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I use KOReader and Calibre and browse my books in the imported directory structure. I have a column in my Calibre database where I store the target path and then a slightly hacky "save template" to ensure that the files are stored in that structure on my device.
My paths are generally Fiction/Non-Fiction followed by one or two sub-directories (author or genre/sub-genre) - I try not to go too much deeper as there is still only a limited path length.
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