updated Doxyfile with auto-generated content from doxygen 1.8.1.2.  Fixed bad exludes, enabled preprocessor parsing.
ignore doxygen generated content
copy over js to local html output folder
using updated, and much more default, doxygen style
added cinder link to new (slim) doxygen header. turned on search bar.
don't use website's doxygen header, it is out of date
Merge remote-tracking branch 'origin/doxygen_updated' into dev