removing the old R code from the v2 branch
making structural changes to the input files for re-run
placed IHS tables in the new ETC folder
added the contract-y thing from Martin so that we dont lose that.
issues in the conversion to shapefile due to the MultiPolygon shores layer section not being commented out.  Cleaned up for now and script is successful.
adding the new codebase to github.
removed some unneeded files and now have only what was used in Version 3 of the run.