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I've just been poking around on the app store and downloaded a couple of readers which I had previously rejected for my own use. Neosoar book reader may do what you want, partially It integrates with Dropbox in such a way that whatever is in Neosoar is also in Dropbox. At least, thats the claim on its current intro screen. I havent tried it myself. For PDF, Goodreader can upload direct to Dropbox, as well. Not sure if thats a sync thing, or just an upload thing. eg in Neosoar, if its deleted from the reader, it will also be deleted from Dropbox (but that doesnt have to be a problem if you make copies to keep in a different folder)
To get books into Neosoar, you'll need an external source which can use "Open In" to get the books into Neosoar. It also has its own book store which I have not explored at all. Neosoar also doesnt seem to allow metadata editing.
In all seriousness... Calibre is the best way forward, even if everything else is on the iPad.
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