Run 'just ci-all' for a whole files

[testfailed]

I added just ci-all script to run ci (pre-commit hooks) in a controlled way, getting the same results for anyone running this script.

# Run ci for all files using pre-commit
ci-all:
  pre-commit run --all-files

Also, I ran just ci-all for a whole files, most of them were fixed automatically by nixpkgs-fmt hook, but I had to make some manual changes.

The purpose of this PR is that I sometimes want to do format for a whole files without conflicts with your upstream commits. It wouldn't make conflicts after this PR if pre-commit hook for git commit is set up properly, not requiring to invoke ci, ci-all scripts manually.

If you want to exclude certain file paths or file types, e.g. *.md or .*/(grief|guppy|gusto).*.nix, I'll add them to exclude: for pre-commit hooks.

Thanks for the great work. It's well organized, and structure diagrams are really helpful for newcomers like me 👍

[EmergentMind]

Thanks for this. I must not have run pre-commit install when I moved my lab to a vm.

The linting on .md is okay, there's some stuff that I don't like about it but it will make things more convenient for people down stream... and now that I actually have pre-commit running properly there should be less noise for you :)

You'll see that I committed a minor followup change to the PR to remove the script exclusions. They should have been executable. Also comment out sops check because I'm storing my secrets in a private repo now and the check wasn't finding what it was looking for.

Glad you're enjoying my work. I'm always open to suggestions. Good luck on you NixOS journey :)