I don't like Calibre's folder structure either. However, Calibre doesn't delete the original files and ebooks are relatively small so I just keep multiple copies. One is a set of books organized in my preferred folder architecture and the other set, the Calibre library. There's nothing stopping anyone from doing that. Even if you have 10 thousand books at 2MB/book (a very generous estimate), that's still just 20GB (40GB for 2 copies). Nowadays, you can get 1TB hard drives for less than $100.
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