How do I run my application as superuser from Eclipse?

You can follow these steps to compile/debug applications as superuser.

1. Rename your java-application

   sudo mv /usr/lib/jvm/java-6-openjdk/jre/bin/java /usr/lib/jvm/java-6-openjdk/jre/bin/java.ori

2. Create following script and store it as /usr/lib/jvm/java-6-openjdk/jre/bin/java

   #!/bin/bash
   # file:  /usr/lib/jvm/java-6-openjdk/jre/bin/java
   # descr: Starter for jdk. Runs jdk as root when 
   #        cmd-line-arg "--run-as-root" is specified.
   #
   jre="/usr/lib/jvm/java-6-openjdk/jre/bin/java.ori"
   run_as_root=false
   args=
   
   # Filter command-line argument
   for arg in "$@"
   do
     case "$arg" in
     --run-as-root)  run_as_root=true
                     ;;
     *)              args="$args $arg"
                     ;;
   
     esac
   done
   
   # Remove leading whitespaces
   args=$(echo $args | sed -e 's/^[ \t]*//')
   
   if $run_as_root
   then
     echo "WARNING: Running as root!"
     gksu "$jre $args"
   else
     $jre $args
   fi
   

3. Change the permissions to make it executable

   sudo chmod 0755 /usr/lib/jvm/java-6-openjdk/jre/bin/java

4. Startup eclipse

5. Go to Window->Preferences->Java->Installed JREs
6. Duplicate java-6-openjdk to java-6-openjdk-root
7. Edit JRE and add “–run-as-root” as Default VM Argument

To run projects as root you need to follow these steps:

1. Go to Project->Properties->Java Build Path
2. Double-Click the JRE System Library and choose in Alternate JRE “java-6-openjdk-root”

Note: The idea is from http://www.eclipse.org/forums/index.php/mv/msg/87353/724852/#msg_724852