title: Nested GIT Repository mistake method to remove it?
body: <p>I have just realised I ran a 
      'git init' 
  command from a sub-directory by mistake and then created a master repo at the root of my project.</p>
  
  <p>This was a mistake, so I ran the 
      'rm -fr' </p>
  
  <p>command (delete) on the nested directory '.git' not in the root of the project - thinking that this would solve my issue (how wrong I was)</p>
  
  <p>The problem is now that when I push the project to GitHub the nested folder is greyed out as if it was ignored.</p>
  
  <p>Is there any way to undo what I have done? or do I just have to start again? I'm new to this and was trying to complete a sample app tutorial but the directory I've seemingly ruined is essential to the deployment in a production env.</p>