Codeigniter has a javascript class: http://codeigniter.com/user_guide/libraries/javascript.html
You will download the jquery library via:
$this->load->library('jquery');
You can then paste this into your header section of your view:
<?php echo $library_src;?> <?php echo $script_head;?>
For additional javascript files, I usually create a resource folder in my application folder and then use the base_url function to link to files such as:
<script src="<?php echo base_url('resources/name-of-js-file.js');?>" type="text/javascript"></script>
source share