[fulafel]

There's a mechanism exactly for this purpouse in Linux: pivot_root. It's used in the standard boot process to switch from the initrd (initial ramdisk) environment to the real system root.

ec2-spotter classic uses this, but you can also make a pivoting AMI of your favourite Linux distribution.

One thing to watch out for is how to keep the OS automatic kernel updates working. AMIs are rarely updated and you're going to have a "damn vulnerable linux" if you don't get the updates just after booting a new image.