Does NATS provide some api for managing its topology, i e create new cluster, combine it in supercluster, create gateway etc. In docs I see only file configuration, but is there another way for configuring nats?
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No, there is no API to handle topology. Leveraging gossip protocol should ease the process - when adding a new node to the cluster, you don't need to alter the configuration of the current ones, nor let clients know.
https://docs.nats.io/running-a-nats-service/nats_admin/upgrading_cluster