Sorry for my english, i just have again this problem on 1.9.0 arduino ide beta version that i can not use this pin again as an output and input, with previous ide versions i just modified the pins_arduino.h on Arduino\hardware\arduino\avr\variants\leonardo, try my h file version, maybe can help someone, on the code just call the pin as "31" for PORTE2.
pins_arduino.h (9.7 KB)