title: git filter-branch with --subdirectory-filter removes all files
body: <p>I would like to to a pretty standard repository split-up.
  The original repository has to following structure:</p>
  
  <pre><code>root
  |-AAA
  |-BBB
    |-BBB1
    |-BBB2
  |-CCC
  </code></pre>
  
  <p>I tried to extract the directory BBB1 and all its contents into an individual repository using the command</p>
  
  <pre><code>git filter-branch --subdirectory-filter BBB/BBB1 -- --all
  </code></pre>
  
  <p>which leads to git rewriting a bunch of commits and ends with git's final statement</p>
  
  <pre><code>Ref 'refs/heads/master' was rewritten
  </code></pre>
  
  <p>So this seems perfectly fine for me.
  But when I take a look into the <em>root</em> directory after git has finished, the repository no longer contains any source files but only the <em>.git</em> folder at <em>root</em>. Browsing this repository with SourceTree I can see in the log the (probably) correct commits which would have affected <em>BBB1</em> only, <strong>but each commit no longer references any files as they are all gone!</strong></p>
  
  <p>What am I doing wrong? Why are all the files gone, even the ones I actually filtered for?</p>
  
  <p>Thanks in advance!</p>
  
  <p>Simon</p>