Remove unnecessary usage of the internal FileRepository class

Change-Id: Iae7b4e550d75798dc66edf6c9e03ea826f072f33
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

31 files changed, 93 insertions, 86 deletions

diff --git a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/AdaptableFileTreeIteratorTest.java b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/AdaptableFileTreeIteratorTest.java
index e7615bea19..291fad5958 100644
--- a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/AdaptableFileTreeIteratorTest.java
+++ b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/AdaptableFileTreeIteratorTest.java
@@ -24,7 +24,7 @@ import org.eclipse.egit.core.ContainerTreeIterator;
 import org.eclipse.egit.core.op.ConnectProviderOperation;
 import org.eclipse.egit.core.project.RepositoryMapping;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.jgit.treewalk.WorkingTreeIterator;
 import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
@@ -41,7 +41,7 @@ public class AdaptableFileTreeIteratorTest extends GitTestCase {
 	public void setUp() throws Exception {
 		super.setUp();
 
-		repository = new FileRepository(gitDir);
+		repository = FileRepositoryBuilder.create(gitDir);
 		repository.create();
 
 		file = new File(project.getProject().getLocation().toFile(), "a.txt");
diff --git a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/ContainerTreeIteratorResourceFilterTest.java b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/ContainerTreeIteratorResourceFilterTest.java
index ca7a8822c0..7f5be1fd37 100644
--- a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/ContainerTreeIteratorResourceFilterTest.java
+++ b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/ContainerTreeIteratorResourceFilterTest.java
@@ -31,7 +31,8 @@ import org.eclipse.core.runtime.Path;
 import org.eclipse.egit.core.AdaptableFileTreeIterator;
 import org.eclipse.egit.core.ContainerTreeIterator;
 import org.eclipse.egit.core.op.ConnectProviderOperation;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.treewalk.AbstractTreeIterator;
 import org.eclipse.jgit.treewalk.TreeWalk;
 import org.junit.Before;
@@ -51,13 +52,13 @@ import org.junit.Test;
  */
 public class ContainerTreeIteratorResourceFilterTest extends GitTestCase {
 
-	private FileRepository repository;
+	private Repository repository;
 
 	@Before
 	public void setUp() throws Exception {
 		super.setUp();
 
-		repository = new FileRepository(gitDir);
+		repository = FileRepositoryBuilder.create(gitDir);
 		repository.create();
 
 		connectProject(project.getProject());
diff --git a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/GitProjectSetCapabilityTest.java b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/GitProjectSetCapabilityTest.java
index 82b183be2c..3eb19c538f 100644
--- a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/GitProjectSetCapabilityTest.java
+++ b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/GitProjectSetCapabilityTest.java
@@ -33,7 +33,7 @@ import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.team.core.ProjectSetSerializationContext;
 import org.eclipse.team.core.TeamException;
@@ -283,7 +283,7 @@ public class GitProjectSetCapabilityTest {
 
 	private File createRepository(IPath location, String url, String branch) throws Exception {
 		File gitDirectory = new File(location.toFile(), Constants.DOT_GIT);
-		Repository repo = new FileRepository(gitDirectory);
+		Repository repo = FileRepositoryBuilder.create(gitDirectory);
 		repo.getConfig().setString(ConfigConstants.CONFIG_REMOTE_SECTION, "origin", ConfigConstants.CONFIG_KEY_URL, url);
 		repo.getConfig().setString(ConfigConstants.CONFIG_BRANCH_SECTION, branch, ConfigConstants.CONFIG_KEY_REMOTE, "origin");
 		repo.create();
diff --git a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/TestRepository.java b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/TestRepository.java
index 986acb1347..4b3377178e 100644
--- a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/TestRepository.java
+++ b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/TestRepository.java
@@ -49,7 +49,7 @@ import org.eclipse.jgit.lib.RefUpdate;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevWalk;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.transport.URIish;
 import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.jgit.util.FileUtils;
@@ -71,7 +71,7 @@ public class TestRepository {
 	 * @throws IOException
 	 */
 	public TestRepository(File gitDir) throws IOException {
-		FileRepository tmpRepository = new FileRepository(gitDir);
+		Repository tmpRepository = FileRepositoryBuilder.create(gitDir);
 		tmpRepository.create();
 		tmpRepository.close();
 		// use repository instance from RepositoryCache!
diff --git a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/internal/mapping/HistoryTest.java b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/internal/mapping/HistoryTest.java
index 1f6d67a5f0..4680bf0d59 100644
--- a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/internal/mapping/HistoryTest.java
+++ b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/internal/mapping/HistoryTest.java
@@ -28,7 +28,7 @@ import org.eclipse.egit.core.test.GitTestCase;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.team.core.RepositoryProvider;
 import org.eclipse.team.core.history.IFileHistory;
@@ -60,7 +60,7 @@ public class HistoryTest extends GitTestCase {
 		// ensure we are working on an empty repository
 		if (gitDir.exists())
 			FileUtils.delete(gitDir, FileUtils.RECURSIVE | FileUtils.RETRY);
-		thisGit = new FileRepository(gitDir);
+		thisGit = FileRepositoryBuilder.create(gitDir);
 		workDir = thisGit.getWorkTree();
 		thisGit.create();
 
