Actually, the links look ok (at least on single-file output), but we lost the <h1><a name="My Stuff">My Stuff</a></h1> stuff. So the links have nowhere to go.
I'm betting we lost some of the subtleties buried behind "why is Dave's prototype munging the <h1> tags more than once?" puzzling. :) Too tired to sort it out tonight.
Actually, the links look ok (at least on single-file output), but we lost the
<h1><a name="My Stuff">My Stuff</a></h1>
stuff. So the links have nowhere to go.