added higher level nesting 'sites' and nested ecosystems within sites
Get input and output directories from commandline.
Change some variable names.
Merge branch 'master' of github.com:ebimodeling/ghgvcR

Conflicts:
	R/ghgvc.R
	src/ghgvc_script.R
auto-updated documentation
used new example multisite config file; finished nesting in ghgvc2 function