Change cloning semantics, EnterSimulation simplification, housekeeping.

Discussion/description of most changes [here](https://groups.google.com/d/msg/cyclus-dev/QOZFL1l48pA/oL7Vwa3gkQQJ).  fixes #400, #399.  Removed a lot of static method and member stuff from Model class.  Companion PR in cycamore.