This is the method to choose when working on new low-level drivers, kernel improvements or new FPGA configurations. In such cases you have to control the board in by your host development system right upon a POR (power-on reset). For this you have to set the jumpers on your MicroZed board as follows
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This will boot the device from JTAG. The settings of the jumpers will be read only at power-on! Hence, make sure to cycle the supply power after changing the jumper settings. A soft reset (through the JTAG or by pressing the reset button on the board will reset the board but will not sample the boot mode pins connected to the jumpers.