kbuild: fix mismatch between .version and include/generated/compile.h

Since commit 56d58936 ("kbuild: do not create orphan built-in.a or
obj-y objects"), scripts/link-vmlinux.sh does nothing when descending
into init/.

Once the version number becomes out of sync between .version and
include/generated/compile.h, it is not self-healing.

[How to reproduce]

 $ echo 100 > .version
 $ make

You will see the number in the .version is always bigger than that in
compile.h by one. After this, every time you run 'make', the vmlinux is
re-linked even when none of source files is updated.

Fixes: 56d58936 ("kbuild: do not create orphan built-in.a or obj-y objects")
Signed-off-by: Masahiro Yamada <masahiroy@kernel.org>