Fixed bib issues

@Simongoring
I fixed a few issues with the bib file. The ??? you see here:
"These findings basically echo those of Graham et al. (???) who showed that taxon response is largely individualistic."
is because that reference does not exist in Neotoma.bib. You just need to add it in.
Rendered output files

@Simongoring: Make sure these look ok.
Added a Makefile

From the command line, you can type make all to render the PDF and word documents. If nothing in `Neotoma_paper.Rmd` has changed, then it wont unnecessarily rerun things.

With some editors like Sublime Text, it will automatically detect the Makefile and set the build system so a command + B will build all 3 output files (md, docx and pdf)
Working through JWilliams' revisions.  Cleaning code to reflect recent changes to the `neotoma` package that helped clean up the code.

Also recompiled & re-pandoc'd
Added Grimm to bib file.
Text changes up until the Pinus section.  Added Word docs to an alternate directory and created a flag for the locked word docs (~$ files).  Most code changes reflect recent changes to `neotoma`.