Upgrade question

Is there any way to upgrade without users risk overwriting modified files? Maybe a list with the changed files and a list of the code changes, for example like phpBB:
http://www.phpbbhacks.com/forums/phpbb-2-0-22-to-2-0-23-code-changes-vt72196.html

I need to upgrade 2.5.1 to 2.6

Thank you