I've used w3t auth (I made a separate include file with several functions that take care of the stuff i need, file that is not located anywere near the w3t directory) and it worked without any problem. Moreover, I've changed the setcookie call in main.inc.php to include an extra parameter ".mydomain.ro" so the cookie is set domain wide -- without it the cookie will be set to the 'w3t_domain/install_path/' only. This way I can acces the cookie from another host on the same domain and perform user auth. against the w3t user database. For my extra needs I've also created new fields in the w3t_Users table, entries that I use/edit with custom scripts.
