Pre-commit: fix the shellcheck and hadolint findings and remove the SKIP #368

The Pre-commit workflow merged with #343 runs every hook except shellcheck and hadolint-docker, which it skips with SKIP: shellcheck,hadolint-docker in the env: of the Run pre-commit on all files step, because the repository still has findings for both. As long as the skip is there, those two hooks protect nothing.

Plan: run both hooks on all files, fix the findings (a shell script that is correct today stays correct; each change is checked by running the script or its test), and remove the SKIP line and its comment in the same pull request, so the workflow runs every hook.

Acceptance:

• uvx pre-commit run --all-files is green with no SKIP.
• The SKIP line and the comment naming this follow-up are gone from .github/workflows/pre-commit.yml.
• Every changed shell script or Dockerfile is exercised by the existing CI jobs, and those are green.

Follows #343.