Make the getFilePath more extensible and more used in QM.
Make the getFilePath more extensible and more used in QM.

The whole file handling thing here could use some work.
There's slightly confusing code duplication making it hard
to see where the paths actually get defined.
The use of "scratch" versus file store is not totally
clear either.
Some classes copy self.settings.scratchDirectory into
self.scratchDirectory, and some classes don't. I think
to make things worse some classes may inherit from both.

I have a hunch this is broken: I am getting a lot of errors like:
"Incorrect connectivity for optimized geometry in file /Users/rwest/Code/RMG-Py/QMscratch/pm3/QKVOVZNSCDPZFS-UHFFFAOYSA-mult1.out"
(but perhaps they are genuine)

nickvandewiele/RMG-Py,nyee/RMG-Py,pierrelb/RMG-Py,chatelak/RMG-Py,pierrelb/RMG-Py,nickvandewiele/RMG-Py,nyee/RMG-Py,chatelak/RMG-Py