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The numbers are the database IDs. The directories that calibre creates are for its own purposes, and you shouldn't directly try to manipulate their contents. You can keep a parallel copy of your books in a separate directory structure if you wish, with whatever naming scheme you prefer, but don't tempt fate by trying to change calibre's directory structure. You can also export books from calibre's database with whatever naming scheme you like. Just don't mess with calibre's copy.
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