title: Merging directory changes when projects have continued
body: <p>I have created a branch from master to bring a lot of C# projects into one. However, some of the other projects in the repository have continued development, but have been moved. I'll try and give an example:</p>
  <p>My repository contains:</p>
  <ul>
  <li>Project A</li>
  <li>Project B</li>
  <li>Project C</li>
  <li>Project D</li>
  <li>Project E</li>
  </ul>
  <p>I have rearranged the repository into directories:</p>
  <ul>
  <li>Directory 1
  <ul>
  <li>Project A</li>
  <li>Project B</li>
  <li>Project C</li>
  </ul>
  </li>
  <li>Directory 2
  <ul>
  <li>Project D</li>
  <li>Project E</li>
  </ul>
  </li>
  </ul>
  <p>I've been making changes on project A, B, and C, and when I merge these will be fine. However, projects D and E have continued development merged into master branch, so my copies of them are out of date.</p>
  <p>How do I merge these changes into master in a way that keeps the newest development on projects D and E, but also moves them into these directories?</p>