Drop `#include "irq.h"` in `cpu.h`, which was there for a legacy work around.
A bunch of missing includes of `irq.h` materialized due to this and were
fixed.
Moving atmega_stdio_init() to cpu_init() just before periph_init() guarantees
that stdio is available to allow DEBUG() in periph_init(). This also helps to
unify the boot up process of ATmega boards and de-duplicates the stdio init from
board_init().
