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If Calibre were to utilize BLOBs (Binary Large Objects) in a database to store the eBooks no one would have any access to them at all. Yes, the databases would be larger than many people are accustomed too, but then there would be no question at all about path names et al.
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My problem with the bad folder organization is precisely that i can't easily access the books outside calibre.
it forces me to use calibre to sync books with my e-reader, but I like to just copy - past. I don't want to be dependent on the software.