title: git subtree pull says that the working tree has modifications, but git status says it doesn't. What gives?
body: <p>If I do this in one of my repositories:</p>
  
  <pre><code>git subtree pull --prefix=frameworks/AquaticPrime --squash AquaticPrime
  </code></pre>
  
  <p>I get this:</p>
  
  <pre><code>Working tree has modifications.  Cannot add.
  </code></pre>
  
  <p>If I do this (in the same place, of course):</p>
  
  <pre><code>git status
  </code></pre>
  
  <p>I get this:</p>
  
  <pre><code># On branch master
  nothing to commit (working directory clean)
  </code></pre>
  
  <p>I'm not quite sure what's going on here. The git status command implies that I don't have modifications, so I'm assuming that the git subtree pull is referring to modifications in a different branch related to the subtree, but it's not entirely clear.</p>
  
  <p>Can anyone provide enlightenment?</p>