The function removes <br /> tags inside <pre> tags and also make possible writing html.

fixPreTags.php

private function fixPreTags($str) {
    $parts = explode('<pre>', $str);
    $newStr = '';
    if(count($parts) > 1) {
        foreach ($parts as $p) {
            $parts2 = explode('</pre>', $p);
            if(count($parts2) > 1) {
                $code = str_replace('<br />', '', $parts2[0]);
                $code = str_replace('<br/>', '', $code);
                $code = str_replace('<br>', '', $code);
                $code = str_replace('<', '&lt;', $code);
                $newStr .= '<pre class="prettyprint linenums">'.$code.'</pre>';
                $newStr .= $parts2[1];
            } else {
                $newStr .= $p;
            }
        }
    } else {
        $newStr = $str;
    }
    return $newStr;
}