ffdn.org/sites/all/modules/admin_menu/admin_devel/admin_devel.module

<?php

/**
 * @file
 * Administration and debugging functionality for developers and site builders.
 */

/**
 * Implements hook_form_FORMID_alter().
 */
function admin_devel_form_admin_menu_theme_settings_alter(&$form, &$form_state) {
  $form['actions']['wipe_rebuild'] = array(
    '#type' => 'submit',
    '#value' => t('Rebuild system links'),
    '#submit' => array('admin_devel_form_admin_menu_theme_settings_alter_rebuild_submit'),
    // @todo Not necessarily ready for mass-consumption yet.
    '#access' => FALSE,
  );
}

/**
 * Form submit handler to wipe and rebuild all 'module' = 'system' menu links.
 */
function admin_devel_form_admin_menu_theme_settings_alter_rebuild_submit($form, &$form_state) {
  // Delete all auto-generated menu links derived from menu router items.
  db_delete('menu_links')
    ->condition('module', 'system')
    ->execute();
  // Rebuild menu links from current menu router items.
  menu_rebuild();

  drupal_set_message(t('System links derived from menu router paths have been rebuilt.'));
}