leave makefile generation to the real configure

call it with the "secret" -top-level option, which shifts the makefile
generation one level up.

this makes the configure call the last thing we do, thus also avoiding
the problems we had with the -help switch (and the previous attempts at
fixing it).

Change-Id: I80ba4a09b260a140a9d1b976277c30fd1436b4d6
Reviewed-by: Thiago Macieira <thiago.macieira@intel.com>