gitserver: Ensure we always update clone_status

Created by: ryanslade

Fixes an issue where clone_status was only being updated when actually cloning a new repo and was ignored when updating existing repos.

Closes https://github.com/sourcegraph/sourcegraph/issues/37432

Test plan

Unit tests updated

Manually tested by clearing my database but not deleting local files. Confirmed that prior to fix repos appeared as not_cloned but after fix they appear as cloned