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Sorting indices is probably not the biggest performance issue when writing problem files, but it's an obvious one. With PyPy and CPython 3.6 and later, we can assume that dictionary keys are ordered. Hence, we can create deterministic problem files without sorting.
I suggest that we use sorted representations for 3.5 and earlier, and unsorted for 3.6 and later. The only real challenge with this involves testing, and it will likely require two sets of baselines.