Right, firstly there seems to be loads of information out there but not for this specific problem (that I can find). Mega thanks to anyone who can help.
I have an Arduino Nano hooked up to my Pi (2B) on the rx/tx lines, crossed and via a LLC.
I want to use avrdude to program my Arduino over the serial connection, on top of the normal bootloader. What command line command do I use to do this?
All the posts I have read use SPI and overwrite the bootloader which is not what I want.
This must be possible because that is exactly how the normal USB programming works.
PS: I have a transistor on the reset pin hooked up to rPi GPIO25 which I can use to manually toggle the reset when needed (or I can just press the button!)