diff --git a/core/includes/config.inc b/core/includes/config.inc
index c89537d..b949199 100644
--- a/core/includes/config.inc
+++ b/core/includes/config.inc
@@ -29,27 +29,27 @@ function config_install_default_config($type, $name) {
     $source_storage = new FileStorage($config_dir);
     $target_storage = drupal_container()->get('config.storage');
 
+    // Ignore manifest files.
+    $config_changes = config_sync_get_changes($source_storage, $target_storage, FALSE);
+
     // If this module defines any ConfigEntity types, then create a manifest file
     // for each of them with a listing of the objects it maintains.
     foreach (config_get_module_config_entities($name) as $entity_type => $entity_info) {
       $manifest_config = config('manifest.' . $entity_info['config_prefix']);
-      $manifest_data = array();
       foreach ($source_storage->listAll($entity_info['config_prefix']) as $config_name) {
         list(, , $id) = explode('.', $config_name);
-        $manifest_data[$id]['name'] = $config_name;
+        $manifest_config->set("$id.name", $config_name);
       }
-      $manifest_config->setData($manifest_data)->save();
+      $manifest_config->save();
     }
 
-    $config_changes = array(
-      'delete' => array(),
-      'create' => array(),
-      'change' => array(),
-    );
-    $config_changes['create'] = $source_storage->listAll();
     if (empty($config_changes['create'])) {
       return;
     }
+    // Do not overwrite or delete pre-existing configuration.
+    $config_changes['change'] = array();
+    $config_changes['delete'] = array();
+
     $remaining_changes = config_import_invoke_owner($config_changes, $source_storage, $target_storage);
     config_sync_changes($remaining_changes, $source_storage, $target_storage);
   }
@@ -112,44 +112,51 @@ function config($name) {
  *   The storage to synchronize configuration from.
  * @param Drupal\Core\Config\StorageInterface $target_storage
  *   The storage to synchronize configuration to.
+ * @param bool $require_manifest
+ *   (optional) Whether to determine changes based on manifest files. Defaults
+ *   to TRUE.
  *
  * @return array|bool
  *   An assocative array containing the differences between source and target
  *   storage, or FALSE if there are no differences.
  */
-function config_sync_get_changes(StorageInterface $source_storage, StorageInterface $target_storage) {
+function config_sync_get_changes(StorageInterface $source_storage, StorageInterface $target_storage, $require_manifest = TRUE) {
+  $config_changes = array(
+    'create' => array(),
+    'change' => array(),
+    'delete' => array(),
+  );
+  $all_source_names = $source_storage->listAll();
+  $all_target_names = $target_storage->listAll();
+
   // Config entities maintain 'manifest' files that list the objects they
   // are currently handling. Each file is a simple indexed array of config
   // object names. In order to generate a list of objects that have been
   // created or deleted we need to open these files in both the source and
   // target storage, generate an array of the objects, and compare them.
-  $source_config_data = array();
-  $target_config_data = array();
-  foreach ($source_storage->listAll('manifest') as $name) {
-    if ($source_manifest_data = $source_storage->read($name)) {
-      $source_config_data = array_merge($source_config_data, $source_manifest_data);
+  if ($require_manifest) {
+    $source_config_data = array();
+    $target_config_data = array();
+    foreach ($source_storage->listAll('manifest') as $name) {
+      if ($source_manifest_data = $source_storage->read($name)) {
+        $source_config_data = array_merge($source_config_data, $source_manifest_data);
+      }
+      if ($target_manifest_data = $target_storage->read($name)) {
+        $target_config_data = array_merge($target_config_data, $target_manifest_data);
+      }
     }
-
-    if ($target_manifest_data = $target_storage->read($name)) {
-      $target_config_data = array_merge($target_config_data, $target_manifest_data);
+    foreach (array_diff_key($target_config_data, $source_config_data) as $name => $value) {
+      $config_changes['delete'][] = $value['name'];
+    }
+    foreach (array_diff_key($source_config_data, $target_config_data) as $name => $value) {
+      $config_changes['create'][] = $value['name'];
     }
   }
-
-  $config_changes = array(
-    'create' => array(),
-    'change' => array(),
-    'delete' => array(),
-  );
-
-  foreach (array_diff_key($target_config_data, $source_config_data) as $name => $value) {
-    $config_changes['delete'][] = $value['name'];
-  }
-
-  foreach (array_diff_key($source_config_data, $target_config_data) as $name => $value) {
-    $config_changes['create'][] = $value['name'];
+  else {
+    $config_changes['delete'] = array_diff($all_target_names, $all_source_names);
+    $config_changes['create'] = array_diff($all_source_names, $all_target_names);
   }
-
-  foreach (array_intersect($source_storage->listAll(), $target_storage->listAll()) as $name) {
+  foreach (array_intersect($all_source_names, $all_target_names) as $name) {
     // Ignore manifest files
     if (substr($name, 0, 9) != 'manifest.') {
       $source_config_data = $source_storage->read($name);