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Why use either program - you can simply drag -n-drop books to the reader and use the internal collection to organize them , the books app also allow you to sort your books a number of different ways and has a search function as well I have 2000 plus books in 92 collections and have no problems finding stuff by keeping it simple you can organize stuff the way you want and you can avoid all the sync problems. i use calibre for conversions and the reader software for firmware updates, use dropbox for wireless transfers
KISS is always the best policy
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