/etc/my-cnf file get overwritten during RPM installation in 5.5.
Old file is saved as /etc/my.cnf.rpmsave
Other distributions (mageia, fedora, Oracle MySQL RPMs) do not change user's /etc/my.cnf. Looking into other distro's RPMs gives the clue -
/etc/my.cnf is installed with atributes %config(noreplace), while our installation is has just %config attribute.