clean up check_chapters function and re-document for roxygen 2

I updated the documentation to be compatible with the newly-released version of roxygen. To update your local version of R, simply type `install.packages('roxygen')`.

The other major addition is a reformatting of `check_chapters` to avoid duplication in the error messages. Additionally, a use of `call. = FALSE` in the `stop(...)`s was suggested to avoid displaying unnecessary call stacks when the content of the error messages is self-evident.