I think the best thing to do would be to start a new project (i.e. repository) which includes the stan-dev/stan as a submodule (which in turn has stan-dev/math as a submodule). Alternatively, include a tagged version of Stan and Math into the project.
It’s fine to use CmdStan as a blueprint, but my guess is that most of the things in there will not be relevant for a project like this.