In the DATA/UNIVERSE/SYSTEM/<system> folder you'll find an INI in each respective directory. I've been trying without success to get the New Berlin -> Sigma 13 jumphole working in MP, but here's what I've found so far:
The file I'm working with is <above dir structure>/RH01/rh01.ini. If you scroll down to the bottom you'll see a section that looks like this:
[Object
nickname = Rh01_to_Bw05_hole
ids_name = 260721
pos = 28710, 0, 21099
rotate = 0, -155, 0
Archetype = jumphole
msg_id_prefix = gcs_refer_system_Bw05
ids_info = 60212
jump_effect = jump_effect_hole
visit = 128
goto = Bw05, Bw05_to_Rh01_hole, gate_tunnel_bretonia
If you change the "visit = 128" to "visit = 0" then the jumphole will at least show up on your map with the right label, however I still get "Access Denied" when trying to dock with it. I've tried changing the ids with no success (that just changed to a different jumphole which STILL said "Access Denied" and commenting out the subsequent [zone sections beneath that [object.
If anyone has any more info on how to activate the jumpgates in MP, please let me know!
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Oh, and commenting out the locked gates in the initialworld.ini doesn't really seem to help, though I did it anyway. Pretty sure that only affects single player.