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The EnergyPlus development team uses a TableDiff utility that compares output HTML table files and summarizes differences. I don't know if it's publicly available but we could easily make it so. I also don't know if that is exactly what you are looking for. LBNL recently developed a utility for comparing IDF files. And I am not sure about the public status of that either, but will check. Calling @YixingChen.