This is the preferred method when writing applications on the MicroZed board using the existing runtime library together with the board support package.
What is happening after a reset? to choose hen working on new low-level drivers, kernel improvements or new FPGA configurations. In such cases you have to control the board 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 powerup! Hence, make sure to cycle the supply power after changing the jumper settings.