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I understand, ZeroNet internally uses torrent.
Have you seen the following paper?
Bittorrent over Tor isn't a good idea
Torrent clients (libraries) use socks proxy settings for connectivity. Not anonymity. The threat in essence boils down to torrent clients using fancy techniques (similar to "sudo ifconfig"), finding out their real external clearnet IP, and then sending that IP through the proxy.
Connection from Tor exit coming and including the information "hi, my real name is...".
Are you sure, that zeronet's usage of torrent does not suffer from the same issue?
@HelloZeroNet one attack I can think of off the top of my head for example is: