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iirc, perl classic is modular so you can delete the folders for any parts you're not using to save some bloat. Aside from that I doubt there'll be any problem running both and mix/matching parts from them apart from the obvious slight waste of resources. Plenty of people run aguf for most frames and a seperate addon for the raid frames.
Any particular reason why you want to keep perl rather than just swapping it out completely for aguf?
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