There are one or two ways of going about this,but mostly I'm going to concentrate on the default java ways.
Actual answer - Use JPackage. JLink is just the image of a runtime. JPackage is your distributable
Support for native packaging formats to give the end user a more natural installation experience. Specifically, the tool will support the following formats:
Windows: msi, exe
macOS: pkg, app in a dmg (drag the app into the Applications directory)
Linux: deb, rpm
The application will be installed in the typical default directory for each platform unless the end-user specifies an alternate directory during the installation process (for example, on Linux the default directory will be /opt).
The ability to specify JDK and application arguments at packaging time that will be used when launching the application
The ability to package applications in ways that integrate into the native platform, for example:
Setting file associations to allow launching an application when a file with an associated suffix is opened
Launching from a platform-specific menu group, such as Start menu items on Windows
Option to specify update rules for installable packages (such as in rpm/deb)
1) - Specify an @Args file
You can make an @args file that you can deploy (bundled) with your jlink app, and reference it when starting the application
java @args -m module/main
2) Use the new environment variable
JDK_JAVA_OPTIONS=--add-opens java.base/java.lang=...... -Xmx1G -Djdk.logging.provider=
https://docs.oracle.com/javase/9/tools/java.htm#JSWOR624
3) Use the JLink/JMod to specify main class in module
https://maven.apache.org/plugins/maven-jmod-plugin/plugin-info.html
<plugin>
<artifactId>maven-jmod-plugin</artifactId>
<version>3.0.0-alpha-1</version>
<extensions>true</extensions>
<configuration>
<module>
<mainClass>mainClass</mainClass>
</configuration>
</plugin>
4) Use JLink to create a custom launcher/Edit JDK_VM_OPTIONS
<plugin>
<artifactId>maven-jlink-plugin</artifactId>
<version>3.0.0-alpha-2-SNAPSHOT</version>
<extensions>true</extensions>
<configuration>
<noHeaderFiles>true</noHeaderFiles>
<noManPages>true</noManPages>
<stripDebug>true</stripDebug>
<verbose>true</verbose>
<compress>2</compress>
<launcher>customjrelauncher=module/mainClass</launcher>
</configuration>
<dependencies>
<dependency>
<groupId>org.ow2.asm</groupId>
<artifactId>asm</artifactId>
<version>${maven.asm.version}</version>
</dependency>
</dependencies>
</plugin>
In the generated .sh/.bat there is a variable to specify any custom addon's
You can also specify the main class descriptor in your module-info using moditect if you are using it:
<plugin>
<groupId>org.moditect</groupId>
<artifactId>moditect-maven-plugin</artifactId>
<executions>
<execution>
<id>add-module-infos</id>
<phase>package</phase>
<goals>
<goal>add-module-info</goal>
</goals>
<configuration>
<overwriteExistingFiles>true</overwriteExistingFiles>
<module>
<mainClass>mainClassLocation</mainClass>
</module>
</configuration>
</execution>
</executions>
</plugin>