kbuild: fix directory traversal bug

Previously kbuild choked over the following:
obj-y += ../../../arch/i386/kernel/bootflag.o

This has resulted in some rather ugly workarounds in
current x86_64 tree.
This patch fixes kbuild to allow the above and enable
potential cleanups in x86_64 and maybe in other places.

Signed-off-by: Sam Ravnborg <sam@ravnborg.org>