Update package metadata for `pkgdown` website

[jasonratcliff]

General updates to R package configuration files used by pkgdown to build a package website.

• DESCRIPTION

  • Add Collate field to control source ordering for R6 class inheritance

    • Set by @include tag

• NAMESPACE

  • Initial commit for currently exported functions

• man/*.Rd

  • Roxygen-generated package documentation files

[jasonratcliff]

Gitpod prebuild error triggered by extra Collate field generated from local file R/literature.R:

Error installing package 'thesis':
==================================

* installing *source* package ‘thesis’ ...
** using staged installation
** R
Error in .install_package_code_files(".", instdir) : 
files in 'Collate' field missing from '/workspace/thesis/R':
  literature.R
ERROR: unable to collate and parse R files for package ‘thesis’
* removing ‘/workspace/thesis/renv/staging/1/thesis’
Error: install of package 'thesis' failed [error code 1]
Traceback (most recent calls last):
11: renv::install(".")
10: renv_install_impl(records)
 9: renv_install_staged(records)
 8: renv_install_default(records)
 7: handler(package, renv_install_package(record))
 6: renv_install_package(record)
 5: withCallingHandlers(renv_install_package_impl(record), error = function(e) {
        vwritef("\tFAILED")
        writef(e$output)
    })
 4: renv_install_package_impl(record)
 3: r_cmd_install(package, path)
 2: r_exec_error(package, output, "install", status)
 1: stop(error)
Execution halted
exit