Various changes to clean up generation and solve link issues.
Added various improvements to the system:

- apply-plugins: Added a plugin system that can handle creating a list of
  categories or even custom code.
- resolve-links: Added code to resolve [something]() into a standard link as
  a form of short-hand.
- Various improvements to the other programs to make them work correctly,
  generate consistent order, and other things I can't remember at this point.