diff --git a/core/includes/module.inc b/core/includes/module.inc
index 6064e05..b5d189c 100644
--- a/core/includes/module.inc
+++ b/core/includes/module.inc
@@ -41,7 +41,7 @@ function system_list($type) {
       'filepaths' => array(),
     );
     // Build a list of themes.
-    $enabled_themes = (array) \Drupal::config('core.extension')->get('theme');
+    $enabled_themes = \Drupal::config('core.extension')->get('theme') ?: array();
     // @todo Themes include all themes, including disabled/uninstalled. This
     //   system.theme.data state will go away entirely as soon as themes have
     //   a proper installation status.
diff --git a/core/includes/update.inc b/core/includes/update.inc
index 0bca244..56fc1ff 100644
--- a/core/includes/update.inc
+++ b/core/includes/update.inc
@@ -23,21 +23,22 @@
  * Disables any extensions that are incompatible with the current core version.
  */
 function update_fix_compatibility() {
+  $extension_config = \Drupal::config('core.extension');
+  $save = FALSE;
   foreach (array('module', 'theme') as $type) {
-    $config = \Drupal::config("system.$type");
-    $save = FALSE;
-    foreach ($config->get('enabled') as $name => $weight) {
+    foreach ($extension_config->get($type) as $name => $weight) {
       if (update_check_incompatibility($name, $type)) {
-        $config->clear("enabled.$name");
+        $extension_config->clear("$type.$name");
+        if ($type === 'theme') {
+          $extension_config->set("disabled.theme.$name", 0);
+        }
         $save = TRUE;
       }
     }
-    if ($save) {
-      if ($type == 'module') {
-        $config->set('enabled', module_config_sort($config->get('enabled')));
-      }
-      $config->save();
-    }
+  }
+  if ($save) {
+    $extension_config->set('module', module_config_sort($extension_config->get('module')));
+    $extension_config->save();
   }
 }
 
diff --git a/core/modules/config/tests/config_test/lib/Drupal/config_test/TestInstallStorage.php b/core/modules/config/tests/config_test/lib/Drupal/config_test/TestInstallStorage.php
index cefb13f..f85de95 100644
--- a/core/modules/config/tests/config_test/lib/Drupal/config_test/TestInstallStorage.php
+++ b/core/modules/config/tests/config_test/lib/Drupal/config_test/TestInstallStorage.php
@@ -23,11 +23,11 @@ class TestInstallStorage extends InstallStorage {
    */
   protected function getAllFolders() {
     if (!isset($this->folders)) {
+      $this->folders = $this->getComponentNames('core', array('core'));
       // @todo Refactor getComponentNames() to use the extension list directly.
       $listing = new ExtensionDiscovery();
-      // Test all profiles.
       $listing->setProfileDirectories(array());
-      $this->folders = $this->getComponentNames('profile', array_keys($listing->scan('profile')));
+      $this->folders += $this->getComponentNames('profile', array_keys($listing->scan('profile')));
       $this->folders += $this->getComponentNames('module', array_keys($listing->scan('module')));
       $this->folders += $this->getComponentNames('theme', array_keys($listing->scan('theme')));
     }
diff --git a/core/modules/config/tests/config_test/lib/Drupal/config_test/TestSchemaStorage.php b/core/modules/config/tests/config_test/lib/Drupal/config_test/TestSchemaStorage.php
index 34b8642..dd782a9 100644
--- a/core/modules/config/tests/config_test/lib/Drupal/config_test/TestSchemaStorage.php
+++ b/core/modules/config/tests/config_test/lib/Drupal/config_test/TestSchemaStorage.php
@@ -30,9 +30,10 @@ public function __construct() {
    */
   protected function getAllFolders() {
     if (!isset($this->folders)) {
+      $this->folders = $this->getComponentNames('core', array('core'));
       // @todo Refactor getComponentNames() to use the extension list directly.
       $listing = new ExtensionDiscovery();
-      $this->folders = $this->getBaseDataTypeSchema();
+      $listing->setProfileDirectories(array());
       $this->folders += $this->getComponentNames('profile', array_keys($listing->scan('profile')));
       $this->folders += $this->getComponentNames('module', array_keys($listing->scan('module')));
       $this->folders += $this->getComponentNames('theme', array_keys($listing->scan('theme')));