You have several options:
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You can install WP-CLI – http://wp-cli.org/
This will allow you to updates from the command line of your server. -
Use revision control, Git, Mercurial, etc. That way you just pull in updates to your staging server or localhost and push updates to your sever.
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Using a build script.
You can have a build script located locally or on your server than will update wordpress for you via the command line or even cron job.
There is a list of build scripts here: http://wpgear.org/ under “Command line fu”. -
Write your own bash/ruby/whatever script
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Use a plugin, there are several that have this as a feature.