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Cool project! If I need physical access to the board, why would I not program it with a physical interface

This project is a part of a commercial usage, where the entire product was located remotely, thus it was not possible to manually flash the STM everytime.

Why do you need physical access to use this?

for switching BOOT0, reset etc?

You can automate that using flipflops or maybe MOSFETs.

Not my point though. Use case for over the air update is when one has no access to the device or its debug interfaces. So, the implementation must provide for a way to remotely handle entering programming mode, etc. IMO, the disclaimer section should be a part of the implementation.

You're entitled to your opinion.

My opinion is that if you read the page, which is only like 10 paragraphs anyway, you can clearly see how it works and decide for yourself if it's useful for you.

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