title: Unable to update submodule in github due to exist directory
body: <p>I am using submodule to control my plugin in MacVim.
  When I tried to update the submodule using <code>git update submodule</code>
  It comes out:</p>
  
  <pre><code>fatal: destination path 'bundle/ShowMark' already exists and is not an empty directory.
  Clone of 'git://github.com/vim-scripts/ShowMarks.git' into submodule path 'bundle/ShowMark' failed
  </code></pre>
  
  <p>I tried my own solution:
  remove the directory and then <code>git update submodule</code>
  It works but the MacVim cannot run properly. MacVim cannot open any new/old files.</p>