I'm pretty sure I have this right, and it used to work... just upgraded to ij13 but I dont think that's the problem. it's as though I dont have the path right but it the same one I always used...
here's what's in my app descriptor:
<icon>
<image48x48>icons/icon_48.png</image48x48>
</icon>
and the folder structure in my output folder looks correct:
app-descriptor.xml
icons
icon_48.png