Add cross-references from env variables doc to CLI options doc (for issue #171)

This pull request adds (and does a little clean up of) documentation cross-references from the `env` variables to their respective command-line options. This satisfies a promise made in the introductory text, and I think it resolves #171.

(On a related note, I encountered and fixed several grammatical and formatting errors in this doc while adding the cross-references, but it seemed inappropriate to include those changes in this pull request. What is the preferred level of granularity—in commits and PRs—for submitting such changes?)