kbuild: pkg: clean up package files/dirs from the top Makefile

I am not a big fan of the $(objtree)/ hack for clean-files/clean-dirs.

These are created in the top of $(objtree), so let's clean them up
from the top Makefile.

Signed-off-by: Masahiro Yamada <yamada.masahiro@socionext.com>