iCleaner can be run via command line (command: icleaner).
It will automatically run as root user, so you don't need to su beforehand.
The command line interface is a stripped down version of the GUI app, which can be invoked via any terminal app or SSH console. It's mainly there as a security measure, considering you can even run it if your device is in a respring loop and you only have SSH access.
It can also be used to restore Daemons, Tweaks and Preference Bundles to their default state.