getopt and commandArgs examples, and AF/OR update to use getopt()

scripts/commandArgs-example.r

@@ -0,0 +1,9 @@
+#!/usr/bin/env Rscript
+print('R Argument Test')
+
+cmd <- paste(commandArgs(), collapse=" ")
+cat("How R was invoked:\n");
+cat(cmd, "\n")
+
+args <- commandArgs(trailingOnly = TRUE)
+cat(c('Command Line Arguments supplied: ', args))