% git statusNeedless to say, my heart skipped a beat. I have a ton of un-backed-up branches in this tree. There's many things that can cause this, according to a quick web search. However, a college told me they've seen this and the most common problem is with .git/HEAD. Looking at mine, it was 0 bytes long. This file has pointer to the latest branch checked out. Since I'd just checked out master, I was able to fix this by creating .git/HEAD:
fatal: not a git repository (or any of the parent directories): .git
ref: refs/heads/masterand life was good.