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Shutting Down Safely
Although shutting down ChromeOS with an active chroot may work, it isn't recommended. Chroots on SD cards are particularly susceptible to corruption.
To cleanly umount the chroot, first logoff/exit any graphical environment you are running (how to do this depends on the graphical environment, although switching back to the Crouton tab and hitting CTRL-C should normally work if your chroot is running in the foreground), then type
exit. You should see something like this.
Unmounting /mnt/stateful_partition/crouton/chroots/jessie... Sending SIGTERM to processes under /mnt/stateful_partition/crouton/chroots/jessie... chronos@localhost /usr/local/bin $
It is safe to shut down ChromeOS at this point.