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Changed the defaults for options
--zbest, --bbflux and --desi_footprint to be true as defult. Now in order to set them false we have to give --no-zbest, --no-bbflux, and no-desifootprint.
@andreufont @HiramHerrera @andreicuceu I think those are the only arguments that make sense to change for now... let me know if there are other suggestions.
I also updated a bit the notebook about reproducibility to work with the latest version of the mocks. I simplified the notebook and included some information about the truth files. This can be improved in a future PR is we want to...