Follow the boot time default pulls as documented in section 6.2 of the
SoC datasheet. If you don't then there will always be a slight glitch between power being applied and any form of software having taken over, processed whatever input, and set your GPIOs to any non-default setting.
By default GPIOs 0-8 pull up, whilst 9-27 pull down. No, those defaults can't be changed.
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