It might concern me when GitHub is going to require Microsoft's version of Git, which isn't fully compatible with the standard Git.
GitHub already announced that they are going to adopt Microsoft's Git Virtual File System. This feels a lot like the Embrace and Extend.
What "Microsoft's version of Git" are you referring to here? It can't be GVFS, because that's a virtual file system driver that's separate from the git protocol and repository.
This one: github.com/Microsoft/git
The recommended install when you are going to install GVFS, also the only one which Microsoft tests with GVFS.
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