From this point I will use `integration` instead of `qt eclipse integration`.

I like edit PRO-file manually - without GUI (especially GUI was removed in latest version of integration). When PRO-file edited I save it! But when I add new files to project integration suggest to add file to PRO-file. If I allow integration add these files automatically then integration restores my PRO-files and removes all my manually added modifications - so sad! Now I have to cancel integration's suggests and add new files manually to keep safe my work!