[PATCH v2 0/3] PCI/PM: Do not save the config space of an inaccessible device

[PATCH v2 0/3] PCI/PM: Do not save the config space of an inaccessible device

[Francisco Beltrán Millalén]

When a PCI device becomes inaccessible while the system is suspending,
pci_save_state() stores all ones over its saved config space, and
pci_restore_state() writes that back on resume to a device that answers
again.  On a MacBookPro14,3 this happens to the upstream bridge of a
Thunderbolt 3 controller that drops off the bus while the system is
suspending: after resume the bridge has bus numbers ff/ff/ff and
Secondary Bus Reset asserted, and the xHCI controllers behind it are
removed.  Resume also waits about 65 seconds for a device behind a dead
bridge, because an all-ones Link Status reads as an active link.

Patch 2 makes pci_save_state() refuse to save an inaccessible device,
using pci_dev_config_accessible() from commit e18d1abc3bff ("PCI: Avoid
saving config space state if inaccessible"), so that system suspend is
covered and not only resets.  Patch 1 prepares the USB PCI HCD for it;
without patch 1, patch 2 makes pci_pm_suspend_noirq() warn.  Patch 3
stops the link wait code from taking an all-ones Link Status for an
active link.

Patch 1 touches drivers/usb.  Bjorn, if you take the series, it would
need an ack from Greg or Alan.

Changes since v1:
- v1 2/4 and 3/4 took an all-ones Vendor and Device ID to mean that the
  device was inaccessible, but that is always the case for SR-IOV VFs,
  so they broke saving and restoring VFs (as I said in reply to v1).
  2/3 now uses pci_dev_config_accessible(), which reads the Command and
  Status registers.
- Dropped v1 3/4 ("PCI/PM: Do not restore a config space snapshot that
  is all ones"): it would never restore a VF, and it did not protect
  what it claimed to, as pci_restore_state() restores the PCIe
  capability state before the standard header.
- 1/3: rewrote the commit message and moved the wakeup handling for a
  dead root hub ahead of the early return.  Alan's Acked-by is dropped.
- 2/3: the second accessibility check now runs after the capabilities
  are saved, and state_saved is only set if both checks pass.
- 3/3: also cover pcie_wait_for_link_status().
- The v1 cover letter spoke of an earlier version; that version was
  never posted.
- Based on pci/next.

v1: https://lore.kernel.org/all/20260924124221.12374-1-fbeltranmillalen@gmail.com/

Testing:
On a MacBookPro14,3 (two Alpine Ridge controllers), v6.18.49 with
e18d1abc3bff backported and this series, S3 entered by closing the lid
(158 s asleep), a USB disk on one controller and nothing on the other:

- In pci_pm_suspend_noirq() the bridges of both controllers, including
  the upstream bridge 04:00.0, were inaccessible and their state was not
  saved ("Device config space inaccessible; unable to save state").
- On resume the controller with nothing attached came back: 04:00.0
  kept bus numbers 04/05/79 and Bridge Control 0x0002, the link came up
  at 8 GT/s and its xHCI controller resumed.  Before the series the same
  bridge came back with ff/ff/ff and Bridge Control 0x005f (Secondary
  Bus Reset asserted), and both xHCI controllers were removed.
- The controller with the disk did not come back (its link does not
  train, which is a separate problem); resume waited 1 s for its xHCI
  controller instead of 65 s.
- No "State of device not saved" warning.

With the separate Alpine Ridge quirk applied, the xHCI controllers of an
empty controller are inaccessible in hcd_pci_suspend_noirq(); four S3
cycles went through patch 1 without warnings and everything resumed.

When the machine wakes up again after a few seconds (with the lid open
it does, after about 3.5 s), the empty controller does not come back
either, with v1 as with v2, so there is nothing for the series to
preserve.  The "1 of 2 controllers instead of 0 of 2" in the v1 cover
letter holds only for the longer sleeps.

I have no SR-IOV hardware, so the VF case is untested, and the machine
never reaches the pcie_wait_for_link_status() change.

