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@caffeineoverload - interesting. Can you run calibre in debug mode and see if there are any errors being thrown? Also I am slightly confused - is it that you have no Goodreads Sync menu at all, or just that it does not have the "Customise plugin" option above "Help" at the bottom of it?
To answer your other question, what do you mean by "refresh an accounts shelves"? What exactly are you trying to do? If you are wanting to assign a tag or custom column value to your books in Calibre based on them being on a Goodreads shelf, then you use the "Sync from shelf" option, once you have setup your "Sync action" for that shelf in the plugin preferences.
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