userGuide vignette

 - increase level of all headings
 - add two example figures
 - replace javascript/d3 code in default chartOpts with R code
userGuide: explain file argument, and charts within Rmd docs
userGuide: fix dup chunk label
userGuide: link to Rmarkdown vignette on web
Split of detailed chartOpts as separate vignette
Clean up Makefile
userGuide vignette: Clean up the beginning