Several fixes to the docs

[xylar]

This merge fixes issues, primarily with the tutorial for developers, related to the documentation.

Checklist

• Documentation has been built locally and changes look as expected

[xylar]

Testing

I built the docs on Chrysalis, and they can be found (when the web portal is feeling cooperative) at:
https://web.lcrc.anl.gov/public/e3sm/diagnostic_output/ac.xasay-davis/analysis_testing/chrysalis/fix-docs/docs/

[xylar]

I added some more improvements to the docs and config commits suggested by @eclare108213. I built the docs locally on my laptop and they look as expected.