libfetchers/git: fix every occasion of a permission error
libfetchers/git: fix every occasion of a permission error

I'm afraid I missed a few problematic `git(1)`-calls while implementing
PR #6440, sorry for that! Upon investigating what went wrong, I realized
that I only tested against the "cached"-case by accident because my
git-checkout with my system's flake was apparently cached during my
debugging.

I managed to trigger the original issue again by running:

    $ git commit --allow-empty -m "tmp"
    $ sudo nixos-rebuild switch --flake .# -L --builders ''

Since `repoDir` points to the checkout that's potentially owned by
another user, I decided to add `--git-dir` to each call affecting
`repoDir`.

Since the `tmpDir` for the temporary submodule-checkout is created by
Nix itself, it doesn't seem to be an issue.

Sorry for that, it should be fine now.

NixOS/nix,NixOS/nix,NixOS/nix,NixOS/nix,NixOS/nix