I deleted the file /etc/initramfs-tools/conf.d/driver-policy, which
contained "MODULES=dep", and the error messages went away.  (The machine
actually didn't boot in the end, but I think that was a GRUB problem,
not an initramfs problem.)

-- 
update-initramfs "missing md root"
https://bugs.launchpad.net/bugs/601380
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