We developed a lot of the protocols and technologies ourselves, and could talk about them for hours :) Let me know if you have a specific area you want me to discuss.
In short, AeroFS is a decentralized data management system running on top of p2p overlay networking.
The overlay network layer presents to the data management layer a transport-agnostic view of the Internet, and addresses peers using network-independent identifiers. In this way, data management can talk to any peer regardless of network topologies and firewall restrictions, as if the world is flat :)
The data management layer controls data versioning and update propagation in a fully decentralized way. As I described in another comment, we use version-vector-like data structures to track versions and mange conflicts. We use modified epidemic algorithms (http://portal.acm.org/citation.cfm?id=41841) for fast update propagation. AeroFS distinguish between peers and super peers. Super peers can help update propagation and peer communication in many ways.
