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I updated the spec in #168 to at least correct the encoding of the secondary slot in the genesis configuration and for configuration update digests.
Current status is that the secondary slot will not be specified for now, as there will be no secondary slot in Sassafras, which should replace Babe in the long run.
There are currently two secondary slot modes in substrate and both are in use (plain in Kusama, VRF in Polkadot).
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