Fix CLI docs action

[i-oden]

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1. Description / Summary

This PR fixes the issue with the action publishing the CLI docs to GitHub Pages.
The issue is due to Python 3.13 having removed some packages, which is why I have included the legacy versions of them in the requirements-dev.txt.
@rv0lt Also fixed the deployment of the docs by bumping some of the sphinx packages but that also meant that the majority of the docs were not visible and there were no links to the different commands.

This is in no way the best option, but this fixes it. We should however, as discussed, change this entire process to use some action that is well maintained, or create our own action which we would have full permissions on and could fix when issues arise.

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[rv0lt]

My mind is already giving up, but I have been testing in branch ghp-test and I found out the issue is within the action

matthiaszepper/sphinx-action-v4

It uses by default python 3.13 which has compatibility issues with this cffi module. I have been trying workarounds but to no avail sadly.

The other issue with python 3.13 is that this module was removed
https://docs.python.org/3.11/library/imghdr.html

Which is need for sphinx to make the documents.

And, don't expect Sphinx to add support for python 3.13 until 2026 xd
https://www.sphinx-doc.org/en/master/internals/release-process.html

---

EDIT: After inspecting more deeply (yapping incoming)

This action is a forked for another one, that this creator suggested was abandonded (whereas the original one allows specifying a version and does not default to latests) and it's now, surprise, abandoned
https://github.com/MatthiasZepper/sphinx-action-v4

I believe it will be MUCH better to just have extra steps and generate the document ourselves instead of relying on libraries maintained by random people...

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 47.88%. Comparing base (7972db5) to head (a5aba24).
Report is 117 commits behind head on dev.

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #730      +/-   ##
==========================================
+ Coverage   47.76%   47.88%   +0.12%     
==========================================
  Files          31       31              
  Lines        2889     2890       +1     
==========================================
+ Hits         1380     1384       +4     
+ Misses       1509     1506       -3     

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[i-oden]

@ScilifelabDataCentre/teamhermes When there's an approval of this you can merge.