boards: adjusted peripheral confs to GPIO changes

boards/airfy-beacon/include/periph_conf.h

boards/arduino-due/include/periph_conf.h

boards/arduino-mega2560/include/periph_conf.h

boards/cc2538dk/include/periph_conf.h

boards/fox/include/periph_conf.h

boards/iot-lab_M3/include/periph_conf.h

boards/msbiot/include/board.h

boards/msbiot/include/periph_conf.h

boards/mulle/board.c

boards/mulle/include/periph_conf.h

boards/nucleo-f091/include/periph_conf.h

boards/nucleo-f334/include/periph_conf.h

boards/nucleo-l1/include/periph_conf.h

boards/openmote/include/periph_conf.h

boards/pba-d-01-kw2x/include/periph_conf.h

boards/saml21-xpro/board.c

boards/saml21-xpro/include/periph_conf.h

boards/samr21-xpro/include/board.h

boards/samr21-xpro/include/periph_conf.h

boards/spark-core/include/periph_conf.h