To debug a Java program being run on the command line from Eclipse you can start the Java program in remote debugging mode:
java -Xdebug -Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=y -jar myProgram.jar
The program will wait for you to attach the Eclipse debugger to it. Open Eclipse and choose:
Run > Debug Configurations... > Remote Java Application > New
Make sure to enter the same port that you chose on the command line. The default is port 8000. Now hit “Debug” and you’re off!