Index: admin_menu.install
===================================================================
RCS file: /cvs/drupal-contrib/contributions/modules/admin_menu/admin_menu.install,v
retrieving revision 1.4.2.6.2.5
diff -u -p -r1.4.2.6.2.5 admin_menu.install
--- admin_menu.install	17 Jun 2009 10:13:18 -0000	1.4.2.6.2.5
+++ admin_menu.install	11 Jul 2009 19:18:03 -0000
@@ -87,27 +87,23 @@ function admin_menu_update_6300() {
 }
 
 /**
- * Add "admin_menu" menu.
+ * Add the "admin_menu" menu.
  */
 function admin_menu_update_6301() {
   $ret = array();
+  // Delete obsolete variable.
   variable_del('admin_menu_rebuild_links');
   // Create menu.
   $ret[] = _admin_menu_install_menu();
   // Clean-up menu links from earlier versions.
   db_query("DELETE FROM {menu_links} WHERE module = 'admin_menu' OR menu_name = 'admin_menu'");
-  // @todo hook_menu_alter() has no effect on customized menu items. During an
-  //   upgrade from earlier versions, it is possible that users altered
-  //   administrative items. Those will be located at the top-level of the menu
-  //   without this (very crude) reset. Suggestions welcome.
-  db_query("DELETE FROM {menu_links} WHERE router_path LIKE 'admin%%'");
   return $ret;
 }
 
+/*
 function admin_menu_form_update_script_selection_form_alter(&$form, $form_state) {
   if ($form['start']['admin_menu']['#default_value'] <= 6301) {
     drupal_set_message("<strong>BACKUP YOUR DATABASE!</strong> Administration menu's upgrade path resets and deletes all custom administrative menu items.", 'error');
   }
 }
-
-# UPDATE `test_drupal6`.`system` SET `schema_version` = '6300' WHERE `system`.`filename` = 'sites/all/modules/admin_menu/admin_menu.module' LIMIT 1 ;
+*/
Index: admin_menu.module
===================================================================
RCS file: /cvs/drupal-contrib/contributions/modules/admin_menu/admin_menu.module,v
retrieving revision 1.43.2.17.2.15
diff -u -p -r1.43.2.17.2.15 admin_menu.module
--- admin_menu.module	4 Jul 2009 13:48:29 -0000	1.43.2.17.2.15
+++ admin_menu.module	11 Jul 2009 19:18:49 -0000
@@ -121,7 +121,7 @@ function admin_menu_menu_alter(&$items) 
         }
         // Skip invisible MENU_CALLBACKs, but make sure that it is not a
         // MENU_NORMAL_ITEM, which shares the MENU_VISIBLE_IN_BREADCRUMB bit.
-        if ($item['type'] == MENU_CALLBACK) {
+        if ($item['type'] === MENU_CALLBACK) {
           continue;
         }
         $items[$path]['menu_name'] = 'admin_menu';
@@ -130,14 +130,23 @@ function admin_menu_menu_alter(&$items) 
   }
 
   // Remove 'admin', so children appear on the top-level.
-  // @todo If 'admin' gets visible, all children are not re-parented at all. If
-  //   it gets invisible, the menu system still displays it.
-  $items['admin']['_visible'] = FALSE;
+  $items['admin']['type'] = MENU_CALLBACK;
   // Remove local tasks on 'admin'.
   $items['admin/by-task']['_visible'] = FALSE;
   $items['admin/by-module']['_visible'] = FALSE;
 
-  // Flush client-side caches.
+  // menu_link_save() looks up the parent's menu_name directly in the database
+  // instead of taking data in hook_menu() into account. When installing
+  // admin_menu, {menu_links} contains the default value of 'navigation', which
+  // is thereby applied to all items, even if this function altered them. There
+  // is no other way to override this behavior.
+  // Additionally, if links below admin/ were moved or customized in any way and
+  // those are moved back into the administration menu, then the menu system
+  // will not calculate/assign the proper menu link parents when the parent item
+  // (here: 'admin') is marked as customized.
+  db_query("UPDATE {menu_links} SET menu_name = 'admin_menu', customized = 0 WHERE router_path = 'admin'");
+
+  // Flush client-side caches whenever the menu is rebuilt.
   module_invoke('admin_menu', 'flush_caches');
 }