A few issues with readthedocs

[Prooffreader]

1. There should be a link to index.rst in the menu
2. On index.html, the "Note" section is cut off at " or you can..."
3. in API section, autodoc does not show docstring for message argument of .run() method
4. Blank config templates should have subheaders for toctree
5. Add a section explaining "message" arg to run() in Tutorial