I\'m working on an embedded Linux project. Our build process makes an image that gets flashed to a device. Many of our files require root ownership for the system to work co
I would structure your system so that the source files don't care what owner they are. You can check these in and out of git without worrying what permissions they have or who the owner is (especially since "owner" isn't meaningful across all the systems a git deployment is likely to serve).
When you want to generate the embedded image, copy everything to a new directory and then set the permissions as you need.