Oral and skin plot fixes

Pull request addresses the following issues:
* Makes pie charts of most abundant taxa
* Calculates most abundant taxa from the whole table
* Handles a number of bugs in generate_otu_signifigance, make_pie_charts, and make_phyla_plots.
* Includes basic metadata information in latex macro

Based on updates refined in *formatting-updates*.

I think I fixed all conflicts with upstream master.