Not crazy about the way Xcode 4.2 has laid out the files on disk. It creates a project file, then a single subfolder next to it that has all the code. We want the project file to be in that same folder, then the workspace file (if any) to be the folder’s sibling. Makes for more portable layouts.
However, I can’t STAND the lack of Save-as in Lion, and now, apparently Xcode 4.2 as well. At least with TextEdit I just grabbed the version from SL and it works. No such luck with Xcode as as you know, it’s a completely different animal than Xcode 3.x.
So… how does one move/rename the project file relative to the source code?
Here is how you do it (I’m using in Xcode 4.3):
First, move your project file
1. Start out by closing the Xcode project
1. Move ProjectName.xcodeproj into the folder with all your code
1. Open the XCode project by clicking ProjectName.xcodeproj
Second, re-map your files
1. You do not need to remap the files one by one, you only need to map the groups
1. Open the “File Inspector” with ⌥⌘1 or
View->Utilities->Show File Inspector1. Click each group, then click the square icon (see screenshot below) and choose the folder your project file is in.
Icon to click:

“None” will show up when you choose the same folder your .xcodeproj file is in.
Conclusion:
I have a large project which contains ~650 files, but only 12 groups, so it takes just a few minutes to re-map everything.
Note:
Sometimes when mapping the files it doesn’t recognize a folder change if the name is the same (ie. two folders with the same name). You may have to pick any other folder temporarily, then choose the actual project folder and the None indicator will appear.