Shared/Contiki/Makefile.contiki (FREERTOS): correct default setting

This caused a build failure in Demo/WM09.
Makefile.contiki: do not override Contiki Makefile variables directly

Instead, introduce variables CONTIKI_EXTRA_* and leave their use to the
Contiki side. Directly overriding variables also prevented them from
being changed on the Contiki side, which broke the whole logic of the
build process.
Makefile.stm32 (FREERTOS): correct default setting

Same change as in commit 843ea0cda0ca695724bb6b037a3b324374f32f27
Shared/Contiki/gpio.[ch] (gpio_r): add pull up/down setting; redo setup logic

This is a little awkward because the STM32 library doesn't support more
selective GPIO pin changes (e.g., only changing the pull resistor without
possibly affecting anything else.)