Update files to pass cran checks
the new version of markdown (0.5.5) is on CRAN now

so you do not need to install it from Github; in the next version of `knitr`, I will depend on `markdown >= 0.5.5`, so `install.packages('knitr')` will solve the problem of dependencies
Merge branch 'patch-1' of git://github.com/yihui/knitrBootstrap into yihui-patch-1
Add markdown dependency

This can be removed once the new version of knitr is on cran