#define PIN_LED (1 << PC7)

void setup() {
DDRF = 0xFF; PORTF = 0;
DDRE = 0xFF; PORTE = 0;
DDRD = 0xFF; PORTD = 0;
DDRC = 0xFF; PORTC = 0;
DDRB = 0xFF; PORTB = 0;
}

void loop() {
  PORTE |= 1<<PE6;
  digitalWrite(13,  PINE & 1<<PE6 ); //issue here. if I change to PORTE will work
  delay(3000);
  PORTC &= ~PIN_LED;       
  PORTE &= ~(1<<PE6);
}

 digitalWrite(13, digitalRead(7));

void digitalWrite(uint8_t pin, uint8_t val)
{
        uint8_t timer = digitalPinToTimer(pin);
        uint8_t bit = digitalPinToBitMask(pin);
        uint8_t port = digitalPinToPort(pin);
        volatile uint8_t *out;

        if (port == NOT_A_PIN) return;

        // If the pin that support PWM output, we need to turn it off
        // before doing a digital write.
        if (timer != NOT_ON_TIMER) turnOffPWM(timer);

        out = portOutputRegister(port);

        uint8_t oldSREG = SREG;
        cli();

        if (val == LOW) {
                *out &= ~bit;
        } else {
                *out |= bit;
        }

        SREG = oldSREG;
}