Github was working. Then when I commented and I went to github UI and I looked at the repo, for one of the folders I saw a green folder and I can't click on it to drill down. How do I fix this?
Even further when I check out the repo and I switch to the branch, there is nothing there. Where did the data go?
This is a submodule. Basically, this is a pointer to a specific commit of another repository.
One would usually rely on a submodule in the following (not exhaustive) list of situations
You can find more information about submodules by reading the following resources
Below, an example of how GitHub currently display a submodule. On the right of the name, you'll notice the abbreviated form of the commit sha (7a361e9) which is being referenced by this submodule.

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