1,3-Hexadiene input file now saves QMfiles in the output directory.

This makes it slower to run, because it won't re-use old files if you
delete the output folder between runs, but that makes it a better test,
and this is one of our Makefile test targets (`make eg2`).
`make eg2` will delete the output directory before running, so we now wipe
the slate clean of old QMfiles.

Author: rwest

examples/rmg/1,3-hexadiene/input.py

@@ -65,7 +65,7 @@
 quantumMechanics(
     software='mopac',
     method='pm3',
-    fileStore='QMfiles', # relative to where you run it? defaults to inside the output folder.
+    # fileStore='QMfiles', # relative to where you run it from. Defaults to inside the output folder if not defined.
     scratchDirectory = None, # not currently used
     onlyCyclics = True,
     maxRadicalNumber = 0,