harden: reject shell=True in run_command (#3132)

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.

src/specify_cli/workflows/steps/shell/__init__.py

@@ -31,7 +31,7 @@ class ShellStep(StepBase):
         # control commands; catalog-installed workflows should be reviewed
         # before use (see PUBLISHING.md for security guidance).
         try:
-            proc = subprocess.run(
+            proc = subprocess.run(  # noqa: S602 -- intentional shell=True (see NOTE above)
                 run_cmd,
                 shell=True,
                 capture_output=True,