title: You have both xxx and xxx/yyy.zz error: Error building trees
body: <p>When I run git status I have something like:</p>
  
  <pre><code>$ git status
  # On branch assets
  # Changes to be committed:
  #   (use "git reset HEAD &lt;file&gt;..." to unstage)
  #
  #   modified:   index.html
  #   new file:   sections
  #   new file:   sections/asset/asset.ctrl.js
  #   new file:   sections/asset/asset.tpl.html
  #
  # Changes not staged for commit:
  #   (use "git add/rm &lt;file&gt;..." to update what will be committed)
  #   (use "git checkout -- &lt;file&gt;..." to discard changes in working directory)
  #
  #   deleted:    sections
  </code></pre>
  
  <p>The sections directory has existed since the project started, so not sure why it thinks it's a new file or needs to be deleted. When I try to commit I get:</p>
  
  <pre><code>You have both sections and sections/asset/asset.ctrl.js
  error: Error building trees
  </code></pre>
  
  <p>Any ideas how I can commit my work?</p>