title: git does not merge all files after resolving conflict
body: <p>So I'm not sure if this is a known issue, but lets go through what happened:</p>
  
  <ol>
  <li><p>I create a feature branch off master, and start working on my feature</p></li>
  <li><p>Master is being updated with other features which I don't have in my own feature branch yet.</p></li>
  <li><p>I am done with my feature branch, and I merge in master into my feature branch so that I solve problems before creating a pull-request to master.  Also, I checkout master and make sure to git pull from origin to get the latest copy of master.</p></li>
  <li><p>I run <code>git merge master</code> in my feature branch and get merge conflicts.<br>
  I resolve those conflicts and add everything (conflict files and new/modified files) and then commit.</p></li>
  <li><p>I run <code>git merge master</code> again in my feature branch and get <code>Already up-to-date.</code></p></li>
  </ol>
  
  <p>Now my problem is that some files are not merged from master.  Master clearly has files that have been changed but did not get picked up in my merge.  So now when I make my pull-request it is saying I modified certain files that I never touched and attempting to undo changes in master.</p>
  
  <p>Can anyone tell me what I did wrong and how I can fix this issue?</p>