I'm pretty sure I came across the same issue yesterday: I ran a dist-upgrade on an X99-based system (the first for several months) and the system was left unbootable. My root system is on raid and booting failed with mdadm errors about it not being able to find any of the raid arrays listed in /etc/mdadm/mdadm.conf.
>From the initramfs shell (having eventually found a PS/2 keyboard!), I could see no disks or partitions under /dev. I even tried booting off a (recent - downloaded to rescue this system!) testing installation DVD and had the same problem: it got so far and then lost the DVD drive! As before, a shell showed no disk or partition devices under /dev. After a lot of panic, I eventually worked out that a simple "modprobe ahci" at the initramfs prompt and exiting it allowed the system to boot properly. The problem (at least for me) is that the ahci module isn't getting loaded automatically on boot. Load it by hand and it boots normally. I suspect this would work for others with a similar setup. I don't know enough about the minutiae of the boot process to debug this much more but I assume that it is udev that should be pulling in any needed modules based on the hardware. As part of the upgrade (looking back now), udev was upgraded from 239-13 to 240-2. I did think about trying to get the initrd to force loading the ahci module but that's never been needed in the past! Cheers, Laz
