Restructures documentation reference section

[skrawcz]

This section was getting unwieldly. It is now
less overwhelming. This will be better for SEO too.

Changes

1. breaks things out into explicit files
2. changes the sphinx build to be htmlDir
3. removes some to be organized docs
4. fixes up a few typos
5. fixes links to match new structure

How I tested this

• Locally

Notes

• this should help with SEO.

Checklist

• PR has an informative and human-readable title (this will be pulled into the release notes)
• Changes are limited to a single goal (no scope creep)
• Code passed the pre-commit check & code is left cleaner/nicer than when first encountered.
• Any change in functionality is tested
• New functions are documented (with a description, list of inputs, and expected output)
• Placeholder code is flagged / future TODOs are captured in comments
• Project documentation has been updated if adding/changing functionality.