Packages do not resolve as source correctly if not registered at root module

[hach-que]

If packages are registered in a Protobuild module that's in a subfolder of a Git repo (rather than being at the root), then the "git submodule" commands Protobuild runs do not correctly account for the fact they need to run at the root of the Git repository, and that they need to include the prefix path to the Protobuild module.