You're only loading the parser, but you aren't doing anything with it. You need a line like
$my_html = Markdown::defaultTransform($my_text);
...to convert markdown to HTML. Like this:
<?php
require_once ('subfolder/MarkdownExtra.inc.php');
require_once ('subfolder/includetest.php');
?>
<html>
<body>
<?php Markdown::defaultTransform("[Test](www.google.com)"); ?>
</body>
</html>
I haven't used this before. I'm just going by the docs that I can find.