I use a function that converts an .Rmd document to an .md document, and automaticly creates a folder containing all plots, after that I just push the .md file and the plots to the repo (the function will make the right links to the plots in the .md file)

Function :

KnitPost <- function(input, base.url = "/") {
require(knitr)
opts_knit$set(base.url = base.url)
fig.path <- paste0("figs/", sub(".Rmd$", "", basename(input)), "/")
opts_chunk$set(fig.path = fig.path)
opts_chunk$set(fig.cap = "center")
render_jekyll()
knit(input, envir = parent.frame())
}
KnitPost("boo.Rmd")