CHanged wildcard to asterisk throughout.
Merge branch 'master' of http://github.com/SimonGoring/neotoma_paper
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
Editing the README.  Minor conflict resolved by accepting changes from main repo.

Merge branch 'master' of http://github.com/SimonGoring/neotoma_paper

Conflicts:
	Neotoma_paper.Rmd