* Make 'any' the default markup role for Sphinx docs
* Automate generation of reference docs with doxygen and breathe
* Improve reference docs coverage
The missing empty line after `.. code-block::` resulted in incorrectly
parsed restructuredtext (sphinx warnings) and the code blocks were not
generated in the html output.
The `exclude_patterns` change just silences the orphaned file warning.
[ci skip]