Git operations search for .git dir

[agoose77]

I was testing nbgitpuller locally inside the nbgitpuller checkout on my machine. I initially cloned projectpythia/radar-cookbook, under /radar-cookbook (where / is the Git root for the nbgitpuller clone).

After deleting the .git directory, I was surprised to observe that there were no errors reported. When then deleting other files that are present in the remote, they were not restored by nbgitpuller.

I expect that the cause for this error is that we don't pass GIT_DIR in our use of the Git CLI, which means that upon deleting /foo/.git, the Git CLI finds /.git instead.