I’m not sure why some instructions make simple task difficult, but here is how I upgrade WordPress…
Backup current ‘wordpress’ directory and database.
cp -a wordpress/* /usr/local/bk/wordpress/
mysqldump --user=root --password=XXX wordpress > /usr/local/bk/wordpress/wordpress.sql
Download and extract latest version of WordPress.
This will unpack a directory called ‘wordpress’ so be careful where you do this and how.
tar -xzf latest.tar.gz
Copy the newer wordpress files over the current base. This will not overwrite files ‘.htaccess’ or ‘wp-config.php’, or anything else that was placed or generated after the initial install.
cp -r --reply=yes wordpress/* /path/to/current/wordpress/dir/
Run upgrade script.