docs: updates cli reference docs

[lukegalbraithrussell]

Summary

This PR is a manual update of the CLI reference docs to use the new format created in #194 and #195

Requirements

• I've read and understood the Contributing Guidelines and have done my best effort to follow them.
• I've read and agree to the Code of Conduct.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 62.91%. Comparing base (859d4f1) to head (fd89332).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@ Coverage Diff @@## main #198 +/- ##
==========================================
- Coverage 62.94% 62.91% -0.03% 
==========================================
Files 212 212 Lines 21782 21782 ==========================================
- Hits 13711 13705 -6 - Misses 7009 7013 +4 - Partials 1062 1064 +2 

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[zimeg]

@lukegalbraithrussell LGTM! And thank you for splitting these changes 🙏 ✨

Please feel free to merge when the time is right. I added this to the v3.6.0 milestone since I believe some of the changes included have updated error outputs from that release, but of course no blocker!