Quote: "Just seems to me that everything should be contained in one project folder, instead of scripts here, map there, etc."
That is how the engine itself is coded. Scripts need to be in the scriptbank folder, segments in the segments folder, maps in the mapbank folder. Otherwise you will have nothing but issues and frustrations.
As I mentioned before, test games only use the "gamebank\mygame" folder and the fpi files that are in there (gameover, gamewon, setuplevel, titlepage, loadingpage). When you build, it will use either the folder that corresponds from your project name or default to the "mygame" file and therefore use the fpi files in whichever folder it uses. So all the developer (you) have to do is keep track of where you put your huds, having the correct path in scripts that use huds, saving map(s) in the mapbank folder, and what game project folder to use. Everything else is pretty much in the proper place.

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