How do I know which pins and cells are in the JTAG Boundary register?
The BSDL file completely describes the JTAG Boundary scan architecture. To find out where your pin is in the Boundary register, please refer to the BSDL file for the device.
In the BSDL file, if your pin is listed as "Linkage", it is not in the chain. For example, VCCs and GNDs are not in the chain and are declared as linkage vectors. For Spartan-II devices, the power down and power down status pins are not in the chain.
The program pin is the most difficult to interpret in the BSDL file. The program pin should always be driven externally with a 1; if it is not, the JTAG TAP controller in the device will be reset and the chain will break.