What is it that you actually want to achieve? If you just want to make sure you have all books in one directory I would have thought rsync was the logical answer.
For example, the command:
Code:
rsync -avzP /home/scott/dir2/ /home/scott/dir1/
should result in dir1 containing its original files and the files in dir2 that were not already in dir 1.
Adding the n option will do a dry run, listing on the console what actions would be performed.
Code:
rsync -anvzP /home/scott/dir2/ /home/scott/dir1/
This is a very simple explanation of using rsync in these types of circumstances:
https://www.digitalocean.com/communi...ories-on-a-vps
My recommendation would be to use Calibre to manage your ebooks. Once imported, you could safely delete the original source. You should, of course, keep at least one backup of your Calibre directories.