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For Kobo you should try KOReader if you want to duplicate the file structure replication that is seen on the Nook via the my files > your directory name > whatever directory name > etc directory name > you get the idea directory name
However as I migrated from Nook to Kobo, I can tell you using Calibre to create collections is a thing of beauty. I find collections (what Nook would call shelves) are very handy. And one book can be in as many collections as you would like.
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