As the question says, how to package a Netbeans Maven project exactly the way a Netbeans native project is packaged:
In your pom.xml file ...
1) Add this code to your project->properties node. This will define your main class in a central place for use in many plugins.
<properties>
<mainClass>project.Main.class</mainClass>
</properties>
2) Add this code to your project->build->plugins node. It will collect all your jar dependencies into a lib folder AND compile your main class jar with the proper classpath reference:
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<phase>install</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/lib</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>${mainClass}</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
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