = new Tree(db);
-		almostEmptyTree.addEntry(new FileTreeEntry(almostEmptyTree, emptyId,
-				"empty".getBytes(), false));
+		TreeFormatter almostEmptyTree = new TreeFormatter();
+		almostEmptyTree.append("empty", FileMode.REGULAR_FILE, emptyId);
 		final ObjectId almostEmptyTreeId = insertTree(almostEmptyTree);
 		CommitBuilder commit = new CommitBuilder();
 		commit.setTreeId(almostEmptyTreeId);
@@ -747,14 +718,6 @@ public class T0003_BasicTest extends SampleDataRepositoryTestCase {
 		return emptyId;
 	}
 
-	private ObjectId insertTree(Tree tree) throws IOException {
-		try (ObjectInserter oi = db.newObjectInserter()) {
-			ObjectId id = oi.insert(Constants.OBJ_TREE, tree.format());
-			oi.flush();
-			return id;
-		}
-	}
-
 	private ObjectId insertTree(TreeFormatter tree) throws IOException {
 		try (ObjectInserter oi = db.newObjectInserter()) {
 			ObjectId id = oi.insert(tree);

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/RefTreeDatabaseTest.java

@@ -0,0 +1,685 @@
+/*
+ * Copyright (C) 2010, 2013, 2016 Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.reftree;
+
+import static org.eclipse.jgit.lib.Constants.HEAD;
+import static org.eclipse.jgit.lib.Constants.R_HEADS;
+import static org.eclipse.jgit.lib.Constants.R_TAGS;
+import static org.eclipse.jgit.lib.Ref.Storage.LOOSE;
+import static org.eclipse.jgit.lib.Ref.Storage.PACKED;
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
+import static org.eclipse.jgit.transport.ReceiveCommand.Result.LOCK_FAILURE;
+import static org.eclipse.jgit.transport.ReceiveCommand.Result.OK;
+import static org.eclipse.jgit.transport.ReceiveCommand.Result.REJECTED_NONFASTFORWARD;
+import static org.eclipse.jgit.transport.ReceiveCommand.Result.REJECTED_OTHER_REASON;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+import java.text.MessageFormat;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.internal.storage.dfs.DfsRepositoryDescription;
+import org.eclipse.jgit.internal.storage.dfs.InMemoryRepository;
+import org.eclipse.jgit.junit.TestRepository;
+import org.eclipse.jgit.lib.AnyObjectId;
+import org.eclipse.jgit.lib.BatchRefUpdate;
+import org.eclipse.jgit.lib.CommitBuilder;
+import org.eclipse.jgit.lib.NullProgressMonitor;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectIdRef;
+import org.eclipse.jgit.lib.ObjectInserter;
+import org.eclipse.jgit.lib.ObjectReader;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.RefDatabase;
+import org.eclipse.jgit.lib.RefUpdate;
+import org.eclipse.jgit.lib.SymbolicRef;
+import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.revwalk.RevTag;
+import org.eclipse.jgit.revwalk.RevWalk;
+import org.eclipse.jgit.transport.ReceiveCommand;
+import org.junit.Before;
+import org.junit.Test;
+
+public class RefTreeDatabaseTest {
+	private InMemRefTreeRepo repo;
+	private RefTreeDatabase refdb;
+	private RefDatabase bootstrap;
+
+	private TestRepository<InMemRefTreeRepo> testRepo;
+	private RevCommit A;
+	private RevCommit B;
+	private RevTag v1_0;
+
+	@Before
+	public void setUp() throws Exception {
+		repo = new InMemRefTreeRepo(new DfsRepositoryDescription("test"));
+		bootstrap = refdb.getBootstrap();
+
+		testRepo = new TestRepository<>(repo);
+		A = testRepo.commit().create();
+		B = testRepo.commit(testRepo.getRevWalk().parseCommit(A));
+		v1_0 = testRepo.tag("v1_0", B);
+		testRepo.getRevWalk().parseBody(v1_0);
+	}
+
+	@Test
+	public void testSupportsAtomic() {
+		assertTrue(refdb.performsAtomicTransactions());
+	}
+
+	@Test
+	public void testGetRefs_EmptyDatabase() throws IOException {
+		assertTrue("no references", refdb.getRefs(ALL).isEmpty());
+		assertTrue("no references", refdb.getRefs(R_HEADS).isEmpty());
+		assertTrue("no references", refdb.getRefs(R_TAGS).isEmpty());
+	}
+
+	@Test
+	public void testGetRefs_HeadOnOneBranch() throws IOException {
+		symref(HEAD, "refs/heads/master");
+		update("refs/heads/master", A);
+
+		Map<String, Ref> all = refdb.getRefs(ALL);
+		assertEquals(2, all.size());
+		assertTrue("has HEAD", all.containsKey(HEAD));
+		assertTrue("has master", all.containsKey("refs/heads/master"));
+
+		Ref head = all.get(HEAD);
+		Ref master = all.get("refs/heads/master");
+
+		assertEquals(HEAD, head.getName());
+		assertTrue(head.isSymbolic());
+		assertSame(LOOSE, head.getStorage());
+		assertSame("uses same ref as target", master, head.getTarget());
+
+		assertEquals("refs/heads/master", master.getName());
+		assertFalse(master.isSymbolic());
+		assertSame(PACKED, master.getStorage());
+		assertEquals(A, master.getObjectId());
+	}
+
+	@Test
+	public void testGetRefs_DetachedHead() throws IOException {
+		update(HEAD, A);
+
+		Map<String, Ref> all = refdb.getRefs(ALL);
+		assertEquals(1, all.size());
+		assertTrue("has HEAD", all.containsKey(HEAD));
+
+		Ref head = all.get(HEAD);
+		assertEquals(HEAD, head.getName());
+		assertFalse(head.isSymbolic());
+		assertSame(PACKED, head.getStorage());
+		assertEquals(A, head.getObjectId());
+	}
+
+	@Test
+	public void testGetRefs_DeeplyNestedBranch() throws IOException {
+		String name = "refs/heads/a/b/c/d/e/f/g/h/i/j/k";
+		update(name, A);
+
+		Map<String, Ref> all = refdb.getRefs(ALL);
+		assertEquals(1, all.size());
+
+		Ref r = all.get(name);
+		assertEquals(name, r.getName());
+		assertFalse(r.isSymbolic());
+		assertSame(PACKED, r.getStorage());
+		assertEquals(A, r.getObjectId());
+	}
+
+	@Test
+	public void testGetRefs_HeadBranchNotBorn() throws IOException {
+		update("refs/heads/A", A);
+		update("refs/heads/B", B);
+
+		Map<String, Ref> all = refdb.getRefs(ALL);
+		assertEquals(2, all.size());
+		assertFalse("no HEAD", all.containsKey(HEAD));
+
+		Ref a = all.get("refs/heads/A");
+		Ref b = all.get("refs/heads/B");
+
+		assertEquals(A, a.getObjectId());
+		assertEquals(B, b.getObjectId());
+
+		assertEquals("refs/heads/A", a.getName());
+		assertEquals("refs/heads/B", b.getName());
+	}
+
+	@Test
+	public void testGetRefs_HeadsOnly() throws IOException {
+		update("refs/heads/A", A);
+		update("refs/heads/B", B);
+		update("refs/tags/v1.0", v1_0);
+
+		Map<String, Ref> heads = refdb.getRefs(R_HEADS);
+		assertEquals(2, heads.size());
+
+		Ref a = heads.get("A");
+		Ref b = heads.get("B");
+
+		assertEquals("refs/heads/A", a.getName());
+		assertEquals("refs/heads/B", b.getName());
+
+		assertEquals(A, a.getObjectId());
+		assertEquals(B, b.getObjectId());
+	}
+
+	@Test
+	public void testGetRefs_TagsOnly() throws IOException {
+		update("refs/heads/A", A);
+		update("refs/heads/B", B);
+		update("refs/tags/v1.0", v1_0);
+
+		Map<String, Ref> tags = refdb.getRefs(R_TAGS);
+		assertEquals(1, tags.size());
+
+		Ref a = tags.get("v1.0");
+		assertEquals("refs/tags/v1.0", a.getName());
+		assertEquals(v1_0, a.getObjectId());
+		assertTrue(a.isPeeled());
+		assertEquals(v1_0.getObject(), a.getPeeledObjectId());
+	}
+
+	@Test
+	public void testGetRefs_HeadsSymref() throws IOException {
+		symref("refs/heads/other", "refs/heads/master");
+		update("refs/heads/master", A);
+
+		Map<String, Ref> heads = refdb.getRefs(R_HEADS);
+		assertEquals(2, heads.size());
+
+		Ref master = heads.get("master");
+		Ref other = heads.get("other");
+
+		assertEquals("refs/heads/master", master.getName());
+		assertEquals(A, master.getObjectId());
+
+		assertEquals("refs/heads/other", other.getName());
+		assertEquals(A, other.getObjectId());
+		assertSame(master, other.getTarget());
+	}
+
+	@Test
+	public void testGetRefs_InvalidPrefixes() throws IOException {
+		update("refs/heads/A", A);
+
+		assertTrue("empty refs/heads", refdb.getRefs("refs/heads").isEmpty());
+		assertTrue("empty objects", refdb.getRefs("objects").isEmpty());
+		assertTrue("empty objects/", refdb.getRefs("objects/").isEmpty());
+	}
+
+	@Test
+	public void testGetRefs_DiscoversNew() throws IOException {
+		update("refs/heads/master", A);
+		Map<String, Ref> orig = refdb.getRefs(ALL);
+
+		update("refs/heads/next", B);
+		Map<String, Ref> next = refdb.getRefs(ALL);
+
+		assertEquals(1, orig.size());
+		assertEquals(2, next.size());
+
+		assertFalse(orig.containsKey("refs/heads/next"));
+		assertTrue(next.containsKey("refs/heads/next"));
+
+		assertEquals(A, next.get("refs/heads/master").getObjectId());
+		assertEquals(B, next.get("refs/heads/next").getObjectId());
+	}
+
+	@Test
+	public void testGetRefs_DiscoversModified() throws IOException {
+		symref(HEAD, "refs/heads/master");
+		update("refs/heads/master", A);
+
+		Map<String, Ref> all = refdb.getRefs(ALL);
+		assertEquals(A, all.get(HEAD).getObjectId());
+
+		update("refs/heads/master", B);
+		all = refdb.getRefs(ALL);
+		assertEquals(B, all.get(HEAD).getObjectId());
+		assertEquals(B, refdb.exactRef(HEAD).getObjectId());
+	}
+
+	@Test
+	public void testGetRefs_CycleInSymbolicRef() throws IOException {
+		symref("refs/1", "refs/2");
+		symref("refs/2", "refs/3");
+		symref("refs/3", "refs/4");
+		symref("refs/4", "refs/5");
+		symref("refs/5", "refs/end");
+		update("refs/end", A);
+
+		Map<String, Ref> all = refdb.getRefs(ALL);
+		Ref r = all.get("refs/1");
+		assertNotNull("has 1", r);
+
+		assertEquals("refs/1", r.getName());
+		assertEquals(A, r.getObjectId());
+		assertTrue(r.isSymbolic());
+
+		r = r.getTarget();
+		assertEquals("refs/2", r.getName());
+		assertEquals(A, r.getObjectId());
+		assertTrue(r.isSymbolic());
+
+		r = r.getTarget();
+		assertEquals("refs/3", r.getName());
+		assertEquals(A, r.getObjectId());
+		assertTrue(r.isSymbolic());
+
+		r = r.getTarget();
+		assertEquals("refs/4", r.getName());
+		assertEquals(A, r.getObjectId());
+		assertTrue(r.isSymbolic());
+
+		r = r.getTarget();
+		assertEquals("refs/5", r.getName());
+		assertEquals(A, r.getObjectId());
+		assertTrue(r.isSymbolic());
+
+		r = r.getTarget();
+		assertEquals("refs/end", r.getName());
+		assertEquals(A, r.getObjectId());
+		assertFalse(r.isSymbolic());
+
+		symref("refs/5", "refs/6");
+		symref("refs/6", "refs/end");
+		all = refdb.getRefs(ALL);
+		assertNull("mising 1 due to cycle", all.get("refs/1"));
+		assertEquals(A, all.get("refs/2").getObjectId());
+		assertEquals(A, all.get("refs/3").getObjectId());
+		assertEquals(A, all.get("refs/4").getObjectId());
+		assertEquals(A, all.get("refs/5").getObjectId());
+		assertEquals(A, all.get("refs/6").getObjectId());
+		assertEquals(A, all.get("refs/end").getObjectId());
+	}
+
+	@Test
+	public void testGetRef_NonExistingBranchConfig() throws IOException {
+		assertNull("find branch config", refdb.getRef("config"));
+		assertNull("find branch config", refdb.getRef("refs/heads/config"));
+	}
+
+	@Test
+	public void testGetRef_FindBranchConfig() throws IOException {
+		update("refs/heads/config", A);
+
+		for (String t : new String[] { "config", "refs/heads/config" }) {
+			Ref r = refdb.getRef(t);
+			assertNotNull("find branch config (" + t + ")", r);
+			assertEquals("for " + t, "refs/heads/config", r.getName());
