GNOME-Shell – How to Reduce Tray Icon Padding on Ubuntu with GNOME 3

The solution is to add the Notification Area applet. Taken from this question No Banshee notification area icon in Gnome 3 classic session

For Java Apps:

• Actually for JDownloader case, It's a modular design. Tray icon comes as a plugin that can be disabled from:

  JDownloader → Addons → Addon Manager → Extensions → Uncheck Activate box for JD Light Tray

• For Java applications general case, It is possible to use Java security manager by writing a custom policy rules.

  1. Create java.policy file in ~/.jdownloader contains:

     grant codeBase "file:/home/user/.jdownloader/-" {
     
     // full access
     //    permission java.security.AllPermission;
     
     // AWTPermission full or only selected elements from it
     //    permission java.awt.AWTPermission "*";
     
         permission java.awt.AWTPermission "accessClipboard";
         permission java.awt.AWTPermission "accessEventQueue";
     //    permission java.awt.AWTPermission "accessSystemTray";
         permission java.awt.AWTPermission "createRobot";
         permission java.awt.AWTPermission "fullScreenExclusive";
         permission java.awt.AWTPermission "listenToAllAWTEvents";
         permission java.awt.AWTPermission "readDisplayPixels";
         permission java.awt.AWTPermission "replaceKeyboardFocusManager";
         permission java.awt.AWTPermission "setAppletStub";
         permission java.awt.AWTPermission "setWindowAlwaysOnTop";
         permission java.awt.AWTPermission "showWindowWithoutWarningBanner";
         permission java.awt.AWTPermission "toolkitModality";
         permission java.awt.AWTPermission "watchMousePointer";
     
     // Added by try and learn
         permission java.io.FilePermission "/-", "read,write,delete";
         permission java.util.PropertyPermission "*", "read,write";
         permission java.util.logging.LoggingPermission "control";
         permission java.lang.RuntimePermission "*";
         permission java.net.NetPermission "*";
         permission java.security.SecurityPermission "*";
         permission javax.net.ssl.SSLPermission "*";
         permission java.net.SocketPermission "*", "connect,resolve";
         permission java.lang.reflect.ReflectPermission "*";
     };
     

  2. Modify jdownloader launch script to use custom policy

     sudo nano /usr/bin/jdownloader
     

     Add: -Djava.security.manager -Djava.security.policy=java.policy to java command call:

     exec java ${JAVA_OPTIONS}  -Djava.security.manager -Djava.security.policy=java.policy -jar JDownloader.jar $*
     

These are the minimum rules that allowed me to launch jdownloader. You may need to add more permissions. Because there is no deny option you have to write all needed grant rules.

References:

• java.awt: Class SystemTray
• java.awt: Class AWTPermission

• java.security: Class BasicPermission

  See Direct Known Subclasses if you want to write a general template that grant AllPermission except accessSystemTray. So you can use it for all remaining java apps.

BTW, try to comment one of the rules by adding // to the beginning of line; So you can see how the error of denied permissions looks like. It tells you which permission you should to add. Also notice that I have used many - & * trying to extend rules as I'm looking for a quick solution (default was AllPermission anyway) and I'm not looking to jail the application.

Here is a template to start with, trying to grant all possible permissions:

grant codeBase "file:/home/user/.jdownloader/-" {

//    permission java.security.AllPermission;

//    permission java.awt.AWTPermission "*";

    permission java.awt.AWTPermission "accessClipboard";
    permission java.awt.AWTPermission "accessEventQueue";
//    permission java.awt.AWTPermission "accessSystemTray";
    permission java.awt.AWTPermission "createRobot";
    permission java.awt.AWTPermission "fullScreenExclusive";
    permission java.awt.AWTPermission "listenToAllAWTEvents";
    permission java.awt.AWTPermission "readDisplayPixels";
    permission java.awt.AWTPermission "replaceKeyboardFocusManager";
    permission java.awt.AWTPermission "setAppletStub";
    permission java.awt.AWTPermission "setWindowAlwaysOnTop";
    permission java.awt.AWTPermission "showWindowWithoutWarningBanner";
    permission java.awt.AWTPermission "toolkitModality";
    permission java.awt.AWTPermission "watchMousePointer";


    permission javax.sound.sampled.AudioPermission "*";
    permission javax.security.auth.AuthPermission "*";
//    permission javax.security.auth.kerberos.DelegationPermission "";
    permission javax.xml.bind.JAXBPermission "*";
    permission java.nio.file.LinkPermission "hard";
    permission java.nio.file.LinkPermission "symbolic";
    permission java.util.logging.LoggingPermission "control";
//    permission java.lang.management.ManagementPermission "*";
    permission javax.management.MBeanServerPermission "*";
    permission javax.management.MBeanTrustPermission "*";
    permission java.net.NetPermission "*";
    permission java.util.PropertyPermission "*", "read,write";
    permission java.lang.reflect.ReflectPermission "*";
    permission java.lang.RuntimePermission "*";
    permission java.security.SecurityPermission "*";
    permission java.io.SerializablePermission "*";
    permission java.sql.SQLPermission "*";
    permission javax.net.ssl.SSLPermission "*";
    permission javax.management.remote.SubjectDelegationPermission "*";
    permission javax.xml.ws.WebServicePermission "*";
//    permission  "*";

    permission java.io.FilePermission "/-", "read,write,execute,delete,readlink";
    permission javax.management.MBeanPermission "*", "*";
//    permission javax.security.auth.PrivateCredentialPermission "", "read";
    permission javax.security.auth.kerberos.ServicePermission "*", "initiate,accept";
    permission java.net.SocketPermission "*", "accept,connect,listen,resolve";
    permission java.net.URLPermission "*";
};

Note:

Java Policy Tools is a GUI tool to edit policy files. It make it more easy t find out all available options from drop box. It should be already install with Java package.