Add PDFs to iBooks, without making a copy to com.apple.BKAgentService folder TL;DR: How do I get rid of duplicate PDF files between the com.apple.BKAgentService iBooks folder and their original location?

My SSD is running out of space, so I'm doing some cleanup. A point that has come to my attention is a lot of duplication of PDF files added to my iBooks library (which I'm forced to use for viewing these files in my iPhone and iPad -- if Apple didn't force iBooks down my throat, I would steer as clear as possible from this abomination.)

As I recall, at some point in time, iBooks wouldn't copy your PDFs to the com.apple.BKAgentService folder -- I believe it was used for your purchased iBooks from Apple, or for PDFs/ePubs you downloaded in iOS Safari and then clicked on "Open in iBooks".

It looks like this is different now. When adding a PDF to iBooks, a copy is automatically made to the com.apple.BKAgentService folder, which is woefully inefficient.

Of course I could delete the other copy (not in com.apple.BKAgentService) of my PDF, but I like to keep them organized by folders, kinda like iTunes does with //.mp3. If this is were possible inside the com.apple.BKAgentService folder, this would be an acceptable solution to me.

I've also thought of individually symlinking each file in the com.apple.BKAgentService folder to their original location. Although this would be a lot of work, it would also be an acceptable solution to me, but I have no idea if this is going to wreak havoc with iBooks.

Any other solutions to the problem are welcome.
I eventually solved the problem by hard-linking the files between my folder and the com.apple.BKAgentService folder, with the aid of some shell scripts to automate the process. Everything still seems to be working fine.