+++ niczero [Apr 29 12 06:49 ]:
>    It would be very useful if there was a --qualified_auto_links that made
>    all
>    auto links be qualified with their chapter ref.
>    Currently
>    # Foo
>    ## Bar
>    means the subheading gets an auto link of "bar", but I'd like the
>    option
>    of having it as "foo_bar" so it's not impacted by the possibility of
>    another chapter having a (sub)heading of 'Bar'.

Pandoc won't produce duplicate identifiers.  If you have two
sections named "Bar", the first will get the id "bar", and the
second will get "bar-1", etc. See the README section on header
identifiers.

Also see the --id-prefix option.

John