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That WP auto-update has its own problems, namely making sure your PHP timeout is set, as well as having the memory limit and right file size limit (if it's an upload, I can't remember). It works ok for add-ons, but I don't trust it for full WP upgrades.

I've screwed up an WP auto-update because some PHP variable was set too low, and I needed to update "the old fashioned way".