[all variants] How to keep my bootable clone up to date?

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http://ubuntuforums.org – I finally managed to make a bootable clone of my old and new systems (I moved from Ubuntu 10.04 to Xubuntu 12.04). It was important to me to be able to boot the clone with the original system drive still installed, so I had to modify the UUIDs, etc/fstab, and /etc/initramfs-tools/conf.d/resume, and then perform update-initramfs, grub-install and update-grub on the clone. So keeping my documents up-to-date should be simple with Grsync. I think that should work for /home to capture any setting changes. But... what about /root? Seems like if I get updated to a new kernel on the running syste (Hardware)