Running Java program outside Jdeveloper -- issue with dependent libaries

Question

Hello, I am using Jdeveloper 11.1.1.7 and have built a java application that imports XML Files into Oracle, then exports an XML file for others to pick up.  I use jaxb, java persistance, and javax.mail etc....
when I run the application in Jdeveloper it works properly, and now I am trying to place the application in my u:\temp directory to test run from the command line.  Later I will move this all to linux to run.
In Jdeveloper I followed the directions about adding all the dependent jars into the application using the File Groups ( http://tompeez.wordpress.com/2011/06/01/creating-a-jar-file-in-jdeveloper/ )
Doing this creates a very big jar file with all of the dependent jar files in it called xmlseprocessing.jar  and then I run it as such in dos
set classpath=.;javax.mail_1.4.jar;xmlseprocessing.jar
u:
cd u:\temp
C:\Oracle11117\Middleware\jdk160_24\bin\javac commandLineStartup.java
C:\Oracle11117\Middleware\jdk160_24\bin\java  commandLineStartup
I get this error: 
Exception in thread "main" java.lang.NoClassDefFoundError: javax/mail/MessagingException
I look on the internet, and finally decide to grab the javax.mail_1.4.jar and put it in my u:\temp directory, and update the classpath, and run it, but then I get this error.
Exception in thread "main" java.lang.NoClassDefFoundError: javax/persistence/Persistence
        at in_jpa_db_objects.JavaServiceFacade.<init>(JavaServiceFacade.java:19)
        at util_import_factory.OraConnInput.OraCleaner(OraConnInput.java:43)
        at startup.startImport.processIncomingXMLs(startImport.java:49)
        at startup.startAll.startupProcesses(startAll.java:92)
        at commandLineStartup.main(commandLineStartup.java:23)
Caused by: java.lang.ClassNotFoundException: javax.persistence.Persistence
        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:305)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:246)
        ... 5 more
My assumption is that I am going to have to grab every jar, add it to my local directory and create a very long path like oracle does when starting the application from jdeveloper (see below)
QUESTION:  Given that I have added all of the required libraries to the xmlseprocessing.jar -- why is this happening?  Any solution?  Am I doing something wrong?
Points awarded!!!!  Any help would be greatly appreciated.
This is what I see in the log window when I run the application in Jdeveloper. 
C:\Oracle11117\Middleware\jdk160_24\bin\javaw.exe -clientlasspath C:\JDeveloper\mywork\xmlProcessing20131021_1100\.adf;C:\JDeveloper\mywork\xmlProcessing20131021_1100\XML_SE\classes;C:\Oracle11117\Middleware\wlserver_10.3\server\lib\weblogic.jar;C:\Oracle11117\Middleware\modules\com.oracle.toplink_1.0.0.0_11-1-1-5-0.jar;C:\Oracle11117\Middleware\modules\org.eclipse.persistence_1.1.0.0_2-1.jar;C:\Oracle11117\Middleware\modules\com.bea.core.antlr.runtime_2.7.7.jar;C:\Oracle11117\Middleware\modules\javax.persistence_1.0.0.0_2-0-0.jar;C:\Oracle11117\Middleware\oracle_common\modules\oracle.xdk_11.1.0\xmlparserv2.jar;C:\Oracle11117\Middleware\oracle_common\modules\oracle.xdk_11.1.0\xml.jar;C:\Oracle11117\Middleware\modules\javax.jsf_1.1.0.0_1-.jar;C:\Oracle11117\Middleware\modules\javax.ejb_3.0.1.jar;C:\Oracle11117\Middleware\modules\javax.enterprise.deploy_1.2.jar;C:\Oracle11117\Middleware\modules\javax.interceptor_1.0.jar;C:\Oracle11117\Middleware\modules\javax.jms_1.1.1.jar;C:\Oracle11117\Middleware\modules\javax.jsp_1.2.0.0_2-.jar;C:\Oracle11117\Middleware\modules\javax.jws_2.0.jar;C:\Oracle11117\Middleware\modules\javax.activation_1.1.0.0_1-1.jar;C:\Oracle11117\Middleware\modules\javax.mail_1.1.0.0_1-4-.jar;C:\Oracle11117\Middleware\modules\javax.xml.soap_1.3.1.0.jar;C:\Oracle11117\Middleware\modules\javax.xml.rpc_1.2.1.jar;C:\Oracle11117\Middleware\modules\javax.xml.ws_2.1.1.jar;C:\Oracle11117\Middleware\modules\javax.management.j2ee_1.0.jar;C:\Oracle11117\Middleware\modules\javax.resource_1.5.1.jar;C:\Oracle11117\Middleware\modules\javax.servlet_1.0.0.0_2-5.jar;C:\Oracle11117\Middleware\modules\javax.transaction_1.0.0.0_1-ar;C:\Oracle11117\Middleware\modules\javax.xml.stream_1.1.1.0.jar;C:\Oracle11117\Middleware\modules\javax.security.jacc_1.0.0.0_1-1.jar;C:\Oracle11117\Middleware\modules\javax.xml.registry_1.0.0.0_1-0.jar;C:\Oracle11117\Middleware\jdeveloper\ide\macros\..\..\..\oracle_common\modules\oracle.jdbc_11.1.1\ojdbc6dms.jar;C:\Oracle11117\Middleware\jdeveloper\ide\macros\..\..\..\oracle_common\modules\oracle.nlsrtl_11.1.0\orai18n.jar;C:\Oracle11117\Middleware\oracle_common\modules\oracle.odl_11.1.1\ojdl.jar;C:\Oracle11117\Middleware\oracle_common\modules\oracle.dms_11.1.1\dms.jar -Djavax.net.ssl.trustStore=C:\Oracle11117\Middleware\wlserver_10.3\server\lib\DemoTrust.jks commandLineStartup

