Git doesn't treat a repository like a standard file system where you can just slap a permission setting on a folder. It tracks snapshots of the entire directory tree. Every commit generates a cryptographic hash that relies on the exact state of all files and folders included in that commit.

If GitHub allowed you to "hide" certain folders from public users, the hashes wouldn't match up for them. If a public user tried to clone the repo, their Git client would see missing data, and the whole cryptographic chain would break. GitHub would essentially have to invent a completely new version control system, or drastically fork Git, to make this work natively.
Practical Workarounds You Can Use Today

Since a single mixed-visibility repo isn't feasible right now, here are the standard ways developers handle this exact scenario:

• Git Submodules: This is the closest thing to what the request is asking for. You create a main Public Repository and a separate Private Repository. You then include the private repository inside the public one as a "submodule." Anyone can clone the public repo, but only authorized users can pull the actual code inside the private submodule folder.

• Separate Repositories & Package Managers: Keep the open-source code in a public repo and publish it as a package (like on npm, PyPI, Maven, or GitHub Packages). Then, use a private repo for your internal project that simply imports your public package as a dependency.

• Strict .gitignore Practices: If you just need to keep configuration files or secrets (like .env files with API keys) private, they should never be committed to the repo at all. Add them to your .gitignore file and use template files (like .env.example) for the public repository so others know what variables they need to provide.