Create a package with some java files in.
Now create a sub package called img, and place an image file inside.
When the code is compiled, the img package and it's image resource is not copied over to the .class area. 

Example project which demonstrates the problem can be found here:
http://bitbucket.org/danielburrell/decent-irc/downloads

This is not a test case, it is a small project I'm working on which demonstrates the problem. 

The com.solong.irc.systemTray package contains a SystemTrayView class which requests a resource on line 59: img/tray.gif which should be available since img/tray.gif exists in the systemTray package.
However when the project is run from the IDE, if you inspect the 
decent-irc\target\classes\com\solong\irc\systemTray 
directory, you see there is no img folder, and no tray.gif either.

This is a resource and it should be copied over. Currently having to manually copy it over as a workaround. 
Eclipse automatically handles this.