Ok, I figured out what happened now – nothing had upgraded at all
– the tar.gz had unpacked to a subdirectory /wordpress
– my mv-fu wasn’t able to move entire trees without deleting everything first (I had already make backups of wp-config.php and wp-content)
For future reference, is there a command in tar which causes a directory to be omitted from the path when extracting? (I usually just use tar -zxvf [archive])
So: resolved but with questions for next time