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Unused Pin/Port declaration

Hello everyone,


I developed a "custom Arduino2560 board", and it aims to be used with a Labview application using LINX.

I would like to have more details about how to first program it.


Some of the pin are unused(unbound), and I know that I will have to declare it somewhere to activate internal pull-up resistor by this way for example:


My questions are:


- Can someone tell me what is the difference between a firmware and a bootloader?


- Where those lines have to be implemented? In the pre-built firmware generated by LINX?


Thank you

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