Re. sudo/root issues,

I don't know how Hamster Filer is handling this, but is seems that it tries to restart itself using sudo (don't know, haven't installed it yet

The "proper" way is IMHO to install the program with the setuid bit (so that it will run with the privileges of its owner, i.e. root), and then, if the option to run as root is not active, the program should just drop privileges