Do I have to build the provided boards to build for a custom one?

Is there anything that pynq or me can reuse, or can I just work on my custom board straight away?

Update: After the several hour build of Pynq-Z1 (I moved the other folders), my custom board built from scratch (hdf file) relatively quickly (1 - 1.5 h)

To rebuild for your board specifically, you can use a similar structure & approach as for the Ultra96 (GitHub - Avnet/Ultra96-PYNQ: Board files to build Ultra 96 PYNQ image see the readme).

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