ccs-flatten/Makefile: distinguish {,deep}clean + fix mispaste

Signed-off-by: Jan Pokorný <jpokorny@redhat.com>
run-clean: new helper cleaning dirs as per .gitignore

...which itself got new convention: not-add, not-remove
files are below "# KEEP" mark.

Signed-off-by: Jan Pokorný <jpokorny@redhat.com>