title: Cannot checkout master branch from branch with submodule
body: <p>I have a directory in my repo (call it <code>blah</code>) which contains some files that I manualy copied from another repo (<code>repo-blah</code>). One day, I decide to get smart and make this <code>blah</code> directory a submodule, so that I don't have to manually recopy the files any time they change in <code>repo-blah</code>, and so that I can make changes to those files in my repo and have a gitish way of updating <code>repo-blah</code>.</p>
  
  <p>I'd been working on the master branch, so I make another branch called <code>sub-blah-branch</code> where I remove the blah directory from the index:</p>
  
  <pre><code>$ git rm -r blah
  </code></pre>
  
  <p>and then create a submodule for it:</p>
  
  <pre><code>$ git submodule add uri/to/repo-blah blah
  </code></pre>
  
  <p>I commit everything, and make sure the repo is clean:</p>
  
  <pre><code>$ git status
  # On branch sub-blah-branch
  nothing to commit (working directory clean)
  </code></pre>
  
  <p>Then, whilst feeling pretty cool about all this submodule stuff, I try to checkout the master branch. But I get this:</p>
  
  <pre><code>$ git checkout master
  error: The following untracked working tree files would be overwritten by checkout:
      blah/[every file that I had manually copied from repo-blah]
  Please move or remove them before you can switch branches.
  Aborting
  </code></pre>
  
  <p><a href="http://git-scm.com/book/ch6-6.html" rel="noreferrer">Pro Git's chapter on submodules</a> tells me that when switching from branches that have created submodules, the contents of those submodules aren't automatically removed, and instead become untracked once the repo switches branches. In this situation, I can't switch to <code>master</code> without doing <code>rm -rf</code> on the <code>blah</code> directory first.</p>
  
  <p>Is there a better way to deal with this problem?</p>
  
  <p>I'm using git version 1.7.9.5</p>