I think you should able to set under config.php
define('LIMIT_TO_DIRECTORY',false); // limit index to given (sub)directory where (sub)directories of give (sub)directory are NOT indexed
// for limit to directory, URL format must either have file at end or ending slash at end
// e.g.,
http://www.domain.com/dirs/ (WITH ending slash) or
http://www.domain.com/dirs/dirs/index.php