diff --git a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/op/CloneOperationTest.java b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/op/CloneOperationTest.java
index e46c41fb46..1ed7b03810 100644
--- a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/op/CloneOperationTest.java
+++ b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/op/CloneOperationTest.java
@@ -28,7 +28,7 @@ import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.RevCommit;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.transport.URIish;
 import org.eclipse.jgit.util.FileUtils;
 import org.junit.Before;
@@ -63,7 +63,7 @@ public class CloneOperationTest extends DualRepositoryTestCase {
 				"refs/heads/master", "origin", 0);
 		clop.run(null);
 
-		Repository clonedRepo = new FileRepository(new File(workdir2,
+		Repository clonedRepo = FileRepositoryBuilder.create(new File(workdir2,
 				Constants.DOT_GIT));
 		assertEquals(
 				"",
@@ -112,7 +112,7 @@ public class CloneOperationTest extends DualRepositoryTestCase {
 		clop.addPostCloneTask(new ConfigurePushAfterCloneTask("origin",
 				"HEAD:refs/for/master", new URIish("file:///pushtarget")));
 		clop.run(null);
-		Repository clonedRepo = new FileRepository(new File(workdir2,
+		Repository clonedRepo = FileRepositoryBuilder.create(new File(workdir2,
 				Constants.DOT_GIT));
 		assertEquals(
 				"",
@@ -140,7 +140,7 @@ public class CloneOperationTest extends DualRepositoryTestCase {
 		clop.addPostCloneTask(new ConfigureFetchAfterCloneTask("origin",
 				"refs/notes/review:refs/notes/review"));
 		clop.run(null);
-		Repository clonedRepo = new FileRepository(new File(workdir2,
+		Repository clonedRepo = FileRepositoryBuilder.create(new File(workdir2,
 				Constants.DOT_GIT));
 		assertTrue(
 				clonedRepo.getConfig()
diff --git a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/op/ConnectProviderOperationTest.java b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/op/ConnectProviderOperationTest.java
index 0adcdb3687..1b67e5daf5 100644
--- a/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/op/ConnectProviderOperationTest.java
+++ b/org.eclipse.egit.core.test/src/org/eclipse/egit/core/test/op/ConnectProviderOperationTest.java
@@ -34,7 +34,7 @@ import org.eclipse.egit.core.test.GitTestCase;
 import org.eclipse.egit.core.test.TestRepository;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.team.core.RepositoryProvider;
 import org.junit.Test;
 
@@ -54,7 +54,7 @@ public class ConnectProviderOperationTest extends GitTestCase {
 	@Test
 	public void testNewRepository() throws CoreException, IOException {
 
-		Repository repository = new FileRepository(gitDir);
+		Repository repository = FileRepositoryBuilder.create(gitDir);
 		repository.create();
 		repository.close();
 		ConnectProviderOperation operation = new ConnectProviderOperation(
@@ -72,7 +72,7 @@ public class ConnectProviderOperationTest extends GitTestCase {
 		IEclipsePreferences p = InstanceScope.INSTANCE.getNode(Activator
 				.getPluginId());
 		p.putBoolean(GitCorePreferences.core_autoIgnoreDerivedResources, true);
-		Repository repository = new FileRepository(gitDir);
+		Repository repository = FileRepositoryBuilder.create(gitDir);
 		repository.create();
 		repository.close();
 		project.setBinFolderDerived();
diff --git a/org.eclipse.egit.core/src/org/eclipse/egit/core/RepositoryCache.java b/org.eclipse.egit.core/src/org/eclipse/egit/core/RepositoryCache.java
index 2ff0867bb2..54a060f475 100644
--- a/org.eclipse.egit.core/src/org/eclipse/egit/core/RepositoryCache.java
+++ b/org.eclipse.egit.core/src/org/eclipse/egit/core/RepositoryCache.java
@@ -22,7 +22,7 @@ import java.util.List;
 import java.util.Map;
 
