editing the conf is no longer needed. (at least i'm about 90% sure)
This is why i'm redoing the wiki.
In theory, you SHOULD be able to add this single line to your .rtorrent.rc to make all plugins "stick"
of course, edit it for your php binary locaton, webroot and user.
Code:
execute = {sh,-c,/usr/bin/php /var/www/rutorrent/php/initplugins.php WEB_AUTH_USER_NAME &}
so if you use webauth, and your webusername is tom, you'd make it:
Code:
execute = {sh,-c,/usr/bin/php /var/www/rutorrent/php/initplugins.php tom &}
(if you do this, you should also have a dir called /var/www/rutorrent/conf/users/tom/ with your config files in it. This will also give you the option to set different plugin settings per user by creating a plugins dir, and then saving the specific configs there)