This will probably only work on *nix systems, but I wanted to automate the setup of new projects and be able to build binaries and run them in Stella.
https://github.com/joeyjoejoejr/cookiecutter-atari2600
It has a basic project pulled from the amazing tutorials in this forum and uses the python library http://cookiecutter.readthedocs.org/en/latest/.
Assuming you have the prerequisites, python, ruby(system defaults are fine) cookiecutter, DASM and Stella you should be able to create your project, and then run the default kernel with "make run"
I hope someone else who hasn't build out their own workflow might find this a useful starting place.