Doxia is a content generation framework, supporting a variety of markup languages, MarkdownPapers provides a doxia module that enables writing content in markdown format.
Write all your docs in src/site/markdown/ with md as file extension, then configure your maven-site-plugin and include markdownpapers-doxia-module as dependency.
Take a look at the site source code.
...
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.0-beta-3</version>
<configuration>
<reportPlugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>2.2</version>
<configuration>
<dependencyDetailsEnabled>false</dependencyDetailsEnabled>
<dependencyLocationsEnabled>false</dependencyLocationsEnabled>
</configuration>
<reports>
<report>license</report>
<report>project-team</report>
</reports>
</plugin>
</reportPlugins>
</configuration>
<dependencies>
<dependency>
<groupId>org.tautua.markdownpapers</groupId>
<artifactId>markdownpapers-doxia-module</artifactId>
<version>${use latest}</version>
</dependency>
</dependencies>
</plugin>
...