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I have over time transferred the majority of my library into Calibre and then removed the originals so I avoid duplication. Actually if anything I have reduced my reqirements as the transfer into Calibre has encouraged me to any duplicates thqat were in my original library, but were filed in different places within my original folder structure.
I then keep backup off-line of my Calibre library to protect against disaster, but I would have to do that regardless of the directory structure used.
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