Improve documentation

[olivroy]

• Take advantage of roxygen markdown support
• Update links
• Generate package docs with roxygen2.
• Add @keywords internal, so that the functions that are not user-facing do not appear in the function index on the pkgdown site (nor in R help system), but still exported. copy from roxygen2 docs: There’s one exception: @keywords internal. It’s useful because it removes the function from the documentation index; it’s useful for functions aimed primarily at other developers, not typical users of the package.
• Fixup the defunct docs
• Have ?sf point to st_sf() rather than the package docs.
• Fixup aliases: they should be separated by spaces, not commas (there still may be some problems of duplicate aliases?)
• Update @name vs @rdname Reference roxygen2 (generally, @name should be used to override the default name of the man page, and @rdame should be used to document other things in the same man page.

I recommend you look primarly at the diff of Rd files, as it will be more telling of the impacts of the changes.

[edzer]

Great clean-up, thanks!