Fix path to QMfiles (and clean up after the error)

Earlier versions were saving QMfiles in a silly place.
From now on they should be in RMG-Py root directory,
and we also move the old ones to that location, to clean
up on computers that ran earlier versions of the script.
Added command line option --noqm to avoid QM thermo calcs.

If your model has a bunch of polyaromatic things, this option will
make it run much faster (albeit with worse thermo estimates).