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 
 /**
  * Central cache for Repository instances
@@ -49,7 +49,7 @@ public class RepositoryCache {
 		Reference<Repository> r = repositoryCache.get(gitDir);
 		Repository d = r != null ? r.get() : null;
 		if (d == null) {
-			d = new FileRepository(gitDir);
+			d = FileRepositoryBuilder.create(gitDir);
 			repositoryCache.put(gitDir, new WeakReference<Repository>(d));
 		}
 		return d;
diff --git a/org.eclipse.egit.core/src/org/eclipse/egit/core/internal/ProjectReferenceImporter.java b/org.eclipse.egit.core/src/org/eclipse/egit/core/internal/ProjectReferenceImporter.java
index 627d684d61..bb15a729ff 100644
--- a/org.eclipse.egit.core/src/org/eclipse/egit/core/internal/ProjectReferenceImporter.java
+++ b/org.eclipse.egit.core/src/org/eclipse/egit/core/internal/ProjectReferenceImporter.java
@@ -40,7 +40,8 @@ import org.eclipse.egit.core.op.ConnectProviderOperation;
 import org.eclipse.jgit.lib.Config;
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.transport.URIish;
 import org.eclipse.osgi.util.NLS;
 import org.eclipse.team.core.TeamException;
@@ -211,9 +212,10 @@ public class ProjectReferenceImporter {
 	private static boolean repositoryAlreadyExistsForUrl(File repositoryPath,
 			URIish gitUrl) {
 		if (repositoryPath.exists()) {
-			FileRepository existingRepository;
+			Repository existingRepository;
 			try {
-				existingRepository = new FileRepository(repositoryPath);
+				existingRepository = FileRepositoryBuilder
+						.create(repositoryPath);
 			} catch (IOException e) {
 				return false;
 			}
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/common/LocalRepositoryTestCase.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/common/LocalRepositoryTestCase.java
index 3327b8cb9f..ecf247ba83 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/common/LocalRepositoryTestCase.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/common/LocalRepositoryTestCase.java
@@ -44,12 +44,14 @@ import org.eclipse.egit.ui.test.ContextMenuHelper;
 import org.eclipse.egit.ui.test.Eclipse;
 import org.eclipse.egit.ui.test.TestUtil;
 import org.eclipse.jface.dialogs.IDialogConstants;
+import org.eclipse.jgit.internal.storage.file.FileRepository;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.RefUpdate;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.lib.RepositoryBuilder;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.transport.URIish;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
@@ -204,7 +206,8 @@ public abstract class LocalRepositoryTestCase extends EGitTestCase {
 
 		File gitDir = new File(new File(testDirectory, repoName),
 				Constants.DOT_GIT);
-		Repository myRepository = new FileRepository(gitDir);
+		Repository myRepository = new RepositoryBuilder().setGitDir(gitDir)
+				.build();
 		myRepository.create();
 
 		// we need to commit into master first
@@ -277,9 +280,9 @@ public abstract class LocalRepositoryTestCase extends EGitTestCase {
 
 	protected static File createRemoteRepository(File repositoryDir)
 			throws Exception {
-		FileRepository myRepository = lookupRepository(repositoryDir);
+		Repository myRepository = lookupRepository(repositoryDir);
 		File gitDir = new File(testDirectory, REPO2);
-		Repository myRemoteRepository = new FileRepository(gitDir);
+		Repository myRemoteRepository = FileRepositoryBuilder.create(gitDir);
 		myRemoteRepository.create();
 		// double-check that this is bare
 		assertTrue(myRemoteRepository.isBare());
@@ -569,7 +572,7 @@ public abstract class LocalRepositoryTestCase extends EGitTestCase {
 	}
 
 	protected static Collection<Ref> getRemoteRefs(URIish uri) throws Exception {
-		final Repository db = new FileRepository(new File("/tmp")); //$NON-NLS-1$
+		final Repository db = FileRepositoryBuilder.create(new File("/tmp")); //$NON-NLS-1$
 		int timeout = 20;
 		ListRemoteOperation listRemoteOp = new ListRemoteOperation(db, uri,
 				timeout);
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/internal/decorators/DecoratableResourceAdapterTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/internal/decorators/DecoratableResourceAdapterTest.java
index f94e9e2d5d..2b13f83ea9 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/internal/decorators/DecoratableResourceAdapterTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/internal/decorators/DecoratableResourceAdapterTest.java
@@ -32,8 +32,8 @@ import org.eclipse.egit.ui.internal.decorators.IDecoratableResource.Staged;
 import org.eclipse.egit.ui.test.TestUtil;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.MergeResult.MergeStatus;
+import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.RevCommit;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
 import org.eclipse.jgit.util.FileUtils;
 import org.junit.After;
 import org.junit.Before;
@@ -64,7 +64,7 @@ public class DecoratableResourceAdapterTest extends LocalRepositoryTestCase {
 		gitDir = createProjectAndCommitToRepository();
 		project = ResourcesPlugin.getWorkspace().getRoot().getProject(PROJ1);
 
-		FileRepository repo = lookupRepository(gitDir);
+		Repository repo = lookupRepository(gitDir);
 		git = new Git(repo);
 		indexDiffCacheEntry = Activator.getDefault().getIndexDiffCache()
 				.getIndexDiffCacheEntry(repo);
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/internal/synchronize/model/GitModelCacheTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/internal/synchronize/model/GitModelCacheTest.java
index 0f7ef5c16f..96235ca235 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/internal/synchronize/model/GitModelCacheTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/internal/synchronize/model/GitModelCacheTest.java
@@ -21,7 +21,7 @@ import org.eclipse.egit.core.synchronize.GitCommitsModelCache.Change;
 import org.eclipse.egit.core.synchronize.StagedChangeCache;
 import org.eclipse.egit.ui.Activator;
 import org.eclipse.jgit.api.Git;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.lib.Repository;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
@@ -102,7 +102,7 @@ public class GitModelCacheTest extends GitModelTestCase {
 
