Still no solutions for 9 months?
Anyway, did you try the Plugin that help you do automatic upgrade? That might be helpful.
I would suggest, make a backup copy of everything in root domain (incase you need it in future), delete all the files and try installing wordpress.
OR, you can straightaway install the wordpress and the installation will clear the files for you.
BUT, be safe, Do a back up 🙂
Did you specify the installation directory?
