How to avoid duplicating files that goes on an iPad? I would like to upload PDF files on an iPad. After adding them to the iTunes Library (iTunes -> Files -> Add to Library), and syncing, they are uploaded on the iPad, but are also copied locally in ~/Music/iTunes/iTunes Media/Books.

Is there a way to prevent the files from being copied in my home directory ? I just want them at two places: an external hard drive, and the iPad.
On a Mac: Drag the files into iTunes with the option key down and the files won't be copied to your iTunes Media folder.

That's the exact result you like.

There is also the option to change it so you don't have to press option key:  

You can press option key after changing that setting to copy it on purpose. (Exact opposite of default setting)

Good luck :)