The .txt file just contains the game code for what projects are under what category and their various effects and the appropriate references to log entries etc. It should be fairly flexible - but I don't think without hard-code changes and extra UI stuffs if you can get it to do direct user-chosen targets. I'm not sure though if I should post the uncompiled versions at this time.
I think SJ's points on the directed versus random intel were pretty valid. Perhaps in a future patch, directed projects could be added in at higher cost.