Is there a better way to setup/run this Java program?

My file structure looks liked this:

cse408 - lib  
       - pics  
       - App.java  
       - ImageUtil.java  
       - Menu.java  

And to compile/run I use the following commands:

***To Compile***
LD_LIBRARY_PATH=/home/soldiermoth/Downloads/6.4.0/lib javac -classpath lib/jmagick.jar:. App.java
****************

****To Run******
LD_LIBRARY_PATH=/home/soldiermoth/Downloads/6.4.0/lib java -classpath lib/jmagick.jar:. App
****************

As you may be able to tell I have a dependency on an installed jmagick library where the jmagick.so file is in 6.4.0/lib

Mostly I'm wondering about how I'm handling dependencies and how I could do it better especially cross platform.

It's more common to have source files under a source directory, and then in the package structure beneath that.

so I'd expect to see

cse408 - lib  
       - pics  
       - src
           App.java  
           ImageUtil.java  
           Menu.java 

At the very least. If your code is in the com.soldier.moth package, I'd expect

cse408 - lib  
       - pics  
       - src
           - com
               - soldier
                    - moth        
                        App.java  
                        ImageUtil.java  
                        Menu.java