I recently upgraded to Cordova 2.9.0 from 2.3.0. After following all the upgrade instructions, I was able to get the app to launch in the simulator. However, in Xcode I see
We opened the project in Xcode, and looked in the Project navigator sidebar.
Under the virtual "Plugins" folder we noticed that the files for some plugins were missing from this folder.
The solution was to right-click on Plugins and select Add Files to "ProjectName"...
Then we navigated into the plugin's folder and added all the .swift and .m and .h files there.
Doing this created new references in the file platforms/ios/[ProjectName].xcodeproj/project.pbxproj so we kept those changes.