Thanks @Dug for the hint of the build phase. I ended up going in a different direction than deleting ...
After checking the assembly phases - compile the sources, find the files that are grayed out (currently they do not have a link to the actual file) to determine the files in question.
If the files are still in use, find them in the Project Navigator (left column) and you will see that they are colored red because Xcode has only a link, not a location for the actual file.
Select each red file, and then go to the file inspector (right column). You will see "Location". Find the files by clicking on the gray folder and finding them in the file structure outside of Xcode.
If you are working with a repo, it may be easier for you to simply delete the red files, choose File> Add Files To ... and just add them so that the link is more general and does not point directly to the location of your machine file.
This happened to me after merging the project file, in which I was forked for a long time from the main repo, so several places in the files were lost in the merger.
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