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I only store a dozen or so books on my iPad. I use Calibre on my computer to manage my ebook collection. I have the Calibre server running and can view my books via the iPad's Safari browser, click on a book and open it in iBooks.
iBooks did add collections in the last version -- haven't tried to see if I could put epubs and pdf's in the same collection. I use GoodReader to read my pdf's anyway. I use DropBox to manage my pdf's as well, and do not keep them all on my iPad.
I can also remote into my PC from my iPad if I want to have full control of Calibre from my iPad.
Lee
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