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I use calibre, which takes care of the HDD end for me. I know people have a strange thing about using the filesystem for their metadata, but where do you file a book by Abel and Baker jointly? I just let calibre worry about that, and I deal with books, not computer files. Thankfully, my Sony is reasonably smart about what to do with the books it gets. I use tags to sort my books into collections -- for instance, Cryoburn is in a "SF" collection, a "fiction" collection, and a TBR collection, plus a "Miles Vorkosigan" series, though I'm not currently using series on the Sony -- and then I can find them by author, title, or category.
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