I have a VS Code project that is a Workspace Application where I've had to make some modifications to code in both zephyr and mcuboot directly. My codebase is in a git repository, but the zephyr and mcuboot directories are themselves git repositories. This appears to be a fundamental aspect of how the west build system works, and it is not happy when I try to remove their .git folders to get their files included in the surrounding repository.
Since I can't push my personal changes to those sub-repositories, someone else checking out the codebase won't get my changes, as they aren't tracked by my main repository.
What is the recommended way to maintain source control in a situation like this? Can I rework the west build system to not completely break when I remove those .git folders? Or to maybe get it to apply a local git patch to them when they're first pulled?