The way I do development is that I create everything on a Local XAMPP installation – all Production websites, plugin code, etc etc etc. Once I am done with the Development version of anything then I copy things individually. ie a Theme, ie a Plugin, ie anything else. I am firm believer in never doing a mass site clone. It would probably go fine most of the time, but 1 experience in hell would be enough for me never to go there again. I get a lot of emails from folks about this so it does happen when mass cloning.
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