The Makefile.includes contain a hardcoded ../../../../../libopencm3
path for the TOOLCHAIN_DIR variable. They also contained another copy
of this hardcoded path, that is now generated from $TOOLCHAIN_DIR.
This allows to have a symbolic link to a Makefile.include in an
out-of-tree project and reuse the Makefile infrastructure.
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.
