stuart_setup and stuart_ci_setup are two separate ways to do a one-time initialization of the project. stuart_setup will initialize any submodules specified as necessary in the settings file while stuart_ci_setup will clone any repo's to the specified location as specified in the settings file. stuart_setup is not a replacement for git, and should be a one-time call to initialize the repository. Any maintenance of the project's submodules is expected to be done manually with git.

However, their names have caused confusion amonst users of edk2-pytool-extensions.

The proposal here is to merge stuart_setup and stuart_ci_setup into a single command, stuart_init. This will clear up confusion with developers who thing stuart_setup should be called whenever they want to get their repo to top of tree. the consumer can choose to either setup their project via submodule or cloned repository by overriding GetRequiredSubmodules() or GetDependencies(). The new invocable, stuart_init will then call GetRequiredSubmodules() and GetDependencies() and initialize any specified, instead of a developer needing to call stuart_ci_setup and/or stuart_setup.