My first feedback! Cool.
add panel: don't know what you want
notes.ini setting: I agree.
layout: not sure what you mean. Top-Down? Right-left?
diagram as page: I felt it was useful to have the documentation within the database itself. I'll think of the option of displaying the result in a separate eclipse window. To be frank it all depends on my eclipse rcp skilz, which I am currently learning. (Steep curve btw)
Regarding your example, that would mean changing the internal logic. At the moment I'm determining the relationship based on the 'Use' keyword. What you suggest would mean a lot more work, i.e. a function dependency chart. I tried that, and the diagrams become saturated with information and unreadable pretty quickly. Libraries coming from another database are already highlited (they are displayed in a separate box)
My immediate next step is getting the selection to be hidden when in the client, but I haven't quite worked out how to do that right now.