There are a couple of make scripts to facilitate building the documents. It is best to use
them, as they will ensure references are added correctly etc. To use them, make sure you 
are in the root directory of the project (the same directory as the file) and that
pdflatex and bibtex are in your $PATH, then:

	make manuscript	
	
Note that there is a .gitignore file for ignoring all the usual latex nuisance files. It
also includes an exception for any file with .local anywhere in the name. If you have any
files you want to keep in your working directory but don't want to include in the
repository, just include .local anywhere in the file name.

Finally, if you just want to build the PDF and don't care about references and figures,
then you can just use pdflatex manuscript from the tex/ directory.