Francisco Beltrán Millalén (3):
  usb: hcd-pci: Honour pci_save_state() failure
  PCI/PM: Do not save the config space of an inaccessible device
  PCI: Do not mistake an absent device for an active link

 drivers/pci/pci.c          | 69 ++++++++++++++++++++++++++------------
 drivers/usb/core/hcd-pci.c | 15 +++++++--
 2 files changed, 61 insertions(+), 23 deletions(-)

[PATCH v2 1/3] usb: hcd-pci: Honour pci_save_state() failure

[Francisco Beltrán Millalén]

hcd_pci_suspend_noirq() ignores the return value of pci_save_state() and
goes on to pci_prepare_to_sleep().

The next patch makes pci_save_state() fail, without marking the state as
saved, when the config space of the device is not accessible.  For such
a controller pci_prepare_to_sleep() does not work either:
pci_set_low_power_state() reads the PM control register as all ones and
marks the device D3cold.  pci_pm_suspend_noirq() then finds a device
whose power state changed without its state being saved, and warns.
With an earlier version of the next patch on a MacBookPro14,3, whose
Thunderbolt xHCI controllers can be inaccessible at this point:

  xhci_hcd 0000:7d:00.0: PCI PM: State of device not saved by hcd_pci_suspend_noirq+0x0/0x180
  WARNING: CPU: 7 PID: 96793 at drivers/pci/pci-driver.c:888 pci_pm_suspend_noirq+0x2f4/0x300

Check the return value and, if the state could not be saved, return 0
without putting the controller into a low-power state.  The PCI core
then handles it as it handles a driver without a suspend_noirq callback:
it tries to save the state and to put the device into a low-power state
itself, which fails in the same way, but without the warning, as the
power state did not change inside the driver callback.

Move the check that disables wakeup for a dead root hub ahead of it, so
that it is not skipped.

Today pci_save_state() only fails if a capability save buffer is missing
or the VC state cannot be saved.  In that case the controller is now left
in D0 instead of being put into a low-power state with an incomplete
saved state.

Assisted-by: LLM
Signed-off-by: Francisco Beltrán Millalén <fbeltranmillalen@gmail.com>
---
v2:
- Rewrote the commit message: the failure handled here comes from the
  next patch, not from pci_save_state() as it is today.
- Disable wakeup for a dead root hub before the early return.
- Dropped Alan's Acked-by because of both changes.

 drivers/usb/core/hcd-pci.c |   15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/drivers/usb/core/hcd-pci.c b/drivers/usb/core/hcd-pci.c
index cd2234759..7f8a56425 100644
--- a/drivers/usb/core/hcd-pci.c
+++ b/drivers/usb/core/hcd-pci.c
@@ -541,8 +541,6 @@ static int hcd_pci_suspend_noirq(struct device *dev)
 	if (retval)
 		return retval;
 
-	pci_save_state(pci_dev);
-
 	/* If the root hub is dead rather than suspended, disallow remote
 	 * wakeup.  usb_hc_died() should ensure that both hosts are marked as
 	 * dying, so we only need to check the primary roothub.
@@ -551,6 +549,19 @@ static int hcd_pci_suspend_noirq(struct device *dev)
 		device_set_wakeup_enable(dev, 0);
 	dev_dbg(dev, "wakeup: %d\n", device_may_wakeup(dev));
 
+	/*
+	 * If the state could not be saved, most likely because the controller
+	 * is no longer accessible, putting it into a low-power state would
+	 * fail as well and leave it marked as D3cold, and the PCI core would
+	 * then warn that its state was not saved.  Leave it to the PCI core
+	 * instead, as for a driver without a suspend_noirq callback.
+	 */
+	retval = pci_save_state(pci_dev);
+	if (retval) {
+		dev_dbg(dev, "--> not suspending, state not saved\n");
+		return 0;
+	}
+
 	/* Possibly enable remote wakeup,
 	 * choose the appropriate low-power state, and go to that state.
 	 */

[PATCH v2 2/3] PCI/PM: Do not save the config space of an inaccessible device

[Francisco Beltrán Millalén]

pci_save_state() reads the standard header into dev->saved_config_space
and marks it valid without checking that the device answered.  If the
device is not accessible, every read returns all ones, the previous
snapshot is overwritten, and pci_restore_state() writes the all-ones
values back once the device answers again.  On a bridge that sets every
writable bit of the Bridge Control register, Secondary Bus Reset
included, and sets the primary, secondary and subordinate bus numbers
to 0xff, which cuts off everything below it.

