Rewrote reference generator with `doxygenfile` directive.
Readapted jinja-based templates.
Trigger generation of output xml files in `conf.py`.
Updated reference documentation.
Fix typos.
Add missing `rtd_doxyfile` doxygen config file.
Remove sphinx_rtd_theme from `requirements.txt`.

Make sure we do: pip install sphinx_rtd_theme on local machines.
Generate relative paths for `doxygenfile` directive` instead.
Regenerated reference documentation.
Merge pull request #73 from DO-CV/doc-fix-ref-documentation

[DOC] Fix cross-referencing in documentation.