Fix on the removal of centrally managed modules

cern_integration.info

 name = CERN Integration
 package = CERN
 description = Provides CERN site integration for Drupal.
-version = "7.X-1.10"
+version = "7.X-1.11"
 core = 7.x
 
 dependencies[] = shib_auth

cern_integration.module

@@ -561,12 +561,14 @@ function cern_integration_form_domain_301_redirect_admin_form_alter(&$form, &$fo
 function cern_integration_update_projects_alter(&$projects)
 {
     // Remove all centrally managed modules.
-    foreach (module_list() as $module) {
-        if (preg_match('/^sites\/all\/modules\//', drupal_get_path('module', $module))) {
-            // This works only if the module name matches the project name.
-            unset($projects[$module]);
+    foreach (system_list("module_enabled") as $module) {
+        if (preg_match('/^sites\/all\/modules\//', drupal_get_path('module', $module->name))) {
+            if(isset($module->info["project"])){
+                unset($projects[$module->info["project"]]);
+            }
         }
     }
+ 
     // Remove all centrally managed themes and their subthemes.
     $array_themes = list_themes();
     foreach ($array_themes as $theme_obj) {