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cookiecutter
A cross-platform command-line utility that creates projects from cookiecutters (project templates), e.g. Python package projects, C projects.
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Yea GitHub templates should really be more used for reproducing an empty repository and not for starting a new coding project. What I mean by that is the template repo should contain git and GitHub specific things, like .gitignore file or .github directory. I also tend to include a .editorconfig file. What you are looking to do is more about a project template. Most coding languages and frameworks provide their own version of templates that are better used for this. My workflow I have is I will start a new repository from my GitHub template and then run the necessary command for the language to generate a project template. I have my own project template I have defined. Here is an example.
Good alternatives that are more complex to use but allow for more customization would be things like Cookiecutter: https://github.com/cookiecutter/cookiecutter
Or if you like a declarative approach you could look into Projen: https://github.com/projen/projen