The methods on this page have not been tested for upstart boot scripts.
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Debian and Ubuntu non-upstart services
On Ubuntu 12.04, upstart boot scripts can be identified by their entries in /etc/init.d being symlinks to /lib/init/upstart-job.
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update-rc.d -f <service name> disablefor s in /etc/rc*.d/S*<service name>; do mv $s ${s/.d\/S/.d\/K}; donesysv-rc-conf <service name>followed by interactively changing the default symlinks. sysv-rc-conf is not installed by default.
Ubuntu upstart services
echo manual >> /etc/init/service_name.override
Reference
Non-upstart
From Securing Debian Manual section "3.6.1 Disabling daemon services"
Quote:
| ... the files under /etc/init.d are configuration files and should not get overwritten due to package upgrades if you have made local changes to them |
Based on that, any disabling technique that leaves at least one /etc/rc*.d/[KS]* symlink which is different from the symlinks in the upgrade package should be fine.