I'm using Xcode 8. I recently inherited a project with several hundred files (including source and image files). I rearranged them on my local drive and the file names (appropriately) become red in the folder list on the left side of Xcode. I selected files/folders in this folder list, click on the "Hide or show Utilities" button to display the "Identity and Type" pane on the right side of Xcode, clicked on the little folder icon next to the Location, and selected the files'/folders' new locations. The text in that pane was updated to the new location and the file/folder names changed from red to black. So far, so good. I did this to all of the file/folder names until none of them were displayed in red.
However, when I go to build the project, I get numerous warning messages similar to, "image.png /Users/Me/Project/images/image.png is missing from working copy." The path shown in the error message is the file's OLD location. When I look at that image in the file list, it is displayed in black. When I select that file and look at the Full Path in the pane on the right, it shows the file's current location (e.g., "/Users/Me/Project/images/newfolder/image.png"). I'm unsure where in the project the old location is being stored. FWIW, I've tried Cleaning the project...
Thanks for insights.