apt-get remove app.. has always worked in linux env. and has always cleaned the files that has been changed on installed.. apt-get is a STRONG tool and keeps track on what is installed and where.. sure dont mess with init and such thing they do indeed mess up the system if you dont know what your doing .. but hey linux is a great thing and its ment to be meessed up some times .. think of it that its a great way to clean up your system LOL