4 files changed, 17 insertions, 10 deletions
diff --git a/modules/system/system.admin.inc b/modules/system/system.admin.inc
index c478e0465..fe6af7436 100644
--- a/modules/system/system.admin.inc
+++ b/modules/system/system.admin.inc
@@ -1203,7 +1203,7 @@ function system_modules_submit($form, &$form_state) {
       $sort[$module] = $files[$module]->sort;
     }
     array_multisort($sort, $modules_to_be_enabled);
-    module_enable($modules_to_be_enabled);
+    module_enable($modules_to_be_enabled, FALSE);
   }
   // Disable the modules that need disabling.
   if (!empty($disable_modules)) {
@@ -1225,7 +1225,7 @@ function system_modules_submit($form, &$form_state) {
       $sort[$module] = $files[$module]->sort;
     }
     array_multisort($sort, $new_modules);
-    drupal_install_modules($new_modules);
+    module_enable($new_modules, FALSE);
   }
 
   $current_module_list = module_list(TRUE);
diff --git a/modules/system/system.install b/modules/system/system.install
index c7ef22fd3..b6c02d4e5 100644
--- a/modules/system/system.install
+++ b/modules/system/system.install
@@ -2082,8 +2082,7 @@ function system_update_7018() {
  */
 function system_update_7020() {
   $module_list = array('field_sql_storage', 'field');
-  drupal_install_modules($module_list);
-  module_enable($module_list);
+  module_enable($module_list, FALSE);
 }
 
 /**
@@ -2305,8 +2304,7 @@ function system_update_7027() {
     ->condition('type', 'module')
     ->condition('name', $module_list)
     ->execute();
-  drupal_install_modules($module_list);
-  module_enable($module_list);
+  module_enable($module_list, FALSE);
 }
 
 /**
diff --git a/modules/system/system.module b/modules/system/system.module
index ef5b72af0..58d135ffb 100644
--- a/modules/system/system.module
+++ b/modules/system/system.module
@@ -2203,7 +2203,18 @@ function system_rebuild_module_data() {
   ksort($modules);
   system_get_files_database($modules, 'module');
   system_update_files_database($modules, 'module');
-  // Refresh bootstrap status.
+  $modules = _module_build_dependencies($modules);
+  return $modules;
+}
+
+/**
+ * Refresh bootstrap column in the system table.
+ *
+ * This is called internally by module_enable/disable() to flag modules that
+ * implement hooks used during bootstrap, such as hook_boot(). These modules
+ * are loaded earlier to invoke the hooks.
+ */
+function _system_update_bootstrap_status() {
   $bootstrap_modules = array();
   foreach (bootstrap_hooks() as $hook) {
     foreach (module_implements($hook) as $module) {
@@ -2219,8 +2230,6 @@ function system_rebuild_module_data() {
     $query->condition('name', $bootstrap_modules, 'NOT IN');
   }
   $query->execute();
-  $modules = _module_build_dependencies($modules);
-  return $modules;
 }
 
 /**
diff --git a/modules/system/system.test b/modules/system/system.test
index 03545ce94..4e49ade61 100644
--- a/modules/system/system.test
+++ b/modules/system/system.test
@@ -208,7 +208,7 @@ class ModuleDependencyTestCase extends ModuleTestCase {
     $this->assert(count($checkbox) == 1, t('Checkbox for the module is disabled.'));
 
     // Force enable the system_dependencies_test module.
-    module_enable(array('system_dependencies_test'));
+    module_enable(array('system_dependencies_test'), FALSE);
 
     // Verify that the module is forced to be disabled when submitting
     // the module page.