For hints about what is missing go to the Navigator view in Eclipse, find the .classpath file within your project and open it up. Within that you will find the classpath that Eclipse is using when you run from within Eclipse. Compare that to what you have on the command line and
you should find something missing.
Note that there are different "kinds" of elements in Eclipse's classpath, you can figure out what they are from context.
BTW, you probably don't want to change the .classpath file.