This 2-pin jumper at this moment for anything. Was left one free pin in the PLD.
Jumper 3-pin is MCU RESET. As the microcontroller can be used Atmel 89Cx051 or AVR2313/ATtiny2313/4313. The first is reset 1s, second 0s. Therefore, 3 pins.
And finally, the 10-pin connector, the JTAG (Altera style) for PLD programming.