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Calibre will automatically rename books for you, and even create subdirectories and other nice stuff.
But calibre does this when you send books to a device or to a folder on a disk. You just change the save and send to device templates.
Inside the calibre internal library, where all the books are before you send them to device or save to disk, it is different. You should stay out of there and not touch or change anything! Preferably not even look! Calibre maintains everything there, if you change anything calibre will most likely loose track of it. And you may lose books and metadata.
Use the functions in calibre to save and send books instead.
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