 <p>The Problem was the <code>git clean</code> <code>git clean</code> removes <strong>any</strong> untracked file from the current working tree.</p> <p>You could set up <code>.gitignore</code> files for the untracked files and leave the <code>-x</code> flag away. You should have a look at the <em>manpage</em> for <code>git-clean</code>. If you don't have a unix system: <a href="http://linux.die.net/man/1/git-clean" rel="nofollow">http://linux.die.net/man/1/git-clean</a></p>