Move Doxyfile to doxygen subdirectory, remove html dir.

Since the Doxygen-generated files must reside in the root directory of the
gh-pages branch, needed to get rid of the 'html' directory and configure
Doxygen to output everything in the root directory. To keep things somewhat
clean and tidy, the Doxyfile was moved into a new doxygen/ directory.
Draft Doxygen documentation in the right place.