 	@Test
 	public void shouldReturnChildren() throws Exception {
-		FileRepository repo = lookupRepository(leftRepoFile);
+		Repository repo = lookupRepository(leftRepoFile);
 		writeTrashFile(repo, "dir/a.txt", "trash");
 		writeTrashFile(repo, "dir/b.txt", "trash");
 		writeTrashFile(repo, "dir/c.txt", "trash");
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/submodule/SubmoduleAddTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/submodule/SubmoduleAddTest.java
index 870ae5e97f..49ea478a73 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/submodule/SubmoduleAddTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/submodule/SubmoduleAddTest.java
@@ -22,7 +22,7 @@ import org.eclipse.egit.ui.test.ContextMenuHelper;
 import org.eclipse.egit.ui.test.TestUtil;
 import org.eclipse.egit.ui.view.repositories.GitRepositoriesViewTestBase;
 import org.eclipse.jface.dialogs.IDialogConstants;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.lib.Repository;
 import org.eclipse.swtbot.swt.finder.junit.SWTBotJunit4ClassRunner;
 import org.eclipse.swtbot.swt.finder.widgets.SWTBotShell;
 import org.eclipse.swtbot.swt.finder.widgets.SWTBotTree;
@@ -57,7 +57,7 @@ public class SubmoduleAddTest extends GitRepositoriesViewTestBase {
 		assertProjectExistence(PROJ1, true);
 		refreshAndWait();
 		assertHasRepo(repositoryFile);
-		FileRepository repo = lookupRepository(repositoryFile);
+		Repository repo = lookupRepository(repositoryFile);
 
 		SWTBotTree tree = getOrOpenView().bot().tree();
 		tree.getAllItems()[0].select();
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/submodule/SubmoduleSyncTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/submodule/SubmoduleSyncTest.java
index f8972a72b2..07345cb0fc 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/submodule/SubmoduleSyncTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/submodule/SubmoduleSyncTest.java
@@ -27,7 +27,6 @@ import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
 import org.eclipse.jgit.transport.URIish;
 import org.eclipse.swtbot.swt.finder.junit.SWTBotJunit4ClassRunner;
 import org.eclipse.swtbot.swt.finder.widgets.SWTBotTree;
@@ -61,7 +60,7 @@ public class SubmoduleSyncTest extends GitRepositoriesViewTestBase {
 		assertProjectExistence(PROJ1, true);
 		refreshAndWait();
 		assertHasRepo(repositoryFile);
-		FileRepository repo = lookupRepository(repositoryFile);
+		Repository repo = lookupRepository(repositoryFile);
 
 		SubmoduleAddCommand command = new SubmoduleAddCommand(repo);
 		String path = "sub";
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/submodule/SubmoduleUpdateTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/submodule/SubmoduleUpdateTest.java
index a0815bdd67..21f0a0e9e9 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/submodule/SubmoduleUpdateTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/submodule/SubmoduleUpdateTest.java
@@ -29,7 +29,6 @@ import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
 import org.eclipse.jgit.transport.URIish;
 import org.eclipse.swtbot.swt.finder.junit.SWTBotJunit4ClassRunner;
 import org.eclipse.swtbot.swt.finder.widgets.SWTBotTree;
@@ -63,7 +62,7 @@ public class SubmoduleUpdateTest extends GitRepositoriesViewTestBase {
 		assertProjectExistence(PROJ1, true);
 		refreshAndWait();
 		assertHasRepo(repositoryFile);
-		FileRepository repo = lookupRepository(repositoryFile);
+		Repository repo = lookupRepository(repositoryFile);
 		ObjectId repoHead = repo.resolve(Constants.HEAD);
 
 		SubmoduleAddCommand command = new SubmoduleAddCommand(repo);
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/test/team/actions/CreatePatchActionTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/test/team/actions/CreatePatchActionTest.java
index 1bace42a35..656a945cc5 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/test/team/actions/CreatePatchActionTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/test/team/actions/CreatePatchActionTest.java
@@ -33,7 +33,7 @@ import org.eclipse.jgit.api.ResetCommand.ResetType;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.TagBuilder;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.jgit.util.IO;
 import org.eclipse.jgit.util.RawParseUtils;
@@ -107,7 +107,7 @@ public class CreatePatchActionTest extends LocalRepositoryTestCase {
 		perspective = bot.activePerspective();
 		bot.perspectiveById("org.eclipse.pde.ui.PDEPerspective").activate();
 		File gitDir = createProjectAndCommitToRepository();
-		repo = new FileRepository(gitDir);
+		repo = FileRepositoryBuilder.create(gitDir);
 
