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Gnunet over other overlay networks?

Would operating a gnunet network within other overlay networks, such as cjdns, work as expected?

From what I can tell, you'll need at least one operating and responsive hostlist server that you can provide to new users in that network.

So long as you have the hostlist server, a gnunet testbed network over cjdns should be possible.

Is there anything else I should keep in mind?

In principle, GNUnet can run over almost anything (and we don't need a hostlist, strictly speaking --- UDP/WLAN broadcast / multicast can also work, depending on your underlay). However, the setup complexity (installing cjdns, Tor, whatever) is likely significant, and then there is the question of what overheads such an additional underlay would create --- and what the benefit you expect to get is (as in: is it worth it). That depends of course on a lot of factors, so there is no general answer. We do know that the Tor community doesn't like P2P networks running over Tor. Also, maybe you can get some of the same benefits more efficiently and/or with easier setup by writing a GNUnet transport plugin instead.