autotools_rework

The purpose of this branch is to make changes to the autotools files,
particularly configure.ac. This will remove a lot of old cruft and update
the input files. This effort was started in January 2015 and should be
completed within the year.

This branch tracks the trunk.

Dana Robinson and Allen Byrne are the owners of this branch.

This branch should be closed when the bulk of the autotools work is
complete and has been merged into the trunk and 1.8 branch. This
work should be completed by mid-2015.