+			assertEquals("for " + t, A, r.getObjectId());
+		}
+	}
+
+	@Test
+	public void testFirstExactRef() throws IOException {
+		update("refs/heads/A", A);
+		update("refs/tags/v1.0", v1_0);
+
+		Ref a = refdb.firstExactRef("refs/heads/A", "refs/tags/v1.0");
+		Ref one = refdb.firstExactRef("refs/tags/v1.0", "refs/heads/A");
+
+		assertEquals("refs/heads/A", a.getName());
+		assertEquals("refs/tags/v1.0", one.getName());
+
+		assertEquals(A, a.getObjectId());
+		assertEquals(v1_0, one.getObjectId());
+	}
+
+	@Test
+	public void testExactRef_DiscoversModified() throws IOException {
+		symref(HEAD, "refs/heads/master");
+		update("refs/heads/master", A);
+		assertEquals(A, refdb.exactRef(HEAD).getObjectId());
+
+		update("refs/heads/master", B);
+		assertEquals(B, refdb.exactRef(HEAD).getObjectId());
+	}
+
+	@Test
+	public void testIsNameConflicting() throws IOException {
+		update("refs/heads/a/b", A);
+		update("refs/heads/q", B);
+
+		// new references cannot replace an existing container
+		assertTrue(refdb.isNameConflicting("refs"));
+		assertTrue(refdb.isNameConflicting("refs/heads"));
+		assertTrue(refdb.isNameConflicting("refs/heads/a"));
+
+		// existing reference is not conflicting
+		assertFalse(refdb.isNameConflicting("refs/heads/a/b"));
+
+		// new references are not conflicting
+		assertFalse(refdb.isNameConflicting("refs/heads/a/d"));
+		assertFalse(refdb.isNameConflicting("refs/heads/master"));
+
+		// existing reference must not be used as a container
+		assertTrue(refdb.isNameConflicting("refs/heads/a/b/c"));
+		assertTrue(refdb.isNameConflicting("refs/heads/q/master"));
+
+		// refs/txn/ names always conflict.
+		assertTrue(refdb.isNameConflicting(refdb.getTxnCommitted()));
+		assertTrue(refdb.isNameConflicting("refs/txn/foo"));
+	}
+
+	@Test
+	public void testUpdate_RefusesRefsTxnNamespace() throws IOException {
+		ObjectId txnId = getTxnCommitted();
+
+		RefUpdate u = refdb.newUpdate("refs/txn/tmp", false);
+		u.setNewObjectId(B);
+		assertEquals(RefUpdate.Result.LOCK_FAILURE, u.update());
+		assertEquals(txnId, getTxnCommitted());
+
+		ReceiveCommand cmd = command(null, B, "refs/txn/tmp");
+		BatchRefUpdate batch = refdb.newBatchUpdate();
+		batch.addCommand(cmd);
+		batch.execute(new RevWalk(repo), NullProgressMonitor.INSTANCE);
+
+		assertEquals(REJECTED_OTHER_REASON, cmd.getResult());
+		assertEquals(MessageFormat.format(JGitText.get().invalidRefName,
+				"refs/txn/tmp"), cmd.getMessage());
+		assertEquals(txnId, getTxnCommitted());
+	}
+
+	@Test
+	public void testUpdate_RefusesDotLockInRefName() throws IOException {
+		ObjectId txnId = getTxnCommitted();
+
+		RefUpdate u = refdb.newUpdate("refs/heads/pu.lock", false);
+		u.setNewObjectId(B);
+		assertEquals(RefUpdate.Result.REJECTED, u.update());
+		assertEquals(txnId, getTxnCommitted());
+
+		ReceiveCommand cmd = command(null, B, "refs/heads/pu.lock");
+		BatchRefUpdate batch = refdb.newBatchUpdate();
+		batch.addCommand(cmd);
+		batch.execute(new RevWalk(repo), NullProgressMonitor.INSTANCE);
+
+		assertEquals(REJECTED_OTHER_REASON, cmd.getResult());
+		assertEquals(JGitText.get().funnyRefname, cmd.getMessage());
+		assertEquals(txnId, getTxnCommitted());
+	}
+
+	@Test
+	public void testBatchRefUpdate_NonFastForwardAborts() throws IOException {
+		update("refs/heads/master", A);
+		update("refs/heads/masters", B);
+		ObjectId txnId = getTxnCommitted();
+
+		List<ReceiveCommand> commands = Arrays.asList(
+				command(A, B, "refs/heads/master"),
+				command(B, A, "refs/heads/masters"));
+		BatchRefUpdate batchUpdate = refdb.newBatchUpdate();
+		batchUpdate.addCommand(commands);
+		batchUpdate.execute(new RevWalk(repo), NullProgressMonitor.INSTANCE);
+		assertEquals(txnId, getTxnCommitted());
+
+		assertEquals(REJECTED_NONFASTFORWARD,
+				commands.get(1).getResult());
+		assertEquals(REJECTED_OTHER_REASON,
+				commands.get(0).getResult());
+		assertEquals(JGitText.get().transactionAborted,
+				commands.get(0).getMessage());
+	}
+
+	@Test
+	public void testBatchRefUpdate_ForceUpdate() throws IOException {
+		update("refs/heads/master", A);
+		update("refs/heads/masters", B);
+		ObjectId txnId = getTxnCommitted();
+
+		List<ReceiveCommand> commands = Arrays.asList(
+				command(A, B, "refs/heads/master"),
+				command(B, A, "refs/heads/masters"));
+		BatchRefUpdate batchUpdate = refdb.newBatchUpdate();
+		batchUpdate.setAllowNonFastForwards(true);
+		batchUpdate.addCommand(commands);
+		batchUpdate.execute(new RevWalk(repo), NullProgressMonitor.INSTANCE);
+		assertNotEquals(txnId, getTxnCommitted());
+
+		Map<String, Ref> refs = refdb.getRefs(ALL);
+		assertEquals(OK, commands.get(0).getResult());
+		assertEquals(OK, commands.get(1).getResult());
+		assertEquals(
+				"[refs/heads/master, refs/heads/masters]",
+				refs.keySet().toString());
+		assertEquals(B.getId(), refs.get("refs/heads/master").getObjectId());
+		assertEquals(A.getId(), refs.get("refs/heads/masters").getObjectId());
+	}
+
+	@Test
+	public void testBatchRefUpdate_NonFastForwardDoesNotDoExpensiveMergeCheck()
+			throws IOException {
+		update("refs/heads/master", B);
+		ObjectId txnId = getTxnCommitted();
+
+		List<ReceiveCommand> commands = Arrays.asList(
+				command(B, A, "refs/heads/master"));
+		BatchRefUpdate batchUpdate = refdb.newBatchUpdate();
+		batchUpdate.setAllowNonFastForwards(true);
+		batchUpdate.addCommand(commands);
+		batchUpdate.execute(new RevWalk(repo) {
+			@Override
+			public boolean isMergedInto(RevCommit base, RevCommit tip) {
+				fail("isMergedInto() should not be called");
+				return false;
+			}
+		}, NullProgressMonitor.INSTANCE);
+		assertNotEquals(txnId, getTxnCommitted());
+
+		Map<String, Ref> refs = refdb.getRefs(ALL);
+		assertEquals(OK, commands.get(0).getResult());
+		assertEquals(A.getId(), refs.get("refs/heads/master").getObjectId());
+	}
+
+	@Test
+	public void testBatchRefUpdate_ConflictCausesAbort() throws IOException {
+		update("refs/heads/master", A);
+		update("refs/heads/masters", B);
+		ObjectId txnId = getTxnCommitted();
+
+		List<ReceiveCommand> commands = Arrays.asList(
+				command(A, B, "refs/heads/master"),
+				command(null, A, "refs/heads/master/x"),
+				command(null, A, "refs/heads"));
+		BatchRefUpdate batchUpdate = refdb.newBatchUpdate();
+		batchUpdate.setAllowNonFastForwards(true);
+		batchUpdate.addCommand(commands);
+		batchUpdate.execute(new RevWalk(repo), NullProgressMonitor.INSTANCE);
+		assertEquals(txnId, getTxnCommitted());
+
+		assertEquals(LOCK_FAILURE, commands.get(0).getResult());
+
+		assertEquals(REJECTED_OTHER_REASON, commands.get(1).getResult());
+		assertEquals(JGitText.get().transactionAborted,
+				commands.get(1).getMessage());
+
+		assertEquals(REJECTED_OTHER_REASON, commands.get(2).getResult());
+		assertEquals(JGitText.get().transactionAborted,
+				commands.get(2).getMessage());
+	}
+
+	@Test
+	public void testBatchRefUpdate_NoConflictIfDeleted() throws IOException {
+		update("refs/heads/master", A);
+		update("refs/heads/masters", B);
+		ObjectId txnId = getTxnCommitted();
+
+		List<ReceiveCommand> commands = Arrays.asList(
+				command(A, B, "refs/heads/master"),
+				command(null, A, "refs/heads/masters/x"),
+				command(B, null, "refs/heads/masters"));
+		BatchRefUpdate batchUpdate = refdb.newBatchUpdate();
+		batchUpdate.setAllowNonFastForwards(true);
+		batchUpdate.addCommand(commands);
+		batchUpdate.execute(new RevWalk(repo), NullProgressMonitor.INSTANCE);
+		assertNotEquals(txnId, getTxnCommitted());
+
+		assertEquals(OK, commands.get(0).getResult());
+		assertEquals(OK, commands.get(1).getResult());
+		assertEquals(OK, commands.get(2).getResult());
+
+		Map<String, Ref> refs = refdb.getRefs(ALL);
+		assertEquals(
+				"[refs/heads/master, refs/heads/masters/x]",
+				refs.keySet().toString());
+		assertEquals(A.getId(), refs.get("refs/heads/masters/x").getObjectId());
+	}
+
+	private ObjectId getTxnCommitted() throws IOException {
+		Ref r = bootstrap.exactRef(refdb.getTxnCommitted());
+		if (r != null && r.getObjectId() != null) {
+			return r.getObjectId();
+		}
+		return ObjectId.zeroId();
+	}
+
+	private static ReceiveCommand command(AnyObjectId a, AnyObjectId b,
+			String name) {
+		return new ReceiveCommand(
+				a != null ? a.copy() : ObjectId.zeroId(),
+				b != null ? b.copy() : ObjectId.zeroId(),
+				name);
+	}
+
+	private void symref(final String name, final String dst)
+			throws IOException {
+		commit(new Function() {
+			@Override
+			public boolean apply(ObjectReader reader, RefTree tree)
+					throws IOException {
+				Ref old = tree.exactRef(reader, name);
+				Command n = new Command(
+					old,
+					new SymbolicRef(
+						name,
+						new ObjectIdRef.Unpeeled(Ref.Storage.NEW, dst, null)));
+				return tree.apply(Collections.singleton(n));
+			}
+		});
+	}
+
+	private void update(final String name, final ObjectId id)
+			throws IOException {
+		commit(new Function() {
+			@Override
+			public boolean apply(ObjectReader reader, RefTree tree)
+					throws IOException {
+				Ref old = tree.exactRef(reader, name);
+				Command n;
+				try (RevWalk rw = new RevWalk(repo)) {
+					n = new Command(old, Command.toRef(rw, id, name, true));
+				}
+				return tree.apply(Collections.singleton(n));
+			}
+		});
+	}
+
+	interface Function {
+		boolean apply(ObjectReader reader, RefTree tree) throws IOException;
+	}
+
+	private void commit(Function fun) throws IOException {
+		try (ObjectReader reader = repo.newObjectReader();
+				ObjectInserter inserter = repo.newObjectInserter();
+				RevWalk rw = new RevWalk(reader)) {
+			RefUpdate u = bootstrap.newUpdate(refdb.getTxnCommitted(), false);
+			CommitBuilder cb = new CommitBuilder();
+			testRepo.setAuthorAndCommitter(cb);
+
+			Ref ref = bootstrap.exactRef(refdb.getTxnCommitted());
+			RefTree tree;
+			if (ref != null && ref.getObjectId() != null) {
+				tree = RefTree.read(reader, rw.parseTree(ref.getObjectId()));
+				cb.setParentId(ref.getObjectId());
+				u.setExpectedOldObjectId(ref.getObjectId());
+			} else {
+				tree = RefTree.newEmptyTree();
+				u.setExpectedOldObjectId(ObjectId.zeroId());
+			}
+
+			assertTrue(fun.apply(reader, tree));
+			cb.setTreeId(tree.writeTree(inserter));
+			u.setNewObjectId(inserter.insert(cb));
+			inserter.flush();
+			switch (u.update(rw)) {
+			case NEW:
+			case FAST_FORWARD:
+				break;
+			default:
+				fail("Expected " + u.getName() + " to update");
+			}
+		}
+	}
+
+	private class InMemRefTreeRepo extends InMemoryRepository {
+		private final RefTreeDatabase refs;
+
+		InMemRefTreeRepo(DfsRepositoryDescription repoDesc) {
+			super(repoDesc);
+			refs = new RefTreeDatabase(this, super.getRefDatabase(),
+					"refs/txn/committed");
+			RefTreeDatabaseTest.this.refdb = refs;
+		}
+
+		public RefDatabase getRefDatabase() {
+			return refs;
+		}
+	}
+}

