news about the Rscript engine http://stackoverflow.com/q/15271406/559676
the `output` argument in process_file() is unused
child documents just return the compiled string; no longer write files for them

this should also solve the problem http://stackoverflow.com/q/15352935/559676
bin/knit no longer uses the --pdf argument
recompile all examples; changes are mainly due to the T1 encoding in my LyX preferences

the bib is also updated
roxygenize
bump version