Some of the templates settings available for Markdown builds are:

Field

Description

Clean output directory

Optionally clean the output directory before generation starts. Warning: this will delete any file and folder in the output directory.

Generate compact Markdown

Generated Markdown is more compact, but less readable.

Line width

Preferred number of characters per line before wrapping. Purely cosmetic effect.

Use Setext-style headings

If enabled, headings are underlined. If not, atx-style headings with leading hash marks (#) is used.

See also: GitHub wiki Markdown documentation settings 

See the How to define build settings in HelpNDoc step-by-step guide.