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Do Ethereum 2.0 clients, such as Lighthouse, Nimbus, or Prysm implement any standard on defining different chain specifications or genesis blocks comparable to how legacy Ethereum clients do?

Would it be possible to bootstrap new beacon-chain testnets based on a specification file fed into the beacon-chain client implementations? If so, how?

I came across the following configs/ in the eth-2.0-specs but I'm not sure whether they serve as specification or actual client configurations.

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Yep, they sure do! You can find a bunch of published specifications here:

https://github.com/eth2-clients/eth2-testnets

They are indeed based upon the "configs/ in the eth-2.0-spec" link you provided.

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