drush site synchronization with aliases
The drush rsync command does not bootstrap your site, so it cannot find your alias files.  Move your alias files to a global location (e.g. $HOME/.drush).

Also, since @dev and @stage are multisites with the same document root, it does not make any sense to rsync from one to the other, because they share the same files.  You might want to drush rsync @stage:%files @dev:%files.