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/RefTreeTest.java

@@ -0,0 +1,303 @@
+/*
+ * Copyright (C) 2016, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.internal.storage.reftree;
+
+import static org.eclipse.jgit.lib.Constants.HEAD;
+import static org.eclipse.jgit.lib.Constants.R_HEADS;
+import static org.eclipse.jgit.lib.Constants.R_TAGS;
+import static org.eclipse.jgit.lib.Ref.Storage.LOOSE;
+import static org.eclipse.jgit.lib.Ref.Storage.NEW;
+import static org.eclipse.jgit.transport.ReceiveCommand.Result.LOCK_FAILURE;
+import static org.eclipse.jgit.transport.ReceiveCommand.Result.NOT_ATTEMPTED;
+import static org.eclipse.jgit.transport.ReceiveCommand.Result.REJECTED_OTHER_REASON;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertTrue;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collections;
+
+import org.eclipse.jgit.errors.MissingObjectException;
+import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.internal.storage.dfs.DfsRepositoryDescription;
+import org.eclipse.jgit.internal.storage.dfs.InMemoryRepository;
+import org.eclipse.jgit.junit.TestRepository;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectIdRef;
+import org.eclipse.jgit.lib.ObjectInserter;
+import org.eclipse.jgit.lib.ObjectReader;
+import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.SymbolicRef;
+import org.eclipse.jgit.revwalk.RevBlob;
+import org.eclipse.jgit.revwalk.RevTag;
+import org.eclipse.jgit.revwalk.RevWalk;
+import org.eclipse.jgit.transport.ReceiveCommand;
+import org.junit.Before;
+import org.junit.Test;
+
+public class RefTreeTest {
+	private static final String R_MASTER = R_HEADS + "master";
+	private InMemoryRepository repo;
+	private TestRepository<InMemoryRepository> git;
+
+	@Before
+	public void setUp() throws IOException {
+		repo = new InMemoryRepository(new DfsRepositoryDescription("RefTree"));
+		git = new TestRepository<>(repo);
+	}
+
+	@Test
+	public void testEmptyTree() throws IOException {
+		RefTree tree = RefTree.newEmptyTree();
+		try (ObjectReader reader = repo.newObjectReader()) {
+			assertNull(HEAD, tree.exactRef(reader, HEAD));
+			assertNull("master", tree.exactRef(reader, R_MASTER));
+		}
+	}
+
+	@Test
+	public void testApplyThenReadMaster() throws Exception {
+		RefTree tree = RefTree.newEmptyTree();
+		RevBlob id = git.blob("A");
+		Command cmd = new Command(null, ref(R_MASTER, id));
+		assertTrue(tree.apply(Collections.singletonList(cmd)));
+		assertSame(NOT_ATTEMPTED, cmd.getResult());
+
+		try (ObjectReader reader = repo.newObjectReader()) {
+			Ref m = tree.exactRef(reader, R_MASTER);
+			assertNotNull(R_MASTER, m);
+			assertEquals(R_MASTER, m.getName());
+			assertEquals(id, m.getObjectId());
+			assertTrue("peeled", m.isPeeled());
+		}
+	}
+
+	@Test
+	public void testUpdateMaster() throws Exception {
+		RefTree tree = RefTree.newEmptyTree();
+		RevBlob id1 = git.blob("A");
+		Command cmd1 = new Command(null, ref(R_MASTER, id1));
+		assertTrue(tree.apply(Collections.singletonList(cmd1)));
+		assertSame(NOT_ATTEMPTED, cmd1.getResult());
+
+		RevBlob id2 = git.blob("B");
+		Command cmd2 = new Command(ref(R_MASTER, id1), ref(R_MASTER, id2));
+		assertTrue(tree.apply(Collections.singletonList(cmd2)));
+		assertSame(NOT_ATTEMPTED, cmd2.getResult());
+
+		try (ObjectReader reader = repo.newObjectReader()) {
+			Ref m = tree.exactRef(reader, R_MASTER);
+			assertNotNull(R_MASTER, m);
+			assertEquals(R_MASTER, m.getName());
+			assertEquals(id2, m.getObjectId());
+			assertTrue("peeled", m.isPeeled());
+		}
+	}
+
+	@Test
+	public void testHeadSymref() throws Exception {
+		RefTree tree = RefTree.newEmptyTree();
+		RevBlob id = git.blob("A");
+		Command cmd1 = new Command(null, ref(R_MASTER, id));
+		Command cmd2 = new Command(null, symref(HEAD, R_MASTER));
+		assertTrue(tree.apply(Arrays.asList(new Command[] { cmd1, cmd2 })));
+		assertSame(NOT_ATTEMPTED, cmd1.getResult());
+		assertSame(NOT_ATTEMPTED, cmd2.getResult());
+
+		try (ObjectReader reader = repo.newObjectReader()) {
+			Ref m = tree.exactRef(reader, HEAD);
+			assertNotNull(HEAD, m);
+			assertEquals(HEAD, m.getName());
+			assertTrue("symbolic", m.isSymbolic());
+			assertNotNull(m.getTarget());
+			assertEquals(R_MASTER, m.getTarget().getName());
+			assertEquals(id, m.getTarget().getObjectId());
+		}
+
+		// Writing flushes some buffers, re-read from blob.
+		ObjectId newId = write(tree);
+		try (ObjectReader reader = repo.newObjectReader();
+				RevWalk rw = new RevWalk(reader)) {
+			tree = RefTree.read(reader, rw.parseTree(newId));
+			Ref m = tree.exactRef(reader, HEAD);
+			assertEquals(R_MASTER, m.getTarget().getName());
+		}
+	}
+
+	@Test
+	public void testTagIsPeeled() throws Exception {
+		String name = "v1.0";
+		RefTree tree = RefTree.newEmptyTree();
+		RevBlob id = git.blob("A");
+		RevTag tag = git.tag(name, id);
+
+		String ref = R_TAGS + name;
+		Command cmd = create(ref, tag);
+		assertTrue(tree.apply(Collections.singletonList(cmd)));
+		assertSame(NOT_ATTEMPTED, cmd.getResult());
+
+		try (ObjectReader reader = repo.newObjectReader()) {
+			Ref m = tree.exactRef(reader, ref);
+			assertNotNull(ref, m);
+			assertEquals(ref, m.getName());
+			assertEquals(tag, m.getObjectId());
+			assertTrue("peeled", m.isPeeled());
+			assertEquals(id, m.getPeeledObjectId());
+		}
+	}
+
+	@Test
+	public void testApplyAlreadyExists() throws Exception {
+		RefTree tree = RefTree.newEmptyTree();
+		RevBlob a = git.blob("A");
+		Command cmd = new Command(null, ref(R_MASTER, a));
+		assertTrue(tree.apply(Collections.singletonList(cmd)));
+		ObjectId treeId = write(tree);
+
+		RevBlob b = git.blob("B");
+		Command cmd1 = create(R_MASTER, b);
+		Command cmd2 = create(R_MASTER, b);
+		assertFalse(tree.apply(Arrays.asList(new Command[] { cmd1, cmd2 })));
+		assertSame(LOCK_FAILURE, cmd1.getResult());
+		assertSame(REJECTED_OTHER_REASON, cmd2.getResult());
+		assertEquals(JGitText.get().transactionAborted, cmd2.getMessage());
+		assertEquals(treeId, write(tree));
+	}
+
+	@Test
+	public void testApplyWrongOldId() throws Exception {
+		RefTree tree = RefTree.newEmptyTree();
+		RevBlob a = git.blob("A");
+		Command cmd = new Command(null, ref(R_MASTER, a));
+		assertTrue(tree.apply(Collections.singletonList(cmd)));
+		ObjectId treeId = write(tree);
+
+		RevBlob b = git.blob("B");
+		RevBlob c = git.blob("C");
+		Command cmd1 = update(R_MASTER, b, c);
+		Command cmd2 = create(R_MASTER, b);
+		assertFalse(tree.apply(Arrays.asList(new Command[] { cmd1, cmd2 })));
+		assertSame(LOCK_FAILURE, cmd1.getResult());
+		assertSame(REJECTED_OTHER_REASON, cmd2.getResult());
+		assertEquals(JGitText.get().transactionAborted, cmd2.getMessage());
+		assertEquals(treeId, write(tree));
+	}
+
+	@Test
+	public void testApplyWrongOldIdButAlreadyCurrentIsNoOp() throws Exception {
+		RefTree tree = RefTree.newEmptyTree();
+		RevBlob a = git.blob("A");
+		Command cmd = new Command(null, ref(R_MASTER, a));
+		assertTrue(tree.apply(Collections.singletonList(cmd)));
+		ObjectId treeId = write(tree);
+
+		RevBlob b = git.blob("B");
+		cmd = update(R_MASTER, b, a);
+		assertTrue(tree.apply(Collections.singletonList(cmd)));
+		assertEquals(treeId, write(tree));
+	}
+
+	@Test
+	public void testApplyCannotCreateSubdirectory() throws Exception {
+		RefTree tree = RefTree.newEmptyTree();
+		RevBlob a = git.blob("A");
+		Command cmd = new Command(null, ref(R_MASTER, a));
+		assertTrue(tree.apply(Collections.singletonList(cmd)));
+		ObjectId treeId = write(tree);
+
+		RevBlob b = git.blob("B");
+		Command cmd1 = create(R_MASTER + "/fail", b);
+		assertFalse(tree.apply(Collections.singletonList(cmd1)));
+		assertSame(LOCK_FAILURE, cmd1.getResult());
+		assertEquals(treeId, write(tree));
+	}
+
+	@Test
+	public void testApplyCannotCreateParentRef() throws Exception {
+		RefTree tree = RefTree.newEmptyTree();
+		RevBlob a = git.blob("A");
+		Command cmd = new Command(null, ref(R_MASTER, a));
+		assertTrue(tree.apply(Collections.singletonList(cmd)));
+		ObjectId treeId = write(tree);
+
+		RevBlob b = git.blob("B");
+		Command cmd1 = create("refs/heads", b);
+		assertFalse(tree.apply(Collections.singletonList(cmd1)));
+		assertSame(LOCK_FAILURE, cmd1.getResult());
+		assertEquals(treeId, write(tree));
+	}
+
+	private static Ref ref(String name, ObjectId id) {
+		return new ObjectIdRef.PeeledNonTag(LOOSE, name, id);
+	}
+
+	private static Ref symref(String name, String dest) {
+		Ref d = new ObjectIdRef.PeeledNonTag(NEW, dest, null);
+		return new SymbolicRef(name, d);
+	}
+
+	private Command create(String name, ObjectId id)
+			throws MissingObjectException, IOException {
+		return update(name, ObjectId.zeroId(), id);
+	}
+
+	private Command update(String name, ObjectId oldId, ObjectId newId)
+			throws MissingObjectException, IOException {
+		try (RevWalk rw = new RevWalk(repo)) {
+			return new Command(rw, new ReceiveCommand(oldId, newId, name));
+		}
+	}
+
+	private ObjectId write(RefTree tree) throws IOException {
+		try (ObjectInserter ins = repo.newObjectInserter()) {
+			ObjectId id = tree.writeTree(ins);
+			ins.flush();
+			return id;
+		}
+	}
+}

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

@@ -1084,7 +1084,7 @@ public class DirCacheCheckoutTest extends RepositoryTestCase {
 		assertWorkDir(mkmap(linkName, "a", fname, "a"));
 
 		Status st = git.status().call();
-		assertFalse(st.isClean());
+		assertTrue(st.isClean());
 	}
 
 	@Test
@@ -1213,9 +1213,7 @@ public class DirCacheCheckoutTest extends RepositoryTestCase {
 		assertWorkDir(mkmap(fname, "a"));
 
 		Status st = git.status().call();
-		assertFalse(st.isClean());
-		assertEquals(1, st.getAdded().size());
-		assertTrue(st.getAdded().contains(fname + "/dir/file1"));
+		assertTrue(st.isClean());
 	}
 
 	@Test

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

@@ -99,8 +99,7 @@ public class IndexDiffTest extends RepositoryTestCase {
 	public void testAdded() throws IOException {
 		writeTrashFile("file1", "file1");
 		writeTrashFile("dir/subfile", "dir/subfile");
-		Tree tree = new Tree(db);
-		tree.setId(insertTree(tree));
+		ObjectId tree = insertTree(new TreeFormatter());
 
 		DirCache index = db.lockDirCache();
 		DirCacheEditor editor = index.editor();
@@ -108,7 +107,7 @@ public class IndexDiffTest extends RepositoryTestCase {
 		editor.add(add(db, trash, "dir/subfile"));
 		editor.commit();
 		FileTreeIterator iterator = new FileTreeIterator(db);
-		IndexDiff diff = new IndexDiff(db, tree.getId(), iterator);
+		IndexDiff diff = new IndexDiff(db, tree, iterator);
 		diff.diff();
 		assertEquals(2, diff.getAdded().size());
 		assertTrue(diff.getAdded().contains("file1"));
@@ -124,18 +123,16 @@ public class IndexDiffTest extends RepositoryTestCase {
 		writeTrashFile("file2", "file2");
 		writeTrashFile("dir/file3", "dir/file3");
 
-		Tree tree = new Tree(db);
-		tree.addFile("file2");
-		tree.addFile("dir/file3");
-		assertEquals(2, tree.memberCount());
-		tree.findBlobMember("file2").setId(ObjectId.fromString("30d67d4672d5c05833b7192cc77a79eaafb5c7ad"));
-		Tree tree2 = (Tree) tree.findTreeMember("dir");
-		tree2.findBlobMember("file3").setId(ObjectId.fromString("873fb8d667d05436d728c52b1d7a09528e6eb59b"));
-		tree2.setId(insertTree(tree2));
-		tree.setId(insertTree(tree));
+		TreeFormatter dir = new TreeFormatter();
+		dir.append("file3", FileMode.REGULAR_FILE, ObjectId.fromString("873fb8d667d05436d728c52b1d7a09528e6eb59b"));
+
+		TreeFormatter tree = new TreeFormatter();
+		tree.append("file2", FileMode.REGULAR_FILE, ObjectId.fromString("30d67d4672d5c05833b7192cc77a79eaafb5c7ad"));
+		tree.append("dir", FileMode.TREE, insertTree(dir));
+		ObjectId treeId = insertTree(tree);
 
 		FileTreeIterator iterator = new FileTreeIterator(db);
-		IndexDiff diff = new IndexDiff(db, tree.getId(), iterator);
+		IndexDiff diff = new IndexDiff(db, treeId, iterator);
 		diff.diff();
 		assertEquals(2, diff.getRemoved().size());
 		assertTrue(diff.getRemoved().contains("file2"));
@@ -157,16 +154,16 @@ public class IndexDiffTest extends RepositoryTestCase {
 
 		writeTrashFile("dir/file3", "changed");
 
-		Tree tree = new Tree(db);
-		tree.addFile("file2").setId(ObjectId.fromString("0123456789012345678901234567890123456789"));
-		tree.addFile("dir/file3").setId(ObjectId.fromString("0123456789012345678901234567890123456789"));
-		assertEquals(2, tree.memberCount());
+		TreeFormatter dir = new TreeFormatter();
+		dir.append("file3", FileMode.REGULAR_FILE, ObjectId.fromString("0123456789012345678901234567890123456789"));
+
+		TreeFormatter tree = new TreeFormatter();
+		tree.append("dir", FileMode.TREE, insertTree(dir));
+		tree.append("file2", FileMode.REGULAR_FILE, ObjectId.fromString("0123456789012345678901234567890123456789"));
+		ObjectId treeId = insertTree(tree);
 
-		Tree tree2 = (Tree) tree.findTreeMember("dir");
-		tree2.setId(insertTree(tree2));
-		tree.setId(insertTree(tree));
 		FileTreeIterator iterator = new FileTreeIterator(db);
-		IndexDiff diff = new IndexDiff(db, tree.getId(), iterator);
+		IndexDiff diff = new IndexDiff(db, treeId, iterator);
 		diff.diff();
 		assertEquals(2, diff.getChanged().size());
 		assertTrue(diff.getChanged().contains("file2"));
@@ -314,17 +311,16 @@ public class IndexDiffTest extends RepositoryTestCase {
 		git.add().addFilepattern("a=c").call();
 		git.add().addFilepattern("a=d").call();
 
-		Tree tree = new Tree(db);
+		TreeFormatter tree = new TreeFormatter();
 		// got the hash id'd from the data using echo -n a.b|git hash-object -t blob --stdin
-		tree.addFile("a.b").setId(ObjectId.fromString("f6f28df96c2b40c951164286e08be7c38ec74851"));
-		tree.addFile("a.c").setId(ObjectId.fromString("6bc0e647512d2a0bef4f26111e484dc87df7f5ca"));
-		tree.addFile("a=c").setId(ObjectId.fromString("06022365ddbd7fb126761319633bf73517770714"));
-		tree.addFile("a=d").setId(ObjectId.fromString("fa6414df3da87840700e9eeb7fc261dd77ccd5c2"));
-
-		tree.setId(insertTree(tree));
+		tree.append("a.b", FileMode.REGULAR_FILE, ObjectId.fromString("f6f28df96c2b40c951164286e08be7c38ec74851"));
+		tree.append("a.c", FileMode.REGULAR_FILE, ObjectId.fromString("6bc0e647512d2a0bef4f26111e484dc87df7f5ca"));
+		tree.append("a=c", FileMode.REGULAR_FILE, ObjectId.fromString("06022365ddbd7fb126761319633bf73517770714"));
+		tree.append("a=d", FileMode.REGULAR_FILE, ObjectId.fromString("fa6414df3da87840700e9eeb7fc261dd77ccd5c2"));
+		ObjectId treeId = insertTree(tree);
 
 		FileTreeIterator iterator = new FileTreeIterator(db);
-		IndexDiff diff = new IndexDiff(db, tree.getId(), iterator);
+		IndexDiff diff = new IndexDiff(db, treeId, iterator);
 		diff.diff();
 		assertEquals(0, diff.getChanged().size());
 		assertEquals(0, diff.getAdded().size());
@@ -356,24 +352,27 @@ public class IndexDiffTest extends RepositoryTestCase {
 				.addFilepattern("a/c").addFilepattern("a=c")
 				.addFilepattern("a=d").call();
 
-		Tree tree = new Tree(db);
+
 		// got the hash id'd from the data using echo -n a.b|git hash-object -t blob --stdin
-		tree.addFile("a.b").setId(ObjectId.fromString("f6f28df96c2b40c951164286e08be7c38ec74851"));
-		tree.addFile("a.c").setId(ObjectId.fromString("6bc0e647512d2a0bef4f26111e484dc87df7f5ca"));
-		tree.addFile("a/b.b/b").setId(ObjectId.fromString("8d840bd4e2f3a48ff417c8e927d94996849933fd"));
-		tree.addFile("a/b").setId(ObjectId.fromString("db89c972fc57862eae378f45b74aca228037d415"));
-		tree.addFile("a/c").setId(ObjectId.fromString("52ad142a008aeb39694bafff8e8f1be75ed7f007"));
-		tree.addFile("a=c").setId(ObjectId.fromString("06022365ddbd7fb126761319633bf73517770714"));
-		tree.addFile("a=d").setId(ObjectId.fromString("fa6414df3da87840700e9eeb7fc261dd77ccd5c2"));
-
-		Tree tree3 = (Tree) tree.findTreeMember("a/b.b");
-		tree3.setId(insertTree(tree3));
-		Tree tree2 = (Tree) tree.findTreeMember("a");
-		tree2.setId(insertTree(tree2));
-		tree.setId(insertTree(tree));
+		TreeFormatter bb = new TreeFormatter();
+		bb.append("b", FileMode.REGULAR_FILE, ObjectId.fromString("8d840bd4e2f3a48ff417c8e927d94996849933fd"));
+
+		TreeFormatter a = new TreeFormatter();
+		a.append("b", FileMode.REGULAR_FILE, ObjectId
+				.fromString("db89c972fc57862eae378f45b74aca228037d415"));
+		a.append("b.b", FileMode.TREE, insertTree(bb));
+		a.append("c", FileMode.REGULAR_FILE, ObjectId.fromString("52ad142a008aeb39694bafff8e8f1be75ed7f007"));
+
+		TreeFormatter tree = new TreeFormatter();
+		tree.append("a.b", FileMode.REGULAR_FILE, ObjectId.fromString("f6f28df96c2b40c951164286e08be7c38ec74851"));
+		tree.append("a.c", FileMode.REGULAR_FILE, ObjectId.fromString("6bc0e647512d2a0bef4f26111e484dc87df7f5ca"));
+		tree.append("a", FileMode.TREE, insertTree(a));
+		tree.append("a=c", FileMode.REGULAR_FILE, ObjectId.fromString("06022365ddbd7fb126761319633bf73517770714"));
+		tree.append("a=d", FileMode.REGULAR_FILE, ObjectId.fromString("fa6414df3da87840700e9eeb7fc261dd77ccd5c2"));
+		ObjectId treeId = insertTree(tree);
 
