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it might be faster to just create a blank library and import a whackload of epubs. i think Calibre is meant to be friendly in how it shows files in it's GUI, but not necessarily in the actual file structure.
it bugged me so much that for each book, i ended up doing a "Save to disk" in my preferred filename format. and then delete from Calibre's library. :P seems dumb, but Calibre does have great clean-up tools.
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