title: git fails to detect renaming
body: <p>One branch (<code>refactoringBranch</code>) had a complete directory restructure. Files were moved chaosly, but the content was preserved.</p>
  
  <p>I tried to merge:
  <code>git merge --no-ff -Xrename-threshold=15 -Xpatience -Xignore-space-change refactoringBranch
  </code></p>
  
  <p>git status shows about half of files renaming recognition. But out of 10000 files in the project half wasn't recognized as moved. </p>
  
  <p>One example would be:</p>
  
  <pre><code># On branch master
  # Changes to be committed:
  
  #   deleted:    404.php
  #   new file:   public_html/404.php
      ...
  #   deleted:    AnotherFile.php
  #   new file:   public_html/AnotherFile.php
      ...
  #   renamed:    contracts/css/view.css -&gt; public_html/contracts/css/view.css
  </code></pre>
  
  <p>Suggestions?</p>
  
  <hr>
  
  <h2>Prehistory</h2>
  
  <p>The refactoring was made outside of git. I did the following:  </p>
  
  <ol>
  <li>Created the <code>refactoringBranch</code> originating on <code>master</code>.  </li>
  <li>Dropped the changed structure inside the <code>refactoringBranch</code>, meaning I had my changes in some other dir and just copy-pasted them over my git repository.  </li>
  <li>Added and committed everything and then tried to merge.</li>
  </ol>
  
  <p>This is was my workflow:</p>
  
  <pre><code>git checkout -b refactoringBranch
  cp -R other/place/* ./
  git add . -A
  git commit -a -m "blabla"
  git checkout master
  git merge --no-ff -Xrename-threshold=15 -Xpatience -Xignore-space-change refactoringBranch
  </code></pre>
  
  <p>The problem arise on the <code>git add . -A</code> step probably.
  Because if rename detection was correct there, I'd assume the merge would go flawless.</p>