Ever since upgrading to Xcode 8 using Swift 2.3 I have several missing files warnings. They are all related to pods that I am using.
The files that are missing are
I tried all of these (and many others) but none of them worked. After hours of trying various fixes, I found that the following procedure worked.
cd "project directory" git add .
You will need to close XCode and reopen or future Commits may fail.
Hope this helps someone.