title: Git doesn't delete directories and files in versioned directories
body: <p>Let's say I have a folder structure in my local repository:</p>
  <pre><code>Folder A
   |_ Folder B
      - File 1
      - File 2
  </code></pre>
  <p>Someone in the team deletes <code>Folder B</code> and its files and pushes some other changes into the upstream branch which I then get with a <code>git pull</code>. Looking into my local repo, the changes are there, but <code>Folder B</code> and all files inside of it is too, they simply weren't deleted. On my next <code>git push</code>, it will add the folder to the remote repo again, resulting in a conflict when other team members are trying to merge.</p>
  <p>What is going on? I checked directory permissions, they are <code>775</code>, and so are files.</p>
  <p>EDIT: Clarifying that files within <code>Folder B</code> weren't deleted either in local repository.</p>