New automata library

Factor out all the automata logic from Analysis.Mode.Execution.NamedInst to
its own library (Dyna.Analysis.Automata) and port everything over.  I won't
claim it's perfect, but I think it's a good start.

Analysis.Automata.Class is probably the right place to start reading.
Tweak version target in Makefile
Update TODO lists
Fix sphinx warning