Function hydrate 

pub async fn hydrate(
    registry: &Arc<McpRegistry>,
    manager: &Arc<SettingsManager>,
) -> Result<()>

Seed the store from the file-derived registry on first boot, then make the registry match the store.

Called once during startup, where tearing the registry down is safe because nothing is connected yet. This is the ONLY path that drops every connection; save deliberately does not (see ApplyOutcome::Deferred).