ok, so what your saying is that you have all the files packed that you want(before you publish). Once you have a file packed into the gsr before publish, remove that file srom your work folder and place it someplace safe in case you need it again( a backup folder). Then "publish" your game (or whatever you made) . During the "publish" process you will keep getting warnings about that file not being there just keep hitting the "I know it's not there button).
This is assuming that i understood you correctly. The thing is is that when you pack a file into the gsr the original file stays in the folder, and if it is there when you "publish" it will go into the .cd folder. Also what do you mean by includes? if you are talking about scripts, packing those is a mistake.
Also, how big is your project, and what edition do you run?