Answer 1

rp0428,
Thank you for your reply.  Please understand that I am on a tight deadline and have spent two weeks writing an application that I cannot run outside of jdeveloper.  I only have some experience with java -- I have been working with Jdeveloper extensively, but have only been deploying to Weblogic, so a lot of this is foreign to me.  
I had not noticed the comments underneath.  I now understand that I need to extract all the jars that are dependent (all the files added to my jar file when I added the File Group Library), and did so.  I also found a blog on this  https://blogs.oracle.com/bwb/resource/Jdev_jar_deployments/Creating_Jar_Deployments_with_JDeveloper.html
So I have all these jars and the jar of the application that was created.   I created a small class called commandLineStartup.java that simply had a main method in it, where I called the program to run in my xmlseprocessing.jar
I created a bat file that set the classpath (which I painstakingly created by taking the startup script that Jdeveloper created when running the program and replaced the various directory structure to match the location was running from
///// a.bat file runs this:
set classpath=C:\temp\xmlseprocessing.jar;%dir%\wlfullclient.jar;C:\temp\javax.mail_1.1.0.0_1-4-1.jar;C:\temp\wljmsclient.jar;C:\temp\com.oracle.toplink_1.0.0.0_11-1-1-5-0.jar;C:\temp\org.eclipse.persistence_1.1.0.0_2-1.jar;C:\temp\com.bea.core.antlr.runtime_2.7.7.jar;C:\temp\javax.persistence_1.0.0.0_2-0-0.jar;C:\temp\xmlparserv2.jar;C:\temp\xml.jar;C:\temp\javax.jsf_1.1.0.0_1-2.jar;C:\temp\javax.ejb_3.0.1.jar;C:\temp\javax.enterprise.deploy_1.2.jar;C:\temp\javax.interceptor_1.0.jar;C:\temp\modules\javax.jms_1.1.1.jar;C:\temp\javax.jsp_1.2.0.0_2-1.jar;C:\temp\javax.jws_2.0.jar;C:\temp\javax.activation_1.1.0.0_1-1.jar;C:\temp\javax.xml.soap_1.3.1.0.jar;C:\temp\javax.xml.rpc_1.2.1.jar;C:\temp\javax.xml.ws_2.1.1.jar;C:\temp\javax.management.j2ee_1.0.jar;C:\temp\javax.resource_1.5.1.jar;C:\temp\javax.servlet_1.0.0.0_2-5.jar;C:\temp\javax.transaction_1.0.0.0_1-1.jar;C:\temp\javax.xml.stream_1.1.1.0.jar;C:\temp\javax.security.jacc_1.0.0.0_1-1.jar;C:\temp\javax.xml.registry_1.0.0.0_1-0.jar;C:\temp\ojdbc6dms.jar;C:\temp\orai18n.jar;C:\temp\ojdl.jar;.
C:\Oracle11117\Middleware\jdk160_24\bin\javac commandLineStartup.java
C:\Oracle11117\Middleware\jdk160_24\bin\java  commandLineStartup
/////  This is the commandLineStartup file
public class commandLineStartup{
    public static void main(String[] args) {
  startup.startAll s = new startup.startAll();
               s.startupProcesses() ;
I found this also on including the meta-inf directory files.   https://blogs.oracle.com/bwb/resource/Jdev_jar_deployments/Creating_Jar_Deployments_with_JDeveloper.html
Now it blows up with this error  java.lang.NoClassDefFoundError: weblogic/utils/NestedException
So I scour the internet and find a solution to create a wlFullClient.jar (http://docs.oracle.com/cd/E12840_01/wls/docs103/client/jarbuilder.html),
Now I run it and get Exception in thread "main" java.lang.NoClassDefFoundError: weblogic/management/WebLogicMBean
And now I get this:  Exception in thread "main" java.lang.NoClassDefFoundError: oracle/dms/console/DMSConsole
This is absolutely crazy.  I am doing this all manually and by hand, which is error prone.  There has got to be a better way of doing it.  Does ant make it so you can deploy and run? Is there some program that does this for me?   What happens when I throw this out on linux?  Another two days of idiotic troubleshooting?
Thank you,
Stuart
All I want to do is run the thing.  I have now spent two days putting files into this and that directory, creating the Jar with and without the dependent jars and trying every combination.
Up to this point I have been impressed with Java.  Now I am about to throw my computer out the window.