I too use the Save As, with the Copy All Audio option checked, and save it all to a new project folder, so that when finished it has a nice clean Audio folder with only referenced audio clips.
 
This only affects me when I have vocals or instruments like guitars or brass - if in a midi only project, or mostly midi, there just aren't the kinds of numbers of audio tracks and their multiple audio clips per track that you would normally see.
 
I HAVE used that clean audio function, but that seemed to take forever, so I just use Save As now, as it is quite speedy. Just ALWAYS remember to double-check the Copy All Audio check box or you will be quite sad.
 
Bob Bone