Changed filenames on glass catalog so that they are easier to track inside the libary.
Got a reply from Zemax that it is okay to include their AGF files, so I added lots more glass files here, and added a comment line at the top of the file indicating the source of the file. Also made a ton of modifications to the main ZemaxGlassReader.py file.
Updated the user manual. Still needs a good deal more work, though.