diff --git a/org.eclipse.jgit.java7.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.java7.test/META-INF/MANIFEST.MF
index 8847a34d3..78764801c 100644
--- a/org.eclipse.jgit.java7.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.java7.test/META-INF/MANIFEST.MF
@@ -5,6 +5,10 @@ Bundle-SymbolicName: org.eclipse.jgit.java7.test
 Bundle-Version: 3.1.0.qualifier
 Bundle-Vendor: %provider_name
 Bundle-RequiredExecutionEnvironment: JavaSE-1.7
-Import-Package: org.eclipse.jgit.junit;version="[3.1.0,3.2.0)",
+Import-Package: org.eclipse.jgit.api;version="[3.1.0,3.2.0)",
+ org.eclipse.jgit.internal.storage.file;version="3.1.0",
+ org.eclipse.jgit.junit;version="[3.1.0,3.2.0)",
  org.eclipse.jgit.lib;version="[3.1.0,3.2.0)",
+ org.eclipse.jgit.revwalk;version="[3.1.0,3.2.0)",
+ org.eclipse.jgit.storage.file;version="[3.1.0,3.2.0)",
  org.eclipse.jgit.util;version="[3.1.0,3.2.0)"
diff --git a/org.eclipse.jgit.java7.test/src/org/eclipse/jgit/lib/DirCacheCheckoutTestWithSymlinks.java b/org.eclipse.jgit.java7.test/src/org/eclipse/jgit/lib/DirCacheCheckoutTestWithSymlinks.java
new file mode 100644
index 000000000..b0d31cd37
--- /dev/null
+++ b/org.eclipse.jgit.java7.test/src/org/eclipse/jgit/lib/DirCacheCheckoutTestWithSymlinks.java
@@ -0,0 +1,99 @@
+/*
+ * Copyright (C) 2013, Christian Halstrick <christian.halstrick@sap.com>
+ * 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.assertTrue;
+
+import java.io.File;
+
+import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
+import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.util.FileUtils;
+import org.junit.Before;
+import org.junit.Test;
+
+public class DirCacheCheckoutTestWithSymlinks extends RepositoryTestCase {
+	@Before
+	public void beforeMethod() {
+		// If this assumption fails the tests are skipped. When running on a
+		// filesystem not supporting symlinks I don't want this tests
+		org.junit.Assume.assumeTrue(FS.DETECTED.supportsSymlinks());
+	}
+
+	@Test
+	public void testDontDeleteSymlinkOnTopOfRootDir() throws Exception {
+		// create a parent folder containing a folder with a test repository
+		File repos = createTempDirectory("repos");
+		File testRepo = new File(repos, "repo");
+		testRepo.mkdirs();
+		Git git = Git.init().setDirectory(testRepo).call();
+		db = (FileRepository) git.getRepository();
+
+		// Create a situation where a checkout of master whould delete a file in
+		// a subfolder of the root of the worktree. No other files/folders exist
+		writeTrashFile("d/f", "f");
+		git.add().addFilepattern(".").call();
+		RevCommit initial = git.commit().setMessage("inital").call();
+		git.rm().addFilepattern("d/f").call();
+		git.commit().setMessage("modifyOnMaster").call();
+		git.checkout().setCreateBranch(true).setName("side")
+				.setStartPoint(initial).call();
+		writeTrashFile("d/f", "f2");
+		git.add().addFilepattern(".").call();
+		git.commit().setMessage("modifyOnSide").call();
+		git.getRepository().close();
+
+		// Create a symlink pointing to the parent folder of the repo and open
+		// the repo with the path containing the symlink
+		File reposSymlink = createTempFile();
+		FileUtils.createSymLink(reposSymlink, repos.getPath());
+
+		Repository symlinkDB = FileRepositoryBuilder.create(new File(
+				reposSymlink, "repo/.git"));
+		Git symlinkRepo = Git.wrap(symlinkDB);
+		symlinkRepo.checkout().setName("master").call();
+
+		// check that the symlink still exists
+		assertTrue("The symlink to the repo should exist after a checkout",
+				reposSymlink.exists());
+	}
+}
diff --git a/org.eclipse.jgit/META-INF/MANIFEST.MF b/org.eclipse.jgit/META-INF/MANIFEST.MF
index 1ddc1cf91..429e2693d 100644
--- a/org.eclipse.jgit/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit/META-INF/MANIFEST.MF
@@ -16,8 +16,12 @@ Export-Package: org.eclipse.jgit.api;version="3.1.0",
  org.eclipse.jgit.ignore;version="3.1.0",
  org.eclipse.jgit.internal;version="3.1.0";x-friends:="org.eclipse.jgit.test,org.eclipse.jgit.http.test",
  org.eclipse.jgit.internal.storage.dfs;version="3.1.0";x-friends:="org.eclipse.jgit.test",
- org.eclipse.jgit.internal.storage.file;version="3.1.0";x-friends:="org.eclipse.jgit.test,
- 	org.eclipse.jgit.junit,org.eclipse.jgit.junit.http,org.eclipse.jgit.http.server",
+ org.eclipse.jgit.internal.storage.file;version="3.1.0";
+  x-friends:="org.eclipse.jgit.test,
+   org.eclipse.jgit.junit,
+   org.eclipse.jgit.junit.http,
+   org.eclipse.jgit.http.server,
+   org.eclipse.jgit.java7.test",
  org.eclipse.jgit.internal.storage.pack;version="3.1.0";x-friends:="org.eclipse.jgit.test",
  org.eclipse.jgit.lib;version="3.1.0",
  org.eclipse.jgit.merge;version="3.1.0",