It requires great diligence and occasionally gets pretty cumbersome if you start new tools on a regular basis.
Why not just use a template for it? Cookiecutter is a CLI tool written in pure Python that enables you to do so. Not only is it working for Python code, but also markdown formats and even other programming languages. We will talk about the ideas behind Cookiecutter and go over how you can create your very own template, so you and others can benefit from your experience.
You can find a recording of my talk on the EuroPython Youtube Channel at https://youtu.be/yxXio-jzAMQ
For more information on this talk please see the official outline at https://ep2015.europython.eu/conference/talks/come-to-the-dark-side-we-have-a-whole-bunch-of-cookiecutters