Basic support for titles within tool help

Basic support for titles within tool help

Preserve reStructuredText title formatting within tool help texts when
printing to console.  For now, manual care is needed to properly nest
the sections in the rst help export (which means that the first
subsection needs to use an underline of ^'s).  This allows removal of
all remaining [BR] tags, improving the HTML help.

Remove extra indentation from gmx wham bullet lists; they result in
unnecessary indentation in the HTML output that looks bad.

Fix formatting of the known issues bullet list by just using the
existing formatting engine, now that bullet lists are properly
supported.

Change-Id: I38a4f442f590515dde724c0cf60f0a862dc9cde7