If I understand what you're doing it sounds like you're adding items to the admin page. If so, there is an upgrade safe way to do this. If you want to do this without using module loader you'd create a file (named whatever you like) in \custom\Extension\modules\Administration\Ext\Admin istration such as MyAdminMenu.php and then create the admin menu items as needed such as:
PHP Code:
$admin_option_defs=array();
$admin_option_defs['mycompany_admin_link']= array($image_path . 'ModuleNameForIconInThemeDirectory','LBL_INTERNAL_LINK_TITLE','LBL_INTERNAL_LINK_DISPLAY','www.google.com');
$admin_group_header[]=array(LBL_COMPANY_ADMIN_DISPLAY_HEADER',',false,$admin_option_defs);
You'd then create a language file for the LBL_*s in a similar fashion in custom\Extension\modules\Administration\Ext\Langua ge.
Then do a Quick Repair & Rebuild on the Administration module and you should see your items on the Admin page.
You can do this as part of a custom module through a manifest file as well. More information on that syntax can be found here: http://www.sugarcrm.com/wiki/index.p...st.php_for_5.0
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