How to safely power on evaluation board?
The jumper they're describing is the power jumper, or J300, which:


  is connected between the 3.3V
  regulated voltage from the regulator and the ATxmega128A1 supply. By replacing the
  jumper with an ammeter, it is possible to measure the current consumption of the
  ATxmega128A1


Here's a board diagram:



The two pins marked "Power jumper" are set up to allow a jumper to be placed across them. A jumper is a block of plastic with an internal conductor and two holes, exactly spaced to fit the two pins (there's a standard spacing; I believe it's 0.1"). You can have the jumper installed, in which case the two pins are shorted, or removed, in which case the two pins are independent. Jumpers are used to optionally connect circuit elements or durably configure boards.

So, if the jumper is present, then it provides a path for power from the main board power supply into the ATxmega128A1 chip. You can pull the jumper and connect an ammeter, which would let you determine how much power the chip alone is consuming.

But, if you leave the jumper off when you apply power to the board, the ATxmega128A1 won't get power, but the rest of the board will. Then, power will flow from the rest of the circuit into the ATxmega128A1 I/O pins, killing the ATxmega128A1. And you don't want to kill the ATxmega128A1.