On a MacBookPro14,3 this happens to the upstream bridge of a
Thunderbolt controller that drops off the bus while the system is
suspending: after resume the bridge answers again, but with bus numbers
ff/ff/ff and Secondary Bus Reset asserted, and the xHCI controllers
behind it are removed.

Commit e18d1abc3bff ("PCI: Avoid saving config space state if
inaccessible") added pci_dev_config_accessible() and checks it before a
reset.  Check it in pci_save_state() itself, so that system suspend,
where the state is saved by pci_pm_suspend_noirq() or by a driver's
suspend_noirq callback, is covered as well.  pci_dev_config_accessible()
reads the Command and Status registers rather than the Vendor and Device
IDs, which always read as all ones on SR-IOV VFs.

Check again after reading, as the device may become inaccessible in the
meantime, and only then replace the previous snapshot of the header and
set state_saved.  The capabilities are saved straight into their own
buffers and are not covered by the second check, and both checks are
racy, as pci_dev_config_accessible() notes.

If the device is not accessible, return -EIO and leave state_saved as it
was.

Assisted-by: LLM
Signed-off-by: Francisco Beltrán Millalén <fbeltranmillalen@gmail.com>
---
v2:
- Use pci_dev_config_accessible() instead of reading the Vendor ID,
  which always reads as all ones on SR-IOV VFs: v1 refused to save the
  state of every VF.  In the v1 thread I said I would use
  pci_device_is_present(), but for a VF that checks the PF and cannot
  tell whether the VF itself answers.
- Do the second check after saving the capabilities, and set
  state_saved only if both checks pass.
- The bus numbers are set to 0xff, not cleared.

 drivers/pci/pci.c |   53 +++++++++++++++++++++++++++++++++++++----------------
 1 file changed, 37 insertions(+), 16 deletions(-)

diff --git a/drivers/pci/pci.c b/drivers/pci/pci.c
index b2879a6be..94de99d31 100644
--- a/drivers/pci/pci.c
+++ b/drivers/pci/pci.c
@@ -1776,31 +1776,52 @@ static void pci_restore_pcix_state(struct pci_dev *dev)
  * pci_save_state - save the PCI configuration space of a device before
  *		    suspending
  * @dev: PCI device that we're dealing with
+ *
+ * If the config space of @dev is not accessible, nothing is saved and the
+ * previous snapshot of the standard header is kept, as writing back the
+ * all-ones values read from such a device would corrupt it once it is
+ * accessible again.
+ *
+ * Return: 0 on success, -EIO if @dev is not accessible, or another
+ * negative errno if a capability could not be saved.
  */
 int pci_save_state(struct pci_dev *dev)
 {
-	int i;
+	u32 config[16];
+	int i, ret;
+
+	if (!pci_dev_config_accessible(dev, "save state"))
+		return -EIO;
+
 	/* XXX: 100% dword access ok here? */
 	for (i = 0; i < 16; i++) {
-		pci_read_config_dword(dev, i * 4, &dev->saved_config_space[i]);
-		pci_dbg(dev, "save config %#04x: %#010x\n",
-			i * 4, dev->saved_config_space[i]);
+		pci_read_config_dword(dev, i * 4, &config[i]);
+		pci_dbg(dev, "save config %#04x: %#010x\n", i * 4, config[i]);
 	}
-	dev->state_saved = true;
 
