Updates to the generated documentation sources

[UncleGrumpy]

Various updates and corrections top the published documentation. Some improvements have been made to the rendering of the documentation, including language highlighting, styled notes, and formatting fixes to make wide text blocks fit in the display. Links have been added for most function and module APIs when they are referenced in the guides. Note, these links will not be enabled until #1037 is merged. They rely on myst_heading_anchors = 5

closes #1008

These changes are made under both the "Apache 2.0" and the "GNU Lesser General Public License 2.1 or later" license terms (dual license).

SPDX-License-Identifier: Apache-2.0 OR LGPL-2.1-or-later