Remove obsolete hidden files.
Workaround the sphinx logo search.

Contrary to the comments in conf.py, sphinx can find html_logo file
only in the base directory.  This is a bug that was fixed upstream,
but remains in stable versions of sphinx.

This change can be reverted once the fix is in stable sphinxes.
Mirror file removals to the master branch.

Files on master can be protected by editing master:.rsync-exclude.