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One trick, that might be relatively easy to arrange, could be to create an alternative tree structure on demand, using something similar to the save to disk template, only populate it using symlinks/shortcuts. That means that there only is one copy of the book on disk, but it can be accessed from several places. That way you can either browse using calibre or some intricate tree structure. It would even be possible to have the same book in several folders at once, using more than one template, and it wouldn't take up much space at all. So the tree could have several different structures to navigate at once. You could browse by genre and then series, or by year and then author and then series. Or whatever.
The mirror structures would have to be read only, of course.
I belive that there already are some that are doing something similar?
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