 		FileTreeIterator iterator = new FileTreeIterator(db);
-		IndexDiff diff = new IndexDiff(db, tree.getId(), iterator);
+		IndexDiff diff = new IndexDiff(db, treeId, iterator);
 		diff.diff();
 		assertEquals(0, diff.getChanged().size());
 		assertEquals(0, diff.getAdded().size());
@@ -383,9 +382,9 @@ public class IndexDiffTest extends RepositoryTestCase {
 		assertEquals(Collections.EMPTY_SET, diff.getUntrackedFolders());
 	}
 
-	private ObjectId insertTree(Tree tree) throws IOException {
+	private ObjectId insertTree(TreeFormatter tree) throws IOException {
 		try (ObjectInserter oi = db.newObjectInserter()) {
-			ObjectId id = oi.insert(Constants.OBJ_TREE, tree.format());
+			ObjectId id = oi.insert(tree);
 			oi.flush();
 			return id;
 		}

org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/T0002_TreeTest.java

@@ -1,319 +0,0 @@
-/*
- * Copyright (C) 2008, Robin Rosenberg <robin.rosenberg@dewire.com>
- * Copyright (C) 2006-2008, Shawn O. Pearce <spearce@spearce.org>
- * and other copyright owners as documented in the project's IP log.
- *
- * This program and the accompanying materials are made available
- * under the terms of the Eclipse Distribution License v1.0 which
- * accompanies this distribution, is reproduced below, and is
- * available at http://www.eclipse.org/org/documents/edl-v10.php
- *
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or
- * without modification, are permitted provided that the following
- * conditions are met:
- *
- * - Redistributions of source code must retain the above copyright
- *   notice, this list of conditions and the following disclaimer.
- *
- * - Redistributions in binary form must reproduce the above
- *   copyright notice, this list of conditions and the following
- *   disclaimer in the documentation and/or other materials provided
- *   with the distribution.
- *
- * - Neither the name of the Eclipse Foundation, Inc. nor the
- *   names of its contributors may be used to endorse or promote
- *   products derived from this software without specific prior
- *   written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
- * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
- * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
- * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
- * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
- * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
- * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-package org.eclipse.jgit.lib;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
-
-import java.io.IOException;
-import java.io.UnsupportedEncodingException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.eclipse.jgit.test.resources.SampleDataRepositoryTestCase;
-import org.junit.Test;
-
-@SuppressWarnings("deprecation")
-public class T0002_TreeTest extends SampleDataRepositoryTestCase {
-	private static final ObjectId SOME_FAKE_ID = ObjectId.fromString(
-			"0123456789abcdef0123456789abcdef01234567");
-
-	private static int compareNamesUsingSpecialCompare(String a, String b)
-			throws UnsupportedEncodingException {
-		char lasta = '\0';
-		byte[] abytes;
-		if (a.length() > 0 && a.charAt(a.length()-1) == '/') {
-			lasta = '/';
-			a = a.substring(0, a.length() - 1);
-		}
-		abytes = a.getBytes("ISO-8859-1");
-		char lastb = '\0';
-		byte[] bbytes;
-		if (b.length() > 0 && b.charAt(b.length()-1) == '/') {
-			lastb = '/';
-			b = b.substring(0, b.length() - 1);
-		}
-		bbytes = b.getBytes("ISO-8859-1");
-		return Tree.compareNames(abytes, bbytes, lasta, lastb);
-	}
-
-	@Test
-	public void test000_sort_01() throws UnsupportedEncodingException {
-		assertEquals(0, compareNamesUsingSpecialCompare("a","a"));
-	}
-
-	@Test
-	public void test000_sort_02() throws UnsupportedEncodingException {
-		assertEquals(-1, compareNamesUsingSpecialCompare("a","b"));
-		assertEquals(1, compareNamesUsingSpecialCompare("b","a"));
-	}
-
-	@Test
-	public void test000_sort_03() throws UnsupportedEncodingException {
-		assertEquals(1, compareNamesUsingSpecialCompare("a:","a"));
-		assertEquals(1, compareNamesUsingSpecialCompare("a/","a"));
-		assertEquals(-1, compareNamesUsingSpecialCompare("a","a/"));
-		assertEquals(-1, compareNamesUsingSpecialCompare("a","a:"));
-		assertEquals(1, compareNamesUsingSpecialCompare("a:","a/"));
-		assertEquals(-1, compareNamesUsingSpecialCompare("a/","a:"));
-	}
-
-	@Test
-	public void test000_sort_04() throws UnsupportedEncodingException {
-		assertEquals(-1, compareNamesUsingSpecialCompare("a.a","a/a"));
-		assertEquals(1, compareNamesUsingSpecialCompare("a/a","a.a"));
-	}
-
-	@Test
-	public void test000_sort_05() throws UnsupportedEncodingException {
-		assertEquals(-1, compareNamesUsingSpecialCompare("a.","a/"));
-		assertEquals(1, compareNamesUsingSpecialCompare("a/","a."));
-
-	}
-
-	@Test
-	public void test001_createEmpty() throws IOException {
-		final Tree t = new Tree(db);
-		assertTrue("isLoaded", t.isLoaded());
-		assertTrue("isModified", t.isModified());
-		assertTrue("no parent", t.getParent() == null);
-		assertTrue("isRoot", t.isRoot());
-		assertTrue("no name", t.getName() == null);
-		assertTrue("no nameUTF8", t.getNameUTF8() == null);
-		assertTrue("has entries array", t.members() != null);
-		assertEquals("entries is empty", 0, t.members().length);
-		assertEquals("full name is empty", "", t.getFullName());
-		assertTrue("no id", t.getId() == null);
-		assertTrue("database is r", t.getRepository() == db);
-		assertTrue("no foo child", t.findTreeMember("foo") == null);
-		assertTrue("no foo child", t.findBlobMember("foo") == null);
-	}
-
-	@Test
-	public void test002_addFile() throws IOException {
-		final Tree t = new Tree(db);
-		t.setId(SOME_FAKE_ID);
-		assertTrue("has id", t.getId() != null);
-		assertFalse("not modified", t.isModified());
-
-		final String n = "bob";
-		final FileTreeEntry f = t.addFile(n);
-		assertNotNull("have file", f);
-		assertEquals("name matches", n, f.getName());
-		assertEquals("name matches", f.getName(), new String(f.getNameUTF8(),
-				"UTF-8"));
-		assertEquals("full name matches", n, f.getFullName());
-		assertTrue("no id", f.getId() == null);
-		assertTrue("is modified", t.isModified());
-		assertTrue("has no id", t.getId() == null);
-		assertTrue("found bob", t.findBlobMember(f.getName()) == f);
-
-		final TreeEntry[] i = t.members();
-		assertNotNull("members array not null", i);
-		assertTrue("iterator is not empty", i != null && i.length > 0);
-		assertTrue("iterator returns file", i != null && i[0] == f);
-		assertTrue("iterator is empty", i != null && i.length == 1);
-	}
-
-	@Test
-	public void test004_addTree() throws IOException {
-		final Tree t = new Tree(db);
-		t.setId(SOME_FAKE_ID);
-		assertTrue("has id", t.getId() != null);
-		assertFalse("not modified", t.isModified());
-
-		final String n = "bob";
-		final Tree f = t.addTree(n);
-		assertNotNull("have tree", f);
-		assertEquals("name matches", n, f.getName());
-		assertEquals("name matches", f.getName(), new String(f.getNameUTF8(),
-				"UTF-8"));
-		assertEquals("full name matches", n, f.getFullName());
-		assertTrue("no id", f.getId() == null);
-		assertTrue("parent matches", f.getParent() == t);
-		assertTrue("repository matches", f.getRepository() == db);
-		assertTrue("isLoaded", f.isLoaded());
-		assertFalse("has items", f.members().length > 0);
-		assertFalse("is root", f.isRoot());
-		assertTrue("parent is modified", t.isModified());
-		assertTrue("parent has no id", t.getId() == null);
-		assertTrue("found bob child", t.findTreeMember(f.getName()) == f);
-
-		final TreeEntry[] i = t.members();
-		assertTrue("iterator is not empty", i.length > 0);
-		assertTrue("iterator returns file", i[0] == f);
-		assertEquals("iterator is empty", 1, i.length);
-	}
-
-	@Test
-	public void test005_addRecursiveFile() throws IOException {
-		final Tree t = new Tree(db);
-		final FileTreeEntry f = t.addFile("a/b/c");
-		assertNotNull("created f", f);
-		assertEquals("c", f.getName());
-		assertEquals("b", f.getParent().getName());
-		assertEquals("a", f.getParent().getParent().getName());
-		assertTrue("t is great-grandparent", t == f.getParent().getParent()
-				.getParent());
-	}
-
-	@Test
-	public void test005_addRecursiveTree() throws IOException {
-		final Tree t = new Tree(db);
-		final Tree f = t.addTree("a/b/c");
-		assertNotNull("created f", f);
-		assertEquals("c", f.getName());
-		assertEquals("b", f.getParent().getName());
-		assertEquals("a", f.getParent().getParent().getName());
-		assertTrue("t is great-grandparent", t == f.getParent().getParent()
-				.getParent());
-	}
-
-	@Test
-	public void test006_addDeepTree() throws IOException {
-		final Tree t = new Tree(db);
-
-		final Tree e = t.addTree("e");
-		assertNotNull("have e", e);
-		assertTrue("e.parent == t", e.getParent() == t);
-		final Tree f = t.addTree("f");
-		assertNotNull("have f", f);
-		assertTrue("f.parent == t", f.getParent() == t);
-		final Tree g = f.addTree("g");
-		assertNotNull("have g", g);
-		assertTrue("g.parent == f", g.getParent() == f);
-		final Tree h = g.addTree("h");
-		assertNotNull("have h", h);
-		assertTrue("h.parent = g", h.getParent() == g);
-
-		h.setId(SOME_FAKE_ID);
-		assertTrue("h not modified", !h.isModified());
-		g.setId(SOME_FAKE_ID);
-		assertTrue("g not modified", !g.isModified());
-		f.setId(SOME_FAKE_ID);
-		assertTrue("f not modified", !f.isModified());
-		e.setId(SOME_FAKE_ID);
-		assertTrue("e not modified", !e.isModified());
-		t.setId(SOME_FAKE_ID);
-		assertTrue("t not modified.", !t.isModified());
-
-		assertEquals("full path of h ok", "f/g/h", h.getFullName());
-		assertTrue("Can find h", t.findTreeMember(h.getFullName()) == h);
-		assertTrue("Can't find f/z", t.findBlobMember("f/z") == null);
-		assertTrue("Can't find y/z", t.findBlobMember("y/z") == null);
-
-		final FileTreeEntry i = h.addFile("i");
-		assertNotNull(i);
-		assertEquals("full path of i ok", "f/g/h/i", i.getFullName());
-		assertTrue("Can find i", t.findBlobMember(i.getFullName()) == i);
-		assertTrue("h modified", h.isModified());
-		assertTrue("g modified", g.isModified());
-		assertTrue("f modified", f.isModified());
-		assertTrue("e not modified", !e.isModified());
-		assertTrue("t modified", t.isModified());
-
-		assertTrue("h no id", h.getId() == null);
-		assertTrue("g no id", g.getId() == null);
-		assertTrue("f no id", f.getId() == null);
-		assertTrue("e has id", e.getId() != null);
-		assertTrue("t no id", t.getId() == null);
-	}
-
-	@Test
-	public void test007_manyFileLookup() throws IOException {
-		final Tree t = new Tree(db);
-		final List<FileTreeEntry> files = new ArrayList<FileTreeEntry>(26 * 26);
-		for (char level1 = 'a'; level1 <= 'z'; level1++) {
-			for (char level2 = 'a'; level2 <= 'z'; level2++) {
-				final String n = "." + level1 + level2 + "9";
-				final FileTreeEntry f = t.addFile(n);
-				assertNotNull("File " + n + " added.", f);
-				assertEquals(n, f.getName());
-				files.add(f);
-			}
-		}
-		assertEquals(files.size(), t.memberCount());
-		final TreeEntry[] ents = t.members();
-		assertNotNull(ents);
-		assertEquals(files.size(), ents.length);
-		for (int k = 0; k < ents.length; k++) {
-			assertTrue("File " + files.get(k).getName()
-					+ " is at " + k + ".", files.get(k) == ents[k]);
-		}
-	}
-
-	@Test
-	public void test008_SubtreeInternalSorting() throws IOException {
-		final Tree t = new Tree(db);
-		final FileTreeEntry e0 = t.addFile("a-b");
-		final FileTreeEntry e1 = t.addFile("a-");
-		final FileTreeEntry e2 = t.addFile("a=b");
-		final Tree e3 = t.addTree("a");
-		final FileTreeEntry e4 = t.addFile("a=");
-
-		final TreeEntry[] ents = t.members();
-		assertSame(e1, ents[0]);
-		assertSame(e0, ents[1]);
-		assertSame(e3, ents[2]);
-		assertSame(e4, ents[3]);
-		assertSame(e2, ents[4]);
-	}
-
-	@Test
-	public void test009_SymlinkAndGitlink() throws IOException {
-		final Tree symlinkTree = mapTree("symlink");
-		assertTrue("Symlink entry exists", symlinkTree.existsBlob("symlink.txt"));
-		final Tree gitlinkTree = mapTree("gitlink");
-		assertTrue("Gitlink entry exists", gitlinkTree.existsBlob("submodule"));
-	}
-
-	private Tree mapTree(String name) throws IOException {
-		ObjectId id = db.resolve(name + "^{tree}");
-		return new Tree(db, id, db.open(id).getCachedBytes());
-	}
-}

org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/ObjectWalkTest.java

@@ -47,11 +47,10 @@ import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertSame;
 import static org.junit.Assert.assertTrue;
 
-import org.eclipse.jgit.lib.Constants;
-import org.eclipse.jgit.lib.FileTreeEntry;
+import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectInserter;
-import org.eclipse.jgit.lib.Tree;
+import org.eclipse.jgit.lib.TreeFormatter;
 import org.junit.Test;
 
 @SuppressWarnings("deprecation")
@@ -220,28 +219,24 @@ public class ObjectWalkTest extends RevWalkTestCase {
 				.fromString("abbbfafe3129f85747aba7bfac992af77134c607");
 		final RevTree tree_root, tree_A, tree_AB;
 		final RevCommit b;
-		{
-			Tree root = new Tree(db);
-			Tree A = root.addTree("A");
-			FileTreeEntry B = root.addFile("B");
-			B.setId(bId);
-
-			Tree A_A = A.addTree("A");
-			Tree A_B = A.addTree("B");
-
-			try (final ObjectInserter inserter = db.newObjectInserter()) {
-				A_A.setId(inserter.insert(Constants.OBJ_TREE, A_A.format()));
-				A_B.setId(inserter.insert(Constants.OBJ_TREE, A_B.format()));
-				A.setId(inserter.insert(Constants.OBJ_TREE, A.format()));
-				root.setId(inserter.insert(Constants.OBJ_TREE, root.format()));
-				inserter.flush();
-			}
-
-			tree_root = rw.parseTree(root.getId());
-			tree_A = rw.parseTree(A.getId());
-			tree_AB = rw.parseTree(A_A.getId());
-			assertSame(tree_AB, rw.parseTree(A_B.getId()));
-			b = commit(rw.parseTree(root.getId()));
+		try (ObjectInserter inserter = db.newObjectInserter()) {
+			ObjectId empty = inserter.insert(new TreeFormatter());
+
+			TreeFormatter A = new TreeFormatter();
+			A.append("A", FileMode.TREE, empty);
+			A.append("B", FileMode.TREE, empty);
+			ObjectId idA = inserter.insert(A);
+
+			TreeFormatter root = new TreeFormatter();
+			root.append("A", FileMode.TREE, idA);
+			root.append("B", FileMode.REGULAR_FILE, bId);
+			ObjectId idRoot = inserter.insert(root);
+			inserter.flush();
+
+			tree_root = objw.parseTree(idRoot);
+			tree_A = objw.parseTree(idA);
+			tree_AB = objw.parseTree(empty);
+			b = commit(tree_root);
 		}
 
 		markStart(b);

org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevCommitParseTest.java

@@ -43,13 +43,18 @@
 
 package org.eclipse.jgit.revwalk;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
 
 import java.io.ByteArrayOutputStream;
 import java.io.UnsupportedEncodingException;
+import java.nio.charset.IllegalCharsetNameException;
+import java.nio.charset.UnsupportedCharsetException;
 import java.util.TimeZone;
 
 import org.eclipse.jgit.junit.RepositoryTestCase;
@@ -303,6 +308,86 @@ public class RevCommitParseTest extends RepositoryTestCase {
 		assertEquals("\u304d\u308c\u3044\n\nHi\n", c.getFullMessage());
 	}
 
