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This paper by Shirahata introduces a notion of "linear comprehension" (that follows the principles of linear logic:
Screen-Shot-2020-06-01-at-11.03.00-AM.png
Comprehensions are what the Mitchell-Benabou language of a topos formalizes. Is there a topos of such linear sets?
it probably won't be a topos
topoi are cartesian as part of their definition
but @Mike Shulman's "affine triposes" may be what you want
actually, no, sorry, that's not right—those have an affine logic, but they don't have pervasive affine-ness requirements in arbitrary morphisms, oops