Hi Paul, that’s a great question! As an admin my main focus on customization is which plugins and so on which I handle with submodules as discussed in part 3 of this series. If you are making customizations directly to the core code, you will have to manage conflicts and choose to keep any of your changes….a tricky business in any case. But Git can at least help you spot and understand differences https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/resolving-a-merge-conflict-using-the-command-line

But how do you prevent all your custom code edits from being overwritten when you pull from the moodle repo