Refactoring CheML in CheML2

Have a much shorter and cleaner implementation of CML parsing and
building.  Also have tests for it implemented
Working on better integrating CML

Things are a little broken right now. They'll be not broken again soon.
Hopefully.
CML is now fully integrated

CheML2 is fully integrated to compound_graphs.  Not going to remove main
or CheML(1) until I'm positive I have everything in cg and cml2 working
as desired
Merge pull request #8 from Dannnno/CheML-work

CML improvements