The fodler hierarchy you see in the project manager, starts from the common top-level path of all the project files. So, when you added something from ../Common, it is now part of the equation and the common top-level path would be 'stuff'. In other words, this is the designed behaviour.
About the compiler error you 're getting, it has nothing to do with the project's layout on disk. At least it shouldn't.
Please enable full build logging (Settings->Compiler->Other) and post the build log here to see what's wrong.