[CI] Update file patterns for specific linting hooks

[guan404ming]

How

• Updat file patterns for specific linting hooks to ensure they only run on relevant file types.

minor update

• Fix linting commands to handle interactive and non-interactive modes
• Add 'pre-commit' to default stages in .pre-commit-config.yaml.
• Add inplace fix flags

[guan404ming]

cc @tqchen

[cchung100m]

LGTM, thanks to @guan404ming 😄

[guan404ming]

cc @tlopex

[tlopex]

Do we really need this update for CI？ cc @tqchen

[tqchen]

I am not sure how it would impact ci since right now ci do not run pre-commit hooks, if it is generally helpful for people who use them then i think we can get it in, @guan404ming to confirm

[guan404ming]

I am not sure how it would impact ci since right now ci do not run pre-commit hooks, if it is generally helpful for people who use them then i think we can get it in, @guan404ming to confirm

By updating file patterns to be more specific, hooks only scan relevant file types instead of checking every file. This reduces file processing and speeds up pre-commit execution in my local test.

While this PR currently focuses on the pre-commit, we can also evaluate the performance improvements to see if it's worth adopting in CI as well.