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Are you using the Trook revision modified by craftycoder (there has been no activity on the original author's part for a long time)? If so, Trook 0.7.15 should work OK with Calibre, at least it does so for me. I do apply a few patches of my own, though, which fix issues with some of the sub-categories -- I have not seen categories displayed as flat text, though. I can provide you with a Gentoo ebuild or the raw patches, just PM me with an address.
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