When integrating the Pods into your project, CocoaPods generates libraries that cannot be easily modified from Xcode. If you're having CocoaPods build frameworks, instead, those cannot be modified at all. You usually have to rerun pod install
or pod update
to let CocoaPods regenerate them if you add files to a Pod.
If you want to reliably add files to a Pod, you should checkout a copy on your machine, somewhere NOT in you project's folder and use something like the following to tell CocoaPods that that one Pod is one you're developing and therefore should integrate differently:
pod MyPod, :path => 'path/to/MyPod.podspec'
Still, even in this case, if you add files to the Pod, although it's easier to add them from Xcode, you might want to rerun the pod command line tool to have CocoaPods reintegrate your pod. However, in this case, you'll only have to make sure your files are added to the right project target in order to add files directly from Xcode.