[sam] Fixed architecture specific macro digitalPinToTimer, added comment to uninplemented portModeRegister

Fix #1833
Merge pull request #2319 from cmaglie/ide-1.5.x-sam-portModeRegister

(Arduino Due/SAM) Removed macro digitalPinToTimer and added comment for portModeRegister
Introducing Atmel toolchain 3.4.4: see https://github.com/arduino/toolchain-avr