run_command() forwarded shell= straight to subprocess.run, so a caller
passing shell=True would invoke a shell. Reject shell=True with ValueError
(keeping the parameter for signature compatibility) and drop shell= from
both subprocess.run calls.
Enable ruff S602/S604/S605 to flag any future shell=True reintroduction,
annotate the one intentional workflow shell sink with # noqa: S602, and
document the shell-step execution risk in workflows/PUBLISHING.md.
