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arbor:
I solved the "Hit any key to stop autoboot" problem with the mcu sending data to u-boot and stopping the boot process.It does require an upgrade to u-boot and if that goes wrong you brick the Yun. The only way to recover after that is to desolder the flash and go through the whole process of writing a new image and soldering the chip back
Sorry for my ignorance, but does this become less risky when moving the root file system from flash to the sd card as in How to expand the storage memory on the Yún - Arduino Yún - Arduino Forum
U-boot is the first 256k of flash on the Atheros side. It's separate from the Rootfs. When the Atheros turns on it looks for a bootloader at the beginning of the flash and runs u-boot. If U-boot is not there or is corrupted then nothing will happen on the Atheros side and the Yun is bricked.
Not that upgrading u-boot isn't safe or fails often with a good working image. But if it does it becomes a pain of a problem.