Every time Apple upgrades Xcode, they change a bunch of stuff. The recent Xcode 4 update was a complete rewrite, including totally new project template and language syntax formats. Worse yet, Apple hasn't yet documented any of it. Effectively, they're turning Xcode into a Cocoa-only IDE, even if it technically still offers external build support.
Anyway, I've given up on Xcode entirely for anything but Mac/iOS programming, and moved over to TextMate, which is a great text editor that's a bit like emacs for the OS X gui. It's very customizable, so I spent some time this weekend building an Atari bundle and packaging that in with some VCS-specific build tools. The result is much easier, leaner, and more automated than it ever was in Xcode.
You can read more and download the installer here. Hope it'll be useful to some of you. Let me know if you have any problems, suggestions, etc.