>> there has to be a way to tell the kernel which partition to boot from and
>> then be able and change it later.

It's telling the boot loader which partition to use to find the
kernel.  Semantics. :)

Yes, can set the boot partition using parted:

    parted -s /dev/sda set ## boot on

Where ## is the partition number.  Not sure if it's possible to set
this flag on the
AppleTV side to switch to booting Linux partition.  Perhaps rEFIt?

Another option may be to have a small boot partition with same files
as the pen drive, that
then has a boot menu that kexec's to your linux or chainloads into
AppleTV.  Could probably
even add some rudimentary lirc support to be able to change the option
using a remote.

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