v1.5.24 Replace .Rnw vignette with .Rmd

- A little formatting remaining for phyloseq-analysis vignette.
- phyloseq-basics.Rnw not removed or adapted yet.
v1.7.1 Migrated phyloseq-basics vignette to vignettes directory (unfinished)
basics Rmd builds, but needs some formatting fixes
1.7.1 All vignettes are now R-Markdown
v1.7.1 Final fixes to Rmd vignettes. All work. Pass all checks. Update installer.R as well.
Merge branch 'Rnw-to-Rmd-vignettes'