Submit handler for shortcut_set_customize().
function shortcut_set_customize_submit($form, &$form_state) {
foreach ($form_state['values']['shortcuts']['links'] as $mlid => $data) {
$link = menu_link_load($mlid);
$link['weight'] = $data['weight'];
menu_link_save($link);
}
drupal_set_message(t('The shortcut set has been updated.'));
}