title: Strange Behaviour on Git Pull Causing: "Error Local Changes... Would Be Overwritten By Merge"
body: <p>I make some changes then run the usual commands:</p>
  
  <pre><code>git add -u
  git commit -m 'some changes'
  git pull
  </code></pre>
  
  <p>but I get errors such as </p>
  
  <pre><code>error: unable to create file 'new_file.py' (Permission denied)
  error: unable to unlink old 'file.py' (Permission denied)
  </code></pre>
  
  <p>so I run</p>
  
  <pre><code>sudo git pull
  </code></pre>
  
  <p>Then, I get the error in the title; 
  when I run git status I see many new changes not staged for commit. I have to add the changes (which I didn't make and only appeared after the failed pull), and commit, before I can pull and merge.</p>
  
  <p>What is going on here?</p>