FPGAs have very large numbers of pins. Ensuring that these are connected and are not shorted to each other requires electrical test vectors and sensing of shorts.
To run up FPGA PCBAs a great solution is boundary scan using a JTAG connection. This lets you drive or sense, in turn, each and every pin on an FPGA or processor without having code loaded into the chip.
Continuity, possible shorted connections or pins stuck high or low can be detected very quickly.
Good low cost solution JTAG Live
We use a simple JTAG pod to do JTAG Live FPGA Boundary Scan Testing. It is really useful for PCBA run up and for short run production testing.
The video shows the use of the JTAG Live Autobuzz test function. In this the AutoBuzz learns the connections on the board allowing rapid testing of connections. It is a great first step in board run up. Watch the video in full screen to see the detail. Click the right bottom corner of the video to see it full screen.