#865 Need to get rid of autotools warnings

[Jack Jansen]

We get all sorts of auto tools warnings, about macros we shouldn't use, and having configure.in in stead of configure.ac, and all that stuff.

We should fix this before the release.

[Kees Blom]

configure.in has been renamed to configure.ac in rev.9025, merged in rev.9062,9067
Some warnings remain during autogen.sh (script uses old versions of some autotools)