The recent fix to glob_files made it so none of the CLS could read from STDIN. I made a small change to glob_files that fixes many cases.

However, many CLS still can't read from STDIN. The problem is that get_outfile() and get_filename() get called on infiles even if the data is coming from STDIN.

It's very useful to be able to do things like
fetchMolecule.py -i benzene | makeInput.py -m b3lyp -b 6-31G -opt -freq -o benzene.com

I've fixed makeInput.py and angle.py and will try to fix the others over the next few days. Some Tony should probably check these fixes though to make sure...