My goal is to create a new icon for sound objects that are saved in another file folder than the arrangement folder. The context menu for these sounds will then have a menu for copying/moving the sound files to the arrangement folder. This can be used in your case to move sounds into arrangement sub folders, but can also be used to make local project copies of e.g. drumloops dragged into an arrangement.
If you use these commands for all your sounds in all your arrangements, then the sounds remaining in your project folder should be the orphan sounds, which you then can delete.