It's much important for Magento theme developer to add their own external js and css file
so that they can use custom JavaScript and css and it much easier in Magento to add this. as just you need
to add local.xml in your own theme and add below structure code in that file
in local.xml under layout folder of your own theme /or default theme that currently in use
<?xml version="1.0" encoding="UTF-8"?>
<layout>
<default>
<reference name="head">
<action method="addCss">
<stylesheet>css/pcds_style.css</stylesheet>
</action>
<action method="addJs">
<script>pcds/jquery.js</script>
</action>
</reference>
</default>
</layout>
here you can replace name of js and css file accordingly yours and folder name too just keep in mind
your css file would be add in below path
/skin/frontend/default/pcds/css/
and js file directly
js/pcds/
folder here PCDS is our own theme name or folder name of default or current theme