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[eluser]CroNiX[/eluser]
Well, as I said, php doesn't get parsed in js files as evidenced by what you just posted (it's not interpreting the php, its posting it literally).

Easiest thing to do is create a js variable in the head of your php template which all of your javascript files can then use.

Code:

var base_url = "<?php echo base_url(); ?>";

Then in your javascript files, just base_url + 'controller/method/etc' to create the urls.