Update PaperFigures.Rmd to use current recommended API

[lwaldron]

e.g. should use curatedMetagenomicData() function instead of eh <- ExperimentHub() and query(eh, "curatedMetagenomicData"). Look for other anachronisms.

[lwaldron]

I still think it's worth updating to use the current API, which will make it easier to update the examples to new versions, more datasets, etc, and also will encourage people to use the recommended method of accessing datasets. I don't think this is a big job :)

[lwaldron]

Significant analyses beyond package documentation are being moved to another repository. Closing and replacing with issue waldronlab/curatedMetagenomicDataAnalyses#1 (rather than transferring, to leave record of the transition)