Using the GitHub Windows client I did a sync to pull remote changes to my local machine, but before finishing the sync, I ran out of disk space and the sync failed.
Looks like the following process had a lock on the .git\index file:
.git\index
ssh-agent.exe C:\Users\Tom\AppData\Local\GitHub\PortableGit_8810fd5c2c79c73adcc73fd0825f3b32fdb816e7\bin\ssh-agent.exe
I killed the process and ran git reset HEAD and looks like I'm back to normal now.
git reset HEAD