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Yep. The problem was that I had tried looking at some plugin code and, among other things, had set up that CALIBRE_CONFIG DIRECTORY environment variable. Since I'd determined I didn't have the right stuff to mess with code any more, I uninstalled all of that and got rid of the associated environment variables. That fixed my issue with the Calibre plugins not updating. I'm assuming Calibre was getting confused and checking the versions in the cloned git repositories instead of looking in the actual plugin directory.
I'm assuming if I'd set up a totally separate "development" Calibre version, I'd have been ok. But, all's well that ends well.
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