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Depending on the platform, one can get one to three levels of loaders which have a some range of configuration items (pins/register config) and programmability before you even to 'application' code. (trying to recall if I've ever hit more than three...) And it's often accessible by the developers and not just the manufacturers. Different mfrs are open to openly annoying about the details of access at that level, but you can often get debugger access at those early bootloader levels, though most embedded dev environments sensibly default to later stages.

Sometimes strange bugs manifest due to misalignments between configs at early boot stages and what the later code needs, so you want to be able to review and change those stages.

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