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