You are correct Michael, those folders and the files below are part of the source files that are being looked at for publishing. I just closed a call with PTC about this same reason. You need to go into your Recipe file for your publishing and set output source to 0.
adapter/outputSource=0
Filename that I changed was "proe2pv.rcp"
Message was edited by: Timothy Swett Reason: added a " at the end of the last line