Markdown

[corybrunson]

This PR contains several roxygen2-related changes, among them:

• a reorganization of the file structure (mostly splitting up long .R files into shorter ones) for more convenient editing and reviewing in future
• changes from TeX-based to Markdown-based syntax with some other judgment-based additions and changes to formatting
• clarification and coordination of @name (and @rdname) and @title tags
• combining of combinadic functions for user convenience
• introduction of @family tags for automatic "See also" linking
• introduction of templates for individual @reference tags and frequently-used @param tags for one-step documentation changes in future
• various clarifications in documentation

Note: I left sample.R unchanged to avoid conflicts with other changes in active and forthcoming PRs.

Finally: The one thing i thought might work but did not try was to change the documentation of simplex_tree to mimic the R6 documentation syntax.

Some of these are obviously outside the scope of "switching to Markdown roxygen2 syntax". I made them because the process of making the Markdown edits convinced me that they would make future edits easier to do and document. But of course everything here is negotiable!