Theory "alternates" support

* This is a feature that Dejan and I want for the upcoming tutorial.
  It allows rapid prototyping of new decision procedure implementations
  (which we may choose to demonstrate), and a new --use-theory command-line
  option to select from different available implementations.  It has no
  affect on the current set of theories, as no "alternates" are defined.

* Also update the new-theory script, which was broken and incomplete.
Add ability to run different regression levels with "make check"