clean up a little bit after #749

note sapply() is which(sapply()) now
replace the old LyX/Rnw vignettes with new R Markdown vignettes

knitr-refcard.lyx is only used as a pandoc template now; run `make vignettes` to create the template
tweak the Makefile; I'm free to check my vignettes now because I no longer have to rely on LaTeX
if .knitEnv$meta is an empty list(), which(list()) will signal an error
more explanation for package developers, per suggestion of JJ
bump version