Xcode 8 - Missing Files warnings

If you don't use Xcode source control but some other git client (like source tree or terminal), you can disable source control in Xcode and then the warnings will disappear.

Xcode > Preferences > Source control and uncheck "Enable source control"

This is just an Xcode bug. If you delete or rename a file without then doing a commit, Xcode sees the discrepancy between the previous git commit and the current state of things and reports these warnings. They go away as soon as you do a git add that includes the file deletion / rename.