The warning will disappear as soon as you commit your changes (Xcode 8).
It seems that this problem may have different causes, but it's often in relation with source control software.
In my case, I solved it by going to Git, and adding the files again. I mean running the following command:
git add .
You can also disable source control by unchecking
Xcode -> Preferences -> Source Control -> Enable Source Control
if you're managing it via command line or any other app.