How do I add 'non-project' files to the project?

I have a project with a structure roughly like this:

base
|---MyApp
|------MyApp.xcodeproj
|------Classes
|---------MyAppObject.m
|---Shared
|------Classes
|---------SharedObject.m

My xcode project file includes both MyAppObject.m and SharedObject.m in build targets, an in my regular workflow I could be modifying shared classes as well as the classes specific to my project.

My problem is that everything under Shared is treated by AppCode as a 'non-project' file (the tab is yellow, and Find Usages (for example) doesn't look in those classes. I've hunted around and can't find a way (like I can in IDEA) to modify the project directories in any way.

I'm running the beta that came out the other day.