Extending codeigniter

To elaborate on what @InsiteFX said: The "core" files are those found in the "system" directory. When a new version of CI is released it typically means replacing all the files/folders in that directory. So, don't mess with them. If you need to extend or replace any of the "system" files with your own version, or if you want to create your own libraries then follow the guidelines provided by the CI documentation.

The files/folders in the "application" directory don't often need replacement in a upgrade. The "Upgrading from a Previous Version" instructions that accompany each new version will usually make clear what, if any, changes are required in the "application" files.