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One of the nice things about Calibre is that it supports putting a book in multiple collections. For the most part, I put books in first their basic collection, thus all SF&F books go into the SF collection, all history books go in the history collection, etc.. Then individual books go into additional collections. For example, I have a collection called favorites, which is where I put all my favorite books that I re-read a lot. Goldsworthy's history on the Punic Wars goes into History and Ancient History and Roman History.
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