Fix various branch/ref issues with bare repositories in Git

Summary:
Ref T2230. Although all the non-bare commands //run// fine in bare repos, not all of them do exactly the same thing.

This could use further cleanup, but at least get it working again for now.

Test Plan: Ran `bin/repository pull`, `bin/repository discover`, viewed Diffusion (looked at branch table), viewed a commit (looked at "Branches"), for bare and non-bare git repos.

Reviewers: avive, btrahan, avivey

Reviewed By: avivey

CC: aran

Maniphest Tasks: T2230

Differential Revision: https://secure.phabricator.com/D7442