title: git skip-worktree on files with merge conflict
body: <p>I have a configuration file <code>abc.cfg</code> with local changes for my environment. To prevent pushing local configs to the remote, I use <code>git update-index --skip-worktree abc.cfg</code> on the file.</p>
  
  <p>Now the upstream has changed <code>abc.cfg</code> with global updates that I need. So I first did <code>--no-skip-worktree abc.cfg</code>, did <code>git stash</code> on it, pulled the upstream, and proceed with <code>git stash apply</code> on the file.</p>
  
  <p>Now there's merge conflicts on <code>abc.cfg</code>. I tried to resolve it, and do <code>git update-index --skip-worktree abc.cfg</code> again, but this time it says:</p>
  
  <pre><code>fatal: Unable to mark file scripts/app.js
  </code></pre>
  
  <p>How should I apply back my local changes without including it in the commits?</p>