-	i = pci_save_pcie_state(dev);
-	if (i != 0)
-		return i;
+	ret = pci_save_pcie_state(dev);
+	if (!ret)
+		ret = pci_save_pcix_state(dev);
+	if (!ret) {
+		pci_save_dpc_state(dev);
+		pci_save_aer_state(dev);
+		pci_save_ptm_state(dev);
+		pci_save_tph_state(dev);
+		ret = pci_save_vc_state(dev);
+	}
+
+	/*
+	 * The device may have become inaccessible while it was being read.
+	 * Keep the previous header snapshot in that case.  The capabilities
+	 * are saved directly into their buffers, so they are not protected.
+	 */
+	if (!pci_dev_config_accessible(dev, "save state"))
+		return -EIO;
 
-	i = pci_save_pcix_state(dev);
-	if (i != 0)
-		return i;
+	memcpy(dev->saved_config_space, config, sizeof(config));
+	dev->state_saved = true;
 
-	pci_save_dpc_state(dev);
-	pci_save_aer_state(dev);
-	pci_save_ptm_state(dev);
-	pci_save_tph_state(dev);
-	return pci_save_vc_state(dev);
+	return ret;
 }
 EXPORT_SYMBOL(pci_save_state);
 

[PATCH v2 3/3] PCI: Do not mistake an absent device for an active link

[Francisco Beltrán Millalén]

When a bridge is no longer accessible, its Link Status register reads
as 0xffff, which has both PCI_EXP_LNKSTA_DLLLA and PCI_EXP_LNKSTA_LT
set.  The code that waits for the link then takes a dead link for an
active one:

  - pci_bridge_wait_for_secondary_bus(), for ports up to 5 GT/s, decides
    that the link is up and waits PCIE_RESET_READY_POLL_MS for the device
    below it;

  - pcie_wait_for_link_status(), used for faster ports and by
    pcie_retrain_link(), reports success at once when waiting for an
    active link, and times out after PCIE_LINK_RETRAIN_TIMEOUT_MS when
    waiting for LT to clear.

Treat an all-ones read as the device being gone.  All callers of
pcie_wait_for_link_status() and pcie_retrain_link() treat any non-zero
return as failure.

On a MacBookPro14,3 whose Thunderbolt controller does not come back from
S3, the downstream ports of the controller are 2.5 GT/s ports that no
longer answer.  Resume spent about 65 seconds waiting for the xHCI
controller behind one of them ("not ready 65535ms after resume"); with
the pci_bridge_wait_for_secondary_bus() change it gives up on that
controller after about one second.  That machine never reaches
pcie_wait_for_link_status() in this situation, so that part has not been
tested.

Assisted-by: LLM
Signed-off-by: Francisco Beltrán Millalén <fbeltranmillalen@gmail.com>
---
v2:
- Also check in pcie_wait_for_link_status() (faster ports and
  pcie_retrain_link()); not tested.
- Say that it is the bridge that is gone.

