added code to generate elements for paper figures
extra scripts for Figure 5
Removed intro from top-level, added opening paragraph
Moved tutorial links to "useful references" page
Removed "rules primer" and "about" from top-level TOC
Began complete re-write of installation instructions
wrote more core docs and removed Monomer.sites_dict
added sympy requirement for doc build
ignore .vagrant file in vm dir
improved docs for installation instructions
Changed changed header tagline in docs
fixed loss-of-precision issue in util.write_params
catch ImportError when testing inline in integrate.py

Saw ImportError on a Windows system (not sure what caused it).
added miriam annotation output to sbml export
added copy of earm estimate_lopez_embedded.py as fig6 script
updated fig6 script to produce proper plots
added numpy to doc requirements
calculate bng path on demand instead of module load
added sympy to doc requirements
mocked scipy in sphinx environment for RTD