Add folder notes

[shntnu]

Incorporates notes by @gwaygenomics

[gwaybio]

I added some minor updates, but this LGTM. I will go ahead and merge!

[gwaybio]

It looks like the Travis build failed:

$ Rscript -e 'deps <- remotes::dev_package_deps(dependencies = NA);remotes::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'
bookdown  (NA -> 5998ab4ef...) [GitHub]
base64enc (NA -> 0.1-3       ) [CRAN]
digest    (NA -> 0.6.18      ) [CRAN]
evaluate  (NA -> 0.13        ) [CRAN]
glue      (NA -> 1.3.1       ) [CRAN]
highr     (NA -> 0.8         ) [CRAN]
htmltools (NA -> 0.3.6       ) [CRAN]
jsonlite  (NA -> 1.6         ) [CRAN]
knitr     (NA -> 1.22        ) [CRAN]
magrittr  (NA -> 1.5         ) [CRAN]
markdown  (NA -> 0.9         ) [CRAN]
mime      (NA -> 0.6         ) [CRAN]
Rcpp      (NA -> 1.0.1       ) [CRAN]
rmarkdown (NA -> 1.12        ) [CRAN]
stringi   (NA -> 1.4.3       ) [CRAN]
stringr   (NA -> 1.4.0       ) [CRAN]
tinytex   (NA -> 0.12        ) [CRAN]
xfun      (NA -> 0.6         ) [CRAN]
yaml      (NA -> 2.2.0       ) [CRAN]
Error in utils::download.file(url, path, method = download_method(), quiet = quiet,  : 
  cannot open URL 'https://api.github.com/repos/rstudio/bookdown/commits/master?access_token=[secure]'
Calls: <Anonymous> ... remote_sha.github_remote -> github_commit -> download -> base_download
Execution halted
The command "Rscript -e 'deps <- remotes::dev_package_deps(dependencies = NA);remotes::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'" failed and exited with 1 during .

@shntnu have we seen this behavior in the past?

[gwaybio]

Wait, now it seems to have worked! Not really sure what happened