+	@Test
+	public void testParse_incorrectUtf8Name() throws Exception {
+		ByteArrayOutputStream b = new ByteArrayOutputStream();
+		b.write("tree 9788669ad918b6fcce64af8882fc9a81cb6aba67\n"
+				.getBytes(UTF_8));
+		b.write("author au <a@example.com> 1218123387 +0700\n".getBytes(UTF_8));
+		b.write("committer co <c@example.com> 1218123390 -0500\n"
+				.getBytes(UTF_8));
+		b.write("encoding 'utf8'\n".getBytes(UTF_8));
+		b.write("\n".getBytes(UTF_8));
+		b.write("Sm\u00f6rg\u00e5sbord\n".getBytes(UTF_8));
+
+		RevCommit c = new RevCommit(
+				id("9473095c4cb2f12aefe1db8a355fe3fafba42f67"));
+		c.parseCanonical(new RevWalk(db), b.toByteArray());
+		assertEquals("'utf8'", c.getEncodingName());
+		assertEquals("Sm\u00f6rg\u00e5sbord\n", c.getFullMessage());
+
+		try {
+			c.getEncoding();
+			fail("Expected " + IllegalCharsetNameException.class);
+		} catch (IllegalCharsetNameException badName) {
+			assertEquals("'utf8'", badName.getMessage());
+		}
+	}
+
+	@Test
+	public void testParse_illegalEncoding() throws Exception {
+		ByteArrayOutputStream b = new ByteArrayOutputStream();
+		b.write("tree 9788669ad918b6fcce64af8882fc9a81cb6aba67\n".getBytes(UTF_8));
+		b.write("author au <a@example.com> 1218123387 +0700\n".getBytes(UTF_8));
+		b.write("committer co <c@example.com> 1218123390 -0500\n".getBytes(UTF_8));
+		b.write("encoding utf-8logoutputencoding=gbk\n".getBytes(UTF_8));
+		b.write("\n".getBytes(UTF_8));
+		b.write("message\n".getBytes(UTF_8));
+
+		RevCommit c = new RevCommit(
+				id("9473095c4cb2f12aefe1db8a355fe3fafba42f67"));
+		c.parseCanonical(new RevWalk(db), b.toByteArray());
+		assertEquals("utf-8logoutputencoding=gbk", c.getEncodingName());
+		assertEquals("message\n", c.getFullMessage());
+		assertEquals("message", c.getShortMessage());
+		assertTrue(c.getFooterLines().isEmpty());
+		assertEquals("au", c.getAuthorIdent().getName());
+
+		try {
+			c.getEncoding();
+			fail("Expected " + IllegalCharsetNameException.class);
+		} catch (IllegalCharsetNameException badName) {
+			assertEquals("utf-8logoutputencoding=gbk", badName.getMessage());
+		}
+	}
+
+	@Test
+	public void testParse_unsupportedEncoding() throws Exception {
+		ByteArrayOutputStream b = new ByteArrayOutputStream();
+		b.write("tree 9788669ad918b6fcce64af8882fc9a81cb6aba67\n".getBytes(UTF_8));
+		b.write("author au <a@example.com> 1218123387 +0700\n".getBytes(UTF_8));
+		b.write("committer co <c@example.com> 1218123390 -0500\n".getBytes(UTF_8));
+		b.write("encoding it_IT.UTF8\n".getBytes(UTF_8));
+		b.write("\n".getBytes(UTF_8));
+		b.write("message\n".getBytes(UTF_8));
+
+		RevCommit c = new RevCommit(
+				id("9473095c4cb2f12aefe1db8a355fe3fafba42f67"));
+		c.parseCanonical(new RevWalk(db), b.toByteArray());
+		assertEquals("it_IT.UTF8", c.getEncodingName());
+		assertEquals("message\n", c.getFullMessage());
+		assertEquals("message", c.getShortMessage());
+		assertTrue(c.getFooterLines().isEmpty());
+		assertEquals("au", c.getAuthorIdent().getName());
+
+		try {
+			c.getEncoding();
+			fail("Expected " + UnsupportedCharsetException.class);
+		} catch (UnsupportedCharsetException badName) {
+			assertEquals("it_IT.UTF8", badName.getMessage());
+		}
+	}
+
 	@Test
 	public void testParse_NoMessage() throws Exception {
 		final String msg = "";

org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevTagParseTest.java

@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.revwalk;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
@@ -361,6 +362,44 @@ public class RevTagParseTest extends RepositoryTestCase {
 		assertEquals("\u304d\u308c\u3044\n\nHi\n", c.getFullMessage());
 	}
 
+	@Test
+	public void testParse_illegalEncoding() throws Exception {
+		ByteArrayOutputStream b = new ByteArrayOutputStream();
+		b.write("object 9788669ad918b6fcce64af8882fc9a81cb6aba67\n".getBytes(UTF_8));
+		b.write("type tree\n".getBytes(UTF_8));
+		b.write("tag v1.0\n".getBytes(UTF_8));
+		b.write("tagger t <t@example.com> 1218123387 +0700\n".getBytes(UTF_8));
+		b.write("encoding utf-8logoutputencoding=gbk\n".getBytes(UTF_8));
+		b.write("\n".getBytes(UTF_8));
+		b.write("message\n".getBytes(UTF_8));
+
+		RevTag t = new RevTag(id("9473095c4cb2f12aefe1db8a355fe3fafba42f67"));
+		t.parseCanonical(new RevWalk(db), b.toByteArray());
+
+		assertEquals("t", t.getTaggerIdent().getName());
+		assertEquals("message", t.getShortMessage());
+		assertEquals("message\n", t.getFullMessage());
+	}
+
+	@Test
+	public void testParse_unsupportedEncoding() throws Exception {
+		ByteArrayOutputStream b = new ByteArrayOutputStream();
+		b.write("object 9788669ad918b6fcce64af8882fc9a81cb6aba67\n".getBytes(UTF_8));
+		b.write("type tree\n".getBytes(UTF_8));
+		b.write("tag v1.0\n".getBytes(UTF_8));
+		b.write("tagger t <t@example.com> 1218123387 +0700\n".getBytes(UTF_8));
+		b.write("encoding it_IT.UTF8\n".getBytes(UTF_8));
+		b.write("\n".getBytes(UTF_8));
+		b.write("message\n".getBytes(UTF_8));
+
+		RevTag t = new RevTag(id("9473095c4cb2f12aefe1db8a355fe3fafba42f67"));
+		t.parseCanonical(new RevWalk(db), b.toByteArray());
+
+		assertEquals("t", t.getTaggerIdent().getName());
+		assertEquals("message", t.getShortMessage());
+		assertEquals("message\n", t.getFullMessage());
+	}
+
 	@Test
 	public void testParse_NoMessage() throws Exception {
 		final String msg = "";

org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/AtomicPushTest.java

@@ -112,12 +112,9 @@ public class AtomicPushTest {
 	public void pushNonAtomic() throws Exception {
 		PushResult r;
 		server.setPerformsAtomicTransactions(false);
-		Transport tn = testProtocol.open(uri, client, "server");
-		try {
+		try (Transport tn = testProtocol.open(uri, client, "server")) {
 			tn.setPushAtomic(false);
 			r = tn.push(NullProgressMonitor.INSTANCE, commands());
-		} finally {
-			tn.close();
 		}
 
 		RemoteRefUpdate one = r.getRemoteUpdate("refs/heads/one");
@@ -131,12 +128,9 @@ public class AtomicPushTest {
 	@Test
 	public void pushAtomicClientGivesUpEarly() throws Exception {
 		PushResult r;
-		Transport tn = testProtocol.open(uri, client, "server");
-		try {
+		try (Transport tn = testProtocol.open(uri, client, "server")) {
 			tn.setPushAtomic(true);
 			r = tn.push(NullProgressMonitor.INSTANCE, commands());
-		} finally {
-			tn.close();
 		}
 
 		RemoteRefUpdate one = r.getRemoteUpdate("refs/heads/one");
@@ -167,8 +161,7 @@ public class AtomicPushTest {
 				ObjectId.zeroId()));
 
 		server.setPerformsAtomicTransactions(false);
-		Transport tn = testProtocol.open(uri, client, "server");
-		try {
+		try (Transport tn = testProtocol.open(uri, client, "server")) {
 			tn.setPushAtomic(true);
 			tn.push(NullProgressMonitor.INSTANCE, cmds);
 			fail("did not throw TransportException");
@@ -176,8 +169,6 @@ public class AtomicPushTest {
 			assertEquals(
 					uri + ": " + JGitText.get().atomicPushNotSupported,
 					e.getMessage());
-		} finally {
-			tn.close();
 		}
 	}
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/BundleWriterTest.java

@@ -168,8 +168,10 @@ public class BundleWriterTest extends SampleDataRepositoryTestCase {
 		final ByteArrayInputStream in = new ByteArrayInputStream(bundle);
 		final RefSpec rs = new RefSpec("refs/heads/*:refs/heads/*");
 		final Set<RefSpec> refs = Collections.singleton(rs);
-		return new TransportBundleStream(newRepo, uri, in).fetch(
-				NullProgressMonitor.INSTANCE, refs);
+		try (TransportBundleStream transport = new TransportBundleStream(
+				newRepo, uri, in)) {
+			return transport.fetch(NullProgressMonitor.INSTANCE, refs);
+		}
 	}
 
 	private byte[] makeBundle(final String name,

org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/ReceivePackAdvertiseRefsHookTest.java

@@ -116,12 +116,9 @@ public class ReceivePackAdvertiseRefsHookTest extends LocalDiskRepositoryTestCas
 
 		// Clone from dst into src
 		//
-		Transport t = Transport.open(src, uriOf(dst));
-		try {
+		try (Transport t = Transport.open(src, uriOf(dst))) {
 			t.fetch(PM, Collections.singleton(new RefSpec("+refs/*:refs/*")));
 			assertEquals(B, src.resolve(R_MASTER));
-		} finally {
-			t.close();
 		}
 
 		// Now put private stuff into dst.
@@ -144,7 +141,8 @@ public class ReceivePackAdvertiseRefsHookTest extends LocalDiskRepositoryTestCas
 	@Test
 	public void testFilterHidesPrivate() throws Exception {
 		Map<String, Ref> refs;
-		TransportLocal t = new TransportLocal(src, uriOf(dst), dst.getDirectory()) {
+		try (TransportLocal t = new TransportLocal(src, uriOf(dst),
+				dst.getDirectory()) {
 			@Override
 			ReceivePack createReceivePack(final Repository db) {
 				db.close();
@@ -154,16 +152,10 @@ public class ReceivePackAdvertiseRefsHookTest extends LocalDiskRepositoryTestCas
 				rp.setAdvertiseRefsHook(new HidePrivateHook());
 				return rp;
 			}
-		};
-		try {
-			PushConnection c = t.openPush();
-			try {
+		}) {
+			try (PushConnection c = t.openPush()) {
 				refs = c.getRefsMap();
-			} finally {
-				c.close();
 			}
-		} finally {
-			t.close();
 		}
 
 		assertNotNull(refs);

org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/RefSpecTest.java

@@ -340,6 +340,41 @@ public class RefSpecTest {
 		assertEquals("refs/heads/foo", c.getSource());
 	}
 
+	@Test
+	public void testWildcardAfterText1() {
+		RefSpec a = new RefSpec("refs/heads/*/for-linus:refs/remotes/mine/*-blah");
+		assertTrue(a.isWildcard());
+		assertTrue(a.matchDestination("refs/remotes/mine/x-blah"));
+		assertTrue(a.matchDestination("refs/remotes/mine/foo-blah"));
+		assertTrue(a.matchDestination("refs/remotes/mine/foo/x-blah"));
+		assertFalse(a.matchDestination("refs/remotes/origin/foo/x-blah"));
+
+		RefSpec b = a.expandFromSource("refs/heads/foo/for-linus");
+		assertEquals("refs/remotes/mine/foo-blah", b.getDestination());
+		RefSpec c = a.expandFromDestination("refs/remotes/mine/foo-blah");
+		assertEquals("refs/heads/foo/for-linus", c.getSource());
+	}
+
+	@Test
+	public void testWildcardAfterText2() {
+		RefSpec a = new RefSpec("refs/heads*/for-linus:refs/remotes/mine/*");
+		assertTrue(a.isWildcard());
+		assertTrue(a.matchSource("refs/headsx/for-linus"));
+		assertTrue(a.matchSource("refs/headsfoo/for-linus"));
+		assertTrue(a.matchSource("refs/headsx/foo/for-linus"));
+		assertFalse(a.matchSource("refs/headx/for-linus"));
+
+		RefSpec b = a.expandFromSource("refs/headsx/for-linus");
+		assertEquals("refs/remotes/mine/x", b.getDestination());
+		RefSpec c = a.expandFromDestination("refs/remotes/mine/x");
+		assertEquals("refs/headsx/for-linus", c.getSource());
+
+		RefSpec d = a.expandFromSource("refs/headsx/foo/for-linus");
+		assertEquals("refs/remotes/mine/x/foo", d.getDestination());
+		RefSpec e = a.expandFromDestination("refs/remotes/mine/x/foo");
+		assertEquals("refs/headsx/foo/for-linus", e.getSource());
+	}
+
 	@Test
 	public void testWildcardMirror() {
 		RefSpec a = new RefSpec("*:*");
@@ -403,21 +438,6 @@ public class RefSpecTest {
 		assertNotNull(new RefSpec("refs/heads/*:refs/heads/*/*"));
 	}
 
-	@Test(expected = IllegalArgumentException.class)
-	public void invalidWhenWildcardAfterText() {
-		assertNotNull(new RefSpec("refs/heads/wrong*:refs/heads/right/*"));
-	}
-
-	@Test(expected = IllegalArgumentException.class)
-	public void invalidWhenWildcardBeforeText() {
-		assertNotNull(new RefSpec("*wrong:right/*"));
-	}
-
-	@Test(expected = IllegalArgumentException.class)
-	public void invalidWhenWildcardBeforeTextAtEnd() {
-		assertNotNull(new RefSpec("refs/heads/*wrong:right/*"));
-	}
-
 	@Test(expected = IllegalArgumentException.class)
 	public void invalidSourceDoubleSlashes() {
 		assertNotNull(new RefSpec("refs/heads//wrong"));

org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/TransportTest.java

@@ -61,13 +61,10 @@ import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.test.resources.SampleDataRepositoryTestCase;
-import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 
 public class TransportTest extends SampleDataRepositoryTestCase {
-	private Transport transport;
-
 	private RemoteConfig remoteConfig;
 
 	@Override
@@ -77,17 +74,6 @@ public class TransportTest extends SampleDataRepositoryTestCase {
 		final Config config = db.getConfig();
 		remoteConfig = new RemoteConfig(config, "test");
 		remoteConfig.addURI(new URIish("http://everyones.loves.git/u/2"));
-		transport = null;
-	}
-
-	@Override
-	@After
-	public void tearDown() throws Exception {
-		if (transport != null) {
-			transport.close();
-			transport = null;
-		}
-		super.tearDown();
 	}
 
