Add the keep-git-dir flag

[HumanBojack]

I added the --keep-git-dir flag in order to preserve the .git directory when cloning.

Note that, if you clone once without the flag the with the flag, the .git file will not be re-added since the clone will be ignored. Maybe this information should be kept in the VDMMETA file? Or a --force option should be added to re-download?

Also, I'm thinking of adding the keep-git-dir as an option to have a more precise control over which repo should have or not their .git directory. I would gladly add it to this PR if you judge it a good addition.

EDIT: I have made the changes but not commited / pushed

[ryapric]

Yeah on further thought, this should be a field on the Spec.Remotes, not a CLI flag, so a) the control is more fine-grained and b) not all remotes will be of the Git type. Thanks for taking a crack at it though!

[HumanBojack]

You're welcome! Would you like for me to push the changes I made to the spec and revert this commit then?