I don't want to say it's impossible, but nobody has found a way to do it yet. No matter what you put into shortest_legal_path and shortest_illegal_path and systems_shortest_path, the game just doesn't calculate the waypoints to go through jump holes. In the Freeworlds mod, we use only jump holes, not jump gates, and we could never get it to work.

If you look in the solararch.ini file, under the entry for "jumphole", you'll see a line:

type = JUMP_HOLE

If you change that to "type = JUMP_GATE" and then the set path will use the jump holes. . . though it will cause crashes if you do that. However, it does show that it's hardcoded to not use objects with the "JUMP_HOLE" type in doing the waypoint calculations.

There is sort of a way around it, but it does cause some major probems as side effects. You can change the hardpoints on the cmp file for the jump hole to be like those in the jumpgate (they are a little bit different, and I don't want to get into how to do it). Then change the "jump_hole" to "jump_gate". This will work for the set path, but it makes it weird when you dock with it. It now has to line up your ship in the right direction instead of being able to jump from any angle. There are also some other weird side effects too. I wouldn't recommend trying it this way.