fixing compilation problem with the examples.
renaming src to theories to make room for plugins.
sketch implementation of reification for ext

- In order to test it completely, I need an actual
  instantiation.
adding to_N
coq_makefile patch to fix dependencies for .ml4
working on reification.

- Reification of very simple terms is working
- This code does not include everything needed for
  reification. I am trying to figure out the appropriate
  licensing for some support code.