Removing obsolete data files, adding documentation for shock generation, tweak to output warning in R script.

change Shock system

Fixes to create shock script and change to createScenario script to take end year as an arguement when implementing shocks.

delete ... file

to take different ssp files as input

Fix for land allocation error in allocAreas method. Unprotected natural area was being calculated on more that one occasion within a timestep resulting in changing proportions of 'other natural' and 'forest' that should be protected. Area(s) of natural land that should be protected now updated at the start of each timestep and remain constant throughout the timestep.