Great to see the upgrade out, but I have to ask ... is there a reason for this:

"Note: Do not upload the folders from the patch overwriting the ones existing on your site. "

I take this to mean each folder has to be manually opened and have its files uploaded separately. Things would be so much simpler if we could just upload everything - would save an awful lot of time. Is there some issue with permissions getting changed if you upload a folder as well as all its subfolders? If see more so, I have never noticed it, using various FTP clients?