title: Remove references of physically removed files from remote Git repository
body: <p>I have deleted a lot of files from my Git repository (from many different directories) physically. </p>
  
  <p>I can still see their reference and if I make a commit to GitHub, old files are still there. </p>
  
  <p>I need to remove those references from the remote repo server (GitHub) and as well as from my local PC. </p>
  
  <p>How can I remove these references from the repositories?</p>