fix: correct behavior of runLinter --update

[thorimur]

This PR changes the behavior of runLinter --update. Previously, this would overwrite the nolints.json file with the full list of current linting violations, meaning that all declarations which violated linters were now nolinted.

However, it is intended to only "remove any declarations that no longer need
to be nolinted" (at least according to the docstring). This means that we should just filter out declarations from the nolints file which no longer fail (i.e., only include those from the nolints file which do still fail).

Since technically we run linters on individual modules, but the nolints.json file may apply to other modules besides the one being linted, we also only filter out those newly non-failing declarations which are from the current module and therefore are actually being linted.

This extra check can introduce some potential (benign) staleness in nolints.json if a nolinted declaration is removed (and thus never appears in any module, and so is never removed by --update). However, these ineffective nolints will not cause any problems, while overzealously deleting nolints from other modules might.

In the future, we might want to consider factoring out the --update behavior so that it is not part of runLinterOnModule, but instead occurs at the top level in main.

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If possible, I'd like someone to verify that this is indeed the intended behavior of --update, and that it's not the case that the docstring is wrong. :)

[thorimur]

WIP

[thorimur]

On zulip, it was mentioned that the current behavior for adding new violations to the nolint file is also useful (or possibly the primary use case!). (Note that the current behavior still needs a tweak because it overeagerly erases nolints that are not from the current module.)

I think both functionalities have a place; maybe --cleanup for this one?

[ghost]

Mathlib CI status (docs):

• ✅ Mathlib branch batteries-pr-testing-1600 has successfully built against this PR. (2026-01-05 21:42:11) View Log