I use a reverse logic for publishing, you might know, becaiuse I mentioned it earlier. I use a projectname.wdl containing several PATH statements, mainly because of wmb levels, but in project code I also create and use full relative path+filenames, which is fine for my custom dynamic level loading, and allows similar file names.
After publishing I simply copy the exe and dll-s to project root folder, and delete the CD folder. This way the development structure is kept, the game root folder is clean.