diff -u b/core/includes/file.inc b/core/includes/file.inc
--- b/core/includes/file.inc
+++ b/core/includes/file.inc
@@ -1443,32 +1443,37 @@
   $files = array();
   // Avoid warnings when opendir does not have the permissions to open a
   // directory.
-  if (is_dir($dir) && $handle = @opendir($dir)) {
-    while (FALSE !== ($filename = readdir($handle))) {
-      if (!preg_match($options['nomask'], $filename) && $filename[0] != '.') {
-        $uri = "$dir/$filename";
-        $uri = file_stream_wrapper_uri_normalize($uri);
-        if (is_dir($uri) && $options['recurse']) {
-          // Give priority to files in this folder by merging them in after any subdirectory files.
-          $files = array_merge(file_scan_directory($uri, $mask, $options, $depth + 1), $files);
-        }
-        elseif ($depth >= $options['min_depth'] && preg_match($mask, $filename)) {
-          // Always use this match over anything already set in $files with the
-          // same $$options['key'].
-          $file = new stdClass();
-          $file->uri = $uri;
-          $file->filename = $filename;
-          $file->name = pathinfo($filename, PATHINFO_FILENAME);
-          $key = $options['key'];
-          $files[$file->$key] = $file;
-          if ($options['callback']) {
-            $options['callback']($uri);
+  if (is_dir($dir)) {
+    if($handle = @opendir($dir)) {
+      while (FALSE !== ($filename = readdir($handle))) {
+        if (!preg_match($options['nomask'], $filename) && $filename[0] != '.') {
+          $uri = "$dir/$filename";
+          $uri = file_stream_wrapper_uri_normalize($uri);
+          if (is_dir($uri) && $options['recurse']) {
+            // Give priority to files in this folder by merging them in after any subdirectory files.
+            $files = array_merge(file_scan_directory($uri, $mask, $options, $depth + 1), $files);
+          }
+          elseif ($depth >= $options['min_depth'] && preg_match($mask, $filename)) {
+            // Always use this match over anything already set in $files with the
+            // same $$options['key'].
+            $file = new stdClass();
+            $file->uri = $uri;
+            $file->filename = $filename;
+            $file->name = pathinfo($filename, PATHINFO_FILENAME);
+            $key = $options['key'];
+            $files[$file->$key] = $file;
+            if ($options['callback']) {
+              $options['callback']($uri);
+            }
           }
         }
       }
-    }
 
-    closedir($handle);
+      closedir($handle);
+    }
+    else {
+      watchdog('file', '@dir can not be opened', array('@dir' => $dir), WATCHDOG_ERROR);
+    }
   }
 
   return $files;
diff -u b/core/includes/install.core.inc b/core/includes/install.core.inc
--- b/core/includes/install.core.inc
+++ b/core/includes/install.core.inc
@@ -1466,10 +1466,6 @@
   module_list_reset();
 
   // Instantiate a new kernel that will not compile the container.
-  // @todo The first two constructor parameters for the Kernel class are for
-  //   environment, e.g. 'prod', 'dev', and a boolean indicating whether it is
-  //   in debug mode. Drupal does not currently make use of either of these,
-  //   though that may change with http://drupal.org/node/1537198.
   $kernel = new DrupalKernel('prod', FALSE, NULL, FALSE);
   $kernel->boot();
   drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
diff -u b/core/includes/module.inc b/core/includes/module.inc
--- b/core/includes/module.inc
+++ b/core/includes/module.inc
@@ -188,16 +188,13 @@
         // Build a list of all enabled modules.
         $lists['module_enabled'][$name] = $name;
         // Build a list of filenames so drupal_get_filename can use it.
-        $lists['filepaths'][] = array(
+        $lists['filepaths'][$name] = array(
           'type' => 'module',
           'name' => $name,
           'filepath' => $module_files[$name],
         );
       }
 
