Simpe method to use JavaScript inside PHP without all the messy code is a global function:

function js_link($src)
{
    //set root path to scripts folder
    if(file_exists("my/html/root/" . $src))
    {
        //we know it will exists within the HTTP Context
        return sprintf("<script type="text/javascript" src="%s"></script>",$src);
    }
    return "<!-- Unable to load " . $src . "-->";
}

Then use:

echo js_link("folder/to/yourscript.js");