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Refactor latest_comparable_paths #3443

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@szy21 pointed out that our long runs were broken due to the reproducibility tests. It looks like #3437 removed this check, which means that the long runs try to run some reproducibility infrastructure in the plot comparison against main part of the driver.

We should probably make that orthogonal to the repro tests, but I had plans to refactor latest_comparable_paths anyway, so this PR adds that check back in, and changes to using compute_bins, which is unit tested (as well as latest_comparable_paths), and this fixes a bug in latest_comparable_paths in that we will no longer incorrectly compare against potentially incompatible commits after reverted commits (when duplicate reference counters exist on main).

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