NO LONGER NECESSARY:
Unless/until I find out how to do that, anyone wanting to use my package will have to manually create the config directory and at least create a husk of an inputs file by opening a terminal and typing:
mkdir .nestopia ; touch .nestopia/nstcontrols
From that point on, everything should work fine. If you are super-scared of hitting the terminal and would feel better with a script, you can download and run this script and it will take care of it for you.
Let me know if you run into any issues or have any questions.