Initialize developer folder in doc/ to contain developer's guide.

- Doxygen config file is moved into doc/doxygen. We might need
  to update the wiki on this.
- doc/developer now contains the Developer's guide. I have *.pdf
  ignored for now, but will probably check it in later so that
  user does not have to generate Latex themselves.
Merge branch 'master' of github.com:mit-crpg/PINSPEC