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Previously we used Setext (underlined) headings by default.
The default is now ATX (`##` style).
* Add the `--markdown-headings=atx|setext` option.
* Deprecate `--atx-headers`.
* Add constructor 'ATXHeadingInLHS` constructor to `LogMessage` [API change].
* Support `markdown-headings` in defaults files.
* Document new options in MANUAL.
Closes #6662.
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This addresses a subsidiary issue in #3674.
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with `--reference-links` and `--reference-location=section`.
Also ensure that there are no empty link references `[]`.
Closes #3674.
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