title: Local files reverted after trying to sync forked GitHub repository
body: <p>I forked the <a href="https://github.com/biopython/biopython" rel="nofollow noreferrer">biopython/biopython</a> repository on GitHub to <a href="https://github.com/BioGeek/biopython" rel="nofollow noreferrer">BioGeek/biopython</a>.</p>
  
  <p>I made some changes in my local repository, <a href="https://github.com/BioGeek/biopython/commit/2875310e8e710b6e84ab9255df945e89affe27d5" rel="nofollow noreferrer">committed</a> them, created a <a href="https://github.com/biopython/biopython/pull/1061" rel="nofollow noreferrer">pull request</a> and they were <a href="https://github.com/biopython/biopython/commit/b667fbce1d916314bc77b7439c6e22196b93e9f5" rel="nofollow noreferrer">merged</a> into the upstream biopython repository. So far, so good.</p>
  
  <p>I make some <a href="https://github.com/BioGeek/biopython/commits/master" rel="nofollow noreferrer">further commits</a> into my repository and in the mean time some <a href="https://github.com/biopython/biopython/commits/master" rel="nofollow noreferrer">other commits</a> are made in the main biopython repository.</p>
  
  <p>Now I want to update my local repository to pull in the changes from the main repository, so I do:</p>
  
  <pre><code>$ git pull upstream master
  remote: Counting objects: 12, done.
  remote: Compressing objects: 100% (5/5), done.
  remote: Total 12 (delta 9), reused 10 (delta 7), pack-reused 0
  Unpacking objects: 100% (12/12), done.
  From https://github.com/biopython/biopython
   * branch                master     -&gt; FETCH_HEAD
     06b6cd64d..6e41879ca  master     -&gt; upstream/master
  First, rewinding head to replay your work on top of it...
  Applying: add header back to 1LCD.pdb file
  Applying: actually check that the warning was raised instead of surpressing it
  $ git status
  On branch master
  Your branch and 'origin/master' have diverged,
  and have 100 and 3 different commits each, respectively.
    (use "git pull" to merge the remote branch into yours)
  Untracked files:
    (use "git add &lt;file&gt;..." to include in what will be committed)
  
      ../Doc/examples/tree1.nwk
  
  nothing added to commit but untracked files present (use "git add" to track)
  </code></pre>
  
  <p>Next I want to update the master branch in my forked repository, so I do:</p>
  
  <pre><code>$ git push origin master
  To https://github.com/BioGeek/biopython.git
   ! [rejected]            master -&gt; master (non-fast-forward)
  error: failed to push some refs to 'https://github.com/BioGeek/biopython.git'
  hint: Updates were rejected because the tip of your current branch is behind
  hint: its remote counterpart. Integrate the remote changes (e.g.
  hint: 'git pull ...') before pushing again.
  hint: See the 'Note about fast-forwards' in 'git push --help' for details.
  </code></pre>
  
  <p>Hmm, <code>rejected</code>. So I pull up the page <a href="https://help.github.com/articles/syncing-a-fork/" rel="nofollow noreferrer">Syncing a fork</a> from GitHub help and follow the instructions from there:</p>
  
  <pre><code>$ git fetch upstream
  $ git checkout master
  Already on 'master'
  Your branch and 'origin/master' have diverged,
  and have 100 and 3 different commits each, respectively.
    (use "git pull" to merge the remote branch into yours)
  </code></pre>
  
  <p>Hmm, I have to use <code>git pull</code>, so I do that</p>
  
  <pre><code>$ git pull
  First, rewinding head to replay your work on top of it...
  Applying: MAF parser, intitial checkin.  Passes unit tests
  [... some 100 lines omitted ...]
  Applying: Update test to match changed exception
  Applying: Thank Jeroen for test_QCPSuperimposer.py update
  Applying: Fix unit test, failed under PyPy 5.6.0
  </code></pre>
  
  <p>But now are the changes I made locally to the files <a href="https://github.com/BioGeek/biopython/commit/1c1f8b3fc6d379af27a508a9852903025253b6be" rel="nofollow noreferrer">1LCD.pdb</a> and <a href="https://github.com/BioGeek/biopython/commit/47d8d8fdd7163a075a1fad4ba9c09ac993fb8500" rel="nofollow noreferrer">test_SeqIO_PdbIO.py</a> gone! I have commited them, so how do I bring them back and where did I go wrong so that I don't get this mess again in the future when I want to sync my fork.</p>