title: jGit CheckoutCommand results in a strange behaviour
body: <p>I'm trying to use <code>CheckoutCommand</code> the following way:</p>
  
  <pre class="lang-java prettyprint-override"><code>Git git = new Git(repository);
  CheckoutCommand checkoutCommand = git.checkout();       
  checkoutCommand.setUpstreamMode(CreateBranchCommand.SetupUpstreamMode.SET_UPSTREAM);
  checkoutCommand.setStartPoint("origin/" + branchName);
  checkoutCommand.setCreateBranch(true);
  checkoutCommand.setForce(true);
  
  checkoutCommand.call();
  </code></pre>
  
  <p>I tried using <code>SetupUpstreamMode.TRACK</code> as well but it still failed.</p>
  
  <p>This results in a strange behaviour:
  the repository contents are deleted and instead a clone from each remote branch is created.</p>
  
  <p>Can you please advise?</p>