title: submitting changes to submodules with EGIt
body: <p>I just installed EGit 2.3.1 on Eclipse Juno.</p>
  
  <p>I checked out this GitHub project:
  <a href="https://github.com/erelsgl/machine-learning" rel="nofollow noreferrer">https://github.com/erelsgl/machine-learning</a>
  which has two submodules - "perceptron" and "classifier".</p>
  
  <p>I made no changes in any of the projects:</p>
  
  <pre><code>$ git status
  # On branch master
  nothing to commit (working directory clean)
  $ git submodule status
   f1002bedc0bbd41866c06d114a299de8a807baf5 classifier (heads/master)
   2a9012c03ea0fb97bd1513a68dd85ba3e6a5f68e perceptron (heads/master)
  $ cd perceptron
  $ git status
  # On branch master
  nothing to commit (working directory clean)
  </code></pre>
  
  <p>However, when I do "Commit" from Eclipse Git Repositories view, standing on the "perceptron" submodule, I see this:</p>
  
  <p><img src="https://i.stack.imgur.com/YQUDM.png" alt="top"></p>
  
  <p><img src="https://i.stack.imgur.com/Co2zq.png" alt="bottom"></p>
  
  <p>i.e., EGit, for some reason, thinks that I have deleted all files in "perceptron", and added them to the "perceptron/" subfolder!</p>
  
  <p>What am I doing wrong?</p>