add support for one repeat per json

[atravitz]

Is your feature request related to a problem? Please describe.
We should no longer enforce 3 replicates per json, as many users want to parallelize and use a more "flat" structure.

Describe the solution you'd like
Eventually in 2.0, I would like to change the default to n=1. In the short-term, we can add this as a yaml input and/or command line flag.