Jeff,
Mark the doc dir as derived (under Properties), then right click > MYEclipse > Remove all Validation errors, and clean/rebuild the project, that should have worked, if not, you need to mark each file as dervied. Setting this property tells any/all of the validators “leave it alone, regardless of it’s condition”. The remove validation markers step is necessary because you aren’t re-validating the file in order to remove the markers, so you need to do it manually.