title: Changes not staged for commit even after git add
body: <p>Here are the git commands which I have typed</p>
  
  <pre><code>$ git add -u -n
  add 'proj1/Foo.scala'
  $ git add .
  $ git add .
  $ git commit -m "message"
  On branch feature/branch
  Your branch is up-to-date with 'origin/feature/branch'.
  Changes not staged for commit:
      modified:   ../proj1/Foo.scala
  </code></pre>
  
  <p>So why did I get the <code>Changes not staged for commit</code>? as you can see that I did <code>git add .</code> twice</p>
  
  <p>Now if I got ahead and do</p>
  
  <pre><code>git add ../proj1/Foo.scala
  </code></pre>
  
  <p>and then do commit it works. Why should I do each file specifically rather than just do <code>git add .</code></p>