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 handling from file-scoped hook scripts.
• Removed git diff --cached based staged-file discovery.
• Kept explicit file arguments as the primary input path for pre-commit.
• Preserved --ci behavior for CI / PR-diff based checks.
• Updated --help output to document bare local runs with:

Note: Running these scripts with --ci outside a CI environment, where neither
GITHUB_BASE_REF nor CI is set, now falls back to checking all tracked
files instead of staged files.

Running the scripts with no file arguments also defaults to checking all
tracked files. This is intentional because pre-commit no longer relies on
script-side staged file discovery; it passes matched files directly via
pass_filenames.

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]

if PR is ready to be reviewed again, please type comment with /ready somewhere in the beginning of any line. also comment/resolve the issues.

/author

[Standing-Man]

/ready

[hubcio]

nit outside the diff hunks: scripts/ci/shellcheck.sh:99-100 and 131-132 still say "Use staged or explicitly provided files when present". --staged was removed in this PR, so the "staged or" wording is misleading. drop it.

also, my prior comment about the --ci-outside-CI behavior change still applies - running scripts with --ci when neither GITHUB_BASE_REF nor CI is set now scans the whole repo via git ls-files instead of staged files. a one-line note in the commit body would help anyone running manually.

[Standing-Man]

/ready