I've been experimenting with both encrypted /boot partitions and booting
from a hidden encrypted volume inside an outer encrypted volume, and have
been successful with Debian based systems. I'd like to get it working with
Qubes, but I've run into some issues.

The implementation requires decrypting the volumes from grub, then a
manual boot of the kernal and initram, then some pre-boot scripts added to
the initramfs are needed to properly decrypt and mount the volumes and
then re-scan and activate LVM volume groups during the handover between
grub, initram and the final boot. However, the Qubes Mananger is
non-functional after boot.

I notice when booting from a normal install, Grub briefly displays
something like:

Loading Xen-4.6.1
Loading vmlinuz-4***
Loading intramfs-4***

In what way does the Xen image get loaded? I think this is what's missing
from my boot sequence. If I'm going through the boot sequence manually, or
loading the components from a bash script in initram, what needs to be
done with the /boot/xen-4.6.1 file?

Any help would be greatly appreciated.

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