 		IFile[] commitables = getAllFiles();
 		ArrayList<IFile> untracked = new ArrayList<IFile>();
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/test/team/actions/MergeToolTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/test/team/actions/MergeToolTest.java
index 650fe6a2a9..62bb7ada53 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/test/team/actions/MergeToolTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/test/team/actions/MergeToolTest.java
@@ -28,7 +28,7 @@ import org.eclipse.jface.dialogs.IDialogConstants;
 import org.eclipse.jgit.api.MergeResult;
 import org.eclipse.jgit.api.MergeResult.MergeStatus;
 import org.eclipse.jgit.junit.TestRepository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.lib.Repository;
 import org.eclipse.swtbot.eclipse.finder.widgets.SWTBotEditor;
 import org.eclipse.swtbot.swt.finder.waits.Conditions;
 import org.eclipse.swtbot.swt.finder.widgets.SWTBotShell;
@@ -49,8 +49,8 @@ public class MergeToolTest extends LocalRepositoryTestCase {
 	@Before
 	public void setUp() throws Exception {
 		File repositoryFile = createProjectAndCommitToRepository();
-		FileRepository repository = lookupRepository(repositoryFile);
-		testRepository = new TestRepository<FileRepository>(repository);
+		Repository repository = lookupRepository(repositoryFile);
+		testRepository = new TestRepository<Repository>(repository);
 	}
 
 	@After
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/variables/DynamicVariablesTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/variables/DynamicVariablesTest.java
index e787cd7b38..90e937aa2a 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/variables/DynamicVariablesTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/variables/DynamicVariablesTest.java
@@ -29,7 +29,8 @@ import org.eclipse.jface.viewers.ISelectionProvider;
 import org.eclipse.jface.viewers.StructuredSelection;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.lib.Constants;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.swtbot.swt.finder.junit.SWTBotJunit4ClassRunner;
 import org.eclipse.team.core.RepositoryProvider;
@@ -46,8 +47,8 @@ public class DynamicVariablesTest extends EGitTestCase {
 	private File gitDir2;
 	private IProject project;
 	private IProject project2;
-	private FileRepository repository;
-	private FileRepository repository2;
+	private Repository repository;
+	private Repository repository2;
 	private Git git;
 
 	private static final String TEST_PROJECT = "TestProject";
@@ -65,7 +66,7 @@ public class DynamicVariablesTest extends EGitTestCase {
 		FileUtils.mkdir(new File(root.getLocation().toFile(),"Sub"), true);
 		gitDir = new File(new File(root.getLocation().toFile(), "Sub"), Constants.DOT_GIT);
 
-		repository = new FileRepository(gitDir);
+		repository = FileRepositoryBuilder.create(gitDir);
 		repository.create();
 
 		project = root.getProject(TEST_PROJECT);
@@ -79,7 +80,7 @@ public class DynamicVariablesTest extends EGitTestCase {
 		project2.create(null);
 		project2.open(null);
 		gitDir2 = new File(project2.getLocation().toFile().getAbsoluteFile(), Constants.DOT_GIT);
-		repository2 = new FileRepository(gitDir2);
+		repository2 = FileRepositoryBuilder.create(gitDir2);
 		repository2.create();
 
 		RepositoryMapping mapping = new RepositoryMapping(project, gitDir);
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/repositories/GitRepositoriesViewBranchHandlingTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/repositories/GitRepositoriesViewBranchHandlingTest.java
index 1a074c0c7d..cb65d9a8ba 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/repositories/GitRepositoriesViewBranchHandlingTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/repositories/GitRepositoriesViewBranchHandlingTest.java
@@ -38,7 +38,7 @@ import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.transport.URIish;
 import org.eclipse.osgi.util.NLS;
 import org.eclipse.swtbot.eclipse.finder.widgets.SWTBotPerspective;
@@ -378,7 +378,7 @@ public class GitRepositoriesViewBranchHandlingTest extends
 
 		String title = NLS.bind(
 				UIText.MergeTargetSelectionDialog_TitleMergeWithBranch,
-				new FileRepository(clonedRepositoryFile).getBranch());
+				FileRepositoryBuilder.create(clonedRepositoryFile).getBranch());
 
 		SWTBotShell mergeDialog = bot.shell(title);
 		// TODO do some merge here
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/repositories/GitRepositoriesViewFetchAndPushTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/repositories/GitRepositoriesViewFetchAndPushTest.java
index 230267c8ee..692f9ea351 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/repositories/GitRepositoriesViewFetchAndPushTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/repositories/GitRepositoriesViewFetchAndPushTest.java
@@ -26,7 +26,6 @@ import org.eclipse.egit.ui.test.JobJoiner;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
 import org.eclipse.jgit.transport.URIish;
 import org.eclipse.osgi.util.NLS;
 import org.eclipse.swtbot.swt.finder.junit.SWTBotJunit4ClassRunner;
@@ -189,7 +188,7 @@ public class GitRepositoriesViewFetchAndPushTest extends
 		Activator.getDefault().getRepositoryUtil().addConfiguredRepository(
 				clonedRepositoryFile2);
 
