Improve structure/formatting of help output

[josh-berry]

A few things I'd like to do to the output of --help to make it more readable (not sure if this should be one or multiple tickets):

• Wrap output according to the user's terminal width
• Re-order and clearly group output so it's: basic usage, long description, required flags, optional flags, generic/common flags
• Properly-format Markdown output, and use the fancy new hyperlink extension that is supported by most modern terminals to link back to the web documentation

[dandavison]

From #649: we could consider using the one-line summaries (text after ###) as the first sentence of the --help description of the command.