Shopify multi-store setup with Github sync

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I have a multi-store setup which will be using same theme. Theme is actively developed and I'm thinking of start using Github sync on all expansion stores, so that changes can get pushed to all stores at the same time, which is a great feature. Each expansion store will have its own branch within Github project and theme changes will pushed to master branch. However, how can I make sure that settings_data.json file doesn't get overwritten when we merge one of our stores branches into the master? is there any way for github to ignore settings_data.json file changes?