AFAIK CZero does a variation on this:
http://www.gamasutra.com/features/20020405/smith_01.htm
(and have a look into the HL2 SDK)
AAS parses the Level BSP File and creates a simplified BSP for itself.
Both don't use waypoints for navigation though.
I've posted some other links previously.
There are at least 3 ways to auto-waypoint a map
- Parsing the Map File
- Recording Player movements
- Analysing the map in the game
Do whatever you prefer...
Btw. I don't need to remind you who started the Podbot craze, do I ?