I would rather see the hotplug-part in device/ as a separate commit.
I think there is a hotplug-capability bit in one of the PCIe standard capability blocks that should be evaluated as well. Can you paste lspci -xxxx output of that thunderbolt device somewhere (mailing list would be fine), maybe there is a more generic solution that does not depend on PCI device ID.
The hotplug code should also hook with cardbus bridges.
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