- Patch #683988 by catch, dww, aspilicious: failure to clear the system_list() entry from {cache_bootstrap()} results in bogus results when you upgrade a module.

modules/system/system.admin.inc

@@ -1240,7 +1240,6 @@ function system_modules_submit($form, &$form_state) {
   registry_rebuild();
   system_rebuild_theme_data();
   drupal_theme_rebuild();
-  cache_clear_all('system_list', 'cache_bootstrap');
   node_types_rebuild();
   menu_rebuild();
   cache_clear_all('schema', 'cache');

modules/system/system.module

@@ -2173,6 +2173,11 @@ function system_update_files_database(&$files, $type) {
     }
   }
   $query->execute();
+
+  // If any module or theme was moved to a new location, we need to reset the
+  // system_list() cache or we will continue to load the old copy, look for
+  // schema updates in the wrong place, etc.
+  system_list_reset();
 }
 
 /**