title: Git checkout/pull doesn't remove directories?
body: <p>I've got my repo @ github. I did some work at home and pushed it to github. It involved some deleting of files and directories. Now I'm on my work box, which had a copy of the code before deleting the files and directories.</p>
  
  <p>I issued the following:</p>
  
  <pre><code>git remote update
  git checkout HEAD
  git pull origin HEAD
  </code></pre>
  
  <p>It deleted all of the files it should have, but not the directories the files were in.</p>
  
  <p>Two questions: </p>
  
  <ol>
  <li>Why did it not remove the directories?</li>
  <li>Is there a git command I can issue in the current state to remove them?</li>
  </ol>