I don't know of anything that does nested collections unless they are just using the file system structure. And to me that isn't a true collection as to get a book into multiple places in the file system, you have to have multiple copies of the book. On a Kobo, a book can be in as many collections as you need.
And before someone jumps on me, yes, you could do it using links. That would require the file system supporting them, and whatever method for adding the books or creating the collections to build the links properly.
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