I have a very large project that currently has all the source code files in a flat directory structure (eg: MyApp/Classes/*). The project structure in Xcode however, is quite complex with thousands of files in nested subfolders. Is there a simple way to update the filesystem to match Xcode 9 now? I have red folders all over the place now due to the new changes...
Updating filesystem to match Xcode 9 folder structure
You don't need to move the files. If you select a group (yellow folder icon in Xcode), and show the file inspector (Command-0), you should see a small button just below the "Location" popup that breaks the connection between the group and an actual (though missing in your case) folder. Multiple selection doesn't seem to work for this, so you will need to do this for each group that's turned red. If you have a lot of groups, it will take a few minutes perhaps, but it shouldn't be more than a temporary annoyance.