 drivers/pci/pci.c |   16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/drivers/pci/pci.c b/drivers/pci/pci.c
index 94de99d31..2e31d18b2 100644
--- a/drivers/pci/pci.c
+++ b/drivers/pci/pci.c
@@ -4586,8 +4586,8 @@ static int pci_pm_reset(struct pci_dev *dev, bool probe)
  * @use_lt: Use the LT bit if TRUE, or the DLLLA bit if FALSE.
  * @active: Waiting for active or inactive?
  *
- * Return 0 if successful, or -ETIMEDOUT if status has not changed within
- * PCIE_LINK_RETRAIN_TIMEOUT_MS milliseconds.
+ * Return 0 if successful, -ENODEV if @pdev is not accessible, or -ETIMEDOUT
+ * if status has not changed within PCIE_LINK_RETRAIN_TIMEOUT_MS milliseconds.
  */
 static int pcie_wait_for_link_status(struct pci_dev *pdev,
 				     bool use_lt, bool active)
@@ -4602,6 +4602,9 @@ static int pcie_wait_for_link_status(struct pci_dev *pdev,
 	end_jiffies = jiffies + msecs_to_jiffies(PCIE_LINK_RETRAIN_TIMEOUT_MS);
 	do {
 		pcie_capability_read_word(pdev, PCI_EXP_LNKSTA, &lnksta);
+		/* All ones means @pdev is gone; it would look like an active link */
+		if (PCI_POSSIBLE_ERROR(lnksta))
+			return -ENODEV;
 		if ((lnksta & lnksta_mask) == lnksta_match)
 			return 0;
 		msleep(1);
@@ -4624,8 +4627,9 @@ static int pcie_wait_for_link_status(struct pci_dev *pdev,
  * according to @use_lt.  It is not verified whether the use of the DLLLA
  * bit is valid.
  *
- * Return 0 if successful, or -ETIMEDOUT if training has not completed
- * within PCIE_LINK_RETRAIN_TIMEOUT_MS milliseconds.
+ * Return 0 if successful, -ENODEV if @pdev is not accessible, or -ETIMEDOUT
+ * if training has not completed within PCIE_LINK_RETRAIN_TIMEOUT_MS
+ * milliseconds.
  */
 int pcie_retrain_link(struct pci_dev *pdev, bool use_lt)
 {
@@ -4858,8 +4862,10 @@ int pci_bridge_wait_for_secondary_bus(struct pci_dev *dev, char *reset_type)
 		if (!dev->link_active_reporting)
 			return -ENOTTY;
 
+		/* All ones means @dev is gone; it would look like an active link */
 		pcie_capability_read_word(dev, PCI_EXP_LNKSTA, &status);
-		if (!(status & PCI_EXP_LNKSTA_DLLLA))
+		if (PCI_POSSIBLE_ERROR(status) ||
+		    !(status & PCI_EXP_LNKSTA_DLLLA))
 			return -ENOTTY;
 
 		return pci_dev_wait(child, reset_type,

Re: [PATCH v2 1/3] usb: hcd-pci: Honour pci_save_state() failure

[sashiko-bot]

> hcd_pci_suspend_noirq() ignores the return value of pci_save_state() and
> goes on to pci_prepare_to_sleep().
> 
> The next patch makes pci_save_state() fail, without marking the state as
> saved, when the config space of the device is not accessible.  For such
> a controller pci_prepare_to_sleep() does not work either:
> pci_set_low_power_state() reads the PM control register as all ones and
> marks the device D3cold.  pci_pm_suspend_noirq() then finds a device
> whose power state changed without its state being saved, and warns.
> With an earlier version of the next patch on a MacBookPro14,3, whose
> Thunderbolt xHCI controllers can be inaccessible at this point:
> 
>   xhci_hcd 0000:7d:00.0: PCI PM: State of device not saved by hcd_pci_suspend_noirq+0x0/0x180
>   WARNING: CPU: 7 PID: 96793 at drivers/pci/pci-driver.c:888 pci_pm_suspend_noirq+0x2f4/0x300
> 
> [ ... ]
> in D0 instead of being put into a low-power state with an incomplete
> saved state.
> 
> Assisted-by: LLM
> Signed-off-by: Francisco Beltrán Millalén <fbeltranmillalen@gmail.com>

Sashiko has reviewed this patch and found no issues. It looks great!

-- 
Sashiko AI review · https://sashiko.dev/#/patchset/20260930141914.6678-1-fbeltranmillalen@gmail.com?part=1

Re: [PATCH v2 3/3] PCI: Do not mistake an absent device for an active link

[sashiko-bot]

