I'm interested in this area. Once, in the past, I wrote
UML::Sequence which runs perl programs to produce sequence diagrams of what they actually do. This leads me to think that you could write a special driver using the debugger hooks to load the modules from your app, then dump out their inheritence relationships, etc. (based on what is loaded and what those modules have in their @ISA and symbol tables). Maybe that could be incorporated with some good POD parsing, but I'm just rambling now.
Phil