The upgrade files include the following instruction:
Before you upgrade anything, make sure you have backup copies of any files you may have modified such as index.php.
Upgrading from any previous WordPress to 2.8:
1. Delete your old WP files, saving ones you've modified.
I have inspected my WP files on the server and there is no way I can see of telling which files I have modified since there are no file dates shown.
How do I know which files they are......or am I missing something.....apart from a deep knowledge of the subject?