Remove deprecated configuration options

[dylwil3]

We should decide whether and when to fully remove some of our deprecated configuration options. I believe the current ones are as follows:

1. Top-level lint options (i.e. those specified in tool.ruff instead of tool.ruff.lint)
2. extend-ignore
3. ignore-init-module-imports
4. builtins-allowed-modules
5. builtins-ignorelist
6. builtins-strict-checking
7. allowed-markup-calls
8. extend-markup-names

[ntBre]

I saw extend-ignore in #12014 today, which links to some other previous context. It sounds like we may even want to un-deprecate this one.

[MichaReiser]

We deferred removing the top-level lint settings because it would create a lot of churn for downstream projects in #12009 and it's not a huge maintenance effort. That doesn't mean that we shouldn't remove them, but we may need to help users to migrate before doing so (maybe something we can bundle with some of our other upcoming setting changes?).