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This is an Information Architecture question. First, your definition. System structure What you and your client describe, sounds like a graph with connected components to me. As such, it will never be effectively defined by a breadcrumbs that can only describe a vertical hierarchy or a tree relationship. Conflict between menu structure and site ...
Categories + meta tags It sounds like you're describing a system of high-level categories or a very shallow tree that is subsequently filtered by meta tags. A hybrid of category identification via a breadcrumb and filter tags is worth consideration. I'm sure this isn't representative of your system, but you get the idea:
As I read your question: - You want to show the overall structure. - It's arranged in the net structure. So it seams you want to show the minimap navigation (like in games). But, you mention that it is about business processes. Here the view (and navigation) depends on the user role and the matter of processes. Process manager (and possibly director) ...
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