 	/**
@@ -99,10 +85,11 @@ public class TransportTest extends SampleDataRepositoryTestCase {
 	@Test
 	public void testFindRemoteRefUpdatesNoWildcardNoTracking()
 			throws IOException {
-		transport = Transport.open(db, remoteConfig);
-		final Collection<RemoteRefUpdate> result = transport
-				.findRemoteRefUpdatesFor(Collections.nCopies(1, new RefSpec(
-						"refs/heads/master:refs/heads/x")));
+		Collection<RemoteRefUpdate> result;
+		try (Transport transport = Transport.open(db, remoteConfig)) {
+			result = transport.findRemoteRefUpdatesFor(Collections.nCopies(1,
+					new RefSpec("refs/heads/master:refs/heads/x")));
+		}
 
 		assertEquals(1, result.size());
 		final RemoteRefUpdate rru = result.iterator().next();
@@ -122,10 +109,11 @@ public class TransportTest extends SampleDataRepositoryTestCase {
 	@Test
 	public void testFindRemoteRefUpdatesNoWildcardNoDestination()
 			throws IOException {
-		transport = Transport.open(db, remoteConfig);
-		final Collection<RemoteRefUpdate> result = transport
-				.findRemoteRefUpdatesFor(Collections.nCopies(1, new RefSpec(
-						"+refs/heads/master")));
+		Collection<RemoteRefUpdate> result;
+		try (Transport transport = Transport.open(db, remoteConfig)) {
+			result = transport.findRemoteRefUpdatesFor(
+					Collections.nCopies(1, new RefSpec("+refs/heads/master")));
+		}
 
 		assertEquals(1, result.size());
 		final RemoteRefUpdate rru = result.iterator().next();
@@ -143,10 +131,11 @@ public class TransportTest extends SampleDataRepositoryTestCase {
 	 */
 	@Test
 	public void testFindRemoteRefUpdatesWildcardNoTracking() throws IOException {
-		transport = Transport.open(db, remoteConfig);
-		final Collection<RemoteRefUpdate> result = transport
-				.findRemoteRefUpdatesFor(Collections.nCopies(1, new RefSpec(
-						"+refs/heads/*:refs/heads/test/*")));
+		Collection<RemoteRefUpdate> result;
+		try (Transport transport = Transport.open(db, remoteConfig)) {
+			result = transport.findRemoteRefUpdatesFor(Collections.nCopies(1,
+					new RefSpec("+refs/heads/*:refs/heads/test/*")));
+		}
 
 		assertEquals(12, result.size());
 		boolean foundA = false;
@@ -171,12 +160,14 @@ public class TransportTest extends SampleDataRepositoryTestCase {
 	 */
 	@Test
 	public void testFindRemoteRefUpdatesTwoRefSpecs() throws IOException {
-		transport = Transport.open(db, remoteConfig);
 		final RefSpec specA = new RefSpec("+refs/heads/a:refs/heads/b");
 		final RefSpec specC = new RefSpec("+refs/heads/c:refs/heads/d");
 		final Collection<RefSpec> specs = Arrays.asList(specA, specC);
-		final Collection<RemoteRefUpdate> result = transport
-				.findRemoteRefUpdatesFor(specs);
+
+		Collection<RemoteRefUpdate> result;
+		try (Transport transport = Transport.open(db, remoteConfig)) {
+			result = transport.findRemoteRefUpdatesFor(specs);
+		}
 
 		assertEquals(2, result.size());
 		boolean foundA = false;
@@ -202,10 +193,12 @@ public class TransportTest extends SampleDataRepositoryTestCase {
 	public void testFindRemoteRefUpdatesTrackingRef() throws IOException {
 		remoteConfig.addFetchRefSpec(new RefSpec(
 				"refs/heads/*:refs/remotes/test/*"));
-		transport = Transport.open(db, remoteConfig);
-		final Collection<RemoteRefUpdate> result = transport
-				.findRemoteRefUpdatesFor(Collections.nCopies(1, new RefSpec(
-						"+refs/heads/a:refs/heads/a")));
+
+		Collection<RemoteRefUpdate> result;
+		try (Transport transport = Transport.open(db, remoteConfig)) {
+			result = transport.findRemoteRefUpdatesFor(Collections.nCopies(1,
+					new RefSpec("+refs/heads/a:refs/heads/a")));
+		}
 
 		assertEquals(1, result.size());
 		final TrackingRefUpdate tru = result.iterator().next()
@@ -225,20 +218,18 @@ public class TransportTest extends SampleDataRepositoryTestCase {
 		config.addURI(new URIish("../" + otherDir));
 
 		// Should not throw NoRemoteRepositoryException
-		transport = Transport.open(db, config);
+		Transport.open(db, config).close();
 	}
 
 	@Test
 	public void testLocalTransportFetchWithoutLocalRepository()
 			throws Exception {
 		URIish uri = new URIish("file://" + db.getWorkTree().getAbsolutePath());
-		transport = Transport.open(uri);
-		FetchConnection fetchConnection = transport.openFetch();
-		try {
-			Ref head = fetchConnection.getRef(Constants.HEAD);
-			assertNotNull(head);
-		} finally {
-			fetchConnection.close();
+		try (Transport transport = Transport.open(uri)) {
+			try (FetchConnection fetchConnection = transport.openFetch()) {
+				Ref head = fetchConnection.getRef(Constants.HEAD);
+				assertNotNull(head);
+			}
 		}
 	}
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/URIishTest.java

@@ -459,6 +459,48 @@ public class URIishTest {
 		assertEquals(u, new URIish(str));
 	}
 
+	@Test
+	public void testSshProtoWithEmailUserAndPort() throws Exception {
+		final String str = "ssh://user.name@email.com@example.com:33/some/p ath";
+		URIish u = new URIish(str);
+		assertEquals("ssh", u.getScheme());
+		assertTrue(u.isRemote());
+		assertEquals("/some/p ath", u.getRawPath());
+		assertEquals("/some/p ath", u.getPath());
+		assertEquals("example.com", u.getHost());
+		assertEquals("user.name@email.com", u.getUser());
+		assertNull(u.getPass());
+		assertEquals(33, u.getPort());
+		assertEquals("ssh://user.name%40email.com@example.com:33/some/p ath",
+				u.toPrivateString());
+		assertEquals("ssh://user.name%40email.com@example.com:33/some/p%20ath",
+				u.toPrivateASCIIString());
+		assertEquals(u.setPass(null).toPrivateString(), u.toString());
+		assertEquals(u.setPass(null).toPrivateASCIIString(), u.toASCIIString());
+		assertEquals(u, new URIish(str));
+	}
+
+	@Test
+	public void testSshProtoWithEmailUserPassAndPort() throws Exception {
+		final String str = "ssh://user.name@email.com:pass@wor:d@example.com:33/some/p ath";
+		URIish u = new URIish(str);
+		assertEquals("ssh", u.getScheme());
+		assertTrue(u.isRemote());
+		assertEquals("/some/p ath", u.getRawPath());
+		assertEquals("/some/p ath", u.getPath());
+		assertEquals("example.com", u.getHost());
+		assertEquals("user.name@email.com", u.getUser());
+		assertEquals("pass@wor:d", u.getPass());
+		assertEquals(33, u.getPort());
+		assertEquals("ssh://user.name%40email.com:pass%40wor%3ad@example.com:33/some/p ath",
+				u.toPrivateString());
+		assertEquals("ssh://user.name%40email.com:pass%40wor%3ad@example.com:33/some/p%20ath",
+				u.toPrivateASCIIString());
+		assertEquals(u.setPass(null).toPrivateString(), u.toString());
+		assertEquals(u.setPass(null).toPrivateASCIIString(), u.toASCIIString());
+		assertEquals(u, new URIish(str));
+	}
+
 	@Test
 	public void testSshProtoWithADUserPassAndPort() throws Exception {
 		final String str = "ssh://DOMAIN\\user:pass@example.com:33/some/p ath";

org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/TreeWalkBasicDiffTest.java

@@ -44,7 +44,6 @@
 package org.eclipse.jgit.treewalk;
 
 import static org.eclipse.jgit.lib.Constants.OBJ_BLOB;
-import static org.eclipse.jgit.lib.Constants.OBJ_TREE;
 import static org.eclipse.jgit.lib.Constants.encode;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
@@ -54,11 +53,10 @@ import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectInserter;
-import org.eclipse.jgit.lib.Tree;
+import org.eclipse.jgit.lib.TreeFormatter;
 import org.eclipse.jgit.treewalk.filter.TreeFilter;
 import org.junit.Test;
 
-@SuppressWarnings("deprecation")
 public class TreeWalkBasicDiffTest extends RepositoryTestCase {
 	@Test
 	public void testMissingSubtree_DetectFileAdded_FileModified()
@@ -72,62 +70,63 @@ public class TreeWalkBasicDiffTest extends RepositoryTestCase {
 
 			// Create sub-a/empty, sub-c/empty = hello.
 			{
-				final Tree root = new Tree(db);
+				TreeFormatter root = new TreeFormatter();
 				{
-					final Tree subA = root.addTree("sub-a");
-					subA.addFile("empty").setId(aFileId);
-					subA.setId(inserter.insert(OBJ_TREE, subA.format()));
+					TreeFormatter subA = new TreeFormatter();
+					subA.append("empty", FileMode.REGULAR_FILE, aFileId);
+					root.append("sub-a", FileMode.TREE, inserter.insert(subA));
 				}
 				{
-					final Tree subC = root.addTree("sub-c");
-					subC.addFile("empty").setId(cFileId1);
-					subC.setId(inserter.insert(OBJ_TREE, subC.format()));
+					TreeFormatter subC = new TreeFormatter();
+					subC.append("empty", FileMode.REGULAR_FILE, cFileId1);
+					root.append("sub-c", FileMode.TREE, inserter.insert(subC));
 				}
-				oldTree = inserter.insert(OBJ_TREE, root.format());
+				oldTree = inserter.insert(root);
 			}
 
 			// Create sub-a/empty, sub-b/empty, sub-c/empty.
 			{
-				final Tree root = new Tree(db);
+				TreeFormatter root = new TreeFormatter();
 				{
-					final Tree subA = root.addTree("sub-a");
-					subA.addFile("empty").setId(aFileId);
-					subA.setId(inserter.insert(OBJ_TREE, subA.format()));
+					TreeFormatter subA = new TreeFormatter();
+					subA.append("empty", FileMode.REGULAR_FILE, aFileId);
+					root.append("sub-a", FileMode.TREE, inserter.insert(subA));
 				}
 				{
-					final Tree subB = root.addTree("sub-b");
-					subB.addFile("empty").setId(bFileId);
-					subB.setId(inserter.insert(OBJ_TREE, subB.format()));
+					TreeFormatter subB = new TreeFormatter();
+					subB.append("empty", FileMode.REGULAR_FILE, bFileId);
+					root.append("sub-b", FileMode.TREE, inserter.insert(subB));
 				}
 				{
-					final Tree subC = root.addTree("sub-c");
-					subC.addFile("empty").setId(cFileId2);
-					subC.setId(inserter.insert(OBJ_TREE, subC.format()));
+					TreeFormatter subC = new TreeFormatter();
+					subC.append("empty", FileMode.REGULAR_FILE, cFileId2);
+					root.append("sub-c", FileMode.TREE, inserter.insert(subC));
 				}
-				newTree = inserter.insert(OBJ_TREE, root.format());
+				newTree = inserter.insert(root);
 			}
 			inserter.flush();
 		}
 
-		final TreeWalk tw = new TreeWalk(db);
-		tw.reset(oldTree, newTree);
-		tw.setRecursive(true);
-		tw.setFilter(TreeFilter.ANY_DIFF);
+		try (TreeWalk tw = new TreeWalk(db)) {
+			tw.reset(oldTree, newTree);
+			tw.setRecursive(true);
+			tw.setFilter(TreeFilter.ANY_DIFF);
 
-		assertTrue(tw.next());
-		assertEquals("sub-b/empty", tw.getPathString());
-		assertEquals(FileMode.MISSING, tw.getFileMode(0));
-		assertEquals(FileMode.REGULAR_FILE, tw.getFileMode(1));
-		assertEquals(ObjectId.zeroId(), tw.getObjectId(0));
-		assertEquals(bFileId, tw.getObjectId(1));
+			assertTrue(tw.next());
+			assertEquals("sub-b/empty", tw.getPathString());
+			assertEquals(FileMode.MISSING, tw.getFileMode(0));
+			assertEquals(FileMode.REGULAR_FILE, tw.getFileMode(1));
+			assertEquals(ObjectId.zeroId(), tw.getObjectId(0));
+			assertEquals(bFileId, tw.getObjectId(1));
 
-		assertTrue(tw.next());
-		assertEquals("sub-c/empty", tw.getPathString());
-		assertEquals(FileMode.REGULAR_FILE, tw.getFileMode(0));
-		assertEquals(FileMode.REGULAR_FILE, tw.getFileMode(1));
-		assertEquals(cFileId1, tw.getObjectId(0));
-		assertEquals(cFileId2, tw.getObjectId(1));
+			assertTrue(tw.next());
+			assertEquals("sub-c/empty", tw.getPathString());
+			assertEquals(FileMode.REGULAR_FILE, tw.getFileMode(0));
+			assertEquals(FileMode.REGULAR_FILE, tw.getFileMode(1));
+			assertEquals(cFileId1, tw.getObjectId(0));
+			assertEquals(cFileId2, tw.getObjectId(1));
 
-		assertFalse(tw.next());
+			assertFalse(tw.next());
+		}
 	}
 }

org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/PathFilterGroupTest.java

@@ -43,11 +43,18 @@
 
 package org.eclipse.jgit.treewalk.filter;
 
+import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEditor;
@@ -58,6 +65,7 @@ import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.errors.StopWalkException;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectReader;
+import org.eclipse.jgit.lib.Sets;
 import org.eclipse.jgit.treewalk.TreeWalk;
 import org.junit.Before;
 import org.junit.Test;
@@ -66,6 +74,8 @@ public class PathFilterGroupTest {
 
 	private TreeFilter filter;
 
+	private Map<String, TreeFilter> singles;
+
 	@Before
 	public void setup() {
 		// @formatter:off
@@ -81,64 +91,75 @@ public class PathFilterGroupTest {
 				};
 		// @formatter:on
 		filter = PathFilterGroup.createFromStrings(paths);
+		singles = new HashMap<>();
+		for (String path : paths) {
+			singles.put(path, PathFilterGroup.createFromStrings(path));
+		}
 	}
 
 	@Test
 	public void testExact() throws MissingObjectException,
 			IncorrectObjectTypeException, IOException {
-		assertTrue(filter.include(fakeWalk("a")));
-		assertTrue(filter.include(fakeWalk("b/c")));
-		assertTrue(filter.include(fakeWalk("c/d/e")));
-		assertTrue(filter.include(fakeWalk("c/d/f")));
-		assertTrue(filter.include(fakeWalk("d/e/f/g")));
-		assertTrue(filter.include(fakeWalk("d/e/f/g.x")));
+		assertMatches(Sets.of("a"), fakeWalk("a"));
+		assertMatches(Sets.of("b/c"), fakeWalk("b/c"));
+		assertMatches(Sets.of("c/d/e"), fakeWalk("c/d/e"));
+		assertMatches(Sets.of("c/d/f"), fakeWalk("c/d/f"));
+		assertMatches(Sets.of("d/e/f/g"), fakeWalk("d/e/f/g"));
+		assertMatches(Sets.of("d/e/f/g.x"), fakeWalk("d/e/f/g.x"));
 	}
 
