Fix several reference errors throughout the documentation and set
``nitpick_ignore`` in ``doc/conf.py``.

Make --jobs a synonym for -j

Add the missing default arguments to two CLI flags, ``-l`` and ``-d``

Co-authored-by: Adam Turner <9087854+aa-turner@users.noreply.github.com>

Using "console" language is better for the console example (including
command-line prompt)

The moved sentence clearly belongs to the discussion of the builders.

To describe the purpose more accurately, the `master_doc` is now renamed
to `root_doc`.  The old name is still available.  But it is recommeneded
to use new one from now on.