First notes for Rosetta common
The new versions of Rosetta(from March 2018), allow users run Rosetta with a configuration file. And this file is basically options file that is loaded at the start of each Rosetta run.
To start with, create a directory that will be home to any Rosetta configurations in your home directory like
mkdir .rosetta && mkdir .rosetta/flags
And Rosetta will now look in that directory each time it is run.