Formatting code
You have several options when it comes to presenting code in your repository.
Jekyll highlight tag
To put code into your pages, one option is to use Jekyll code snippet highlighting.
For example,
{% highlight java %}
public static void main(String args[]) {
System.out.println("Hello world");
}
{% endhighlight %}
</pre>
produces:
public static void main(String args[]) {
System.out.println("Hello world");
}
Jekyll gist tag
For larger code samples, you might prefer to use the Jekyll gist tag.
For example,
<pre>
{% gist philipmjohnson/5288814 %}
</pre>
produces:
Code repo
For documenting executable systems, as opposed to code samples, your best bet is to create a GitHub repo containing the system and provide links to it in your markdown.