Thunderbolt has been a Linux issue for a while now but Andreas is trying to improve the situation. One of the Linux kernel issues has been better supporting Apple hardware where Thunderbolt is very common. Apple's firmware for their hardware doesn't handle hot-plugging as it's supposed to but only initializes devices at boot time and ignores hot-plugging events. This new Cactus Ridge Linux driver allows for supporting hot-plug operations of one-device, no-chaining Thunderbolt devices.
While the Intel Cactus Ridge driver will be a step forward, its still limited in its usefulness due to no support chaining and supports only initializing the first PCI device on a Thunderbolt port, and there's some ACPI issues still to be worked out. These new Linux Thunderbolt patches that might appear in Linux 3.14 can be found on the kernel mailing list.