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Not only is calibre's library under its own control, it is dependent on that scheme to find your books. Make any changes to the calibre library structure, including folder names and filenames, and you will not be able to access your books from within calibre. Once a book has been copied to the library (note that calibre doesn't touch your original file), there is no need to ever go into the calibre folder for any reason; anything you need to do can be done from inside calibre. If ever you do need a library with a flat structure to use outside of calibre, you can use calibre's Save to Disk function to generate one for you.
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