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Is there a specific reason you want to keep your file directory system. You'll probably find that whatever you are using it for can be done at least as well if not better within Calibre.
The biggest advantage I find is that books can be in multiple categories/tags within Calibre and you can search by any of these and find it. Whereas in a file directory system you can only put a book in a single folder(e.g do historical crime fiction books go under Historical Fiction or under Crime?)
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