IMO you need to give priority to the niche you are in rather than worry too much about whether the input falls in your niche. The user can always run a separate old-school diff. But your own output should be rigorously predictable in format, so that people can write code to process it. The only way I see to do that is to have a rigid default behaviour first and have such options as extras. If %change is important in your problem, I would be inclined to have a switch that replaces the functionality with only a statistical analysis that the user can then consider before choosing the next step and that also each such option, not just the default, should stick to the rule of rigorous predictability in the interests of those who will process the output.
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