title: git fatal: multiple stage entries for merged file
body: <p>Git throws an error:</p>
  
  <pre><code>fatal: multiple stage entries for merged file
  </code></pre>
  
  <p>I've been on the side (<a href="https://stackoverflow.com/questions/27330446/getting-a-fatal-error-in-git-for-multiple-stage-entries">Getting a fatal error in git for multiple stage entries</a>) and read the workaround: </p>
  
  <pre><code>cd /patH/to/second/cloned/repo
  git --work-tree=/path/to/first/repo add .
  </code></pre>
  
  <p>Now, the changes can be queried via status, but after that what i have to do now? When I use git add, then everything back to last version. All changes are gone. The changes were removed and my new repo has the old status again. How can i put all change to the new repository?
  I use git version 2.2.0 on OS X 10.10.</p>