### Please describe the problem.
After I run "git annex add" some folders (not empty) 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.

This is regular repository (not direct). 

EDIT:
It seems that all the problem directories have either .git directory in them (I understand that git cannot manage .git but what about all the other files in there?) or are full of symlinks (git annex cannot manage symlinks?)

> You should `git add` symlinks. They are not large files, so 
> are out of scope for git-annex.
> 
> Git repositories cannot contain other git repositories. [[done]]
> --[[Joey]]