EXPERT RESPONSE
Discovery and accurate topology generation is a difficult problem. And spanning trees for VLANs is even tougher. It is an active research topic.
I don't have a particular solution to point you to. However, I would have a look at Avaya's offerings and see if they can provide the tools that you need. Cisco would be another logical choice. Further, I would check into the various academic offerings - quite often simple but effective tools can be found for free, especially if you are willing to act as a proving ground and provide feedback to the researchers.
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