> but does not leave the reply message in the relay which Alyssa pulls from
Well, there is the problem. Just don't do that and you won't need centralization.
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A bit new here, but as I understand it from asking around if someone you don't follow posts in a sub-thread you are not participating in then you won't see the note and common outbox methods may not help with sniffing the relevant relay out, things hitting a math-shaped wall.
With town-square microblogging, most people spend the bulk of their time reading threads by people they don't follow, and with no intent to participate in those threads. I would imagine it'd trigger some people's OCD knowing there might be interesting replies that are invisible to them as they browse through such town-square threads.
Assuming I'm getting that all right, I'm not sure if:
(a) That's a solvable problem with some sort of 'outbox-plus' paradigm
(b) The only way for nostr to get there is old-fashioned third-party crawling and indexing (and associated search-engine-style centralisation risks)
(c) The way forward is to focus on use cases where such a global view is somewhat superfluous, making the question of how to achieve it moot
Love to get your thoughts.