Make qubes-doc installable with pyproject.toml

[parulin]

• Move extensions as part of the qubes_doc package
• Update conf.py
• Update pyproject.toml:
  • Convert qubes_doc to a real package
  • Move some packages to optional dependencies groups
  • Bump sphinx version
• Remove requirements.txt
• Update .readthedocs.yaml to use the new install method
• Update installation instructions accordingly
• Add basic instructions to build the docs in README

After all this, the PDF would still not build on Read The Docs, so a workaround is to remove (almost) unused sphinxnotes-* extensions

Fix QubesOS/qubes-issues#10738
Fix QubesOS/qubes-issues#10737

Thanks to @hippalectryon-0 for some parts. See also: #1642

[parulin]

Tested:

• html build, with the pull request build
• html build, locally with pip
• html build, locally with poetry
• html build, locally with uv
• html build, locally with uv without optional dependencies
• epub and pdf on read the docs

[unman]

I think there is too much being done here, which could be spread across separate PR.
Looking at 10737, I dont think I want to introduce another level of complexity to the build. I've though carefully about this and I do not want to do it - the benefit to users is minimal.

[parulin]

Okay, what changes do you want to keep? The one allowing us to move to Sphinx >9.1?

Note that this PR doesn't change anything to most users. The only difference is that someone who want to create a perfect copy of the official doc website have to install an extra group of dependencies.