Connor: no, I haven't tried kernel options yet.

Dimitrios: I think you're right!  I built a kernel with that single
patch applied, but unfortunately it wasn't enough:

[   30.118089] ahci 0000:02:00.0: JMB361 has only one port, port_map 0x3 -> 0x1
[   30.118094] ahci 0000:02:00.0: nr_ports (2) and implemented port map (0x1) 
don't match, using nr_ports
[   30.118096] ahci 0000:02:00.0: forcing PORTS_IMPL to 0x3

and then again

[   34.106600] ata2: classification failed
[   34.106604] ata2: reset failed (errno=-22), retrying in 8 secs

Looking at the code I think I see the problem with the fix: the port_map
change is dropped a few lines down because it doesn't match the number
of ports advertised in cap.nr_ports.  Resetting the latter ought to fix
it...

-- 
ata errors stop the boot process for 10 minutes
https://bugs.launchpad.net/bugs/244363
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