Many, many changes

On branch master
 Changes to be committed:
	new file:   README.html
	modified:   README.md
	new file:   README.pdf
	new file:   data/H5N1_latlong.txt
	new file:   images/beast.png
	deleted:    images/beast_geo.png
	deleted:    images/beast_skyline.png
	modified:   images/beauti_clocks.png
	new file:   images/beauti_clocks_geo.png
	new file:   images/beauti_import_traits.png
	modified:   images/beauti_mcmc.png
	new file:   images/beauti_mcmc_geo.png
	deleted:    images/beauti_mcmc_logistic.png
	modified:   images/beauti_operators.png
	modified:   images/beauti_partitions.png
	modified:   images/beauti_priors.png
	deleted:    images/beauti_priors_exp.png
	new file:   images/beauti_priors_geo.png
	deleted:    images/beauti_priors_logistic.png
	deleted:    images/beauti_priors_uniform.png
	modified:   images/beauti_sites.png
	modified:   images/beauti_sites_geo.png
	modified:   images/beauti_states_geo.png
	modified:   images/beauti_tips.png
	modified:   images/beauti_tips_guess_dates.png
	modified:   images/beauti_traits.png
	deleted:    images/beauti_traits_create.png
	deleted:    images/beauti_traits_guess.png
	deleted:    images/beauti_trees.png
	deleted:    images/beauti_trees_logistic.png
	deleted:    images/beauti_trees_skyline.png
	new file:   images/beauti_trees_skyride.png
	deleted:    images/figtree_colours.png
	modified:   images/figtree_geo.png
	new file:   images/figtree_mcc_orig.png
	new file:   images/figtree_mcc_reordered.png
	deleted:    images/figtree_skyline.png
	modified:   images/google_earth.png
	deleted:    images/logistic_n0.png
	deleted:    images/logistic_rate.png
	deleted:    images/logistic_t50.png
	new file:   images/phylowood.png
	deleted:    images/tracer_logistic_dialog.png
	deleted:    images/tracer_logistic_history.png
	new file:   images/tracer_logpopsize.png
	modified:   images/tracer_posterior.png
	deleted:    images/tracer_skyline_dialog.png
	deleted:    images/tracer_skyline_history.png
	new file:   images/tracer_skyride_dialog.png
	new file:   images/tracer_skyride_history.png
	new file:   images/treeannotator.png
	deleted:    images/treeannotator_skyline.png
	deleted:    output/pandemic_geo.kml
	deleted:    output/pandemic_geo.log
	deleted:    output/pandemic_geo.mcc
	deleted:    output/pandemic_geo.rates
	deleted:    output/pandemic_geo.root
	deleted:    output/pandemic_geo.trees
	deleted:    output/pandemic_logistic.log
	deleted:    output/pandemic_logistic.trees
	deleted:    output/pandemic_skyline.log
	deleted:    output/pandemic_skyline.mcc
	deleted:    output/pandemic_skyline.trees
	new file:   scripts/beast-to-nhx-phylowood-discrete-location.rb
	new file:   scripts/example_command_line.txt
	new file:   scripts/rootstate.R
	deleted:    xml/pandemic_geo.xml
	deleted:    xml/pandemic_logistic.xml
	deleted:    xml/pandemic_skyline.xml