Update: I've compiled the 4.13.19 kernel without USB 3 support (in the
hope that it would fall back to the USB 2 module - it doesn't - you end
up with no keyboard or trackpad). If you're running a system that has a
BIOS, and it allows you to turn off USB 3.0 support, that seems to be
the only option. Otherwise it appears that you're stuck with
intermittent USB. It sucks that MacBooks don't have ethernet... I'm
using a shared wifi AP even though I have a gigabit cable on my desk :(

There's a ton of USB 3.0 kernel bug tickets on launchpad, and in most
cases they end up expiring due to lack of updates. This one will likely
go the same way.

If ANYONE with a MacBook has managed to get it to work without USB 3.0
in the kernel, post here or PM me.

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https://bugs.launchpad.net/bugs/1668105

Title:
  xhci_hcd module turns off usb host controller on boot

Status in Linux:
  Unknown
Status in linux package in Ubuntu:
  Confirmed

Bug description:
  So we know this xhci_kcd was always shit in that it turns off the
  console usb keyboard for long running computers and that it on abrupt
  termination of Linux puts usb in a 12x slower mode. It is buggy, it
  was always buggy, and its getting worse.

  With Linux 4.8.0-37, this crappy software decides to halt the host
  controller on boot, ie. turn off the console keyboard preventing any
  boot. I cannot think of any situation where anyone would want their
  host controller halted.

  This is MacBook Pro 2015. So, it's already broken in UEFI-grub as it
  always was, ie. every key press takes 8 seconds, but you only need
  two, so you can boot in 16 s.

  I tried to disable the xhci_kcd crap by using kernel parameter
  noxhci_port_switch or modprobe.blacklist=xhci_hcd neither which works.

  Because it has crap in UEFI, the computer will not boot any external
  hard drive or usb fob. The only thing that works is Apple rescue that
  gets rid of the xhci garbage, and the boot os x immediately after
  that.

  So the log output
  xhci_hcd 0000:00:14.0: Timeout while waiting for setup device command
  xhci_hcd 0000:00:14.0: xHCI host not responding to stop endpoint command.
  - and a bit later:
  xhci_hcd 0000:00:14.0: Assuming host is dying, halting host.
  xhci_hcd 0000:00:14.0: HC died; cleaning up

  This clown programming of Linux has to stop. Why would anyone ever want their 
host controller halted?
  --- 
  ApportVersion: 2.20.3-0ubuntu8.2
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC1:  foxyboy    5662 F.... pulseaudio
   /dev/snd/controlC0:  foxyboy    5662 F.... pulseaudio
  CurrentDesktop: GNOME
  DistroRelease: Ubuntu 16.10
  HibernationDevice: RESUME=/dev/mapper/C89-SWAP
  MachineType: Apple Inc. MacBookPro12,1
  Package: linux (not installed)
  ProcFB: 0 inteldrmfb
  ProcKernelCmdLine: BOOT_IMAGE=/vmlinuz-4.8.0-39-generic 
root=/dev/mapper/C89-RFS ro i915.enable_rc6=0
  ProcVersionSignature: Ubuntu 4.8.0-39.42-generic 4.8.17
  RelatedPackageVersions:
   linux-restricted-modules-4.8.0-39-generic N/A
   linux-backports-modules-4.8.0-39-generic  N/A
   linux-firmware                            1.161.1
  Tags:  yakkety
  Uname: Linux 4.8.0-39-generic x86_64
  UpgradeStatus: Upgraded to yakkety on 2016-11-16 (108 days ago)
  UserGroups: adm docker libvirt libvirtd sudo
  _MarkForUpload: True
  dmi.bios.date: 10/26/2015
  dmi.bios.vendor: Apple Inc.
  dmi.bios.version: MBP121.88Z.0167.B15.1510261437
  dmi.board.name: Mac-E43C1C25D4880AD6
  dmi.board.vendor: Apple Inc.
  dmi.board.version: MacBookPro12,1
  dmi.chassis.type: 9
  dmi.chassis.vendor: Apple Inc.
  dmi.chassis.version: Mac-E43C1C25D4880AD6
  dmi.modalias: 
dmi:bvnAppleInc.:bvrMBP121.88Z.0167.B15.1510261437:bd10/26/2015:svnAppleInc.:pnMacBookPro12,1:pvr1.0:rvnAppleInc.:rnMac-E43C1C25D4880AD6:rvrMacBookPro12,1:cvnAppleInc.:ct9:cvrMac-E43C1C25D4880AD6:
  dmi.product.name: MacBookPro12,1
  dmi.product.version: 1.0
  dmi.sys.vendor: Apple Inc.

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