True, if you have modified your files and trust yourself to be really thorough in checking them over, use
Beyond Compare to go through the changed files and upgrade them. I did this here for every upgrade from 5.45c through 5.47d. You get good after a while and can upgrade in a matter of minutes. Navaho has said they plan to release "upgrade zips" too, that only contain the changed files from previous releases, so tat should help as well.
I look forward to every release, it means bugs have been fixed and/ or features added into the base code.
