I'm a 100% behind the idea of sandboxing, one of my apps in the Mac App Store already comes with sandboxing enabled even though it's not required yet, but I feel like the current way to do it can be very limiting. Some perfectly legit applications would be inherently broken with no easy way to fix them. Heck, even Xcode would be broken as you only open the project file directly, how could you edit the source files in the project individually without opening them one by one?

The only way I can think of is having the whole project, including the source files in a single bundle but that would break everything currently out there.