Modify Application without changing files

Hey guys,

Just started using Code Igniter. Awesome PHP Framework!

I have purchased an Code Igniter Application from the Envato Marketplace.

Currently making most of my changes in the APPLICATION and RESOURCE folders

Problem is, when the developer releases an update, it over writes over all my custom modifications.

Is there a 3rd party extension or app for Code Igniter which allows you to Code over the top or should I say override the source code without changing the original file.

For example Opencart use VQMOD and OCMOD

Any guidance would be much appreciated.