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As discussed in #2331, there is no need to have the cookiecutter stuff for autogenerating a project structure. This removes the folder, references in the docs, and dependency in the toml file. This made the entire main.py file redundant as far as I can tell, so I got rid of that as well.
I favor removal over deprecation because MESA 3 allows us to remove. Otherwise, we commit ourselves to maintaining this in MESA 3.