Reorganize so setup.py works, and add exception handling/map checking

[davidlmobley]

This reorganizes the tool so the name is alchemical_setup rather than alchemical-setup and so that setup.py works for installation. Additionally, and more significantly, this adds some additional exception handling and use checking, including:

• Checks that required files are provided by the user and raises an exception if not
• Checks that no atom is mapped twice in map.txt

There are also some fixes to the verbosity settings and print statements, i.e. to remove extraneous prints except when verbose is specified. And I made some improvements to the -h option to make it more self-explanatory.

@FEPanalysis , please review. I'll also open an issue regarding two other small things.

[davidlmobley]

@FEPanalysis - did you review this? I'm ready to merge. I also fixed a number of tab vs space issues which may be an issue in #6 ... (To be more specific - in some cases you had a tab rather than spaces in the code which caused some indentation problems when I edited those functions, if I remember correctly.)

[davidlmobley]

I'll need to update this now that #6 is merged. Will do soon.

[davidlmobley]

@FEPanalysis - if you could also just give this a quick review when you have time (though it's lower priority) you or I can merge once you do so.