-		FileRepository repository = lookupRepository(clonedRepositoryFile2);
+		Repository repository = lookupRepository(clonedRepositoryFile2);
 		// add the configuration for push from cloned2
 		repository.getConfig().setString("remote", "origin", "push",
 				"refs/heads/*:refs/heads/*");
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/repositories/GitRepositoriesViewRepoDeletionTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/repositories/GitRepositoriesViewRepoDeletionTest.java
index 4aa74d218a..bf76143e3e 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/repositories/GitRepositoriesViewRepoDeletionTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/repositories/GitRepositoriesViewRepoDeletionTest.java
@@ -21,7 +21,6 @@ import org.eclipse.egit.ui.test.TestUtil;
 import org.eclipse.jface.dialogs.IDialogConstants;
 import org.eclipse.jgit.api.SubmoduleAddCommand;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
 import org.eclipse.osgi.util.NLS;
 import org.eclipse.swtbot.swt.finder.junit.SWTBotJunit4ClassRunner;
 import org.eclipse.swtbot.swt.finder.widgets.SWTBotShell;
@@ -63,7 +62,7 @@ public class GitRepositoriesViewRepoDeletionTest extends
 				.getPluginLocalizedValue(DELETE_REPOSITORY_CONTEXT_MENU_LABEL));
 		SWTBotShell shell = bot.shell(UIText.DeleteRepositoryConfirmDialog_DeleteRepositoryWindowTitle);
 		shell.activate();
-		FileRepository repo = lookupRepository(repositoryFile);
+		Repository repo = lookupRepository(repositoryFile);
 		String workDir=repo.getWorkTree().getPath();
 		String checkboxLabel = NLS
 				.bind(UIText.DeleteRepositoryConfirmDialog_DeleteWorkingDirectoryCheckbox,
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/synchronize/AbstractSynchronizeViewTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/synchronize/AbstractSynchronizeViewTest.java
index d2a8766497..b5d054e4b4 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/synchronize/AbstractSynchronizeViewTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/synchronize/AbstractSynchronizeViewTest.java
@@ -49,7 +49,7 @@ import org.eclipse.egit.ui.test.TestUtil;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.jgit.util.StringUtils;
 import org.eclipse.swtbot.eclipse.finder.widgets.SWTBotEditor;
@@ -203,7 +203,7 @@ public abstract class AbstractSynchronizeViewTest extends
 	protected void createEmptyRepository() throws Exception {
 		File gitDir = new File(new File(getTestDirectory(), EMPTY_REPOSITORY),
 				Constants.DOT_GIT);
-		Repository myRepository = new FileRepository(gitDir);
+		Repository myRepository = FileRepositoryBuilder.create(gitDir);
 		myRepository.create();
 
 		// we need to commit into master first
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/synchronize/SynchronizeViewGitChangeSetModelTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/synchronize/SynchronizeViewGitChangeSetModelTest.java
index 878c250548..eab89b8b56 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/synchronize/SynchronizeViewGitChangeSetModelTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/synchronize/SynchronizeViewGitChangeSetModelTest.java
@@ -39,7 +39,7 @@ import org.eclipse.egit.ui.internal.UIText;
 import org.eclipse.egit.ui.internal.synchronize.GitChangeSetModelProvider;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.Status;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.lib.Repository;
 import org.eclipse.swt.widgets.Display;
 import org.eclipse.swt.widgets.Label;
 import org.eclipse.swtbot.eclipse.finder.widgets.SWTBotEditor;
@@ -316,7 +316,7 @@ public class SynchronizeViewGitChangeSetModelTest extends
 
 
 		// then file FILE1 should be in index
-		FileRepository repo = lookupRepository(repositoryFile);
+		Repository repo = lookupRepository(repositoryFile);
 		Status status = new Git(repo).status().call();
 		assertThat(Long.valueOf(status.getChanged().size()),
 				is(Long.valueOf(1L)));
@@ -341,7 +341,7 @@ public class SynchronizeViewGitChangeSetModelTest extends
 		bot.activeEditor().save();
 
 		// then file FILE1 should be unchanged in working tree
-		FileRepository repo = lookupRepository(repositoryFile);
+		Repository repo = lookupRepository(repositoryFile);
 		Status status = new Git(repo).status().call();
 		assertThat(Long.valueOf(status.getModified().size()),
 				is(Long.valueOf(1)));
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/synchronize/SynchronizeViewPushTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/synchronize/SynchronizeViewPushTest.java
index 118b109bf2..a255cdaeb1 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/synchronize/SynchronizeViewPushTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/view/synchronize/SynchronizeViewPushTest.java
@@ -20,8 +20,8 @@ import org.eclipse.egit.ui.test.JobJoiner;
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
-import org.eclipse.jgit.storage.file.FileBasedConfig;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.transport.RemoteConfig;
 import org.eclipse.jgit.transport.URIish;
@@ -39,10 +39,10 @@ public class SynchronizeViewPushTest extends AbstractSynchronizeViewTest {
 
 	@Before
 	public void prepare() throws Exception {
-		FileRepository childRepository = lookupRepository(childRepositoryFile);
+		Repository childRepository = lookupRepository(childRepositoryFile);
 
