Merge from theory-break-dependences branch to break Theory and TheoryEngine dependenc...

Merge from theory-break-dependences branch to break Theory and TheoryEngine dependences; now, if you touch theory_engine.h, only a few things in theory need be recompiled (TheoryEngine, SharedTermManager, .... but no theory implementations), along with the PropEngine and SmtEngine.  If you touch a specific theory's .h file, only that theory must be recompiled (along with the TheoryEngine, since it uses traits, and SmtEngine, since it tells the TheoryEngine which theory implementations to use).