The two main connectors on the XEM6010 are labelled JP2 and JP3 and the tables in the manual also reference JP2/JP3.
However, the UCF file supplied with the software distribution references JP1 and JP2 in the comments, not JP2/JP3. It appears that if you interpret these as the labels for the breakout board, then it’s correct. For example, FPGA pin T21 is JP2-41 in the XEM6010 manual, which connects to JP1-41 = JP1B-41 on the breakout board, and the comments say JP1-41 in the UCF file.
The UCF file would be a little confusing if you don’t have a breakout board.