How do I run DataNucleus from within an Eclipse executable JAR?

Question

How do I run a standalone Google AppEngine project using DataNucleus JPA in an Eclipse executable JAR? The customer will run it, so it needs to be packaged. It accesses the local file system so it can't be a web app. I'm not using Maven, just Eclipse Project > Export > Executable JAR (and the Ant script it makes). It works of course when run from within Eclipse. When I run the JAR, I get the following DataNucleus errors:

Caused by: java.io.FileNotFoundException: rsrc:datanucleus-api-jdo-3.1.3.jar (The system cannot find the file specified)

Caused by: org.datanucleus.exceptions.NucleusException: Error reading manifest file "jar:rsrc:datanucleus-api-jdo-3.1.3.jar!/plugin.xml"

javax.persistence.PersistenceException: Explicit persistence provider error(s) occurred for "transactions-optional" after trying the following discovered implementations: org.datanucleus.api.jpa.PersistenceProviderImpl from provider: org.datanucleus.api.jpa.PersistenceProviderImpl

Full Stack Trace

javax.persistence.PersistenceException: Explicit persistence provider error(s) occurred for "transactions-optional" after trying the following discovered implementations: org.datanucleus.api.jpa.PersistenceProviderImpl from provider: org.datanucleus.api.jpa.PersistenceProviderImpl
        at javax.persistence.Persistence.createPersistenceException(Persistence.java:242)
        at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:184)
        at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:70)
        at com.mwv.pic.dao.EMF.getInstance(EMF.java:26)
        at com.mwv.pic.dao.SecondaryDocumentsDao.isSecondaryDocumentUniqueByTitle(SecondaryDocumentsDao.java:80)
        at com.mwv.pic.dao.SecondaryDocumentsDao.addSecondaryDocument(SecondaryDocumentsDao.java:53)
        at com.mwv.Import.createSecondaryDocument(Import.java:294)
        at com.mwv.Import.importAllFiles(Import.java:234)
        at com.mwv.Main$6.run(Main.java:220)
        at java.lang.Thread.run(Unknown Source)
Caused by: org.datanucleus.exceptions.NucleusException: Error reading manifest file "jar:rsrc:datanucleus-api-jdo-3.1.3.jar!/plugin.xml"
        at org.datanucleus.plugin.NonManagedPluginRegistry.registerBundle(NonManagedPluginRegistry.java:482)
        at org.datanucleus.plugin.NonManagedPluginRegistry.registerExtensions(NonManagedPluginRegistry.java:219)
        at org.datanucleus.plugin.NonManagedPluginRegistry.registerExtensionPoints(NonManagedPluginRegistry.java:160)
        at org.datanucleus.plugin.PluginManager.<init>(PluginManager.java:65)
        at org.datanucleus.plugin.PluginManager.createPluginManager(PluginManager.java:427)
        at org.datanucleus.api.jpa.JPAEntityManagerFactory.<init>(JPAEntityManagerFactory.java:328)
        at org.datanucleus.api.jpa.PersistenceProviderImpl.createEntityManagerFactory(PersistenceProviderImpl.java:91)
        at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:150)
        ... 8 more
Caused by: java.io.FileNotFoundException: rsrc:datanucleus-api-jdo-3.1.3.jar (The system cannot find the file specified)
        at java.util.zip.ZipFile.open(Native Method)
        at java.util.zip.ZipFile.<init>(Unknown Source)
        at java.util.zip.ZipFile.<init>(Unknown Source)
        at java.util.jar.JarFile.<init>(Unknown Source)
        at java.util.jar.JarFile.<init>(Unknown Source)
        at org.datanucleus.plugin.NonManagedPluginRegistry.registerBundle(NonManagedPluginRegistry.java:390)
        ... 15 more

Code, EMF.java:26

        instance = Persistence.createEntityManagerFactory("transactions-optional");

JAR files contents

META-INF/MANIFEST.MF

Manifest-Version: 1.0
Ant-Version: Apache Ant 1.8.4
Created-By: 1.7.0_17-b02 (Oracle Corporation)
Main-Class: org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader
Rsrc-Main-Class: com.mwv.Main
Rsrc-Class-Path: ./ google-api-services-drive-v2-rev107-1.16.0-rc.jar 
... a hundred JARs ...
Class-Path: .

Answer 1

This is not an ideal solution but I edited the JAR file with 7-Zip manager, added main.bat and main.sh, and renamed it with .zip extension. The user implicitly assumes to unzip it and run the batch or shell script. The script looks like:

java -cp ./:google-api-services-drive-v2-rev107-1.16.0-rc.jar:...:forms-1.3.0.jar com.mwv.Main

And the .bat file is the same, with : replace with ;. I just copied the MANIFEST.MF (F4 edit in 7-Zip) and manually used some Notepad++ Kung Fu to make the giant class path. The Eclipse generated Ant file could no doubt be modified to automatically include the scripts, but I have not done that yet.