The pins in the jst connector are ordered in the same way as on the discovery board, but the outermost (green) cable is connected to 3V or VDD. Notice that I have removed two jumpers on the discovery board to disconnect the SWD from the microcontroller. An STM32 discovery board with stlinkv2 works perfectly for programming and debugging, and can be connected as shown here (click on the picture to get a larger version where the wire colors can be seen): The connector is a 6-pin micro-jst connector with 2mm pitch, which easily can be found by searching on ebay. When I make custom STM32 PCBs (such as my RF-mote or my ESC), I use an SWD connector for programming and debugging the microcontroller.