I have gotten the opportunity to work with Lattix in the past. I believe the paradigm it represents (a hierarchical dependency matrix) is the future of large-scale system a
There are some open source tools that implement the core functionality of Lattix, DSM (Design or Dependency Structure Matrix) listed here:
http://en.wikipedia.org/wiki/Dependency_Structure_Matrix
The recent release of dtangler 2.0 has an something in its release notes you might find interesting:
dtangler 2.0.0. is released! The major new feature is the ability to read dependency information from a plaintext file. In other words: it's not just for java - now you can generate a dependency structure matrix that describes whatever you want!