While some of the examples include a "board.ld" style file, some of them were
pointing to the libopencm3 provided chip specific ld scripts. When
TOOLCHAIN_DIR has been overridden, those paths were no longer valid/correct.
Replace includes of stm32/YY/xxxx.h with stm32/xxxx.h
Replace stm32/YY/nvic.h with cm3/nvic.h.
In some cases, the include list was resorted alphabetically when it was
complicated and I was reviewing them manually, but most of this was
automatically done.
