diff --git a/src/Gitonomy/Git/Admin.php b/src/Gitonomy/Git/Admin.php
index 7b32794..41a7862 100644
--- a/src/Gitonomy/Git/Admin.php
+++ b/src/Gitonomy/Git/Admin.php
@@ -98,12 +98,13 @@ public static function isValidRepositoryAndBranch($url, $branchName, array $opti
      * @param string $url     url of repository to clone
      * @param bool   $bare    indicates if repository should be bare or have a working copy
      * @param array  $options options for Repository creation
+     * @param array  $args    arguments to be added to the command-line
      *
      * @return Repository
      */
-    public static function cloneTo($path, $url, $bare = true, array $options = [])
+    public static function cloneTo($path, $url, $bare = true, array $options = [], array $args = [])
     {
-        $args = $bare ? ['--bare'] : [];
+        $args = array_merge($args,$bare ? ['--bare'] : []);
 
         return static::cloneRepository($path, $url, $args, $options);
     }
diff --git a/src/Gitonomy/Git/Repository.php b/src/Gitonomy/Git/Repository.php
index fe77a88..82b10fd 100644
--- a/src/Gitonomy/Git/Repository.php
+++ b/src/Gitonomy/Git/Repository.php
@@ -166,9 +166,19 @@ private function initDir($gitDir, $workingDir = null)
             throw new InvalidArgumentException(sprintf('Directory "%s" does not exist or is not a directory', $gitDir));
         } elseif (!is_dir($realGitDir)) {
             throw new InvalidArgumentException(sprintf('Directory "%s" does not exist or is not a directory', $realGitDir));
-        } elseif (null === $workingDir && is_dir($realGitDir.'/.git')) {
+        } elseif (null === $workingDir && is_file($realGitDir . '/.git')) {
+            if (!preg_match('/^gitdir: ?(.+)$/', file_get_contents($realGitDir . '/.git'), $matches)) {
+                throw new InvalidArgumentException(sprintf('Directory "%s" contains a .git file, but it is not in the expected format', $realGitDir));
+            }
+            $foundGitPath = realpath($realGitDir . DIRECTORY_SEPARATOR . $matches[1]);
+            if (!is_dir($foundGitPath)) {
+                throw new InvalidArgumentException(sprintf('Directory "%s" contains a .git file, but the directory it points to cannot be found', $realGitDir));
+            }
+            $workingDir = $realGitDir;
+            $realGitDir = $foundGitPath;
+        } elseif (null === $workingDir && is_dir($realGitDir . '/.git')) {
             $workingDir = $realGitDir;
-            $realGitDir = $realGitDir.'/.git';
+            $realGitDir = $realGitDir . '/.git';
         }
 
         $this->gitDir = $realGitDir;
@@ -598,12 +608,14 @@ public function getLogger()
      *
      * @param string $path path to the new repository in which current repository will be cloned
      * @param bool   $bare flag indicating if repository is bare or has a working-copy
+     * @param array  $options options for Repository creation
+     * @param array  $args arguments to be added to the command-line
      *
      * @return Repository the newly created repository
      */
-    public function cloneTo($path, $bare = true, array $options = [])
+    public function cloneTo($path, $bare = true, array $options = [], array $args = [])
     {
-        return Admin::cloneTo($path, $this->gitDir, $bare, $options);
+        return Admin::cloneTo($path, $this->gitDir, $bare, $options, $args);
     }
 
     /**
diff --git a/tests/Gitonomy/Git/Tests/AbstractTest.php b/tests/Gitonomy/Git/Tests/AbstractTest.php
index 0b9a51b..3731208 100644
--- a/tests/Gitonomy/Git/Tests/AbstractTest.php
+++ b/tests/Gitonomy/Git/Tests/AbstractTest.php
@@ -39,7 +39,7 @@ abstract class AbstractTest extends TestCase
      *
      * @return Repository
      */
-    public static function createEmptyRepository($bare = true)
+    public static function createEmptyRepository($bare = true, $separateGitDir = false)
     {
         $dir = self::createTempDir();
         $repository = Admin::init($dir, $bare, self::getOptions());
@@ -56,6 +56,7 @@ public static function provideFoobar()
         return [
             [self::createFoobarRepository()],
             [self::createFoobarRepository(false)],
+            [self::createFoobarRepository(false, true)]
         ];
     }
 
@@ -75,10 +76,12 @@ public static function provideEmpty()
      *
      * @return Repository
      */
-    public static function createFoobarRepository($bare = true)
+    public static function createFoobarRepository($bare = true, $separateGitDirectory = false)
     {
+        $args = $separateGitDirectory ? ['--separate-git-dir=' . tempnam(sys_get_temp_dir(), 'gitlib_')] : [];
+
         if (null === self::$localRepository) {
-            self::$localRepository = Admin::cloneTo(self::createTempDir(), self::REPOSITORY_URL, $bare, self::getOptions());
+            self::$localRepository = Admin::cloneTo(self::createTempDir(), self::REPOSITORY_URL, $bare, self::getOptions(), $args);
         }
 
         $repository = self::$localRepository->cloneTo(self::createTempDir(), $bare, self::getOptions());