Personally I would just stick with Reader Library.
I have never been able to get my head round Calibre. I know it's a great program but I just can't tolerate the way it works not allowing me to organise my books the way I want to and not the way Calibre thinks it should be.
I like to have my books sorted by genre - biographies, travel, humour, history etc., but Calibre just seems to want to put everything in separate folders based on the author's name.
And another thing why does it need to store the cover and metadata as a separate files? All that information is in the epub file itself. To me that is just wasting space and making things complicated for no reason.
So just stick to Reader Library. Use Calibre for 'editing' if necessary and then remove the book from Calibre's library.
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