Confusion on how SAM-BA work with Due?

Hi, I was reading about SAM-BA and I am kind of confused, does the DUE always boot with SAM-BA or is it initiated via the UART chip? From what I have read it appears to make a program run, the program must load from FLASH0 but based upon what I have read, when the boot-select bit is set, the DUE will always boot into SAM-BA mode and never leave it.

Does the UART programmer exert a system reset on the DUE in order to program it? How does it exit/enter SAM-BA mode on the device?

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