title: Using Github pages with Jekyll in a subdirectory
body: <p>I recently wanted to publish my Jekyll site on Github pages, but it seems that putting everything in a subdirectory is giving some issues, even after I change the <code>source</code> to the correct directory.</p>
  
  <p>My structure looks like this:</p>
  
  <pre><code>- site
     - src (contains all Jekyll stuff)
     - README.md
     - GruntFile.js
     - ...
  </code></pre>
  
  <p>Locally my site builds perfectly and when I go to <code>http://localhost:4040</code> I can see it just nicely, but when I commit this to my Github and visit <code>username.github.io</code> I get a 404, if I go to <code>username.github.io/src</code> I can see part of my site, however all <code>{% include %}</code> are ignored.</p>
  
  <p>In my <code>_config.yml</code> I updated the source: <code>source: ./src</code>, but that doesn't seem to help.</p>
  
  <p>Is there a way to make Github Pages handle subdirectories properly? Basically I want to tell it that my Jekyll site is inside <code>/src</code>, and I want the url to just be <code>username.github.io</code> instead of <code>username.github.io/src</code></p>
  
  <p>I know i can use the pages branch and commit to there, but I would prefer if it could happen automaticly.</p>