first trance of tidying
delete the temp ggmap
remove the AD version of the .Rmd
remove the empty pdf
remove the now obsolete todo list
remove the temporary Rdata files
delete the un-used file
moved revision_notes to misc folder
clean up the Makefile
quotes in library call
remove Simon's R script to build the documents; this was mostly in the Makefile
figures should be in the figure folder; move the object diagram
move the flowchart to figure folder; update Rmd to use correct paths
remove the now-obsolete R code; this functionality is now in neotoma
Revert "delete the un-used file"

This reverts commit 23b332c989cc7078c72cd2aad1c897d4f083541c.
add a markdown option to the Makefile
add output metadata for markdown; indent
no longer need mrgins.sty; set margins in PDF directly via pandoc_args
make the long examples optional by loading a data snapshot
render MD, DOCX and PDF versions of the file