sage: staging-next 2023-01-05 upgrade fixes

[collares]

Description of changes

The last staging-next merge (#209180) caused a few test failures on Sage:

• Matplotlib was upgraded to version 3.6. We import upstream patches (https://git.sagemath.org/sage.git/patch?id2=9.8.beta2&id=5501e0de0dca1cff0355326dd42bd8c7e5749568 and https://git.sagemath.org/sage.git/patch?id2=9.8.beta4&id=64589686c261d33e6b5aff2589bcae8af004bcc6) and delete now-upstreamed patch from sageWithDoc: fix documentation index #189776.
• Sphinx was upgraded to 5.3.0. We import https://git.sagemath.org/sage.git/patch?id2=9.8.beta1&id=8f8af65e54d3a9962cfab40f15dc23f4e955b43f. There is a separate trac ticket to sync sage_autodoc with upstream autodoc (https://trac.sagemath.org/ticket/34730), but I think we can wait for Sage 9.8 to get that one.
• ipywidgets was also upgraded to 8.0.4 and is now throwing a deprecation warning, which I reported as DeprecationWarning due to widgets/interaction.py's on_submit call jupyter-widgets/ipywidgets#3669. I have papered over it for the time being, but I will import an upstream patch from ipywidgets as soon as it is available.

More detail on the last point: Some deprecation notices weren't being reported due to an upstream bug fixed in jupyter-widgets/ipywidgets#3569, and upstream is now in the process of fixing/suppressing the newly-discovered warnings (see the ChangeLog for some examples). Unfortunately I do not have time to investigate the specific problem in more detail right now.

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 23.05 Release Notes (or backporting 22.11 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
  • (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes
• Fits CONTRIBUTING.md.

[timokau]

Thank you for staying on top of this, great work :)

[collares]

Thank you for the review :)