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You're using the filesystem for metadata now, right? So, for instance, you have a folder named "American Literature" full of, well, American literature?
Simply import the books one folder at a time. As you import each folder, tag the newly-imported books en masse with the proper category.
Trust me, once you get started using real metadata instead of a filesystem-based kludge, you'll wonder how you managed to endure the old way. I know because I did.
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