Add unsupported and deprecated --checkup sections

[rolandwalker]

Description

Let --checkup show config options which are read and ignored, as well as config options which are read, but deprecated.

Checklist

• I added this contribution to the changelog.md file.
• I added my name to the AUTHORS file (or it's already there).
• To lint and format the code, I ran

  uv run ruff check && uv run ruff format && uv run mypy --install-types .

[scottnemes]

These config related changes are getting a bit hard to follow, so will have to trust it's doing what you want it to anyway.

I.e. if I have a value like local_infile in .my.cnf, and then comment out the [connection] section of the ~/.myclirc, it only complains about the local_infile one and not the missing [connection] section.