I've made a map (gee, what else is new?) and was testing it with bots. I happened to look at the map .cfg file and noticed that there was no .wpt file with it, just the .ogz file. I completely closed the game and opened it again and went to my map. I used /loadwaypoints and the game message read "loaded 1412 waypoints from packages/base/gulley.wpt". Bots can use the waypoints I loaded. However, I looked again and still could not find the gulley.wpt file. I did a whole computer search and found the file, but could not find where it had been. I copied the .wpt file into the packages/base folder and can now find it there.
While I managed to solve this problem, I want to ask if anyone knows why this happened?
[this occurred on a completely unmodded copy of Sauerbraten: Collect edition]