Git operations search for .git dir

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.