JTAG (Joint Test Action Group) is used to refer to a means of accessing the internal registers of a chip or circuit board. These registers are connected as a series of shift registers and their contents shifted out. This allows testing and control of the chip/board. For example, you can set the external interface signals, give a clock, then shift out the registers to verify that the inputs were properly received.

By shifting data IN it is possible to configure the hardware to perform a specific action, such as driving particular outputs or in the case of a programmer, writing the contents of flash memory.

See http://www.jtag.com/brochure.php?lg=en#1 for a brochure that describes the JTAG interface and how it can be used. See also the datasheet for your particular chip using JTAG (such as Cygnal/SI Labs).

Dennis