I have multiple sites I manage that run WordPress so I try to stay up to date on all of them. If you stay on op of upgrading WordPress then most of the updates are fairly easy and don’t require changing that many files. Instead of uploading the entire set of files again it is easiest to simply upload the modified files. This will allow you to not have to make all of your custom modifications again if you have made customizations to any core WordPress files. Customizing core WordPress files is something I try to stay away from but there are definitely situations where I have modified core files to accomplish various goals. Anyhow since I haven’t found a site that keeps a consistant list of changed WordPress files I am going to try to start providing a list for each upgrade on Question Defense from now on.