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Yes, I'm still affected.
The contents of the directory looks perfectly normal, no duplicate files or folders...
I suspect this is caused by the way Jenkins handles plugin registration, and how it used to handle it in the past. Nowadays, extensionpoints take care of this sort of thing, but back in the day you used to have to register by extending the Plugin class and adding the necessary classes to the appropriate lists using the start() function. So running old plugins on newer versions of Jenkins would exhibit this behaviour, and it explains why the issue goes away when certain plugins get updated.
Ideally these lists (such as BuildStep.PUBLISHERS) should be unique lists, and not allow these duplicates to be added.