Yep. I really like the ~/.aMule/amule.conf name. It just sounds (and looks) so natural, and obvious. Also, keeping preferences.dat is a good idea. For example, I would have never started using amule if there was no way to keep using my hard-earned emule credits. But fortunately, tere is, so keep this.
Regards.
P.S: I've noticed some (all?) of the error pop-ups, say emule application (or smth like that) instead of amule. If possible, would like to see that corrected also. It's no funny for me to remember every time that amule is based on emule.