I’ve always been mystified at the strange instructions for upgrading WordPress — “update all the files, except for …”. With more recent versions this gets easier because it’s possible to move
- wp-content (and so wp-content/plugins and wp-content/themes)
out of the main WordPress directory. Thus an upgrade of core WordPress doesn’t have a chance to modify the files that shouldn’t be modified.
Read more here: Converting To WordPress Rearranging directory structure?