title: Can't unmodify files in git
body: <p>When I merged with another branch, a few of my files became modified automatically.<br>
  I tried to <code>checkout --</code> on the files, but <code>git status</code> still shows them as modified.  </p>
  
  <p>I then tried a custom shell function that normally fixes these kinds of problems for me:  </p>
  
  <pre><code>cd `git rev-parse --show-toplevel`;
  git reset --hard HEAD &amp;&amp; git clean -d -f;
  cd -; 
  git rm -r --cached .
  git reset --hard HEAD
  </code></pre>
  
  <p>The files still showed up as modified.  </p>
  
  <p>I tried  running these chunks of commands through different versions of:   </p>
  
  <pre><code>git config --global core.autocrlf true
  git config --global core.autocrlf false
  git config --global core.autocrlf input
  </code></pre>
  
  <p>The files still show as modified.<br>
  I just want a clean <code>git status</code>...  </p>
  
  <p>Is there a command that is guaranteed to do this?   </p>