Edits to User Guide documentation

[atravitz]

Edits just to the top level and Setup section. Further edits for other sections (and to update graphics) will follow in later PRs.

Developers certificate of origin

• [x ] I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.84%. Comparing base (4c06370) to head (6e44bfb).
Report is 26 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #995      +/-   ##
==========================================
- Coverage   94.59%   92.84%   -1.76%     
==========================================
  Files         134      134              
  Lines        9940     9940              
==========================================
- Hits         9403     9229     -174     
- Misses        537      711     +174     

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fast-tests	92.84% <ø> (?)
slow-tests	?

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[IAlibay]

I'm going to put a block here because it looks like some of the things here will need some discussion / will have differing views.

[ijpulidos]

Much clearer and concise, great work! I just added some comments.

[hannahbaumann]

Thank for you all your work on this @atravitz , this looks great overall! Just left a few suggestions!

[atravitz]

@IAlibay A couple items I addressed but you should take one more look at. I think we need to revisit the ligand network section as a whole. Maybe a follow-up PR?

[atravitz]

let me know if this is better.

[mikemhenry]

+1 to removing see also from the TOC but keeping that section on the page

[mikemhenry]

same with references

[mikemhenry]

Also while we are at it, I think we should have a call to action on this page:
https://openfe--995.org.readthedocs.build/en/995/guide/introduction.html

In between the Introduction and Workflow overview section as a .. note:: that is something like "If you have used openfe, please use this citation xxx." I think some sentence about also sponsoring the project would be good as well.

Also also, feel free to just convert this comment into an issue if you think it warrants further discussion and/or is outside the scope of the PR.

[hannahbaumann]

Thanks, lgtm!