41537a770b46f2376e74af58ba4885749339e81e erroneously stripped the
top_builddir off the per-directory flag setting which works fine for
in-tree builds but is not correct for O=
Just use the full path of the target files to apply the flags to fix
that thinko.
Signed-off-by: Bernhard Reutner-Fischer <rep.dot.nop@gmail.com>