-      // Store a hash of the enabled modules for use when compiling the DIC.
-      $lists['module_enabled_hash'] = hash('sha256', implode(',', array_keys($lists['module_enabled'])));
-
       // Build a list of themes.
       $enabled_themes = config('system.theme')->get('enabled');
       // @todo Themes include all themes, including disabled/uninstalled. This
@@ -218,7 +215,7 @@
         $lists['theme'][$name] = $theme;
         // Build a list of filenames so drupal_get_filename can use it.
         if (isset($enabled_themes[$name])) {
-          $lists['filepaths'][] = array(
+          $lists['filepaths'][$name] = array(
             'type' => 'theme',
             'name' => $name,
             'filepath' => $theme->filename,
@@ -252,6 +249,9 @@
         // Set the theme engine prefix.
         $lists['theme'][$key]->prefix = ($lists['theme'][$key]->info['engine'] == 'theme') ? $base_key : $lists['theme'][$key]->info['engine'];
       }
+      // Store a hash of the enabled modules for use when compiling the DIC.
+      $lists['system_list_hash'] = hash('sha256', implode(',', array_keys($lists['filepaths'])));
+
       cache('bootstrap')->set('system_list', $lists);
     }
     // To avoid a separate database lookup for the filepath, prime the
diff -u b/core/lib/Drupal/Core/DrupalKernel.php b/core/lib/Drupal/Core/DrupalKernel.php
--- b/core/lib/Drupal/Core/DrupalKernel.php
+++ b/core/lib/Drupal/Core/DrupalKernel.php
@@ -48,7 +48,20 @@
    */
   protected $storage;
 
-  public function __construct($environment, $debug, $system_list = NULL, $use_compiled_container = TRUE) {
+  /**
+   * @todo The first two constructor parameters for the Kernel class are for
+   *   environment, e.g. 'prod', 'dev', and a boolean indicating whether it is
+   *   in debug mode. Drupal does not currently make use of either of these,
+   *   though that may change with http://drupal.org/node/1537198.
+   *
+   * @param string $environment
+   * @param bool $debug
+   * @param array $system_list
+   *   The same data structure as system_list().
+   * @param bool $use_compiled_container
+   *   Whether to compile the container to disk or not.
+   */
+  public function __construct($environment, $debug, array $system_list = NULL, $use_compiled_container = TRUE) {
     parent::__construct($environment, $debug);
     $this->useCompiledContainer = $use_compiled_container;
     $this->storage = drupal_php_storage('service_container');
@@ -102,11 +115,8 @@
    *   the old files. See http://drupal.org/node/1759582.
    */
   protected function initializeContainer() {
-    if (!$this->useCompiledContainer) {
-      // In debug mode we do not use a compiled container.
-      $this->container = $this->buildContainer();
-    }
-    else {
+    $this->container = NULL;
+    if ($this->useCompiledContainer) {
       // While the default Symfony class name only depends on the environment, for
       // testing purposes we can't use that because there would be a collision as
       // each test method creates a new kernel. On the other hand, the container
@@ -118,7 +128,7 @@
       // needing to rebuild the DIC at the right time on module enable: simply on
       // the next request the hash will change and so the container will be
       // rebuilt.
-      $class = 'c' . $this->systemList['module_enabled_hash'] . ucfirst($this->environment) . ($this->debug ? 'Debug' : '');
+      $class = 'c' . $this->systemList['system_list_hash'] . ucfirst($this->environment) . ($this->debug ? 'Debug' : '');
       $cache_file = $class . '.php';
 
       // First, try to load.
@@ -127,15 +137,16 @@
       }
       // If the load succeeded or the class already existed, use it.
       if (class_exists($class)) {
-        $this->container = new $class;
+        $fully_qualified_classname = '\\' . $class;
+        $this->container = new $fully_qualified_classname;
       }
-      else {
-        $this->container = $this->buildContainer();
-        if (!$this->dumpDrupalContainer($cache_file, $this->container, $class, $this->getContainerBaseClass())) {
-          // We want to log this as an error but we cannot call watchdog() until
-          // the container has been fully built and set in drupal_container().
-          $error = 'Container cannot be written to disk';
-        }
+    }
+    if (!isset($this->container)) {
+      $this->container = $this->buildContainer();
+      if ($this->useCompiledContainer && !$this->dumpDrupalContainer($cache_file, $this->container, $class, $this->getContainerBaseClass())) {
+        // We want to log this as an error but we cannot call watchdog() until
+        // the container has been fully built and set in drupal_container().
+        $error = 'Container cannot be written to disk';
       }
     }