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I'm confused, I thought that for ctf mode you just placed a flag in-game and then added the needed scripting. What do these lines do then?

-- spawn Holodisk
Holocron1Spawn = GetPathPoint("HolodiskSpawn", 0) --gets the path point
CreateEntity("pol_icon_disk", Holocron1Spawn, "pol_icon_disk") --spawns the disk

And more improtantly how do I get that to work?

you should have a path called "HolodiskSpawn", the code spawns the holodisk on it

Additionally, (correct me if I'm wrong, but I don't think I am) the path should have only one point.