title: Merge error after converting Git submodule to subtree
body: <p>I have a project where I was originally using submodules for some dependent code. It turns out that submodules are not really appropriate for this project (and they are hard to use in practice), so I am converting each submodule to a subtree (using the new <code>git-subtree</code> feature).</p>
  
  <p>In my working repository, I have successfully removed each submodule and have added the old submodule repo as a subtree. No problem with this.</p>
  
  <p>When I go to another clone and attempt to pull from the first one, I get the following error from the merge step:</p>
  
  <pre><code>error: The following untracked working tree files would be overwritten by merge:
          sub/.gitignore
          sub/Makefile
          sub/README
          sub/src/main.c
          ... and so on for all files in sub/
  Aborting
  </code></pre>
  
  <p>It seems that this is because the files in <code>sub/</code> never really existed in the main repository in the first place, and when Git applies the patch to update <code>.gitmodules</code> it doesn't remove the directory with the submodule files. When processing the next commit, where Git tries to create the new files in <code>sub/</code> that <em>are</em> now part of the main repository, all those files conflict with the still-existing files in <code>sub/</code>. </p>
  
  <p>The workaround I have found is to use <code>rm -rf sub</code> before <code>git pull</code>, which avoids this problem.</p>
  
  <p>My question is, is there any command line switch I can use with <code>git merge</code> that says "Overwrite any files that happen to exist in the working directory"? Even better would be a feature where <code>git merge</code> would look at the contents of the existing file, and if the contents are identical to the file it was going to create anyway, suppress the error message and continue.</p>
  
  <p><strong>UPDATE</strong>: I have created Git repositories that demonstrate this problem, to show exactly what I'm talking about. To reproduce:</p>
  
  <pre><code>$ git clone https://github.com/ghewgill/q14224966.git
  $ cd q14224966
  $ git submodule init
  $ git submodule update
  $ git merge origin/branch
  </code></pre>
  
  <p>This should result in the error message</p>
  
  <pre><code>error: The following untracked working tree files would be overwritten by merge:
      sub/Makefile
      sub/README
      sub/src/main.c
  Please move or remove them before you can merge.
  Aborting
  </code></pre>