refactor(ci): rely on pre-commit file arguments

[Standing-Man]

Which issue does this PR close?

Closes #3195.

Rationale

Some pre-commit hook scripts still accepted --staged and used git diff --cached to discover staged files internally.

That duplicated pre-commit's own file selection behavior. Since these hooks now use pass_filenames, pre-commit already passes the matched staged files directly to the scripts. Keeping a second staged-file discovery path made the behavior harder to reason about and easier to drift from pre-commit's filtering rules.

What changed?

• Removed --staged argument handling from file-scoped hook scripts.
• Removed git diff --cached based staged-file discovery.
• Updated help text to no longer mention --staged.
• Kept explicit file arguments as the primary input path for pre-commit.
• Kept full-repository behavior for local/manual runs when no files are provided.
• Preserved --ci behavior for GitHub Actions / PR-diff checks.

Local Execution

• Passed / not passed
  Passed
• Pre-commit hooks ran / not ran
  Ran

AI Usage

1. Which tools? (e.g., GitHub Copilot, Claude, ChatGPT) Codex
2. Scope of usage? (e.g., autocomplete, generated functions, entire implementation)
   Drafted changes and updated the pr-commit scripts based on human direction.
3. How did you verify the generated code works correctly?
   🚧: Not tested locally yet.
4. Can you explain every line of the code if asked?
   Yes. I reviewed the changes

[hubcio]

behavior change worth noting in the commit body: running scripts with --ci outside CI (no GITHUB_BASE_REF, no CI env) now scans the whole repo instead of staged files. not a bug since pre-commit no longer relies on it, but a one-line note in the commit message would help anyone running the scripts manually.

[hubcio]

the local fallback here uses find . while the sibling scripts (binary-artifacts.sh, trailing-newline.sh, trailing-whitespace.sh) use git ls-files for the same fallback. inconsistent. could align to git ls-files -- '*.toml' and also collapse the duplication with the all) branch below since they're now functionally identical.

[Standing-Man]

I’ve replaced find with git ls-files in the latest commit to collect the files to be checked.

[hubcio]

--all is now a no-op (just shift, no FILE_MODE var anymore). help text on line 43 still says (default). flag is harmless but redundant - either drop it or document it as accepted-for-compat.

[hubcio]

same as markdownlint.sh - --all is now a no-op after FILE_MODE removal. help text still claims it's the default. either drop the flag or keep it as a documented compat shim.