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Good grief! What exactly do you want to do with your collections? I've had the same problem but I'm not happy about jailbreaking my device so I'm using calibre to label my files and then put them in a collection. For example, I used calibre to change the book titles in my 'Song of Ice and Fire' collection as "Song 1 - Game of Thrones" "Song 2 - A Clash of Kings" etc.
I then manually created the Song of Ice and Fire collection folder and put the books into it using the paperwhite collection function.
It's a bit tedious but it does work.
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