Here is the code I tested:
<!DOCTYPE html>
<html lang="en">
<head>
<script>
// Just a lil’ script to show off that inline JS gets highlighted
window.console && console.log('foo');
</script>
<meta charset="utf-8" />
<link rel="shortcut icon" href="favicon.png" />
<title>Prism</title>
<link rel="stylesheet" href="style.css" />
<link rel="stylesheet" href="themes/prism.css" data-noprefix />
<script src="prefixfree.min.js"></script>
<script>var _gaq = [['_setAccount', 'UA-33746269-1'], ['_trackPageview']];</script>
<script src="http://www.google-analytics.com/ga.js" async></script>
</head>
<body>
And here is the output:

Thanks for reporting.
Could you provide an online page reproducing the problem?
Hey @TheZoker, I _think_ your new lines might be getting stripped.
If you look at the source code (view-source:http://demo.comboot.io/viewtopic.php?style=2&f=2&t=7&p=66#p66) from the original issue you reported:
<div class="content">
<dl class="codebox"><dt>Code: <a href="#" onclick="selectCode(this); return false;">Select all</a></dt><dd><pre class="line-numbers"><code class="language-markup"><?php <br /> Print "Hello, World!";<br /> ?> <br /><br /> <?php <br /> Echo "Hello, World!";<br /> ?><br /></code></pre></dd></dl>
</div>
It looks like it's all in one line in the markup, so Prism will display it in kind.
Let me know if I'm off base, though!
Oh, sorry I didn't see the other issue on the other repo.
It looks like your line feeds are replaced with <br /> tags, which are stripped during highlighing (like any other HTML tags in the code block).
I think you might fix your issue with a little hook like the following (to be inserted after Prism main script):
Prism.hooks.add('before-highlight', function(env) {
env.element.innerHTML = env.element.innerHTML.replace(/<br\s*\/?>/g,'\n');
env.code = env.element.textContent.replace(/^(?:\r?\n|\r)/,'');
});
@LeaVerou Should we handle this in the official release?
Hi, thanks for the fast answer :)
Just included the code, but now its totaly messed :P
http://demo.comboot.io/viewtopic.php?style=2&f=2&t=34
http://demo.comboot.io/viewtopic.php?style=2&f=2&t=7&p=66#p66 (code completly missing)
The version of Prism you're using seems quite outdated. Have you tried to redownload it from http://prismjs.com/download.html?themes=prism&languages=markup+css+clike+javascript&plugins=line-numbers+autolinker ?
I re-downloaded it and same issue :/
Be sure to empty your browser cache. I can no longer reproduce the issue on the two links you posted previously:
http://demo.comboot.io/viewtopic.php?style=2&f=2&t=34
http://demo.comboot.io/viewtopic.php?style=2&f=2&t=7&p=66#p66
Your right, was cached in my browser :)
Thank you very much!
Most helpful comment
I think you might fix your issue with a little hook like the following (to be inserted after Prism main script):
@LeaVerou Should we handle this in the official release?