tactics for upgrading CodeIgniter?

[eluser]sneakyimp[/eluser]
I'm interested in upgrading my project from CodeIgniter 2.2.0 to the latest version, chiefly to address this bug:
https://github.com/EllisLab/CodeIgniter/issues/1890

The problem I have is that I do NOT want to overwrite files that I have changed. I can easily identify these files are ones that should NOT be overwritten:
ci/application/config/config.php
ci/application/config/database.php
ci/application/controllers/*.php
ci/application/core/*.php
ci/application/models/*.php
ci/application/views/*.php

I'm guessing that just unzipping the latest code igniter source download into my project folder is going to destroy config.php and database.php in the config folder at least. Can anyone recommend a good tactic for upgrading CodeIgniter?