Refactor Kodkod options.

- This cleans up the Kodkod Options class. Comments are cleaned up, and
  the logging/cloning methods have been updated with the
  allSolutionsPerPoint option.
- Note that the interface has been changed with a shorter name.
- MoolloyOptions has been removed, as it only had one option.
- As a result, AlloySolver now directly saves the option, instead of
  setting it to MoolloyOptions and then getting it back out.

Since this commit changes the interface, Alloy has been updated:
de32b38fba461cc9bf6091054898b51553c2a476