These devices are hot-swap compliant. However, there are certain power-sequencing requirements that must be met (see page7 of DS152, Virtex-6 data sheet: http://www.xilinx.com/support/documentation/data_sheets/ds152.pdf for details).
Virtex-6 has clamp diodes to VCCO, similar to Virtex-II Pro, Virtex-4, Virtex-5 FPGA,etc., which means that the currentthrough them shouldbe limited in case Vin is applied before VCCO. The maximum current through a pin is 10 mA, as stated in the data sheet.
XAPP251 (http://www.xilinx.com/support/documentation/application_notes/xapp251.pdf) applies to Virtex-6 devices. See this application note for more information on hot swapping.This application note applies to all devices with a clamp diode to VCCO / GND, including Virtex-6 FPGA.
The Spartan-6 is Hot-swap compliant as stated in the Spartan-6 Family Overview data sheet (DS160).These devices do not have clamp diodes to VCCO, so there are lessrestrictions. The Spartan-6 FPGA input voltage is independent of VCCO (see Table 1, page 1 of DS162, Spartan-6 data sheet for details: http://www.xilinx.com/support/documentation/data_sheets/ds162.pdf).
In Table 2, page 3, of the DC and Switching data sheet (DS162), you can see that you can safely apply a voltage up to 3.95V maximum to the I/O without destroying it.
Diodes are only available for PCI standards - If a Customer is using a PCI standard, then the diodes would exist and the hot-swap/hot-plug compatibility follows the usual rules: the current through the I/Os should be limitedand Vinshould beapplied before VCCO.