> When a bridge is no longer accessible, its Link Status register reads
> as 0xffff, which has both PCI_EXP_LNKSTA_DLLLA and PCI_EXP_LNKSTA_LT
> set.  The code that waits for the link then takes a dead link for an
> active one:
> 
>   - pci_bridge_wait_for_secondary_bus(), for ports up to 5 GT/s, decides
>     that the link is up and waits PCIE_RESET_READY_POLL_MS for the device
>     below it;
> 
>   - pcie_wait_for_link_status(), used for faster ports and by
>     pcie_retrain_link(), reports success at once when waiting for an
>     active link, and times out after PCIE_LINK_RETRAIN_TIMEOUT_MS when
>     waiting for LT to clear.
> 
> Treat an all-ones read as the device being gone.  All callers of
> pcie_wait_for_link_status() and pcie_retrain_link() treat any non-zero
> return as failure.
> 
> On a MacBookPro14,3 whose Thunderbolt controller does not come back from
> S3, the downstream ports of the controller are 2.5 GT/s ports that no
> longer answer.  Resume spent about 65 seconds waiting for the xHCI
> controller behind one of them ("not ready 65535ms after resume"); with
> the pci_bridge_wait_for_secondary_bus() change it gives up on that
> controller after about one second.  That machine never reaches
> pcie_wait_for_link_status() in this situation, so that part has not been
> tested.
> 
> Assisted-by: LLM
> Signed-off-by: Francisco Beltrán Millalén <fbeltranmillalen@gmail.com>

Sashiko has reviewed this patch and found no issues. It looks great!

-- 
Sashiko AI review · https://sashiko.dev/#/patchset/20260930141914.6678-1-fbeltranmillalen@gmail.com?part=3

Re: [PATCH v2 2/3] PCI/PM: Do not save the config space of an inaccessible device

[sashiko-bot]

> pci_save_state() reads the standard header into dev->saved_config_space
> and marks it valid without checking that the device answered.  If the
> device is not accessible, every read returns all ones, the previous
> snapshot is overwritten, and pci_restore_state() writes the all-ones
> values back once the device answers again.  On a bridge that sets every
> writable bit of the Bridge Control register, Secondary Bus Reset
> included, and sets the primary, secondary and subordinate bus numbers
> to 0xff, which cuts off everything below it.
> 
> On a MacBookPro14,3 this happens to the upstream bridge of a
> Thunderbolt controller that drops off the bus while the system is
> suspending: after resume the bridge answers again, but with bus numbers
> ff/ff/ff and Secondary Bus Reset asserted, and the xHCI controllers
> behind it are removed.
> 
> [ ... ]
> If the device is not accessible, return -EIO and leave state_saved as it
> was.
> 
> Assisted-by: LLM
> Signed-off-by: Francisco Beltrán Millalén <fbeltranmillalen@gmail.com>

Sashiko has reviewed this patch and found no issues. It looks great!

-- 
Sashiko AI review · https://sashiko.dev/#/patchset/20260930141914.6678-1-fbeltranmillalen@gmail.com?part=2

Re: [PATCH v2 0/3] PCI/PM: Do not save the config space of an inaccessible device

[Darrell Gum]

On Wed, 30 Sep 2026 11:19:11 -0300, Francisco Beltrán Millalén wrote:
> When a PCI device becomes inaccessible while the system is suspending,
[...]

Hi Francisco,

I tested this series on another MacBookPro14,3, together with your
Alpine Ridge SXFP quirk and the Apple native PME patch. On this
machine the combination takes S3 from never resuming to working, and
it fixes USB-C hotplug while the Thunderbolt xHCIs are
runtime-suspended.

Hardware: MacBookPro14,3 (15", 2017, T1), two Alpine Ridge 4C
controllers:

  upstream bridges    8086:1578   04:00.0, 7a:00.0
  downstream bridges  8086:15d3
  NHI                 8086:15d2   06:00.0, 7c:00.0
  xHCI                8086:15d4   07:00.0, 7d:00.0

The dGPU is a Radeon Pro 555 (1002:67ef, subsystem 106b:017a rev c7).

Kernel: 7.2.5 with the Omarchy distro patches (linux-omarchy
7.2.5-3), plus these, in this order:

  e18d1abc3bff ("PCI: Avoid saving config space state if inaccessible")
  this series, v2 1/3-3/3
  PCI: Extend Apple Thunderbolt power quirk to Alpine Ridge
  ACPI: PCI: take native PME control on Apple machines
  a5be7ad8f5f0 + a22e5e4f2ebb (amdgpu VI reset quirk, incl. 017a)

Everything applied with offsets only (no fuzz) on 7.2.5.
mem_sleep=deep, stock command line.

