CHanged wildcard to asterisk throughout.
Merge branch 'master' of http://github.com/SimonGoring/neotoma_paper
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
Revert "Minor change to the "Other" description in discussion compile_taxa.  Re-rendered following changes to bib file & minor text edits.  This Rmd and docx is the submitted version.  The PDF reflects the unedited knit."

This reverts commit 1ff7634a15656e8211e0dce82a743aae4ef8b8ce.
Cherry picked commit that was removed #34
Revert "Minor change to the "Other" description in discussion compile_taxa.  Re-rendered following changes to bib file & minor text edits.  This Rmd and docx is the submitted version.  The PDF reflects the unedited knit."

This reverts commit 1ff7634a15656e8211e0dce82a743aae4ef8b8ce.
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