Javascript deprecated

I may be missing something here, but jquery is a browser side javascript library, that you load onto your page with some html in the footer, just like a css file in the header. CI does not 'use' jquery. CI does not care what you output to your users browser, and does not care what your user uses or experiences on your page. JavaScript does not run on your server, where your CI is sitting and executing.

Just put the relevant links to your js files and css files into your header view or footer view. It has nothing to do with CI. In the same way you would not load an image into CI to use in a page, you would just output the link to the image and display it however you want.

Have I missed or misunderstood something in your question?

Paul.