When I ran git add from the command line on a file in the currently opened project, I got an error several times in succession in the IDE (stacktraced attached) and the decorators on all files in the project turned to ?s. A command line git status showed that all files in the repository had the status deleted and untracked, whereas before most of them had been tracked and unmodified.
Stacktrace
Logged In: YES
user_id=308431
Originator: NO
I have not seen this before. It looks like a concurrency problem. I think Java Git should provide a better exception for this -- I will address their list.