Leaving the bootloader from an IRQ (eg USB or I2C IRQ) will not work if
MBOOT_LEAVE_BOOTLOADER_VIA_RESET is disabled, ie if mboot jumps directly to
the application. This is because the CPU will still be in IRQ state when
the application starts and IRQs of lower priority will be blocked.
Fix this by setting a flag when the bootloader should finish, and exit the
bootloader always from the main (top level) thread.
This also improves the USB behaviour of mboot: it no longer abruptly
disconnects when the manifest command is sent.
Signed-off-by: Damien George <damien@micropython.org>