tools/counter: Makefile: Remove lingering 'include' directories on make clean

`make` creates 'include' directories where necessary, so remove them as
appropriate on `make clean`.

Signed-off-by: Rong Tao <rongtao@cestc.cn>
Link: https://lore.kernel.org/r/tencent_F85E314661100B0CE2845EB27E2E2F558C09@qq.com/


Signed-off-by: William Breathitt Gray <william.gray@linaro.org>