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Ideally after you make changes to your measures, you would run openstudio measure -u /path/to/measure_dir
(or openstudio measure -t /path/to/dir_of_measures
if there are multiple measures) and commit the updated measure XML file. You could wrap this command in a rake task or perhaps a git pre-commit hook to make it easier to run. Thus the git repo would have measure XMLs that are consistent with the measures, and running the OpenStudio App would not generate any XML file diffs.