directory: Align process to checkout a remote git ref with guix one

It has been observed that the process used by SWH to checkout a remote
git reference can lead to different recursive nar hash values compared
to those computed by guix. This seems related to CR/LF normalization.

So prefer to align the process to checkout a remote git reference with
the one used by guix. It seems also faster than the previous approach.

Also refine the not found repository detection process as previously
some non related git errors could be missed.

Related to #4751.