Short story long, they surround any ndif or pdif shape, including the n+ and p+ shapes needed to make well-taps. Magic auto-generated them when it generated gds's from .mag, but it used to not do it well. There used to be boundary issues when putting two cells next to each other. As far as I know, magic now properly auto-generates them. It's just legacy at this point to have them manually painted on; it's on our to-do list to remove.