Promote envir to named argument in kint2html

Added an explicit named argument envir to the signature of knit2html
(after the ... argument) because calls to knit2html from knit_rd
sepecified an envir argument which was being passed to
markdown::markdonwToHTML (via ...) which does not have that argument
and it was not being passed to kint which is where it was supposed to go.
Merge pull request #489 from BrianDiggs/knitr-rd-envir

Promote envir to named argument in kint2html
Add envir as a parameter to knit2pdf
Merge pull request #490 from viking/knit2pdf-envir

Add envir as parameter to knit2pdf
when caching the package names, exclude the base packages, so don't need to do it when loading packages

note setdiff() does unique() automatically
use writeLines() instead of cat(sep = '\n')
sort the package names before saving them to __packages
Frank's name should be 'Harrell, Jr, Frank E'
add @BrianDiggs for #489
knitr does not really need RTools; Windows users can install from source on RForge
duplicated -> duplicate
add Jeremy Stephens to contributors for #490
roxygenize
cosmetic (the envir argument has been added in #490, so close #491)
bump version
three convenience functions for filenames and extensions (just to save some typing efforts)
a pandoc wrapper; closes #206
roxygenize
adapt to Shiny 0.4 API
disable the progress bar