Hi Peter,

I have Mavericks and iBooks takes any ePub or PDF I drop into it just fine, and 
syncs them to my iPad and iPhone.
iBooks accepts .epub format eBooks, & PDFs - Kindle accepts .mobi format eBooks.

A little information about iBooks on Mavericks:

You put the eBooks in iBooks. Then iTunes syncs (through the iBooks Store) 
where your book-specific info is stored in your account, so you must be logged 
in to the store on each device) (although not necessarily at the same time) in 
order for the information to be uploaded from one place to the cloud and then 
downloaded to another.
Syncing isn’t limited to iBooks Store purchases. Other books you put in 
iBooks—those downloaded from the Web, for instance—can still have their 
bookmarks and annotations synced across devices.

On the Mac, the books are stored (as you have already found), in a series of 
folders inside a folder that’s normally hidden from users. 
The path is ~/ Library/Containers/com.apple.BKAgentService/Data/Documents/ 
iBooks/Books, and it’s the Library folder in the path that’s hidden.
 (You can access this Library folder from the Finder by holding Option as you 
open the Go menu, and then choose Library; after that, open each of the folders 
named in that folder path.)
And inside this enigma are: folders for each of your books, named with long 
random-looking strings of alphanumeric characters and containing many odd files 
and sometimes other folders. PDFs, however, sit calmly inside that inner Books 
folder without subfolders or substitute names.
It’s obvious that we are not meant to enter this sanctum. And there’s little 
reason to. Store-bought books can be downloaded again if anything happens to 
your iBooks copy, and items you installed in another way (from the Web, for 
instance) are only copies of the original, and can be copied from iBooks by 
merely dragging them out of the Library window.

iTunes-iBooks Transfer:
If you’ve used iBooks on your mobile device and synced your books through 
iTunes, and then upgraded to Mavericks, you have a ready-made library to 
transfer onto the waiting shelves of Mac iBooks.

The first time you launch iBooks, it checks if you have an iTunes library of 
books and, if so, it grabs them all. 
If you have other ebook files & PDFs, you can add them to iBooks on the Mac. - 
ePub files, from within iBooks: Choose File > Add to Library, or dropping it 
onto the iBooks icon in the Dock, or dragging it into the iBooks Library window.
PDFs, drag & drop works both onto the iBooks icon & into the iBooks Library 
window.

Note: The file is copied into iBooks; the original file remains wherever you 
left it. So, if you delete it from iBooks, it’s the copy in your Library that’s 
erased, not the original.

Over 9000 ePub files to move is going to take a long time to add to iBooks 
Library.

Cheers,
Ronni

On 22 Feb 2014, at 5:03 pm, Peter Crisp <[email protected]> wrote:

> Hi, I have some epub files on an external drive that were in my previous 
> iTunes library and now I have moved to Mavericks, iBooks is now a standalone 
> app. When iBooks starts up it says “iBooks is moving your library …”. Shortly 
> after it quits saying “iBooks has quit unexpectedly but will continue to move 
> your library”. I’ve located where the iBooks storage folder is in the library 
> and only a few files have moved over - I have over 9000 of them - (don’t ask).
> 
> So I wait quite a while for the external drive light to stop flickering - and 
> still just a few epubs in place. Still iBooks will not complete the process. 
> Lots of online chatter on the same issue - is iBooks ok for anyone here?
> 
> Any ideas how I can read these now or do i have to go to Kindle?
> 
> Regards
> 
> Pete.

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