Putting commands to build R in the main Makefile.

This doesn't work: after installing knitr with:

~~~
install.packages("knitr")
install.packages("markdown")
~~~

the command `make preview` produces:

~~~
~/lessons/r-novice-inflammation: make preview
pandoc -s -t html \
       --template=_layouts/page \
       --filter=tools/filters/blockquote2div.py \
       --filter=tools/filters/id4glossary.py \
       -Vheader="$(cat _includes/header.html)" -Vbanner="$(cat _includes/banner.html)" -Vfooter="$(cat _includes/footer.html)" -Vjavascript="$(cat _includes/javascript.html)" \
       -o 00-first-timers.html 00-first-timers.md
Rscript -e "knitr::knit('$(basename 01-starting-with-data.Rmd)', output = '$(basename 01-starting-with-data.md)')"

processing file: 01-starting-with-data.Rmd
  |.                                                                |   2%
  ordinary text without R code

  |..                                                               |   4%
label: unnamed-chunk-1 (with options)
List of 1
 $ include: logi FALSE

Quitting from lines 7-9 (01-starting-with-data.Rmd)
Error in file(filename, "r", encoding = encoding) :
  cannot open the connection
Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> source -> file

Execution halted
make: *** [01-starting-with-data.md] Error 1
~~~
Source chunk-options.R from its new location in subdirectory tools.
Merge pull request #1 from jdblischak/fix-build

Source chunk-options.R from its new location in subdirectory tools.
Merge branch 'gh-pages' into consolidating-makefile
Merge pull request #5 from gvwilson/consolidating-makefile

Putting commands to build R in the main Makefile.