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As I said in that long-winded post of mine (and in my .sig), calibre isn't for managing files; calibre is for managing books. A book can consist of any number of files. Let calibre do its own thing. It works much better than the OS filesystem for storing metadata. Really it does. Once you've gotten used to it, you'll wonder why you ever bothered trying to remember if a book by Smith & Jones was stored under "\smith" or "\jones". The key is to stop thinking about your books as files and start thinking of them as books.
And given that a 1.5 TB external hard drive is $99 at buy.com, with free shipping, don't stress about the space.
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