The DMG for the Mac version of Duke 3D doesn't appear to include the source or a Harvester manual, though it seems to be based on Boxer, not just DosBox. The Mac PKG for Ultima does have the source (dosbox_svn.zip), but no (edit: out of place) manuals as far as I can tell.
I wonder if the Harvester manual you're seeing is a GoG artifact from reusing the same DosBox setup as Harvester and they forgot to remove it, as the source from Ultima includes a file called "harvester_mouse_clean.diff".