@Aljoscha
SSB indexes links, and allows querying them using the links method. it indexes links to blobs, feeds, and messages, in any message, but only in top-level properties of a message or second-level properties if the rel is "link", i think. so deeply nested links are not detected. but links like these would be:

{
  type: '...',
  thing: Ref,
  things: [Ref, {link: Ref}]
}

where Ref is an ssb ref (blob, feed, or msg id).

contact messages have special meaning at the protocol level: they are used to determine what feeds you will request from your peers (and what feeds you will not offer, if a contact is blocked). pub messages are used for discovering addresses of pubs to connect to. i don't think any other messages currently are given special meaning in scuttlebot.