Do you think Tor should be run over IPsec, or IPsec over Tor? Please be specific as of why you made this decision.
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As far as I understand from the Tor page: my first question is what is the relation between Tor and IPSEC?
Secondly, Tor is just for instead of taking a direct route from source to destination, data packets on the Tor network take a random pathway through several relays that cover your tracks so no observer at any single point can tell where the data came from or where it's going.
It also states that to create a private network pathway with Tor, the user's software or client incrementally builds a circuit of encrypted connections through relays on the network.
When I look in this perspective, Tor is just changing the IP addresses from source to destination and IP address as you may know are in the network layer, so IPSEC is in-between the datalink layer and network layer.
They work in different osi layers, one works in transport layer(Tor), and the other in Ip layer(ipsec), so it depends what you need:
Real example: You can't do a port scanning or use other fingerprinting tools such as nessus through TOR because the results won't be accurate because they send lots of malformed TCP packets that simply don't work through proxysocks (port forwarding), but you can use TOR for ssh-tunneling.