Managing changes to configure.in as patches

[Jérôme Marant <jmarant@free.fr>]

Hi,

I'm trying to find a good way to manage changes to configure.in
as patches.
Until now, running aclocal, autoconf and others from debian/rules
was considered as a bad practice. So, people run them manualy out
of the debian packaging.

However, doing like this is annoying especialy when changes to
configure.in go with some changes to source files: I'd like to
keep everything in a single (d)patch.
Currently, I can see no other way than running autotools from
debian/rules.

Is there any other way to achieve this?

Thanks in advance.

-- 
Jérôme Marant