title: git ignoring a directory, it's like it doesn't exist
body: <p>I have a cloned repo. There's a directory, call it a/b/c that <strong>used to be</strong> its own repo, i.e. there was a/b/c/.git/ etc.</p>
  
  <p>Now I want the files managed in the main repo. I don't care about the history in a/b/c, so I deleted the .git dir in a/b/c</p>
  
  <p>But the problem is that <code>git status</code> is ignoring a/b/c completely. I can't <code>git add</code> it. It's as though I'd put the path into .gitignore (I haven't).</p>
  
  <p>Obviously before, it made sense for git to ignore a subdir with a .git dir in it, but now how does it know the difference?</p>
  
  <p>Is there somewhere else that ignore files are listed other than .gitignore and .git/info/excludes? There's nothing in the .git/config file?</p>
  
  <p>I've been asked what git status says. Not much:</p>
  
  <pre><code>/path/to/root/dir $ git status
  # On branch fred
  nothing to commit (working directory clean)
  </code></pre>
  
  <p>And what git add says. Even less (nothing)</p>
  
  <pre><code>/path/to/root/dir $ git add a/b/c
  </code></pre>