Make sure the indexes file matches what's in the project

Last build "failed" because it was waiting for user input on whether we should delete an index or not. Lets make sure that the indexes in the project match the file (it was asking if we wanted to delete an index from the project since it wasn't here in the file, but we should check to see if it's an old one that can be deleted, or a new one that needs to be added to the file).