-		FileRepository repository = lookupRepository(repositoryFile);
-		FileBasedConfig config = repository.getConfig();
+		Repository repository = lookupRepository(repositoryFile);
+		StoredConfig config = repository.getConfig();
 		RemoteConfig remoteConfig = new RemoteConfig(config, "origin");
 		remoteConfig.addURI(new URIish(childRepository.getDirectory().getParentFile().toURI().toURL()));
 		remoteConfig.addFetchRefSpec(new RefSpec("+refs/heads/*:refs/remotes/origin/*"));
@@ -59,7 +59,7 @@ public class SynchronizeViewPushTest extends AbstractSynchronizeViewTest {
 	@Test
 	public void shouldUpdateTrackingBranchOnPush() throws Exception {
 		makeChangesAndCommit(PROJ1);
-		FileRepository repository = lookupRepository(repositoryFile);
+		Repository repository = lookupRepository(repositoryFile);
 		ObjectId headId = repository.resolve(Constants.HEAD);
 
 		String trackingBranch = Constants.R_REMOTES + "origin/master";
@@ -75,7 +75,7 @@ public class SynchronizeViewPushTest extends AbstractSynchronizeViewTest {
 		SWTBotShell resultDialog = bot.shell(NLS.bind(UIText.ResultDialog_title, destinationString));
 		resultDialog.close();
 
-		FileRepository remoteRepository = lookupRepository(childRepositoryFile);
+		Repository remoteRepository = lookupRepository(childRepositoryFile);
 		ObjectId masterOnRemote = remoteRepository.resolve("master");
 		assertThat("Expected push to update branch on remote repository", masterOnRemote, is(headId));
 
