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The get_systems command just records what you used. So if you add 1+1 then GMP/MPIR is involved, though thats not really cite-worthy. If you are pushing the envelope in large integer computations, then you should definitely cite GMP/MPIR. Use your own judgement to decide what to cite.
Your question does hit on a difficult question: How to automatically decide what needs to be cited and what doesn't. Its probably fair to say that contributions to scientific software are under-cited. There is a citation package in the works that'll make it easier to cite things, and where individual methods can be marked as "cite-worthy" or not.
