A lot of deleted files warning "is missing from working copy"

Did you try using Xcode's Product menu w/the option key pressed, selecting 'clean build folder'...?

I've tried Clean All, deleting Derived Data folder, quitting XCode, I still get these wanrings. The worst part is I'm now getting warnigns for files from other projects that have never been part of my current project.

Turns out that the warnings were from a project I hadn't worked on in nearly a year, that somehow was active in source control for my brand new project. I don't use the XCode built in source control, I use Github with terminal commands or the Github desktop app. Nothing I found would update XCode and I couldn't figure out how to break the connection to the older project so I just turned off source control within XCode and the warnings are gone.

I use SourceTree as my UI for my Git repository. If I stage all unstaged files the warnings disappear.

After cleaning the build area, if you are using git, you might have to right mouse button on the offended files and Source Control->Commit each one and push it to your server too just to make xcode feel all better.

it is confusing, but when using source control, after deleting files the deleted files have to be committed to the repository.

why you need to commit "deleted" files to the repository, i don't know.

in the git commit dialog Xcode presents, the deleted files are unchecked during the commit and identified by an exclamation mark thus not committed... of course they should be unchecked, i am not committing files to the repository: i am deleting them!!!!!!

but i suppose committing deleted files tells the repo they are deleted.