title: Troubleshooting misplaced .git directory (nothing to commit)
body: <p>I started getting this message. No matter what I edit and try to commit, it says there is nothing to commit. Looks like git does not see my working directory and looking somewhere else. </p>
  
  <p>If I run <code>git status</code> it outputs the same:</p>
  
  <pre><code>nothing to commit (working directory clean)
  </code></pre>
  
  <p>If I create new branch and edit something, then same thing happens. This started happening when I needed to fix merge clashes. When I wanted to merge my one branch with master branch, I had to manually fix it and I needed my files to look exactly as in that branch overwriting master branch those same files. So I added those files and it let me merge it. But then no matter what I change it shows as there is nothing to commit. </p>
  
  <p>What could be done here?</p>