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calibre "forces" you to keep only one copy. The extra copy for itunes is present because of itunes (or more precisely because Apple dont want you to use anything other than itunes to send files to their devices). There is nothing that prevents you from working on files in the calibre library, so there is no need to keep an extra copy to work on. The only restriction is that you don't move the files around outside of calibre.
As for the network backend, once again, it is *optional*. Don't use it if you dont want to, in which case calibre will continue to work as it does today.
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