I have a two archives, one is x.jar (compressed) and x.ear (exploded). x.ear contains a fileset, which includes x.jar. So my directory structure is:

x.jar
ear/x.ear/
ear/x.ear/x.jar

x.jar contains compiled Java classes. When I make a change in the Java code, the x.jar is properly updated, however, the x.ear contains the old version of x.jar. I have to select "Build Archive" action from the menu.