title: git repo says it's up-to-date after pull but files are not updated
body: <p>I have 3 repos. A bare repo which I use as a master repo, a dev repo in which I make and test changes, and prod repo from which scripts are executed in the prod environment.</p>
  
  <p>After I have tested changes in the dev repo I push them to the bare repo and they are auto pulled down into the prod repo on a cronjob using a basic script (carrying out git pull command).</p>
  
  <p>I followed through the above procedure for a change, but the altered file will not update in the prod repo.</p>
  
  <ul>
  <li>The change is checked in and pushed in the dev repo </li>
  <li>The pull has been done to the prod repo</li>
  <li>The git logs for all repos are identical and all show the checkin for this change</li>
  <li>git branch gives me "* master" for all repos</li>
  <li>git status for all repos gives me:
   # On branch master
   nothing to commit, working directory clean</li>
  <li>git pull gives me "Already up-to-date" for the dev &amp; prod repos</li>
  </ul>
  
  <p>Using git extensions for a graphical view, it appears each repo is up to date and at the head.</p>
  
  <p>I've tried:</p>
  
  <pre><code>git checkout HEAD  
  git pull origin master  
  git reset --hard HEAD  
  git reset --hard origin/master  
  git reset origin/master  
  </code></pre>
  
  <p>Can anyone help here?</p>