External JS with CI / PHP

[eluser]mjstenbe[/eluser]
I moved all my JS code to an external file. Now I have issues with AJAX functions referring to <?php echo base_url();?>. Any good advice on how to deal with these? I'd rather not hardcode any paths to my application.

What would be the ideal location for external JS and CSS files? Now Im using /system/application/libraries?

Any tips are welcome.

Thanks,
Mika