Best explanation of the network topology yet, if I'm reading this correctly this removes the problem of not being able to participate on the global network just because the application you chose to interact with it is considered an "evil server" and banned from participation like mastodon, in other words, user accounts aren't associated with a home server that determines who they can interact with, is that right?
How does an application decide whose repos to index?
Same logic as a search engine might apply to the Web - some kind of crawling rules. That said, the network tends to use Relay services to optimize it. The Relays are essentially dumb caches that provide a firehose from multiple servers. We introduced them to make it easier for new applications to pull from the network, but they're optional; you can setup your own relay or crawl/subscribe directly with servers.
EDIT: to answer your question - this means the relay tends to decide what gets indexed.
How does an application decide whose repos to index?