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### Please describe the problem.
After I run git annex add some folders in current directory remain unannexed and git shows them as untracked. Even git annex add "problemDirName" does nothing. git annex add --force doesn't help either. 

### What steps will reproduce the problem?
No idea :( sometimes it happens and sometimes not.

### What version of git-annex are you using? On what operating system?
5.20141013 on Debian testing

### Please provide any additional information below.

git add works fine. It correctly stages the files.