Using CodeIgniter with EE 2.0

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Anyone? Derek? I know this is possible and somewhat fringe use of the product…

I have read the following article: http://paramore.is/think/entry/harnessing-the-power-of-codeigniter-in-expressionengine-2.0/

By modifying some of the code I am able to use CodeIgniter within an existing EE install. The downs side of this approach is that it completely by passes all native EE functionality. For example the ability to use tags such as {exp:channel:channel_name}… or any other tags provided by plugins. I am using structure, it would be nice not to have rewrite code that duplicates it’s functionality for the views that I am handling with CI instead of EE.

Does anyone know if it is possible to load CodeIgniter and still be able to use EE’s default functionality in conjunction with it? If so what is the process?

Thanks