Limit modules added by javapackager

GabeV :

I am trying to reduce the size of my application by limiting the modules that it includes. I already did this for my runtime using jlink. However, when I run javapackager using the --add-modules and --limit-modules options with a comma-separated list of the same small set of modules I used for the runtime, it insists on adding all of the modules anyway. It doesn't seem to want to honor the option I'm giving it. How can I get the tool to limit the modules it adds to my app bundle?

"Adding modules: [java.base, java.desktop, java.naming, java.sql, java.xml, java.logging, 
    java.management, java.scripting, java.compiler, java.rmi, java.activation, jdk.charsets, jdk.xml.dom, 
    java.datatransfer, jdk.httpserver, javafx.base, java.security.sasl, jdk.zipfs, jdk.crypto.ec, 
    jdk.management.agent, java.sql.rowset, javafx.swing, jdk.jsobject, jdk.sctp, java.smartcardio, 
    jdk.unsupported, jdk.scripting.nashorn, java.security.jgss, javafx.graphics, javafx.fxml, jdk.dynalink, 
    javafx.media, jdk.accessibility, jdk.security.jgss, javafx.web, java.xml.crypto, jdk.jfr, jdk.packager.services, jdk.net, javafx.controls, 
    java.prefs, jdk.naming.rmi, jdk.jdwp.agent, java.instrument, jdk.management, 
    jdk.security.auth, java.management.rmi, jdk.naming.dns, jdk.localedata] to runtime image."
outputDir = ...
modulePath = [/Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home/jmods]
addModules = [java.base, java.desktop, java.naming, java.sql, java.xml, java.logging, java.management, java.scripting, java.compiler, java.rmi, java.activation, jdk.charsets, 
    jdk.xml.dom, java.datatransfer, jdk.httpserver, javafx.base, java.security.sasl, jdk.zipfs, jdk.crypto.ec, jdk.management.agent, java.sql.rowset, javafx.swing, jdk.jsobject, 
    jdk.sctp, java.smartcardio, jdk.unsupported, jdk.scripting.nashorn, java.security.jgss, javafx.graphics, javafx.fxml, jdk.dynalink, javafx.media, jdk.accessibility, jdk.security.jgss, javafx.web, java.xml.crypto, jdk.jfr, 
    jdk.packager.services, jdk.net, javafx.controls, java.prefs, jdk.naming.rmi, jdk.jdwp.agent, java.instrument, jdk.management, jdk.security.auth, java.management.rmi, jdk.naming.dns, jdk.localedata]
limitModules = [java.base, java.desktop, java.naming, java.sql, java.xml, java.logging, java.management, java.scripting, java.compiler, java.rmi, java.activation]

Here is the command that I run, with some things like username replaced:

/Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home/bin/javapackager -deploy -native image \
-name Commander -title Commander -vendor "username" \
-appclass com.username.commander.ui.AppWindow \
-srcdir /Users/username/Dropbox/coding/commander/Commander-java/packageJars \
-outdir /Users/username/Dropbox/coding/commander/Commander-java/target \
-outfile Commander \
-Bruntime=target/jre-9.0.1 -Bicon=src/main/resources/icons/commander.icns \
-BappVersion=1.0 \
-Bmac.CFBundleIdentifier=com.username.Commander \
-BmainJar=commander-0.0.1-SNAPSHOT-jar-with-dependencies.jar \
--add-modules java.base,java.desktop,java.naming,java.sql,java.xml,java.logging,java.management,java.scripting,java.compiler,java.rmi,java.activation \
--limit-modules java.base,java.desktop,java.naming,java.sql,java.xml,java.logging,java.management,java.scripting,java.compiler,java.rmi,java.activation \
-nosign -v

GabeV :

So it turns out that the reason why it wasn't honoring my options is because my app jar is not a Java 9 module. It's a plain old jar. In Java 9, javapackager uses jlink to generate the runtime and will not try to limit the number of modules because it can't determine the module dependencies. The -Bruntime option is only for Java Web Start applications. If you want javapackager to not use jlink, you have to use the one in JDK 8.

I cannot turn my app jar into a module due to the complexity involved with all the 3rd party dependencies (you can see the details in this question). And I can't use JDK 8 because I need some APIs added to the Desktop module in Java 9. So, I found a workaround to get a slimmer runtime into the app using the Java 9 javapackager:

Generate a slimmer runtime using jlink by specifying only the modules that you need using the --add-modules option. You can use the jdeps command to figure out which modules are needed by all the jars in your app.
Generate the .app with the full runtime using javapackger as usual.
Open up your generated .app file (macOS) or for Windows, use something that will let you edit the .exe or .msi installer (don't know how to do this myself).
On macOS, replace the contents of <myApp>.app/Contents/PlugIns/Java.runtime/Contents/Home with those of your slimmer runtime. Do something similar for the Windows installer.