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They're submodules. The actual code is there:

almost as if you need to do something with that submodules file...

I guess they forgot the .DS_Store files.

Will never understand why doesn't Nintendo sue them for this.

Probably because the .DS_Store file predates the Nintendo DS by several years.

I think it may be a joke.

Apparently it stands for "Desktop Services Store". https://www.arno.org/on-the-origins-of-ds-store