title: Git error during clone: error: Untracked working tree file <file> would be overwritten by merge
body: <p>I just deleted my git repo and am cloning it anew. I can't figure out how I might encounter the error below. </p>
  
  <p>I use the same repo on another machine (as do dozens of other people). I tried following the <code>git checkout -f HEAD</code> suggested. It syncs up a lot of files that were missed during hte clone, but it still shows a few dozen modified and missing files somehow. I completely removed the old directory. And <code>df -h</code> shows available disk space.</p>
  
  <pre><code>$ git clone git@github.com:myrepo/src.git
  Cloning into 'src'...
  remote: Counting objects: 83096, done.
  remote: Compressing objects: 100% (309/309), done.
  remote: Total 83096 (delta 351), reused 385 (delta 228), pack-reused 82556
  Receiving objects: 100% (83096/83096), 785.59 MiB | 22.16 MiB/s, done.
  Resolving deltas: 100% (41943/41943), done.
  Checking connectivity... done.
  error: Untracked working tree file 'common/ml/.pylintrc' would be overwritten by merge.
  fatal: unable to checkout working tree
  warning: Clone succeeded, but checkout failed.
  You can inspect what was checked out with 'git status'
  and retry the checkout with 'git checkout -f HEAD'
  </code></pre>