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I know you are probably joking, but didn't MS buy the code?

Yes, Microsoft bought Skype, it didn't create Skype. There have been many substantive changes since then (e.g. much less peer-to-peer in operation).

Is there any peer-to-peer now, I thought they routed everything through their own servers now?

I don't know. It seems stupid to entirely drop peer-to-peer but maybe that's the case now.

only "stupid" if you are opposed to this:

Otherwise, dropping peer to peer is the only way to achieve the projects goals.