The Rev 4 PCB has changed the pinout a bit to allow in-circuit programming. Pin assignments are as follows:

PinNo	Name	Function	Programming	AVR ISP
13	PA0	LED D1 (bottom)
12	PA1	LED D2
11	PA2	LED D3
10	PA3	LED D4
9	PA4/ADC4	Data sensor	P1 - SCK	7
8	PA5	Button (GND when pressed)	P3 - MISO	9
7	PA6/ADC6	Clock sensor	P4 - MOSI	1
6	PA7	LED D5
2	PB0	LED D6
3	PB1	LED D7
5	PB2	LED D8 (top)
4	PB3/RESET		P2 - RESET	5
14	GND	Ground	P6 - GND	4,6,8,10
1	VCC	3.3V	P5 - VCC	2

The "programming" pins are solder points shown in this view: ​layout_prog.png. One can solder wires to the points and connect them to an AVR programmer (10 pin cable) using the pin numbers shown for in-circuit programming.