Man page documentation is incomplete

[sequoiatree]

Finish the man page documentation.

1. Finish the inline documentation in all the R files. (Some things, you may be able to simply copy and paste from the wiki.) In io.R make it clear that every file should have a tsv or csv extension as appropriate, because we use the extension to determine which readr function to use!
2. Do roxygen2::roxygenize().