$criteria = $modx->newQuery( 'modResource' );
$criteria->where(
array(
'parent' => $modx->getOption('site_start'),
'isfolder' => 1,
'deleted' => 0,
'hidemenu' => 0
)
);
$criteria->sortby( 'menuindex' );
$folders = $modx->getCollection( 'modResource', $criteria );