Skip the fiddling with prompts, just sandbox so that these commands are not run (via permissions.deny)

In dire cases, use the PreToolUse hook to inspect/intercept (though it's usually not necessary).

Granted, I haven't tried it for huge projects yet, but after doing that my small-medium sized projects all got ported nicely.

(If you must change the prompt, mention PEP723 as well, it seems to have the same effect as showing a shiny trinket to a magpie ;)