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/wizards/clone/GitCloneWizardTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/wizards/clone/GitCloneWizardTest.java
index ecd360aa8e..fe4bfd2d28 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/wizards/clone/GitCloneWizardTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/wizards/clone/GitCloneWizardTest.java
@@ -25,7 +25,7 @@ import org.eclipse.egit.ui.common.WorkingCopyPage;
 import org.eclipse.egit.ui.internal.UIText;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.osgi.util.NLS;
 import org.junit.BeforeClass;
 import org.junit.Ignore;
@@ -225,7 +225,8 @@ public class GitCloneWizardTest extends GitCloneWizardTestBase {
 		// the integrity of the repository here. Only a few basic properties
 		// we'd expect from a clone made this way, that would possibly
 		// not hold true given other parameters in the GUI.
-		Repository repository = new FileRepository(new File(destRepo, Constants.DOT_GIT));
+		Repository repository = FileRepositoryBuilder.create(new File(destRepo,
+				Constants.DOT_GIT));
 		assertNotNull(repository.resolve("src/" + SampleTestRepository.FIX));
 		// we didn't clone that one
 		assertNull(repository.resolve("src/master"));
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/wizards/clone/GitCloneWizardTestBase.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/wizards/clone/GitCloneWizardTestBase.java
index 3a5308edbf..51a53326f4 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/wizards/clone/GitCloneWizardTestBase.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/wizards/clone/GitCloneWizardTestBase.java
@@ -29,7 +29,7 @@ import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.util.FileUtils;
 import org.junit.After;
 import org.junit.AfterClass;
@@ -72,8 +72,8 @@ public abstract class GitCloneWizardTestBase extends LocalRepositoryTestCase {
 		// the integrity of the repository here. Only a few basic properties
 		// we'd expect from a clone made this way, that would possibly
 		// not hold true given other parameters in the GUI.
-		Repository repository = new FileRepository(new File(destinationRepo,
-				Constants.DOT_GIT));
+		Repository repository = FileRepositoryBuilder.create(new File(
+				destinationRepo, Constants.DOT_GIT));
 		// we always have an origin/master
 		assertNotNull(repository.resolve("origin/master"));
 		// and a local master initialized from origin/master (default!)
diff --git a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/wizards/share/SharingWizardTest.java b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/wizards/share/SharingWizardTest.java
index a973aa99c2..f47b35c963 100644
--- a/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/wizards/share/SharingWizardTest.java
+++ b/org.eclipse.egit.ui.test/src/org/eclipse/egit/ui/wizards/share/SharingWizardTest.java
@@ -46,7 +46,7 @@ import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.junit.MockSystemReader;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.jgit.util.SystemReader;
 import org.eclipse.swtbot.swt.finder.junit.SWTBotJunit4ClassRunner;
@@ -193,15 +193,15 @@ public class SharingWizardTest extends LocalRepositoryTestCase {
 	@Test
 	public void shareProjectWithAlreadyCreatedRepos() throws IOException,
 			InterruptedException, JGitInternalException, GitAPIException {
-		FileRepository repo1 = new FileRepository(new File(
+		Repository repo1 = FileRepositoryBuilder.create(new File(
 				createProject(projectName1), "../.git"));
 		repo1.create();
 		repo1.close();
-		FileRepository repo2 = new FileRepository(new File(
+		Repository repo2 = FileRepositoryBuilder.create(new File(
 				createProject(projectName2), ".git"));
 		repo2.create();
 		repo2.close();
-		FileRepository repo3 = new FileRepository(new File(
+		Repository repo3 = FileRepositoryBuilder.create(new File(
 				createProject(projectName3), ".git"));
 		repo3.create();
 		Git git = new Git(repo3);
diff --git a/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/clone/GitSelectRepositoryPage.java b/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/clone/GitSelectRepositoryPage.java
index de3502bd4a..d3d0302641 100644
--- a/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/clone/GitSelectRepositoryPage.java
+++ b/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/clone/GitSelectRepositoryPage.java
@@ -43,7 +43,7 @@ import org.eclipse.jface.window.Window;
 import org.eclipse.jface.wizard.WizardDialog;
 import org.eclipse.jface.wizard.WizardPage;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.swt.SWT;
 import org.eclipse.swt.events.SelectionAdapter;
 import org.eclipse.swt.events.SelectionEvent;
@@ -217,8 +217,8 @@ public class GitSelectRepositoryPage extends WizardPage {
 			for (String dir : dirsAfter)
 				if (!dirsBefore.contains(dir))
 					try {
-						RepositoryNode node = new RepositoryNode(
-								null, new FileRepository(new File(dir)));
+						RepositoryNode node = new RepositoryNode(null,
+								FileRepositoryBuilder.create(new File(dir)));
 						tv.setSelection(new StructuredSelection(
 								node));
 					} catch (IOException e1) {
diff --git a/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/clone/SourceBranchPage.java b/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/clone/SourceBranchPage.java
index 291a7aa9d6..a8c414193d 100644
--- a/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/clone/SourceBranchPage.java
+++ b/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/clone/SourceBranchPage.java
@@ -49,7 +49,7 @@ import org.eclipse.jgit.api.errors.TransportException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.transport.URIish;
 import org.eclipse.osgi.util.NLS;
 import org.eclipse.swt.SWT;
@@ -308,7 +308,8 @@ class SourceBranchPage extends WizardPage {
 		final ListRemoteOperation listRemoteOp;
 		try {
 			final URIish uri = newRepoSelection.getURI();
-			final Repository db = new FileRepository(new File("/tmp")); //$NON-NLS-1$
+			final Repository db = FileRepositoryBuilder
+					.create(new File("/tmp")); //$NON-NLS-1$
 			int timeout = Activator.getDefault().getPreferenceStore().getInt(
 					UIPreferences.REMOTE_CONNECTION_TIMEOUT);
 			listRemoteOp = new ListRemoteOperation(db, uri, timeout);
diff --git a/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/repository/tree/LinkHelper.java b/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/repository/tree/LinkHelper.java
index bfb61af90a..becc5d0469 100644
--- a/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/repository/tree/LinkHelper.java
+++ b/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/repository/tree/LinkHelper.java
@@ -24,7 +24,7 @@ import org.eclipse.egit.ui.internal.repository.RepositoriesViewContentProvider;
 import org.eclipse.jface.viewers.IStructuredSelection;
 import org.eclipse.jface.viewers.StructuredSelection;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.ui.IEditorInput;
 import org.eclipse.ui.IEditorPart;
 import org.eclipse.ui.IEditorReference;
@@ -95,7 +95,7 @@ public class LinkHelper implements ILinkHelper {
 		for (String repo : repos) {
 			Repository repository;
 			try {
-				repository = new FileRepository(new File(repo));
+				repository = FileRepositoryBuilder.create(new File(repo));
 			} catch (IOException e) {
 				continue;
 			}
diff --git a/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/sharing/ExistingOrNewPage.java b/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/sharing/ExistingOrNewPage.java
index df09fc0aef..4954a99158 100644
--- a/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/sharing/ExistingOrNewPage.java
+++ b/org.eclipse.egit.ui/src/org/eclipse/egit/ui/internal/sharing/ExistingOrNewPage.java
@@ -52,10 +52,11 @@ import org.eclipse.jface.wizard.WizardPage;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.RepositoryBuilder;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevTree;
 import org.eclipse.jgit.revwalk.RevWalk;
-import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.osgi.util.NLS;
 import org.eclipse.swt.SWT;
@@ -377,7 +378,8 @@ class ExistingOrNewPage extends WizardPage {
 				File gitDir = new File(repositoryToCreate.getText(),
 						Constants.DOT_GIT);
 				try {
-					Repository repository = new FileRepository(gitDir);
+					Repository repository = FileRepositoryBuilder
+							.create(gitDir);
 					repository.create();
 					for (IProject project : getProjects(false).keySet()) {
 						// If we don't refresh the project directories right
@@ -510,8 +512,8 @@ class ExistingOrNewPage extends WizardPage {
 			treeItem.setText(2, relativePath.toOSString());
 			try {
 				IProject project = m.getContainer().getProject();
-				FileRepository repo = new FileRepository(m
-						.getGitDirAbsolutePath().toFile());
+				Repository repo = new RepositoryBuilder().setGitDir(
+						m.getGitDirAbsolutePath().toFile()).build();
 				File workTree = repo.getWorkTree();
 				IPath workTreePath = Path.fromOSString(workTree
 						.getAbsolutePath());