At the beginning of assignIndexes() function, when FunctionIndex` and
GlobalIndex variables are created, InputFunctions and InputGlobals
vectors are guaranteed to be empty, because those vectors are only
populated in assignIndexes() function. Current code looks like they
are nonempty, so this patch deletes them for better readability.
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Hmm, I guess at some point in the past InputFunctions and InputGlobals were not empty at the start of this function.
Can you add asserts that they are empty?