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Remember, calibre's library is meant to be a back-up that you don't directly touch. It is not meant to be your one and only copy of these ebook files.
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While I agree with everything said about the file structure being immutable for good reasons, I cannot agree with the last bit.
Calibre is *the* place for my eBooks, and I might take a back-up of my calibre library, but it itself is the primary location, and *not* a back-up at all.