Doc: Restructure clean up.

This commit fixes all warnings about cross-references and file names. It
addresses all mark-up issues. Only the warnings regarding Doxygen
objects and files that are intentionally not added to a toctree are left
unhandled.

Change-Id: I5d840522ea0bade4f183e447745244aecf893c94
Signed-off-by: Rodrigo Caballero <rodrigo.caballero.abraham@intel.com>
24 files changed