Simplify ruff configuration

[vincentmacri]

Also fix a few rules that were only violated a small number of times.

This PR:

• Removes list of rules we want to follow from src/tox.ini to remove duplication
• Defines all rules we wish to follow in pyproject.toml
  • For rulesets that are not stable enough yet (E, PL) we list the rules explicitly instead of enabling all E or all PL rules.
  • We still ignore specific E and PL rules that we don't want to follow because the hope is that once the E and PL rules are fully stable in ruff we will just enable them all and selectively disable the ones we don't want.
• We add a new file .github/workflows/ruff.toml that starts with the pyproject.toml configuration (using extend, so no duplication), and disables all rules that currently fail.
• We also ignore a few troublesome directories in the ruff config, and run ruff on the entire repo. This means tools and scripts are linted now as well.
• I also fixed a handful of rules that were only violated in a couple files, I didn't want to add a rule to the CI ignore list if fixing the rule was a one line change.

The benefits of this are:

• There is now only one file (pyproject.toml) that needs to be modified to add new rules
• We can now locally run the same ruleset as CI with ruff --config .github/workflows/ruff.toml

📝 Checklist

• The title is concise and informative.
• The description explains in detail what this PR is about.
• I have linked a relevant issue or discussion.
• I have created tests covering the changes.
• I have updated the documentation and checked the documentation preview.

⌛ Dependencies