Well, if you don't mind iBooks taking all your ePubs and PDFs and just throwing them all into a folder buried in your user Library directory, then iBooks will work for you. It will keep all your iOS devices abreast of what is on your Mac and you can Sync them and stuff.
What this thread is about is the problem that iBooks takes PDFs and ePubs OUT of iTunes, and renames all the ePUBs to DOGOAD@*$Y#* or whatever it does, leaves the PDFs alone (thankfully) but still throws EVERYTHING into a single folder in a ~/Library
SO what ever structure you had in place to organize PDFs or ePubs in iTunes is gone. That is a problem.
@Eric, I wish that was the only problem! There isn't any way to edit metadata in ibooks, so its not a useful catalog. Also, a great number of my pdfs didn't get moved into ibooks when apple automagically moved them out of itunes. They're actually still in my itunes 'books' folder, so they're not lost, but when I try to add them to ibooks ibooks gets confused and says they're already there. And finally, as far as I can see there is no way to manually manage books using ibooks, you have to 'sync'. I refuse to do that. The recent update did nothing to address any of these concerns so obviously it isn't a priority for Apple.
So I find myself wondering, is calibre the best thing out there currently or are there other better options? Anyone have any experience? I'm starting to really look forward to a day when I can leave the clutches of Apple for the clutches of Google. Why should we pay more for a poor (similarly poor I'm sure) experience? I just kind of feel like, if computing is going to be a pain in the *** anyway then I might as well go with the cheaper alternative.
Kevin Edgecomb presents a simple solution to restore control of ePubs/PDFs back to iTunes as you used to have it.
In the middle of the page.
Just tried it myself and it works fine. Make sure to back up all of your books before you do it just in case.
Hope this helps.