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I am able to access the CommandlineConfiguration.jar and set all the settings, but when I attempt to run the bot itself, I get this:

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cabam@cbm:~$ java -jar /etc/javaop/JavaOp2.jar
Loading plugin: file://etc/javaop/Advertisements.jar
Loading plugin: file://etc/javaop/Alias.jar
Loading plugin: file://etc/javaop/AntiFlood.jar
Loading plugin: file://etc/javaop/Auto-Rejoin.jar
Loading plugin: file://etc/javaop/Autoban.jar
Loading plugin: file://etc/javaop/Away.jar
Loading plugin: file://etc/javaop/BNetLogin.jar
Loading plugin: file://etc/javaop/BasicCommands.jar
Loading plugin: file://etc/javaop/BotMail.jar
Loading plugin: file://etc/javaop/ChannelList.jar
Loading plugin: file://etc/javaop/ChannelProtection.jar
Loading plugin: file://etc/javaop/Clan.jar
Loading plugin: file://etc/javaop/CommandlineConfiguration.jar
   --> Load failed (Plugin 'file://etc/javaop/CommandlineConfiguration.jar' does
n't have required PluginMain.class.
java.lang.ClassNotFoundException: PluginMain
java.lang.ClassNotFoundException: PluginMain
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
        at pluginmanagers.PluginManager.loadFile(PluginManager.java:133)
        at pluginmanagers.PluginManager.loadFile(PluginManager.java:114)
        at pluginmanagers.PluginManager.initialize(PluginManager.java:55)
        at _main.BotStart.main(BotStart.java:34)
Loading plugin: file://etc/javaop/Commands.jar
Loading plugin: file://etc/javaop/ConnectionCommands.jar
Loading plugin: file://etc/javaop/ConsoleDisplay.jar
Loading plugin: file://etc/javaop/Designate.jar
Loading plugin: file://etc/javaop/EmailRegister.jar
Loading plugin: file://etc/javaop/Filters.jar
Loading plugin: file://etc/javaop/Forwarding.jar
Loading plugin: file://etc/javaop/FunStuff.jar
Loading plugin: file://etc/javaop/GlobalCommand.jar
Loading plugin: file://etc/javaop/Greeting.jar
Loading plugin: file://etc/javaop/Help.jar
Loading plugin: file://etc/javaop/IPBan.jar
Loading plugin: file://etc/javaop/JavaOp2.jar
   --> Load failed (Plugin 'file://etc/javaop/JavaOp2.jar' doesn't have required
PluginMain.class.
java.lang.ClassNotFoundException: PluginMain
java.lang.ClassNotFoundException: PluginMain
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
        at pluginmanagers.PluginManager.loadFile(PluginManager.java:133)
        at pluginmanagers.PluginManager.loadFile(PluginManager.java:114)
        at pluginmanagers.PluginManager.initialize(PluginManager.java:55)
        at _main.BotStart.main(BotStart.java:34)
Loading plugin: file://etc/javaop/Ladder.jar
Loading plugin: file://etc/javaop/Logging.jar
Loading plugin: file://etc/javaop/Moderation.jar
Loading plugin: file://etc/javaop/Ping.jar
Loading plugin: file://etc/javaop/Profile.jar
Loading plugin: file://etc/javaop/SelectPlugins.jar
   --> Load failed (Plugin 'file://etc/javaop/SelectPlugins.jar' doesn't have re
quired PluginMain.class.
java.lang.ClassNotFoundException: PluginMain
java.lang.ClassNotFoundException: PluginMain
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
        at pluginmanagers.PluginManager.loadFile(PluginManager.java:133)
        at pluginmanagers.PluginManager.loadFile(PluginManager.java:114)
        at pluginmanagers.PluginManager.initialize(PluginManager.java:55)
        at _main.BotStart.main(BotStart.java:34)
Loading plugin: file://etc/javaop/ShellCommands.jar
Loading plugin: file://etc/javaop/ShowInvisibleUsers.jar
Loading plugin: file://etc/javaop/SimpleEventProcess.jar
Loading plugin: file://etc/javaop/SweepBan.jar
Loading plugin: file://etc/javaop/UserInformation.jar
Loading plugin: file://etc/javaop/UserManagement.jar
Loading plugin: file://etc/javaop/Version.jar
Loading plugin: file://etc/javaop/War3Clan.jar

And it just stops right here.

I am using the most recent version: JavaOp2-beta42 - 03/09/2007

I am new to Ubuntu, so please excuse me if I'm making a simple mistake.

Any help appreciated  :)

EDIT: I just didn't put the plugins in a seperate folder, and didn't configure it to auto load/connect.