This is pretty straightforward (and also completely untested, but afaik, one flag CTF is possible in JA).
All you have to do is add an additional team_ctf_neutralflag ent in your map, in addition to the two other flag ents. I'm shocked that I haven't seen any more maps that have this.
I R Scary Eyeball
16th October 2006
Interesting, I'm going to have to try this out!