Question about the place where books are stored
I use Calibre only for transfering ebooks to my device. So the library of the books on my device is always the same as my Calibre library.
I store my ebook collection in directories on my HD, f.i. Fiction with subdirectories literature, historical fiction, crime etc and finally in those sections per author a final subdirectory. That system suits me fine. However it could be useful to create a Calibre library of the whole collection but I wonder if it is possible to do so but leaving the books in the directory structure where they are. If they are also added in the Calibre directory, that gives a lot of redundancy.
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