title: GitHub does not let me access Subfolders
body: <p><strong>Short:</strong></p>
  
  <p>GitHub has grayed out folders in my repo that I cannot access.  This worries me, as my code changes are in those folders!</p>
  
  <p><strong>Long:</strong></p>
  
  <p>I am developing a ZF2 web application and using git for source control.  ZF2 is modular, so somewhere somehow (most likely with composer.phar or possibly with git clone) I have downloaded some ZF2 modules into project subfolders.  One such ZF2 module is <code>vendor/coolcsn/csn-user</code>.  I have made changes in that ZF2 module.</p>
  
  <p>Problem 1:  when I run git status, I get this:</p>
  
  <pre><code>$ git status
  # On branch master
  # Changes not staged for commit:
  #       modified:   vendor/coolcsn/csn-user (modified content, untracked content)
  </code></pre>
  
  <p>When I run git commit, it says "No changes added to commit".  And I've definitely made some changes.</p>
  
  <p>So then I found that I can change my directory to <code>vendor/coolcsn/csn-user</code>, and do git status and git commit there.  Then I can change back to the root directory of the project, and do a git commit there.  Then, all is fine....  until:</p>
  
  <p>Problem 2:  Until I do a git push to GitHub.  On GitHub my entire project seems to be in place, but the <code>vendor/coolcsn/csn-user</code> is not accessible on GitHub!  It is Grayed Out.  I cannot click on it.  It makes me cry.  I don't know why and I don't know what's up.  I've read something about git submodules.  I don't know if I have git submodules or if they are something else.  I have not consciously set up any submodules myself.  Either way, I am concerned that my GitHub submodule changes are not being tracked, or if they are being tracked, they are hidden, not accessible for viewing.</p>
  
  <p>Possible Solution #1:  I thought that I could REMOVE .git folder in the submodules (if they are submodules) and just do straight commits to GitHub, with my <code>csn-user</code> folder possibly not being grayed out.  But before I do so, I've heard that it is not advisable, and I wanted to check on what all that is going on, and how if anyhow, I can properly use git and GitHub and submodules, and track my changes at the same time.</p>
  
  <p>In particular, looking for a set of steps, instructions, or ideas on how keep my repo accessible and committable both using git and GitHub.</p>