Database Refactor

This is a companion to cyclus/cyclus#840.  I tried to do a little python cleanup while I was here, but it is a bit too far gone to worry about.  

Also note, that I expect the regression tests to fail because the structure of the tables has changed.  I don't think it is worth our time to do a micro-release this close to a full release though I suppose reasonable folks could disagree on this point.