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I use the option in Calibre to add empty book entries and then set up the metadata appropriately. I then add a tag called PAPER.
I guess one could also use a custom column to track this, or perhaps even rely on a search for formats:false (if you do not ever intend to add empty book entries for other purposes).
I have seen other people talking about scanning in the ISBN as an aid to retrieving metadata from the web.
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