At the risk of not being helpful: I have some json files that are updated weekly that I keep under source control in git. The week-to-week updates are often fairly simple, but git was showing some crazy diffs that I knew were way more complicated than the update. I soon realized that the data provider was not consistently sorting the json arrays; when I began sorting the json arrays by rowid everytime before writing it, the diff's were as straightforward as expected.
I think I don't understand the problem you're encountering, because this solution seems too obvious.
