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As of Ubuntu 12.04, what is the proper/clean way to make the system execute a script upon boot? (not upon user login) e.g. running a daemon.

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Actually there is a way to execute user specific commands during boot up time. The commands or scripts that we want to execute should be added to the script /etc/rc.local

The script /etc/rc.local will be similar to a shell script. Make sure it's exit status is 0, add the following line to that script "exit 0".

This /etc/rc.local script is executed at the end of each multiuser runlevel.

From here

Also you can see examples in /etc/init.d/

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You could also try using Upstart which I find to be useful.

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