Dave Girard with a shell script for OS X and Linux that collects Nuke files. This latest version makes a relinked duplicate of your scene. Get and use the script from here!
“Perfect for archiving your work and even has a check to make sure you wouldn’t accidentally clobber your collected files by copying files with duplicate names. Sorry, I can’t make a Windows version since this is just passing the Nuke file through a lot of UNIX filters like sed, it’s not a binary.”