See, that's why I enjoy discussing things with you - this is a great idea! And probably much simpler than what I had in mind.
If I understood correctly, you're suggesting to simply run the clone process again and overwrite existing files? Or should we skip existing files if they exist instead of overwriting? I'd say skip existing and add a message that existing files were skipped. Skipping means any existing customization remains intact, BUT opens the possibility that an updated plugin (not encapsulated) introduced new constants which would not be copied now.



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