First pass at running doxygen on commotiond.
added stub menu for API subsection
Layout and CSS changes for the Doxygen section of the site.
Add change to call doxygen css only on API sections.
added api to top menu & reordered
First pass at a script to autogenerate doxygen pages from github on to the jekyll site.
More tweaks to doxygen scraper.
More changes to the doxygen scraper; use the readme as a landing page etc.
Rewrite the API reference section landing page.
Working on automatically generating menus.
Rework the file structure to move up one level.
More changes towards the API subsection
Change default latex paper type.
Update the API section stylesheet conditional to reflect the moved API section.
Clean up tmp directories when done, and build some menu items.
Update main menu to point at the right spot.
Commiting a doxygen generation run.
Merge branch 'doxygen-2014-05-20_10-56' into staging.
Commit menu changes made by the doxygen script.
Merge branch 'doxygen-2014-05-20_12-00' into staging