introduce autotools deprecation warning

Description

As autotools will be deprecated in the future, we are now printing a warning (with user confirmation) at the end of the configure script. This warning can be disabled with the --enable-silent_deprecation flag.

News snippet

Deprecate autotools.

Checklist

• I have checked that my code follows the Octopus coding standards
• I have added tests for all the new features added in this request.