Somehow atom deleted the project I had open, including the .git directory, so I lost all my work that had not yet been pushed to the remote server.
I’m not sure what I pressed, I was just typing and tried to delete some text I’d miss-typed, and suddenly all my work was gone.
The file sidebar was hidden when it happened, so it didn’t have keyboard focus. There was a confirmation dialog but I had already pressed return before the dialog even opened, so it immediately confirmed and closed before I even had a chance to read the text.
Judging by this screenshot: http://d.pr/i/nV43 the normal/default behaviour of the delete confirmation is to move to trash, however “delete” has keyboard focus, so if you hit spacebar after whatever key binding brings up the dialog it will erase the directory without any way to recover.