I applied and tested all of these together. I did not bisect them,
so beyond what the logs show directly I can't pin a result on one
patch.

Before (stock 7.2.5-3 on the same machine):

- pm_test=platform hard-hung 3 out of 3 times. That includes a fresh
  boot and runs with brcmfmac unloaded, and it did not recover after
  more than 3.5 minutes. pm_test=devices passed.
- Real S3 never resumed. Every attempt needed a forced power-off.
- With both TB xHCIs runtime-suspended (power/control=auto), plugging
  a USB 3 stick into any USB-C port produced no kernel messages at
  all. With power/control=on, it enumerated at SuperSpeed right away.

After (patched kernel):

- _OSC now reads "OS assumes control of [PCIeHotplug SHPCHotplug PME
  AER PCIeCapability LTR DPC]". PME is missing from that line on the
  stock kernel.
- Hotplug: with both xHCIs runtime-suspended, the same stick
  enumerated at SuperSpeed within about 1 s. 7d:00.0 resumed on its
  own and 07:00.0 stayed suspended. Nothing was forced.
- pm_test=platform passes. "quirk: cutting power to Thunderbolt
  controller..." is logged for both 04:00.0 and 7a:00.0.
- Real S3: every attempt resumed. That was about half a dozen real
  S3 cycles over one morning: rtcwake on AC, plus lid-close suspends
  on battery. amdgpu resumed in 1.2 s.
- With a device attached (lid-close S3 on battery, about 1 min
  asleep): a USB 3 stick was enumerated at SuperSpeed on 7d:00.0
  (behind 7a:00.0) before suspend. The quirk logged for both 7a:00.0
  and 04:00.0 with the stick attached. After resume the stick was
  still there with no USB disconnect logged, still at 5000 Mbps, and
  its filesystem mounted and listed fine. Unplugging it and plugging
  it back in about 2 min after resume re-enumerated it at SuperSpeed
  in about 3 s, with power/control=auto.
- On that cycle the xHCI of the other, empty controller logged
  "xhci_hcd 0000:07:00.0: xHC error in resume, USBSTS 0x401, Reinit"
  and recovered. I'm mentioning it only because it's on the path
  your quirk affects; I haven't looked into it further.
- noirq resume takes about 16 s (15.9 s on a real S3 cycle). About
  11 s of that is in each upstream bridge (04:00.0, 7a:00.0), then
  about 5 s in the NHIs (06:00.0, 7c:00.0). Another 14,3 owner
  reports the same split in s2idle (stock kernel plus a local
  Thunderbolt workaround), and says it drops to about 0.5 s with the
  ACPICA change proposed in
  https://github.com/open-acpica/acpica/pull/1235 . I haven't tried
  that here.

Not covered:

- The "plugging into USB-C no longer wakes it" trade-off is
  untested here.
- Only one S3 cycle had a device attached, and it was a USB stick.
  No real Thunderbolt devices and no SR-IOV.
- The stock kernel also lacked the amdgpu quirk, so the real-S3
  before/after mixes both changes. The cleaner Thunderbolt-side
  comparison is pm_test=platform: the devices stage, amdgpu included,
  already passed on stock.

Two workarounds that have nothing to do with Thunderbolt were in place
for every patched-kernel run, in case they show up in other reports:

- d3cold_allowed=0 on the NVMe SSD (02:00.0). On stock, the machine
  never even reached S3 without it. I have not retested without it on
  the patched kernel.
- brcmfmac (BCM43602, 03:00.0) unloaded before suspend and reloaded
  after. Left bound through a real S3, the Wi-Fi firmware state is
  lost.

Thanks for chasing this down. This is the first kernel on which this
machine resumes from S3 at all.

Tested-by: Darrell Gum <d@rrell.co>