Removing README.rst from sphinx theme.

File caused warnings. Had hoped to keep read me around to track
original theme source; thankfully links inline in template can take on
this role.
Ignoring runtime created contents.
Limiting input to doxygen to avoid encoding problems

Some xml output from doxygen is incorrectly encoded. This causes sphinx
to exit due to an expat error.

xmllint highlights the problem as encoding issues. These need to be
fixed but for now can be worked around by restricting doxygen input to
just *.h files.