Ah, I didn't realize the new beta added that. Excellent!
I know the preselection causes automatic command execution for some commands, which is great. It was just baffling when the command pane appeared and suddenly vanished without completion for no apparent reason. Anyway, the new UI you mentioned should help with that.
As a suggestion for the done button, perhaps when the command starts execution, change the text to "Calculating..." and disable the button so it doesn't respond to clicks.
Edit: Actually, an approach more consistent with typical UI would be to immediately change the entire content of the pane to a progress view. Even if a progress bar or percentage is not doable and it just displays "Calculating..." and a cancel button, the content switch makes sense. Usually one expects clicking done or cancel to immediately close the pane or transition to a new content view. Just my $0.02.
Will
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