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It is possible that your platform modifications may have repurposed GPIOs that are otherwise used for JTAG.
- Connect the EVB to your computer
- Build and prepare to download an app
- Hold the reset button on the EVB
- When the app is about to start programming the board (watch the build output) release the reset button on the EVB
- Watch while the app downloads (if it fails, try again, but vary the timing of when you release the reset button)