Clean up top level configure part 1

Hi guys,

the patch in attachment is purely cosmetic. I switched the top level configure to use perl -w rather than just perl and spotted a bunch of warnings.

This patch:

- switches permanently to perl -w
- fixes all the warnings in the script.

Part1 because I plan to re-rewrite the top level configure from scratch by using the only known thing in every system (that being /bin/sh) and make path to perl configurable (not all system use /usr/bin/perl).
I also plan to kill the need of make/defines.mk.input and create make/define.mk directly.

use Usual::ACK::Apply::disclaimer

Cheers
Fabio

I'm going to make him an offer he can't refuse.
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You missed one:

Patrick
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