Xcode 8 - Missing Files warnings

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.

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"

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.

I solve the problem simply by this:

1. Add the culprit to the project

2. Remove the reference

This cleans the internal state of XCode and the message goes away.