I have several XML files which all have dependencies among each other. They are all kept in svn (subersion) repositories. My perl script analysis them and generates the graph.

What I build is one group node for each repository.
Inside this there are group nodes for each (so called) workbench file.
Each of these files can contain several templates and objects.
Each template is made up of several objects not necessarily belonging to the same workbench file the template belongs to.
So in order to visualize the dependencies I will draw edges between each template and all the objects used in that template.

It's just an experiment to get a tool to help me get my files a bit better structured.
I hope I will more easily identify common objects which are used in several templates.