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I tend to manage tags en masse, and have found that can work just as well so long as you are careful with the mass tag search/replace. If I manage books one by one I get the tags mixed-up, and it doesn't help that so many books now come preloaded with tags that may or may not match up with my standard tags.
Calibre can accommodate a lot of different workflows. The important part is to make sure that it's something you can do regularly and keeps your library organized to a standard you feel happy with.
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