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I was just about to make a suggestion on this during the JOSS review.
In addition to making the installation process easier it also enables to keep the repositories in sync, e.g., making sure that an older version of MAESTROeX is always tied to a version of AMReX that work together.
So +1 from my point of view on this (but this is independent of the review).
See AMReX-Astro/Castro#651.
This would make the installation process easier for new users.
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