 	@Test
 	public void testNoMatchButClose() throws MissingObjectException,
 			IncorrectObjectTypeException, IOException {
-		assertFalse(filter.include(fakeWalk("a+")));
-		assertFalse(filter.include(fakeWalk("b+/c")));
-		assertFalse(filter.include(fakeWalk("c+/d/e")));
-		assertFalse(filter.include(fakeWalk("c+/d/f")));
-		assertFalse(filter.include(fakeWalk("c/d.a")));
-		assertFalse(filter.include(fakeWalk("d+/e/f/g")));
+		assertNoMatches(fakeWalk("a+"));
+		assertNoMatches(fakeWalk("b+/c"));
+		assertNoMatches(fakeWalk("c+/d/e"));
+		assertNoMatches(fakeWalk("c+/d/f"));
+		assertNoMatches(fakeWalk("c/d.a"));
+		assertNoMatches(fakeWalk("d+/e/f/g"));
 	}
 
 	@Test
 	public void testJustCommonPrefixIsNotMatch() throws MissingObjectException,
 			IncorrectObjectTypeException, IOException {
-		assertFalse(filter.include(fakeWalk("b/a")));
-		assertFalse(filter.include(fakeWalk("b/d")));
-		assertFalse(filter.include(fakeWalk("c/d/a")));
-		assertFalse(filter.include(fakeWalk("d/e/e")));
+		assertNoMatches(fakeWalk("b/a"));
+		assertNoMatches(fakeWalk("b/d"));
+		assertNoMatches(fakeWalk("c/d/a"));
+		assertNoMatches(fakeWalk("d/e/e"));
+		assertNoMatches(fakeWalk("d/e/f/g.y"));
 	}
 
 	@Test
 	public void testKeyIsPrefixOfFilter() throws MissingObjectException,
 			IncorrectObjectTypeException, IOException {
-		assertTrue(filter.include(fakeWalk("b")));
-		assertTrue(filter.include(fakeWalk("c/d")));
-		assertTrue(filter.include(fakeWalk("c/d")));
-		assertTrue(filter.include(fakeWalk("c")));
-		assertTrue(filter.include(fakeWalk("d/e/f")));
-		assertTrue(filter.include(fakeWalk("d/e")));
-		assertTrue(filter.include(fakeWalk("d")));
+		assertMatches(Sets.of("b/c"), fakeWalkAtSubtree("b"));
+		assertMatches(Sets.of("c/d/e", "c/d/f"), fakeWalkAtSubtree("c/d"));
+		assertMatches(Sets.of("c/d/e", "c/d/f"), fakeWalkAtSubtree("c"));
+		assertMatches(Sets.of("d/e/f/g", "d/e/f/g.x"),
+				fakeWalkAtSubtree("d/e/f"));
+		assertMatches(Sets.of("d/e/f/g", "d/e/f/g.x"),
+				fakeWalkAtSubtree("d/e"));
+		assertMatches(Sets.of("d/e/f/g", "d/e/f/g.x"), fakeWalkAtSubtree("d"));
+
+		assertNoMatches(fakeWalk("b"));
+		assertNoMatches(fakeWalk("c/d"));
+		assertNoMatches(fakeWalk("c"));
+		assertNoMatches(fakeWalk("d/e/f"));
+		assertNoMatches(fakeWalk("d/e"));
+		assertNoMatches(fakeWalk("d"));
+
 	}
 
 	@Test
 	public void testFilterIsPrefixOfKey() throws MissingObjectException,
 			IncorrectObjectTypeException, IOException {
-		assertTrue(filter.include(fakeWalk("a/b")));
-		assertTrue(filter.include(fakeWalk("b/c/d")));
-		assertTrue(filter.include(fakeWalk("c/d/e/f")));
-		assertTrue(filter.include(fakeWalk("c/d/f/g")));
-		assertTrue(filter.include(fakeWalk("d/e/f/g/h")));
-		assertTrue(filter.include(fakeWalk("d/e/f/g/y")));
-		assertTrue(filter.include(fakeWalk("d/e/f/g.x/h")));
-		// listed before g/y, so can't StopWalk here, but it's not included
-		// either
-		assertFalse(filter.include(fakeWalk("d/e/f/g.y")));
+		assertMatches(Sets.of("a"), fakeWalk("a/b"));
+		assertMatches(Sets.of("b/c"), fakeWalk("b/c/d"));
+		assertMatches(Sets.of("c/d/e"), fakeWalk("c/d/e/f"));
+		assertMatches(Sets.of("c/d/f"), fakeWalk("c/d/f/g"));
+		assertMatches(Sets.of("d/e/f/g"), fakeWalk("d/e/f/g/h"));
+		assertMatches(Sets.of("d/e/f/g"), fakeWalk("d/e/f/g/y"));
+		assertMatches(Sets.of("d/e/f/g.x"), fakeWalk("d/e/f/g.x/h"));
 	}
 
 	@Test
@@ -182,6 +203,10 @@ public class PathFilterGroupTest {
 		// less obvious #2 due to git sorting order
 		filter.include(fakeWalk("d/e/f/g/h.txt"));
 
+		// listed before g/y, so can't StopWalk here
+		filter.include(fakeWalk("d/e/f/g.y"));
+		singles.get("d/e/f/g").include(fakeWalk("d/e/f/g.y"));
+
 		// non-ascii
 		try {
 			filter.include(fakeWalk("\u00C0"));
@@ -191,6 +216,44 @@ public class PathFilterGroupTest {
 		}
 	}
 
+	private void assertNoMatches(TreeWalk tw) throws MissingObjectException,
+			IncorrectObjectTypeException, IOException {
+		assertMatches(Sets.<String> of(), tw);
+	}
+
+	private void assertMatches(Set<String> expect, TreeWalk tw)
+			throws MissingObjectException, IncorrectObjectTypeException,
+			IOException {
+		List<String> actual = new ArrayList<>();
+		for (String path : singles.keySet()) {
+			if (includes(singles.get(path), tw)) {
+				actual.add(path);
+			}
+		}
+
+		String[] e = expect.toArray(new String[expect.size()]);
+		String[] a = actual.toArray(new String[actual.size()]);
+		Arrays.sort(e);
+		Arrays.sort(a);
+		assertArrayEquals(e, a);
+
+		if (expect.isEmpty()) {
+			assertFalse(includes(filter, tw));
+		} else {
+			assertTrue(includes(filter, tw));
+		}
+	}
+
+	private static boolean includes(TreeFilter f, TreeWalk tw)
+			throws MissingObjectException, IncorrectObjectTypeException,
+			IOException {
+		try {
+			return f.include(tw);
+		} catch (StopWalkException e) {
+			return false;
+		}
+	}
+
 	TreeWalk fakeWalk(final String path) throws IOException {
 		DirCache dc = DirCache.newInCore();
 		DirCacheEditor dce = dc.editor();
@@ -210,4 +273,25 @@ public class PathFilterGroupTest {
 		return ret;
 	}
 
+	TreeWalk fakeWalkAtSubtree(final String path) throws IOException {
+		DirCache dc = DirCache.newInCore();
+		DirCacheEditor dce = dc.editor();
+		dce.add(new DirCacheEditor.PathEdit(path + "/README") {
+			public void apply(DirCacheEntry ent) {
+				ent.setFileMode(FileMode.REGULAR_FILE);
+			}
+		});
+		dce.finish();
+
+		TreeWalk ret = new TreeWalk((ObjectReader) null);
+		ret.addTree(new DirCacheIterator(dc));
+		ret.next();
+		while (!path.equals(ret.getPathString())) {
+			if (ret.isSubtree()) {
+				ret.enterSubtree();
+			}
+			ret.next();
+		}
+		return ret;
+	}
 }

org.eclipse.jgit.test/tst/org/eclipse/jgit/util/ChangeIdUtilTest.java

@@ -45,7 +45,6 @@ package org.eclipse.jgit.util;
 
 import static org.junit.Assert.assertEquals;
 
-import java.io.IOException;
 import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.junit.MockSystemReader;
@@ -113,7 +112,7 @@ public class ChangeIdUtilTest {
 	}
 
 	@Test
-	public void testId() throws IOException {
+	public void testId() {
 		String msg = "A\nMessage\n";
 		ObjectId id = ChangeIdUtil.computeChangeId(treeId, parentId, p, q, msg);
 		assertEquals("73f3751208ac92cbb76f9a26ac4a0d9d472e381b", ObjectId

org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FileUtilTest.java

@@ -54,6 +54,7 @@ import java.util.regex.Matcher;
 
 import org.eclipse.jgit.junit.JGitTestUtil;
 import org.junit.After;
+import org.junit.Assume;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -424,18 +425,27 @@ public class FileUtilTest {
 	@Test
 	public void testCreateSymlink() throws IOException {
 		FS fs = FS.DETECTED;
-		try {
-			fs.createSymLink(new File(trash, "x"), "y");
-		} catch (IOException e) {
-			if (fs.supportsSymlinks())
-				fail("FS claims to support symlinks but attempt to create symlink failed");
-			return;
-		}
-		assertTrue(fs.supportsSymlinks());
+		// show test as ignored if the FS doesn't support symlinks
+		Assume.assumeTrue(fs.supportsSymlinks());
+		fs.createSymLink(new File(trash, "x"), "y");
 		String target = fs.readSymLink(new File(trash, "x"));
 		assertEquals("y", target);
 	}
 
+	@Test
+	public void testCreateSymlinkOverrideExisting() throws IOException {
+		FS fs = FS.DETECTED;
+		// show test as ignored if the FS doesn't support symlinks
+		Assume.assumeTrue(fs.supportsSymlinks());
+		File file = new File(trash, "x");
+		fs.createSymLink(file, "y");
+		String target = fs.readSymLink(file);
+		assertEquals("y", target);
+		fs.createSymLink(file, "z");
+		target = fs.readSymLink(file);
+		assertEquals("z", target);
+	}
+
 	@Test
 	public void testRelativize_doc() {
 		// This is the javadoc example

org.eclipse.jgit.test/tst/org/eclipse/jgit/util/PathsTest.java

@@ -0,0 +1,118 @@
+/*
+ * Copyright (C) 2016, Google Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.util;
+
+import static org.eclipse.jgit.util.Paths.compare;
+import static org.eclipse.jgit.util.Paths.compareSameName;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.FileMode;
+import org.junit.Test;
+
+public class PathsTest {
+	@Test
+	public void testStripTrailingSeparator() {
+		assertNull(Paths.stripTrailingSeparator(null));
+		assertEquals("", Paths.stripTrailingSeparator(""));
+		assertEquals("a", Paths.stripTrailingSeparator("a"));
+		assertEquals("a/boo", Paths.stripTrailingSeparator("a/boo"));
+		assertEquals("a/boo", Paths.stripTrailingSeparator("a/boo/"));
+		assertEquals("a/boo", Paths.stripTrailingSeparator("a/boo//"));
+		assertEquals("a/boo", Paths.stripTrailingSeparator("a/boo///"));
+	}
+
+	@Test
+	public void testPathCompare() {
+		byte[] a = Constants.encode("afoo/bar.c");
+		byte[] b = Constants.encode("bfoo/bar.c");
+
+		assertEquals(0, compare(a, 1, a.length, 0, b, 1, b.length, 0));
+		assertEquals(-1, compare(a, 0, a.length, 0, b, 0, b.length, 0));
+		assertEquals(1, compare(b, 0, b.length, 0, a, 0, a.length, 0));
+
+		a = Constants.encode("a");
+		b = Constants.encode("aa");
+		assertEquals(-97, compare(a, 0, a.length, 0, b, 0, b.length, 0));
+		assertEquals(0, compare(a, 0, a.length, 0, b, 0, 1, 0));
+		assertEquals(0, compare(a, 0, a.length, 0, b, 1, 2, 0));
+		assertEquals(0, compareSameName(a, 0, a.length, b, 1, b.length, 0));
+		assertEquals(0, compareSameName(a, 0, a.length, b, 0, 1, 0));
+		assertEquals(-50, compareSameName(a, 0, a.length, b, 0, b.length, 0));
+		assertEquals(97, compareSameName(b, 0, b.length, a, 0, a.length, 0));
+
+		a = Constants.encode("a");
+		b = Constants.encode("a");
+		assertEquals(0, compare(
+				a, 0, a.length, FileMode.TREE.getBits(),
+				b, 0, b.length, FileMode.TREE.getBits()));
+		assertEquals(0, compare(
+				a, 0, a.length, FileMode.REGULAR_FILE.getBits(),
+				b, 0, b.length, FileMode.REGULAR_FILE.getBits()));
+		assertEquals(-47, compare(
+				a, 0, a.length, FileMode.REGULAR_FILE.getBits(),
+				b, 0, b.length, FileMode.TREE.getBits()));
+		assertEquals(47, compare(
+				a, 0, a.length, FileMode.TREE.getBits(),
+				b, 0, b.length, FileMode.REGULAR_FILE.getBits()));
+
+		assertEquals(0, compareSameName(
+				a, 0, a.length,
+				b, 0, b.length, FileMode.TREE.getBits()));
+		assertEquals(0, compareSameName(
+				a, 0, a.length,
+				b, 0, b.length, FileMode.REGULAR_FILE.getBits()));
+
+		a = Constants.encode("a.c");
+		b = Constants.encode("a");
+		byte[] c = Constants.encode("a0c");
+		assertEquals(-1, compare(
+				a, 0, a.length, FileMode.REGULAR_FILE.getBits(),
+				b, 0, b.length, FileMode.TREE.getBits()));
+		assertEquals(-1, compare(
+				b, 0, b.length, FileMode.TREE.getBits(),
+				c, 0, c.length, FileMode.REGULAR_FILE.getBits()));
+	}
+}

org.eclipse.jgit.ui/BUCK

@@ -0,0 +1,7 @@
+java_library(
+  name = 'ui',
+  srcs = glob(['src/**']),
+  resources = glob(['resources/**']),
+  deps = ['//org.eclipse.jgit:jgit'],
+  visibility = ['PUBLIC'],
+)

org.eclipse.jgit.ui/src/org/eclipse/jgit/awtui/AwtCredentialsProvider.java

@@ -56,15 +56,20 @@ import javax.swing.JPasswordField;
 import javax.swing.JTextField;
 
 import org.eclipse.jgit.errors.UnsupportedCredentialItem;
+import org.eclipse.jgit.transport.ChainingCredentialsProvider;
 import org.eclipse.jgit.transport.CredentialItem;
 import org.eclipse.jgit.transport.CredentialsProvider;
+import org.eclipse.jgit.transport.NetRCCredentialsProvider;
 import org.eclipse.jgit.transport.URIish;
 
 /** Interacts with the user during authentication by using AWT/Swing dialogs. */
 public class AwtCredentialsProvider extends CredentialsProvider {
 	/** Install this implementation as the default. */
 	public static void install() {
-		CredentialsProvider.setDefault(new AwtCredentialsProvider());
+		final AwtCredentialsProvider c = new AwtCredentialsProvider();
+		CredentialsProvider cp = new ChainingCredentialsProvider(
+				new NetRCCredentialsProvider(), c);
+		CredentialsProvider.setDefault(cp);
 	}
 
