Thanks, I went for dh_auto_clean option.
Here is the explicit answer
https://lists.debian.org/debian-science/2015/05/msg00078.html which is
better for a newbie.

What about (explicit) instructions how to push the package to
http://anonscm.debian.org/cgit/debian-science/packages/gpaw.git
asked at https://lists.debian.org/debian-science/2015/05/msg00079.html?
Or does this question is specific to debian science and I should wait for
their answer?

Marcin

On Sun, May 31, 2015 at 10:57 PM, gregor herrmann <gre...@debian.org> wrote:

> On Sun, 31 May 2015 22:54:58 +0500, Andrey Rahmatullin wrote:
>
> > On Sun, May 31, 2015 at 05:03:29PM +0200, Marcin Dulak wrote:
>
> > > It looks to me like the configuration.log file, which is written during
> > > compilation of gpaw
> > > is treated as a source modification. How should I handle this?
> > You need to removed it in the clean step. With dh(1) it can be done by
> > overriding dh_auto_clean.
>
> Or (matter of taste) by adding the configuration.log to debian/clean.
>
>
> Cheers,
> gregor
>
> --
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