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The key generation step would be done once.  There would be some substantial changes to Genesis.scala to bundle up the various contracts into the single deployment; as part of that, scala code would need to be added to compute the signatures necessary to register the contracts at the given public keys.  The changes to each individual file in casper/src/main/rholang are mostly just removing quotation marks. 

Consensus

From the discussion below in the comments, the consensus is to keep the files separate, but register them at public keys with LONG_MAX nonces.  Each file will import the ones it needs explicitly using the public key.