 	@Override

org.eclipse.jgit/.settings/.api_filters

@@ -1,5 +1,45 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <component id="org.eclipse.jgit" version="2">
+    <resource path="META-INF/MANIFEST.MF" type="org.eclipse.jgit.lib.FileTreeEntry">
+        <filter id="305324134">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.lib.FileTreeEntry"/>
+                <message_argument value="org.eclipse.jgit_4.2.0"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="META-INF/MANIFEST.MF" type="org.eclipse.jgit.lib.GitlinkTreeEntry">
+        <filter id="305324134">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.lib.GitlinkTreeEntry"/>
+                <message_argument value="org.eclipse.jgit_4.2.0"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="META-INF/MANIFEST.MF" type="org.eclipse.jgit.lib.SymlinkTreeEntry">
+        <filter id="305324134">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.lib.SymlinkTreeEntry"/>
+                <message_argument value="org.eclipse.jgit_4.2.0"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="META-INF/MANIFEST.MF" type="org.eclipse.jgit.lib.Tree">
+        <filter id="305324134">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.lib.Tree"/>
+                <message_argument value="org.eclipse.jgit_4.2.0"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="META-INF/MANIFEST.MF" type="org.eclipse.jgit.lib.TreeEntry">
+        <filter id="305324134">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.lib.TreeEntry"/>
+                <message_argument value="org.eclipse.jgit_4.2.0"/>
+            </message_arguments>
+        </filter>
+    </resource>
     <resource path="src/org/eclipse/jgit/attributes/AttributesNode.java" type="org.eclipse.jgit.attributes.AttributesNode">
         <filter comment="attributes weren't really usable in earlier versions" id="338792546">
             <message_arguments>

org.eclipse.jgit/BUCK

@@ -0,0 +1,20 @@
+SRCS = glob(['src/**'])
+RESOURCES = glob(['resources/**'])
+
+java_library(
+  name = 'jgit',
+  srcs = SRCS,
+  resources = RESOURCES,
+  deps = [
+    '//lib:javaewah',
+    '//lib:jsch',
+    '//lib:httpcomponents',
+    '//lib:slf4j-api',
+  ],
+  visibility = ['PUBLIC'],
+)
+
+java_sources(
+  name = 'jgit_src',
+  srcs = SRCS + RESOURCES,
+)

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

@@ -65,9 +65,10 @@ Export-Package: org.eclipse.jgit.annotations;version="4.2.0",
    org.eclipse.jgit.junit,
    org.eclipse.jgit.junit.http,
    org.eclipse.jgit.http.server,
-   org.eclipse.jgit.java7.test,
+   org.eclipse.jgit.pgm.test,
    org.eclipse.jgit.pgm",
  org.eclipse.jgit.internal.storage.pack;version="4.2.0";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.storage.reftree;version="4.2.0";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
  org.eclipse.jgit.lib;version="4.2.0";
   uses:="org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,

org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties

@@ -99,6 +99,7 @@ cannotSquashFixupWithoutPreviousCommit=Cannot {0} without previous commit.
 cannotStoreObjects=cannot store objects
 cannotResolveUniquelyAbbrevObjectId=Could not resolve uniquely the abbreviated object ID
 cannotUnloadAModifiedTree=Cannot unload a modified tree.
+cannotUpdateUnbornBranch=Cannot update unborn branch
 cannotWorkWithOtherStagesThanZeroRightNow=Cannot work with other stages than zero right now. Won't write corrupt index.
 cannotWriteObjectsPath=Cannot write {0}/{1}: {2}
 canOnlyCherryPickCommitsWithOneParent=Cannot cherry-pick commit ''{0}'' because it has {1} parents, only commits with exactly one parent are supported.
@@ -125,14 +126,15 @@ connectionFailed=connection failed
 connectionTimeOut=Connection time out: {0}
 contextMustBeNonNegative=context must be >= 0
 corruptionDetectedReReadingAt=Corruption detected re-reading at {0}
+corruptObjectBadDate=bad date
+corruptObjectBadEmail=bad email
 corruptObjectBadStream=bad stream
 corruptObjectBadStreamCorruptHeader=bad stream, corrupt header
+corruptObjectBadTimezone=bad time zone
 corruptObjectDuplicateEntryNames=duplicate entry names
 corruptObjectGarbageAfterSize=garbage after size
 corruptObjectIncorrectLength=incorrect length
 corruptObjectIncorrectSorting=incorrectly sorted
-corruptObjectInvalidAuthor=invalid author
-corruptObjectInvalidCommitter=invalid committer
 corruptObjectInvalidEntryMode=invalid entry mode
 corruptObjectInvalidMode=invalid mode
 corruptObjectInvalidModeChar=invalid mode character
@@ -151,11 +153,11 @@ corruptObjectInvalidNameNul=invalid name 'NUL'
 corruptObjectInvalidNamePrn=invalid name 'PRN'
 corruptObjectInvalidObject=invalid object
 corruptObjectInvalidParent=invalid parent
-corruptObjectInvalidTagger=invalid tagger
 corruptObjectInvalidTree=invalid tree
 corruptObjectInvalidType=invalid type
 corruptObjectInvalidType2=invalid type {0}
 corruptObjectMalformedHeader=malformed header: {0}
+corruptObjectMissingEmail=missing email
 corruptObjectNameContainsByte=name contains byte 0x%x
 corruptObjectNameContainsChar=name contains '%c'
 corruptObjectNameContainsNullByte=name contains byte 0x00
@@ -181,6 +183,7 @@ corruptObjectPackfileChecksumIncorrect=Packfile checksum incorrect.
 corruptObjectTruncatedInMode=truncated in mode
 corruptObjectTruncatedInName=truncated in name
 corruptObjectTruncatedInObjectId=truncated in object id
+corruptObjectZeroId=entry points to null SHA-1
 couldNotCheckOutBecauseOfConflicts=Could not check out because of conflicts
 couldNotDeleteLockFileShouldNotHappen=Could not delete lock file. Should not happen
 couldNotDeleteTemporaryIndexFileShouldNotHappen=Could not delete temporary index file. Should not happen
@@ -432,6 +435,7 @@ noXMLParserAvailable=No XML parser available.
 objectAtHasBadZlibStream=Object at {0} in {1} has bad zlib stream
 objectAtPathDoesNotHaveId=Object at path "{0}" does not have an id assigned. All object ids must be assigned prior to writing a tree.
 objectIsCorrupt=Object {0} is corrupt: {1}
+objectIsCorrupt3={0}: object {1}: {2}
 objectIsNotA=Object {0} is not a {1}.
 objectNotFound=Object {0} not found.
 objectNotFoundIn=Object {0} not found in {1}.
@@ -595,6 +599,7 @@ transportExceptionInvalid=Invalid {0} {1}:{2}
 transportExceptionMissingAssumed=Missing assumed {0}
 transportExceptionReadRef=read {0}
 transportNeedsRepository=Transport needs repository
+transportProvidedRefWithNoObjectId=Transport provided ref {0} with no object id
 transportProtoAmazonS3=Amazon S3
 transportProtoBundleFile=Git Bundle File
 transportProtoFTP=FTP

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

@@ -43,6 +43,10 @@
  */
 package org.eclipse.jgit.api;
 
+import static org.eclipse.jgit.lib.Constants.OBJ_BLOB;
+import static org.eclipse.jgit.lib.FileMode.GITLINK;
+import static org.eclipse.jgit.lib.FileMode.TYPE_TREE;
+
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.Collection;
@@ -58,12 +62,12 @@ import org.eclipse.jgit.dircache.DirCacheBuilder;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.dircache.DirCacheIterator;
 import org.eclipse.jgit.internal.JGitText;
-import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
+import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectInserter;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.treewalk.FileTreeIterator;
-import org.eclipse.jgit.treewalk.TreeWalk;
+import org.eclipse.jgit.treewalk.NameConflictTreeWalk;
 import org.eclipse.jgit.treewalk.TreeWalk.OperationType;
 import org.eclipse.jgit.treewalk.WorkingTreeIterator;
 import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
@@ -135,15 +139,12 @@ public class AddCommand extends GitCommand<DirCache> {
 			throw new NoFilepatternException(JGitText.get().atLeastOnePatternIsRequired);
 		checkCallable();
 		DirCache dc = null;
-		boolean addAll = false;
-		if (filepatterns.contains(".")) //$NON-NLS-1$
-			addAll = true;
+		boolean addAll = filepatterns.contains("."); //$NON-NLS-1$
 
 		try (ObjectInserter inserter = repo.newObjectInserter();
-				final TreeWalk tw = new TreeWalk(repo)) {
+				NameConflictTreeWalk tw = new NameConflictTreeWalk(repo)) {
 			tw.setOperationType(OperationType.CHECKIN_OP);
 			dc = repo.lockDirCache();
-			DirCacheIterator c;
 
 			DirCacheBuilder builder = dc.builder();
 			tw.addTree(new DirCacheBuildIterator(builder));
@@ -151,62 +152,85 @@ public class AddCommand extends GitCommand<DirCache> {
 				workingTreeIterator = new FileTreeIterator(repo);
 			workingTreeIterator.setDirCacheIterator(tw, 0);
 			tw.addTree(workingTreeIterator);
-			tw.setRecursive(true);
 			if (!addAll)
 				tw.setFilter(PathFilterGroup.createFromStrings(filepatterns));
 
-			String lastAddedFile = null;
+			byte[] lastAdded = null;
 
 			while (tw.next()) {
-				String path = tw.getPathString();
-
+				DirCacheIterator c = tw.getTree(0, DirCacheIterator.class);
 				WorkingTreeIterator f = tw.getTree(1, WorkingTreeIterator.class);
-				if (tw.getTree(0, DirCacheIterator.class) == null &&
-						f != null && f.isEntryIgnored()) {
+				if (c == null && f != null && f.isEntryIgnored()) {
 					// file is not in index but is ignored, do nothing
+					continue;
+				} else if (c == null && update) {
+					// Only update of existing entries was requested.
+					continue;
+				}
+
+				DirCacheEntry entry = c != null ? c.getDirCacheEntry() : null;
+				if (entry != null && entry.getStage() > 0
+						&& lastAdded != null
+						&& lastAdded.length == tw.getPathLength()
+						&& tw.isPathPrefix(lastAdded, lastAdded.length) == 0) {
+					// In case of an existing merge conflict the
+					// DirCacheBuildIterator iterates over all stages of
+					// this path, we however want to add only one
+					// new DirCacheEntry per path.
+					continue;
+				}
+
+				if (tw.isSubtree() && !tw.isDirectoryFileConflict()) {
+					tw.enterSubtree();
+					continue;
+				}
+
+				if (f == null) { // working tree file does not exist
+					if (entry != null
+							&& (!update || GITLINK == entry.getFileMode())) {
+						builder.add(entry);
+					}
+					continue;
+				}
+
+				if (entry != null && entry.isAssumeValid()) {
+					// Index entry is marked assume valid. Even though
+					// the user specified the file to be added JGit does
+					// not consider the file for addition.
+					builder.add(entry);
+					continue;
+				}
+
+				if (f.getEntryRawMode() == TYPE_TREE) {
+					// Index entry exists and is symlink, gitlink or file,
+					// otherwise the tree would have been entered above.
+					// Replace the index entry by diving into tree of files.
+					tw.enterSubtree();
+					continue;
+				}
+
+				byte[] path = tw.getRawPath();
+				if (entry == null || entry.getStage() > 0) {
+					entry = new DirCacheEntry(path);
 				}
-				// In case of an existing merge conflict the
-				// DirCacheBuildIterator iterates over all stages of
-				// this path, we however want to add only one
-				// new DirCacheEntry per path.
-				else if (!(path.equals(lastAddedFile))) {
-					if (!(update && tw.getTree(0, DirCacheIterator.class) == null)) {
-						c = tw.getTree(0, DirCacheIterator.class);
-						if (f != null) { // the file exists
-							long sz = f.getEntryLength();
-							DirCacheEntry entry = new DirCacheEntry(path);
-							if (c == null || c.getDirCacheEntry() == null
-									|| !c.getDirCacheEntry().isAssumeValid()) {
-								FileMode mode = f.getIndexFileMode(c);
-								entry.setFileMode(mode);
-
-								if (FileMode.GITLINK != mode) {
-									entry.setLength(sz);
-									entry.setLastModified(f
-											.getEntryLastModified());
-									long contentSize = f
-											.getEntryContentLength();
-									InputStream in = f.openEntryStream();
-									try {
-										entry.setObjectId(inserter.insert(
-												Constants.OBJ_BLOB, contentSize, in));
-									} finally {
-										in.close();
-									}
-								} else
-									entry.setObjectId(f.getEntryObjectId());
-								builder.add(entry);
-								lastAddedFile = path;
-							} else {
-								builder.add(c.getDirCacheEntry());
-							}
-
-						} else if (c != null
-								&& (!update || FileMode.GITLINK == c
-										.getEntryFileMode()))
-							builder.add(c.getDirCacheEntry());
+				FileMode mode = f.getIndexFileMode(c);
+				entry.setFileMode(mode);
+
+				if (GITLINK != mode) {
+					entry.setLength(f.getEntryLength());
+					entry.setLastModified(f.getEntryLastModified());
+					long len = f.getEntryContentLength();
+					try (InputStream in = f.openEntryStream()) {
+						ObjectId id = inserter.insert(OBJ_BLOB, len, in);
+						entry.setObjectId(id);
 					}
+				} else {
+					entry.setLength(0);
+					entry.setLastModified(0);
+					entry.setObjectId(f.getEntryObjectId());
 				}
+				builder.add(entry);
+				lastAdded = path;
 			}
 			inserter.flush();
 			builder.commit();

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

@@ -47,6 +47,7 @@ import java.io.FileOutputStream;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.file.StandardCopyOption;
 import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.List;
@@ -141,9 +142,13 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 				case RENAME:
 					f = getFile(fh.getOldPath(), false);
 					File dest = getFile(fh.getNewPath(), false);
-					if (!f.renameTo(dest))
+					try {
+						FileUtils.rename(f, dest,
+								StandardCopyOption.ATOMIC_MOVE);
+					} catch (IOException e) {
 						throw new PatchApplyException(MessageFormat.format(
-								JGitText.get().renameFileFailed, f, dest));
+								JGitText.get().renameFileFailed, f, dest), e);
+					}
 					break;
 				case COPY:
 					f = getFile(fh.getOldPath(), false);

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

@@ -331,9 +331,16 @@ public class CheckoutCommand extends GitCommand<Ref> {
 	}
 
 	private String getShortBranchName(Ref headRef) {
-		if (headRef.getTarget().getName().equals(headRef.getName()))
-			return headRef.getTarget().getObjectId().getName();
-		return Repository.shortenRefName(headRef.getTarget().getName());
+		if (headRef.isSymbolic()) {
+			return Repository.shortenRefName(headRef.getTarget().getName());
+		}
+		// Detached HEAD. Every non-symbolic ref in the ref database has an
+		// object id, so this cannot be null.
+		ObjectId id = headRef.getObjectId();
+		if (id == null) {
+			throw new NullPointerException();
+		}
+		return id.getName();
 	}
 
 	/**

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

@@ -61,6 +61,7 @@ import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.NullProgressMonitor;
+import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.RefUpdate;
@@ -235,7 +236,7 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 		}
 
 		if (head == null || head.getObjectId() == null)
-			return; // throw exception?
+			return; // TODO throw exception?
 
 		if (head.getName().startsWith(Constants.R_HEADS)) {
 			final RefUpdate newHead = clonedRepo.updateRef(Constants.HEAD);
@@ -287,20 +288,24 @@ public class CloneCommand extends TransportCommand<CloneCommand, Git> {
 
 	private Ref findBranchToCheckout(FetchResult result) {
 		final Ref idHEAD = result.getAdvertisedRef(Constants.HEAD);
-		if (idHEAD == null)
+		ObjectId headId = idHEAD != null ? idHEAD.getObjectId() : null;
+		if (headId == null) {
 			return null;
+		}
 
 		Ref master = result.getAdvertisedRef(Constants.R_HEADS
 				+ Constants.MASTER);
-		if (master != null && master.getObjectId().equals(idHEAD.getObjectId()))
+		ObjectId objectId = master != null ? master.getObjectId() : null;
+		if (headId.equals(objectId)) {
 			return master;
+		}
 
 		Ref foundBranch = null;
 		for (final Ref r : result.getAdvertisedRefs()) {
 			final String n = r.getName();
 			if (!n.startsWith(Constants.R_HEADS))
 				continue;
-			if (r.getObjectId().equals(idHEAD.getObjectId())) {
+			if (headId.equals(r.getObjectId())) {
 				foundBranch = r;
 				break;
 			}