Fixed most of commands creating a git repo instead of throwing an error

[JohanMabille]

Currently, most of the commands create a .git folder instead of throwing an exception when we execute them in a non-git folder, like git does.

[ianthomas23]

Are the files added to test/data/status_data/embedded_git needed?

[SandrineP]

test/data/status_data/embedded_git shouldn't exist anymore. I believe I removed it in a previous PR.

[JohanMabille]

Are the files added to test/data/status_data/embedded_git needed?

Definitely not, looks like I reintroduced them by mistake

[ianthomas23]

Thanks @JohanMabille