This Patch makes gpio_init precalculate the pin mask once,
This Patch makes gpio_init of atmega_common configure the pin as an input and configure the pullup in the case of GPIO_IN_PU.
GPIO_IN_PU and GPIO_IN need to change pullup so they need to change output (this is coverd by the not touching outputs is not guaranteed statement)
(this is a special case for atmega the pull_up is configured by writing 1 to the port_register which is also the level of the output if the pin is configured to output).

This fix makes it more compliant to comments in periph/gpio.h