We started using JUNG (http://jung.sourceforge.net/index.html) for the
visualization before we became an Eclipse project. Danyel Fisher and his
team have created a very powerful package. We are looking into the issues
of using JUNG with Eclipse. The Ariadne project
http://awareness.ics.uci.edu/~ariadne/index.html has used JUNG with
Eclipse for the purpose of plotting relationships between engineers and
code modules. Is this logically similar to what you want to do with
applications and framework methods?
By the way, Higgins keeps track of relationships within itself. We were
just using JUNG for the display.