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Not sure if this was always the case in pythonista 3, but wrench menu now seems to clear globals. I realize this is not a democracy, but I will register my vote for the ability to have wrench actions run in the current interpreter session. That offers a lot more flexibility to create wrench scripts that aid in debugging.
Maybe an option per wrench action (if there are use cases where global clearing is the preferred approach)

This isn't really the intended behavior; even though I do have this on my todo list, I somehow forgot to address it before the 3.0 release (perhaps also because no one ever complained ;)).