Just got off a conference call with Britton and Dave. The highlights of the discussion were that the contouring is going to get rewritten, in two phases.
1. Dave is going to check in the ability to demand bifurcation of clumps during clump finding; this is an extension of Britton's Clump.py. 2. I'm going to start (some day) on rewriting the contouring algorithm to use one from the paper "Efficient Computation of Topology of Level Sets" by Pascucci and Cole-McLaughlin 2002. This is longer term, but it's faster than the one I wrote a year ago and it gives the entire tree in a single pass.
Britton has some good ideas about other improvements to the clump finder, as well; the upshot of point #2 is that this tree will be trimmable in exactly the same way as the current method, but it will be smaller, faster, and give you more information. It's also parallelizable.