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Calibre is "almost" an all-or-nothing system. You have 2 options:
A. Use Calibre for managing your library, and never go poking into the library folder. Treat it as a black box.
B. Manage the books manually in your own folder structure. Just don't expect Calibre to help you with that.
Choose Option A or Option B, and stick with it. For obvious reasons, most people here will recommend Option A, but there's no wrong answer, except trying to do both.
That said, there's a reason I said Calibre is an "almost" all-or-nothing system. Calibre is also modular. You can associate ebook file types with Calibre's reader, and open them directly in the reader without going through the library management system. You can import books into a temporary library to clean up metadata and do conversions, then export them and delete them from the library.
Find a system that works for you, whether it includes Calibre or not. Just don't try to manage your library in two different ways.
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