Given that the image here looks like it was generated from a .dot file, though, it could have just-as-well been exported as an .svg, where the SVG flowchart-box nodes themselves would have the fragment links attached to them.

As it is, given the comment on how to hand-calculate new <area> coordinates embedded near the <map> on the page, I think they just used Graphvis to output a .gif rendering of the flowchart, and then went in and hand-wrote a separate HTML <map> on top of it. Quite a bit more work, and work that would have to be duplicated if you ever wanted to tweak and re-export the graph itself.