Adjusted settings for making com files

The section of the com file that generated the "post-opt. energy"
mae index appears to only be necessary for argument meo, although
it was being invoked with argument me as well. Made it such that
this only occurs with meo.
Removed tools directory

I never meant to add that tools/remove_dummy.py. It was just a
script that changed some atom names for me, but it's specific
to a particular system I'm working on.