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How does federation work?
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I don't think you do. Instances should merely reach out to other instances it's federated with periodically to get a list of communities and some of their metadata. Ideally, they could ask all of those other instances to notify it when a community is added, modified, or deleted, and then store that metadata.
That should be pretty easy to implement, and maybe it already has, idk.
Sure, but this isn't finding new instances, just new communities on known instances. Indeed, this is not difficult to implement. The reason it's not done already is for resource economy. A lot of instances are already struggling to scale, making them process and store a lot more content with little value for most users of the instance isn't feasible for a lot of servers right now.
A list of communities isn't "a lot more content." Just run it once daily and the problem is solved. Instances don't need to store posts, just community names available on that instance.
If the issue is finding new instances, I think it's fine for it to take some time the first time someone tries to find a community on that instance. But after that, it should immediately have a list of communities from that instance.